Package: a4
Version: 1.6.1
Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting
Suggests: MLP, nlcv, ALL, Cairo
License: GPL-3
Title: Automated Affymetrix Array Analysis Umbrella Package
Description: Automated Affymetrix Array Analysis Umbrella Package
biocViews: Bioinformatics, Microarray
Author: Willem Talloen, Tobias Verbeke
Maintainer: Tobias Verbeke <tobias.verbeke@openanalytics.eu>
MD5sum: 07bc5cbc782e672d63d5e6b6c87adf8c
source.ver: src/contrib/a4_1.6.1.tar.gz
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vignettes: vignettes/a4/inst/doc/a4vignette.pdf
vignetteTitles: a4vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/a4/inst/doc/a4vignette.R
Package: a4Base
Version: 1.6.0
Depends: methods, graphics, grid, Biobase, AnnotationDbi, annaffy, mpm,
genefilter, limma, multtest, glmnet, a4Preproc, a4Core, gplots
Suggests: Cairo, ALL
Enhances: gridSVG, JavaGD
License: GPL-3
Title: Automated Affymetrix Array Analysis Base Package
Description: Automated Affymetrix Array Analysis
biocViews: Bioinformatics, Microarray
Author: Willem Talloen, Tobias Verbeke, Tine Casneuf, An De Bondt,
Steven Osselaer and Hinrich Goehlmann
Maintainer: Tobias Verbeke <tobias.verbeke@openanalytics.eu>
MD5sum: 06406dfd887d97c639c179295f6b5b24
source.ver: src/contrib/a4Base_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/a4Base_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/a4Base_1.6.0.zip
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hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: a4
Package: a4Classif
Version: 1.6.0
Depends: methods, a4Core, a4Preproc, MLInterfaces, ROCR, pamr, glmnet,
varSelRF
Imports: a4Core
Suggests: ALL
License: GPL-3
Title: Automated Affymetrix Array Analysis Classification Package
Description: Automated Affymetrix Array Analysis Classification Package
biocViews: Bioinformatics, Microarray
Author: Willem Talloen, Tobias Verbeke
Maintainer: Tobias Verbeke <tobias.verbeke@openanalytics.eu>
MD5sum: a79af61ae6d5c88e352fab9fbb8fa33a
source.ver: src/contrib/a4Classif_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/a4Classif_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/a4Classif_1.6.0.zip
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hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: a4
Package: a4Core
Version: 1.6.0
Depends: methods, Biobase, glmnet
License: GPL-3
Title: Automated Affymetrix Array Analysis Core Package
Description: Automated Affymetrix Array Analysis Core Package
biocViews: Bioinformatics, Microarray
Author: Willem Talloen, Tobias Verbeke
Maintainer: Tobias Verbeke <tobias.verbeke@openanalytics.eu>
MD5sum: 7b6a3c7b7cddb14f5b2bc0b1781e0379
source.ver: src/contrib/a4Core_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/a4Core_1.6.0.zip
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hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: a4, a4Base, a4Classif
importsMe: a4Classif
Package: a4Preproc
Version: 1.6.0
Depends: methods, AnnotationDbi
Suggests: ALL, hgu95av2.db
License: GPL-3
Title: Automated Affymetrix Array Analysis Preprocessing Package
Description: Automated Affymetrix Array Analysis Preprocessing Package
biocViews: Bioinformatics, Microarray
Author: Willem Talloen, Tobias Verbeke
Maintainer: Tobias Verbeke <tobias.verbeke@openanalytics.eu>
MD5sum: d90391402175f298d1fe89f56c2e91bc
source.ver: src/contrib/a4Preproc_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/a4Preproc_1.6.0.zip
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hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: a4, a4Base, a4Classif
Package: a4Reporting
Version: 1.6.0
Depends: methods, annaffy
Imports: xtable, utils
License: GPL-3
Title: Automated Affymetrix Array Analysis Reporting Package
Description: Automated Affymetrix Array Analysis Reporting Package
biocViews: Microarray
Author: Tobias Verbeke
Maintainer: Tobias Verbeke <tobias.verbeke@openanalytics.eu>
MD5sum: 3c5d221e8f5738788ab8adf0ccffa694
source.ver: src/contrib/a4Reporting_1.6.0.tar.gz
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hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: a4
Package: ABarray
Version: 1.26.0
Imports: Biobase, graphics, grDevices, methods, multtest, stats, tcltk,
utils
Suggests: limma, LPE
License: GPL
Title: Microarray QA and statistical data analysis for Applied
Biosystems Genome Survey Microrarray (AB1700) gene expression
data.
Description: Automated pipline to perform gene expression analysis for
Applied Biosystems Genome Survey Microarray (AB1700) data
format. Functions include data preprocessing, filtering,
control probe analysis, statistical analysis in one single
function. A GUI interface is also provided. The raw data,
processed data, graphics output and statistical results are
organized into folders according to the analysis settings used.
biocViews: Microarray, OneChannel, Preprocessing
Author: Yongming Andrew Sun
Maintainer: Yongming Andrew Sun <sunya@appliedbiosystems.com>
MD5sum: 71c16f7a44ebb75bdbbdcc56655da985
source.ver: src/contrib/ABarray_1.26.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ABarray_1.26.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ABarray_1.26.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ABarray/inst/doc/ABarrayGUI.pdf,
vignettes/ABarray/inst/doc/ABarray.pdf
vignetteTitles: ABarray gene expression GUI interface, ABarray gene
expression
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ABarray/inst/doc/ABarrayGUI.R,
vignettes/ABarray/inst/doc/ABarray.R
Package: aCGH
Version: 1.36.0
Depends: R (>= 2.10), cluster, survival, multtest
Imports: Biobase, cluster, grDevices, graphics, methods, multtest,
stats, survival, splines, utils
License: GPL-2
Archs: i386, x64
Title: Classes and functions for Array Comparative Genomic
Hybridization data.
Description: Functions for reading aCGH data from image analysis output
files and clone information files, creation of aCGH S3 objects
for storing these data. Basic methods for accessing/replacing,
subsetting, printing and plotting aCGH objects.
biocViews: CopyNumberVariants, DataImport, Genetics
Author: Jane Fridlyand <jfridlyand@cc.ucsf.edu>, Peter Dimitrov
<dimitrov@stat.Berkeley.EDU>
Maintainer: Peter Dimitrov <dimitrov@stat.Berkeley.EDU>
MD5sum: 77356c94eb4f384880cd4e4910ac12b6
source.ver: src/contrib/aCGH_1.36.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/aCGH_1.36.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/aCGH_1.36.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/aCGH_1.36.0.tgz
vignettes: vignettes/aCGH/inst/doc/aCGH.pdf
vignetteTitles: aCGH Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/aCGH/inst/doc/aCGH.R
dependsOnMe: ADaCGH2, CRImage
importsMe: snapCGH
suggestsMe: beadarraySNP
Package: ACME
Version: 2.14.0
Depends: R (>= 2.10), Biobase (>= 2.5.5), methods
Imports: graphics, stats
License: GPL (>= 2)
Archs: i386, x64
Title: Algorithms for Calculating Microarray Enrichment (ACME)
Description: ACME (Algorithms for Calculating Microarray Enrichment) is
a set of tools for analysing tiling array ChIP/chip, DNAse
hypersensitivity, or other experiments that result in regions
of the genome showing "enrichment". It does not rely on a
specific array technology (although the array should be a
"tiling" array), is very general (can be applied in experiments
resulting in regions of enrichment), and is very insensitive to
array noise or normalization methods. It is also very fast and
can be applied on whole-genome tiling array experiments quite
easily with enough memory.
biocViews: Bioinformatics
Author: Sean Davis <sdavis2@mail.nih.gov>
Maintainer: Sean Davis <sdavis2@mail.nih.gov>
URL: http://watson.nci.nih.gov/~sdavis
MD5sum: 0643c42174550c40469b27560a54e8ff
source.ver: src/contrib/ACME_2.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ACME_2.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ACME_2.14.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ACME_2.14.0.tgz
vignettes: vignettes/ACME/inst/doc/ACME.pdf
vignetteTitles: ACME
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ACME/inst/doc/ACME.R
Package: ADaCGH2
Version: 1.8.0
Depends: R (>= 2.11.0), tilingArray, aCGH, waveslim, cluster, snapCGH,
snowfall, ff
Suggests: GLAD, DNAcopy, CGHregions, rlecuyer
Enhances: Rmpi, multicore
License: GPL (>= 3)
Archs: i386, x64
Title: Analysis of data from aCGH experiments using parallel computing
and ff objects
Description: Analysis and plotting of array CGH data. Allows usage of
Circular Binary Segementation, wavelet-based smoothing (both as
in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM,
BioHMM, GLAD, CGHseg. Most computations are parallelized.
biocViews: Microarray, CopyNumberVariants
Author: Ramon Diaz-Uriarte <rdiaz02@gmail.com>, Oscar M. Rueda
<rueda.om@gmail.com>. Wavelet-based aCGH smoothing code from Li
Hsu <lih@fhcrc.org> and Douglas Grove <dgrove@fhcrc.org>.
Imagemap code from Barry Rowlingson
<B.Rowlingson@lancaster.ac.uk>. HaarSeg code from Erez
Ben-Yaacov; downloaded from
<http://www.ee.technion.ac.il/people/YoninaEldar/Info/software/HaarSeg.htm>
Maintainer: Ramon Diaz-Uriarte <rdiaz02@gmail.com>
URL: http://launchpad.net/adacgh, http://wavicgh.bioinfo.cnio.es
MD5sum: eb2fb42169ef7626aa6d0dceccde0b23
source.ver: src/contrib/ADaCGH2_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ADaCGH2_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ADaCGH2_1.8.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ADaCGH2/inst/doc/ADaCGH2.pdf
vignetteTitles: ADaCGH2 Overview
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ADaCGH2/inst/doc/ADaCGH2.R
Package: adSplit
Version: 1.28.0
Depends: R (>= 2.1.0), methods (>= 2.1.0)
Imports: AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db
(>= 1.8.1), graphics, grDevices, KEGG.db (>= 1.8.1), methods,
multtest (>= 1.6.0), stats (>= 2.1.0)
Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1)
License: GPL (>= 2)
Archs: i386, x64
Title: Annotation-Driven Clustering
Description: This package implements clustering of microarray gene
expression profiles according to functional annotations. For
each term genes are annotated to, splits into two subclasses
are computed and a significance of the supporting gene set is
determined.
biocViews: Microarray, Bioinformatics, Clustering
Author: Claudio Lottaz, Joern Toedling
Maintainer: Claudio Lottaz <Claudio.Lottaz@klinik.uni-regensburg.de>
URL: http://compdiag.molgen.mpg.de/software/index.shtml
MD5sum: 0751ef28d4531c8a8c4abc7aeefb49c7
source.ver: src/contrib/adSplit_1.28.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/adSplit_1.28.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/adSplit_1.28.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/adSplit/inst/doc/bcb_logo.pdf,
vignettes/adSplit/inst/doc/minerva_bcb.pdf,
vignettes/adSplit/inst/doc/tr_2005_02.pdf
vignetteTitles: bcb_logo.pdf, minerva_bcb.pdf, Annotation-Driven
Clustering
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/adSplit/inst/doc/tr_2005_02.R
Package: affxparser
Version: 1.30.2
Depends: R (>= 2.6.0)
Suggests: R.utils (>= 1.19.3), AffymetrixDataTestFiles
License: LGPL (>= 2)
Archs: i386, x64
Title: Affymetrix File Parsing SDK
Description: Package for parsing Affymetrix files (CDF, CEL, CHP,
BPMAP, BAR). It provides methods for fast and memory efficient
parsing of Affymetrix files using the Affymetrix' Fusion SDK.
Both ASCII- and binary-based files are supported. Currently,
there are methods for reading chip definition file (CDF) and a
cell intensity file (CEL). These files can be read either in
full or in part. For example, probe signals from a few
probesets can be extracted very quickly from a set of CEL files
into a convenient list structure.
biocViews: Infrastructure, DataImport
Author: Henrik Bengtsson, James Bullard, Robert Gentleman, Kasper
Daniel Hansen, Martin Morgan
Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
MD5sum: f0197d2ce532839004ebdcbf0b7fc5de
source.ver: src/contrib/affxparser_1.30.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/affxparser_1.30.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/affxparser_1.30.2.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: ITALICS, pdInfoBuilder, rMAT, Starr
importsMe: affyILM, AffyTiling, cn.farms, GeneRegionScan, ITALICS,
oligo, rMAT
Package: affy
Version: 1.36.1
Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5)
Imports: BiocGenerics, Biobase, affyio (>= 1.13.3), BiocInstaller,
graphics, grDevices, methods, preprocessCore, stats, utils,
zlibbioc
LinkingTo: preprocessCore
Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools
License: LGPL (>= 2.0)
Archs: i386, x64
Title: Methods for Affymetrix Oligonucleotide Arrays
Description: The package contains functions for exploratory
oligonucleotide array analysis. The dependence on tkWidgets
only concerns few convenience functions. 'affy' is fully
functional without it.
biocViews: Microarray, OneChannel, Preprocessing
Author: Rafael A. Irizarry <rafa@jhu.edu>, Laurent Gautier
<lgautier@gmail.com>, Benjamin Milo Bolstad
<bmb@bmbolstad.com>, and Crispin Miller
<cmiller@picr.man.ac.uk> with contributions from Magnus Astrand
<Magnus.Astrand@astrazeneca.com>, Leslie M. Cope
<cope@mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad
Halling <challing@agilixcorp.com>, Wolfgang Huber, James
MacDonald <jmacdon@med.umich.edu>, Benjamin I. P. Rubinstein,
Christopher Workman <workman@cbs.dtu.dk>, John Zhang
Maintainer: Rafael A. Irizarry <rafa@jhu.edu>
MD5sum: ce1da25547feda90c5432b61c2ee9fc9
source.ver: src/contrib/affy_1.36.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/affy_1.36.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/affy_1.36.1.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affy_1.36.1.tgz
vignettes: vignettes/affy/inst/doc/affy.pdf,
vignettes/affy/inst/doc/builtinMethods.pdf,
vignettes/affy/inst/doc/customMethods.pdf,
vignettes/affy/inst/doc/vim.pdf
vignetteTitles: 1. Primer, 2. Built-in Processing Methods, 3. Custom
Processing Methods, 4. Import Methods
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/affy/inst/doc/affy.R,
vignettes/affy/inst/doc/builtinMethods.R,
vignettes/affy/inst/doc/customMethods.R,
vignettes/affy/inst/doc/vim.R
dependsOnMe: affyContam, affycoretools, AffyExpress, affylmGUI,
affyPara, affypdnn, affyPLM, affyQCReport, AffyRNADegradation,
altcdfenvs, arrayMvout, ArrayTools, bgx, Cormotif, dualKS,
ExiMiR, farms, frmaTools, gcrma, LMGene, logitT, maDB, maskBAD,
MLP, panp, plw, puma, qpcrNorm, ReadqPCR, RefPlus, rHVDM, RPA,
simpleaffy, sscore, Starr, webbioc
importsMe: affyILM, affyQCReport, AffyTiling, ArrayExpress,
arrayQualityMetrics, ArrayTools, ChIPXpress, Cormotif, farms,
ffpe, frma, gcrma, GEOsubmission, Harshlight, HTqPCR, lumi,
makecdfenv, MSnbase, plier, plw, puma, pvac, simpleaffy,
tilingArray, TurboNorm, virtualArray, vsn, waveTiling
suggestsMe: AnnotationForge, beadarray, beadarraySNP, BiocCaseStudies,
Biostrings, BufferedMatrixMethods, categoryCompare, ecolitk,
ExpressionView, factDesign, ffpe, GeneRegionScan, limma, made4,
oneChannelGUI, PREDA, siggenes, TurboNorm
Package: affycomp
Version: 1.34.0
Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3)
Suggests: splines, affycompData
License: GPL (>= 2)
Title: Graphics Toolbox for Assessment of Affymetrix Expression
Measures
Description: The package contains functions that can be used to compare
expression measures for Affymetrix Oligonucleotide Arrays.
biocViews: OneChannel, Microarray, Preprocessing
Author: Rafael A. Irizarry <rafa@jhu.edu> and Zhijin Wu
<zwu@stat.brown.edu> with contributions from Simon Cawley
<simon_cawley@affymetrix.com>
Maintainer: Rafael A. Irizarry <rafa@jhu.edu>
MD5sum: 2dfa3507781f8db9656253aafb3f4cf1
source.ver: src/contrib/affycomp_1.34.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/affycomp_1.34.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/affycomp_1.34.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/affycomp/inst/doc/affycomp.pdf
vignetteTitles: affycomp primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/affycomp/inst/doc/affycomp.R
Package: AffyCompatible
Version: 1.18.2
Depends: R (>= 2.7.0), XML (>= 2.8-1), RCurl (>= 0.8-1), methods
Imports: Biostrings
License: Artistic-2.0
Title: Affymetrix GeneChip software compatibility
Description: This package provides an interface to Affymetrix chip
annotation and sample attribute files. The package allows an
easy way for users to download and manage local data bases of
Affynmetrix NetAffx annotation files. The package also provides
access to GeneChip Operating System (GCOS) and GeneChip Command
Console (AGCC)-compatible sample annotation files.
biocViews: Infrastructure, Microarray, OneChannel
Author: Martin Morgan, Robert Gentleman
Maintainer: Martin Morgan <mtmorgan@fhcrc.org>
MD5sum: 9d455b8c8ea154308cfc4ddb99710a4d
source.ver: src/contrib/AffyCompatible_1.18.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/AffyCompatible_1.18.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/AffyCompatible_1.18.2.zip
mac.binary.leopard.ver:
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vignettes: vignettes/AffyCompatible/inst/doc/MAGEAndARR.pdf,
vignettes/AffyCompatible/inst/doc/NetAffxResource.pdf
vignetteTitles: Retrieving MAGE and ARR sample attributes, Annotation
retrieval with NetAffxResource
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/AffyCompatible/inst/doc/MAGEAndARR.R,
vignettes/AffyCompatible/inst/doc/NetAffxResource.R
importsMe: IdMappingRetrieval
Package: affyContam
Version: 1.16.0
Depends: R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata
License: Artistic-2.0
Title: structured corruption of affymetrix cel file data
Description: structured corruption of cel file data to demonstrate QA
effectiveness
biocViews: Infrastructure, Bioinformatics
Author: V. Carey
Maintainer: V. Carey <stvjc@channing.harvard.edu>
MD5sum: c7bd1ea7e9c37cc6d39facd5c08f7e73
source.ver: src/contrib/affyContam_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/affyContam_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/affyContam_1.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/affyContam/inst/doc/affyContam.pdf
vignetteTitles: affy contamination tools
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/affyContam/inst/doc/affyContam.R
Package: affycoretools
Version: 1.30.0
Depends: affy, Biobase, GO.db, KEGG.db
Imports: biomaRt, limma, GOstats, annotate, annaffy, genefilter, gcrma,
splines, xtable, AnnotationDbi, lattice, gplots
Suggests: affydata, hgfocuscdf, rgl
License: Artistic-2.0
Title: Functions useful for those doing repetitive analyses with
Affymetrix GeneChips.
Description: Various wrapper functions that have been written to
streamline the more common analyses that a core Biostatistician
might see.
biocViews: ReportWriting, Microarray, OneChannel, GeneExpression
Author: James W. MacDonald
Maintainer: James W. MacDonald <jmacdon@med.umich.edu>
MD5sum: 254b996ba2583859e77ac294b94b1b3c
source.ver: src/contrib/affycoretools_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/affycoretools_1.30.0.zip
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vignettes: vignettes/affycoretools/inst/doc/affycoretools_biomaRt.pdf,
vignettes/affycoretools/inst/doc/affycoretools.pdf
vignetteTitles: affycoretools biomaRt Integration, affycoretools
Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/affycoretools/inst/doc/affycoretools_biomaRt.R,
vignettes/affycoretools/inst/doc/affycoretools.R
suggestsMe: Agi4x44PreProcess
Package: AffyExpress
Version: 1.24.0
Depends: R (>= 2.10), affy (>= 1.23.4), limma
Suggests: simpleaffy, R2HTML, affyPLM, hgu95av2cdf, hgu95av2, test3cdf,
genefilter, estrogen, annaffy, gcrma
License: LGPL
Title: Affymetrix Quality Assessment and Analysis Tool
Description: The purpose of this package is to provide a comprehensive
and easy-to-use tool for quality assessment and to identify
differentially expressed genes in the Affymetrix gene
expression data.
biocViews: Microarray, OneChannel, QualityControl, Preprocessing,
Bioinformatics, DifferentialExpression, Annotation,
ReportWriting, Visualization
Author: Xiwei Wu <xwu@coh.org>, Xuejun Arthur Li <xueli@coh.org>
Maintainer: Xuejun Arthur Li <xueli@coh.org>
MD5sum: 8b073cd0cf5e47c2eb9e984f07b1b93a
source.ver: src/contrib/AffyExpress_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/AffyExpress_1.24.0.zip
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mac.binary.leopard.ver:
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vignettes: vignettes/AffyExpress/inst/doc/AffyExpress.pdf
vignetteTitles: 1. Primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/AffyExpress/inst/doc/AffyExpress.R
Package: affyILM
Version: 1.10.0
Depends: R (>= 2.10.0), methods, gcrma
Imports: affxparser (>= 1.16.0), affy, graphics, methods, Biobase
Suggests: AffymetrixDataTestFiles
License: GPL version 3
Title: Linear Model of background subtraction and the Langmuir isotherm
Description: affyILM is a preprocessing tool which estimates gene
expression levels for Affymetrix Gene Chips. Input from
physical chemistry is employed to first background subtract
intensities before calculating concentrations on behalf of the
Langmuir model.
biocViews: Microarray, OneChannel, Preprocessing
Author: K. Myriam Kroll, Fabrice Berger, Gerard Barkema, Enrico Carlon
Maintainer: Myriam Kroll and Fabrice Berger <fabrice.berger@gmail.com>
MD5sum: 2aef75dba97bb45afae4c02e87687251
source.ver: src/contrib/affyILM_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/affyILM_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/affyILM_1.10.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/affyILM/inst/doc/affyILM.pdf
vignetteTitles: affyILM1.3.0
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/affyILM/inst/doc/affyILM.R
Package: affyio
Version: 1.26.0
Depends: R (>= 2.6.0), methods
Imports: zlibbioc
License: LGPL (>= 2)
Archs: i386, x64
Title: Tools for parsing Affymetrix data files
Description: Routines for parsing Affymetrix data files based upon file
format information. Primary focus is on accessing the CEL and
CDF file formats.
biocViews: Microarray, DataImport, Infrastructure
Author: Benjamin Milo Bolstad <bmb@bmbolstad.com>
Maintainer: Benjamin Milo Bolstad <bmb@bmbolstad.com>
MD5sum: 49f79ea18618b82e1babfd146faabf68
source.ver: src/contrib/affyio_1.26.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/affyio_1.26.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/affyio_1.26.0.zip
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
dependsOnMe: affylmGUI, sscore
importsMe: affy, crlmm, gcrma, oligo, oligoClasses
suggestsMe: BufferedMatrixMethods
Package: affylmGUI
Version: 1.32.0
Depends: limma, tcltk, affy, BiocInstaller, affyio
Suggests: tkrplot, affyPLM, R2HTML, xtable
License: LGPL
Title: GUI for affy analysis using limma package
Description: A Graphical User Interface for affy analysis using the
limma Microarray package
biocViews: Microarray, OneChannel, DataImport, QualityControl,
Preprocessing, Bioinformatics, DifferentialExpression,
MultipleComparisons, GUI
Author: James Wettenhall and Ken Simpson Division of Genetics and
Bioinformatics, WEHI.
Maintainer: Keith Satterley <keith@wehi.edu.au>
URL: http://bioinf.wehi.edu.au/affylmGUI/
MD5sum: f94f6e0f0be51b2675dcb7074a52ed36
source.ver: src/contrib/affylmGUI_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/affylmGUI_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/affylmGUI_1.32.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/affylmGUI/inst/doc/affylmGUI.pdf,
vignettes/affylmGUI/inst/doc/extract.pdf
vignetteTitles: affylmGUI Vignette, Extracting affy and limma objects
from affylmGUI files
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/affylmGUI/inst/doc/affylmGUI.R,
vignettes/affylmGUI/inst/doc/extract.R
htmlDocs: vignettes/affylmGUI/inst/doc/about.html,
vignettes/affylmGUI/inst/doc/CustMenu.html,
vignettes/affylmGUI/inst/doc/index.html,
vignettes/affylmGUI/inst/doc/windowsFocus.html
dependsOnMe: oneChannelGUI
Package: affyPara
Version: 1.18.0
Depends: R (>= 2.5.0), methods, affy (>= 1.20.0), snow (>= 0.2-3), vsn
(>= 3.6.0), aplpack (>= 1.1.1)
Suggests: affydata
Enhances: affy
License: GPL-3
Title: Parallelized preprocessing methods for Affymetrix
Oligonucleotide Arrays
Description: The package contains parallelized functions for
exploratory oligonucleotide array analysis. The package is
designed for large numbers of microarray data.
biocViews: Microarray, Preprocessing
Author: Markus Schmidberger <schmidb@ibe.med.uni-muenchen.de>,
Esmeralda Vicedo <e.vicedo@gmx.net>, Ulrich Mansmann
<mansmann@ibe.med.uni-muenchen.de>
Maintainer: Markus Schmidberger <MSchmidberger@freenet.de>
URL: http://www.ibe.med.uni-muenchen.de
MD5sum: 57b459595f0764bdba80f84e595b8efa
source.ver: src/contrib/affyPara_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/affyPara_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/affyPara_1.18.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/affyPara/inst/doc/affyPara.pdf,
vignettes/affyPara/inst/doc/vsnStudy.pdf
vignetteTitles: Parallelized affy functions for preprocessing,
Simulation Study for VSN Add-On Normalization and Subsample
Size
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/affyPara/inst/doc/affyPara.R,
vignettes/affyPara/inst/doc/vsnStudy.R
Package: affypdnn
Version: 1.32.0
Depends: R (>= 2.13.0), affy (>= 1.5)
Suggests: affydata, hgu95av2probe
License: LGPL
Title: Probe Dependent Nearest Neighbours (PDNN) for the affy package
Description: The package contains functions to perform the PDNN method
described by Li Zhang et al.
biocViews: OneChannel, Microarray, Preprocessing
Author: H. Bjorn Nielsen and Laurent Gautier (Many thanks to Li Zhang
early communications about the existence of the PDNN program
and related publications).
Maintainer: Laurent Gautier<lgautier@gmail.com>
MD5sum: df3cf0a6b6da79843c3e20338585c4c9
source.ver: src/contrib/affypdnn_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/affypdnn_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/affypdnn_1.32.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/affypdnn/inst/doc/affypdnn.pdf
vignetteTitles: affypdnn
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/affypdnn/inst/doc/affypdnn.R
Package: affyPLM
Version: 1.34.0
Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), affy (>= 1.11.0),
Biobase (>= 2.17.8), gcrma, stats, preprocessCore (>= 1.5.1)
Imports: BiocGenerics, zlibbioc, graphics, grDevices, methods
LinkingTo: preprocessCore
Suggests: affydata, MASS
License: GPL (>= 2)
Archs: i386, x64
Title: Methods for fitting probe-level models
Description: A package that extends and improves the functionality of
the base affy package. Routines that make heavy use of compiled
code for speed. Central focus is on implementation of methods
for fitting probe-level models and tools using these models.
PLM based quality assessment tools.
biocViews: Microarray, OneChannel, Preprocessing, QualityControl
Author: Ben Bolstad <bmb@bmbolstad.com>
Maintainer: Ben Bolstad <bmb@bmbolstad.com>
URL: http://bmbolstad.com
MD5sum: 95793fc13d81edf7db5e11dd49348302
source.ver: src/contrib/affyPLM_1.34.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/affyPLM_1.34.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/affyPLM_1.34.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/affyPLM/inst/doc/AffyExtensions.pdf,
vignettes/affyPLM/inst/doc/MAplots.pdf,
vignettes/affyPLM/inst/doc/QualityAssess.pdf,
vignettes/affyPLM/inst/doc/ThreeStep.pdf
vignetteTitles: affyPLM: Fitting Probe Level Models, affyPLM: Advanced
use of the MAplot function, affyPLM: Model Based QC Assessment
of Affymetrix GeneChips, affyPLM: the threestep function
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/affyPLM/inst/doc/AffyExtensions.R,
vignettes/affyPLM/inst/doc/MAplots.R,
vignettes/affyPLM/inst/doc/QualityAssess.R,
vignettes/affyPLM/inst/doc/ThreeStep.R
dependsOnMe: RefPlus
importsMe: affyQCReport, arrayQualityMetrics, virtualArray
suggestsMe: AffyExpress, affylmGUI, arrayMvout, ArrayTools,
BiocCaseStudies, BiocGenerics, frmaTools, ggbio, metahdep,
oneChannelGUI
Package: affyQCReport
Version: 1.36.0
Depends: Biobase (>= 1.13.16), affy, lattice
Imports: affy, affyPLM, Biobase, genefilter, graphics, grDevices,
lattice, RColorBrewer, simpleaffy, stats, utils, xtable
Suggests: tkWidgets (>= 1.5.23), affydata (>= 1.4.1)
License: LGPL (>= 2)
Title: QC Report Generation for affyBatch objects
Description: This package creates a QC report for an AffyBatch object.
The report is intended to allow the user to quickly assess the
quality of a set of arrays in an AffyBatch object.
biocViews: Microarray,OneChannel,QualityControl
Author: Craig Parman <craig.parman@bifx.org>, Conrad Halling
<conrad.halling@bifx.org>, Robert Gentleman
Maintainer: Craig Parman <craig.parman@bifx.org>
MD5sum: 9712a8f30e08dc7798ac9601ec297a06
source.ver: src/contrib/affyQCReport_1.36.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/affyQCReport_1.36.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/affyQCReport_1.36.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/affyQCReport/inst/doc/affyQCReport.pdf
vignetteTitles: affyQCReport: Methods for Generating Affymetrix QC
Reports
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/affyQCReport/inst/doc/affyQCReport.R
suggestsMe: BiocCaseStudies
Package: AffyRNADegradation
Version: 1.4.0
Depends: R (>= 2.9.0), methods, affy
Suggests: AmpAffyExample
License: GPL-2
Title: Analyze and correct probe positional bias in microarray data due
to RNA degradation
Description: The package helps with the assessment and correction of
RNA degradation effects in Affymetrix 3' expression arrays. The
parameter d gives a robust and accurate measure of RNA
integrity. The correction removes the probe positional bias,
and thus improves comparability of samples that are affected by
RNA degradation.
biocViews: GeneExpression, Microarray, OneChannel, Preprocessing,
QualityControl, Bioinformatics
Author: Mario Fasold
Maintainer: Mario Fasold <fasold@izbi.uni-leipzig.de>
MD5sum: 7f23aa06335b16cd04279a9cce31ecf5
source.ver: src/contrib/AffyRNADegradation_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/AffyRNADegradation_1.4.0.zip
win64.binary.ver:
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mac.binary.leopard.ver:
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vignettes: vignettes/AffyRNADegradation/inst/doc/vignette.pdf
vignetteTitles: AffyRNADegradation Example
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/AffyRNADegradation/inst/doc/vignette.R
Package: AffyTiling
Version: 1.16.1
Depends: R (>= 2.6)
Imports: affxparser, affy (>= 1.16), stats, utils, preprocessCore
License: GPL (>= 2)
Archs: i386, x64
Title: Easy extraction of individual probes in Affymetrix tiling arrays
Description: This package provides easy, fast functions for the
extraction and annotation of individual probes from Affymetrix
tiling arrays.
biocViews: Microarray, Preprocessing
Author: Charles G. Danko <dankoc@gmail.com>
Maintainer: Charles G. Danko <dankoc@gmail.com>
MD5sum: bc48c08feba49130a1702ed2af4267bc
source.ver: src/contrib/AffyTiling_1.16.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/AffyTiling_1.16.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/AffyTiling_1.16.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/AffyTiling/inst/doc/AffyTiling.pdf
vignetteTitles: AffyTiling
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/AffyTiling/inst/doc/AffyTiling.R
Package: AGDEX
Version: 1.6.0
Depends: R (>= 2.10), Biobase, GSEABase
Imports: stats
License: GPL Version 2 or later
Title: Agreement of Differential Expression Analysis
Description: A tool to evaluate agreement of differential expression
for cross-species genomics
biocViews: Microarray, Genetics, Bioinformatics, GeneExpression
Author: Stan Pounds <stanley.pounds@stjude.org>; Cuilan Lani Gao
<cuilan.gao@stjude.org>
Maintainer: Cuilan lani Gao <cuilan.gao@stjude.org>
MD5sum: 84b585c15fbeb006c747284decd87910
source.ver: src/contrib/AGDEX_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/AGDEX_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/AGDEX_1.6.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AGDEX_1.6.0.tgz
vignettes: vignettes/AGDEX/inst/doc/AGDEX.pdf
vignetteTitles: AGDEX.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/AGDEX/inst/doc/AGDEX.R
Package: Agi4x44PreProcess
Version: 1.18.0
Depends: R (>= 2.10), Biobase, limma, annotate, genefilter
Suggests: vsn, affycoretools, hgug4112a.db, GO.db, marray, gplots,
gtools, gdata
License: GPL-3
Title: PreProcessing of Agilent 4x44 array data
Description: Preprocessing of Agilent 4x44 array data
biocViews: Microarray, OneChannel, Preprocessing
Author: Pedro Lopez-Romero <plopez@cnic.es>
Maintainer: Pedro Lopez-Romero <plopez@cnic.es>
MD5sum: 8fe40f90ba22882438174504e74bde8a
source.ver: src/contrib/Agi4x44PreProcess_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Agi4x44PreProcess_1.18.0.zip
win64.binary.ver:
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vignettes: vignettes/Agi4x44PreProcess/inst/doc/Agi4x44PreProcess.pdf
vignetteTitles: Agi4x44PreProcess
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Agi4x44PreProcess/inst/doc/Agi4x44PreProcess.R
Package: agilp
Version: 3.0.0
Depends: R (>= 2.14.0)
License: GPL-3
Title: Agilent expression array processing package
Description: provides a pipeline for the low-level analysis of gene
expression microarray data, primarily Agilent data
Author: Benny Chain <b.chain@ucl.ac.uk>
Maintainer: Benny Chain <b.chain@ucl.ac.uk>
MD5sum: c7c0cd6a36b0902375ef063bff77fd22
source.ver: src/contrib/agilp_3.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/agilp_3.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/agilp_3.0.0.zip
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vignettes: vignettes/agilp/inst/doc/agilp_manual.pdf
vignetteTitles: An R Package for processing expression microarray data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/agilp/inst/doc/agilp_manual.R
Package: AgiMicroRna
Version: 2.8.0
Depends: R (>= 2.10),methods,Biobase,limma,affy (>=
1.22),preprocessCore,affycoretools
Imports: Biobase
Suggests: geneplotter,marray,gplots,gtools,gdata,codelink
License: GPL-3
Title: Processing and Differential Expression Analysis of Agilent
microRNA chips
Description: Processing and Analysis of Agilent microRNA data
biocViews:
Microarray,AgilentChip,OneChannel,Preprocessing,DifferentialExpression,Bioinformatics
Author: Pedro Lopez-Romero <plopez@cnic.es>
Maintainer: Pedro Lopez-Romero <plopez@cnic.es>
MD5sum: 0b7ad6d12deaddd9e5f6470165fcfda4
source.ver: src/contrib/AgiMicroRna_2.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/AgiMicroRna_2.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/AgiMicroRna_2.8.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/AgiMicroRna/inst/doc/AgiMicroRna.pdf
vignetteTitles: AgiMicroRna
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/AgiMicroRna/inst/doc/AgiMicroRna.R
Package: altcdfenvs
Version: 2.20.0
Depends: R (>= 2.7), methods, BiocGenerics (>= 0.1.0), Biobase (>=
2.15.1), affy, makecdfenv, Biostrings, hypergraph
Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db,
hgu133acdf, Rgraphviz, RColorBrewer
License: GPL (>= 2)
Title: alternative CDF environments (aka probeset mappings)
Description: Convenience data structures and functions to handle
cdfenvs
biocViews: Microarray, OneChannel, QualityControl, Preprocessing,
Annotation, ProprietaryPlatforms, Transcription
Author: Laurent Gautier <lgautier@gmail.com>
Maintainer: Laurent Gautier <lgautier@gmail.com>
MD5sum: ef7103c545763cd1c00dc0d269944b51
source.ver: src/contrib/altcdfenvs_2.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/altcdfenvs_2.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/altcdfenvs_2.20.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/altcdfenvs/inst/doc/altcdfenvs.pdf,
vignettes/altcdfenvs/inst/doc/modify.pdf,
vignettes/altcdfenvs/inst/doc/ngenomeschips.pdf
vignetteTitles: altcdfenvs, affy primer, affy primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/altcdfenvs/inst/doc/altcdfenvs.R,
vignettes/altcdfenvs/inst/doc/modify.R,
vignettes/altcdfenvs/inst/doc/ngenomeschips.R
importsMe: Harshlight
Package: annaffy
Version: 1.30.0
Depends: R (>= 2.5.0), methods, Biobase, GO.db, KEGG.db
Imports: AnnotationDbi (>= 0.1.15)
Suggests: hgu95av2.db, multtest, tcltk
License: LGPL
Title: Annotation tools for Affymetrix biological metadata
Description: Functions for handling data from Bioconductor Affymetrix
annotation data packages. Produces compact HTML and text
reports including experimental data and URL links to many
online databases. Allows searching biological metadata using
various criteria.
biocViews: OneChannel, Microarray, Annotation, GO, Pathways,
ReportWriting
Author: Colin A. Smith <annaffy@colinsmith.org>
Maintainer: Colin A. Smith <annaffy@colinsmith.org>
MD5sum: 706772d7ae0b91168fbf826172af773c
source.ver: src/contrib/annaffy_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/annaffy_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/annaffy_1.30.0.zip
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vignettes: vignettes/annaffy/inst/doc/annaffy.pdf
vignetteTitles: annaffy Primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/annaffy/inst/doc/annaffy.R
dependsOnMe: a4Base, a4Reporting, PGSEA, webbioc
importsMe: affycoretools
suggestsMe: AffyExpress, ArrayTools, BiocCaseStudies, maDB
Package: annmap
Version: 1.0.0
Depends: R (>= 2.15.0), methods, GenomicRanges
Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice,
Rsamtools, genefilter, IRanges, BiocGenerics
Suggests: RUnit, rjson
License: GPL-2
Title: Genome annotation and visualisation package pertaining to
Affymetrix arrays and NGS analysis.
Description: annmap provides annotation mappings for Affymetrix exon
arrays and coordinate based queries to support deep sequencing
data analysis. Database access is hidden behind the API which
provides a set of functions such as genesInRange(),
geneToExon(), exonDetails(), etc. Functions to plot gene
architecture and BAM file data are also provided. Underlying
data are from Ensembl.
biocViews: Annotation, Bioinformatics, Microarray, OneChannel,
ReportWriting, Transcription, Visualization
Author: Tim Yates <tyates@picr.man.ac.uk>
Maintainer: Tim Yates <tyates@picr.man.ac.uk>
URL: http://annmap.picr.man.ac.uk
MD5sum: 1ba2dc5cb5cd9d98894ee542ba55ae21
source.ver: src/contrib/annmap_1.0.0.tar.gz
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/annmap_1.0.0.tgz
vignettes: vignettes/annmap/inst/doc/annmap.pdf,
vignettes/annmap/inst/doc/cookbook.pdf,
vignettes/annmap/inst/doc/INSTALL.pdf
vignetteTitles: annmap primer, The Annmap Cookbook, annmap installation
instruction
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/annmap/inst/doc/annmap.R,
vignettes/annmap/inst/doc/cookbook.R,
vignettes/annmap/inst/doc/INSTALL.R
Package: annotate
Version: 1.36.0
Depends: R (>= 2.10), AnnotationDbi (>= 0.1.15)
Imports: Biobase, AnnotationDbi, DBI, xtable, graphics, utils, stats,
methods, XML (>= 0.92-2), BiocGenerics (>= 0.1.13)
Suggests: Biobase, hgu95av2.db, genefilter, Biostrings (>= 2.25.10),
rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, XML
(>= 0.92-2), org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC,
Rgraphviz, RUnit,
License: Artistic-2.0
Title: Annotation for microarrays
Description: Using R enviroments for annotation.
biocViews: Annotation, Pathways, GO
Author: R. Gentleman
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: d10a9c0482613386d825d1e1e1655260
source.ver: src/contrib/annotate_1.36.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/annotate_1.36.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/annotate_1.36.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/annotate/inst/doc/annotate.pdf,
vignettes/annotate/inst/doc/chromLoc.pdf,
vignettes/annotate/inst/doc/GOusage.pdf,
vignettes/annotate/inst/doc/prettyOutput.pdf,
vignettes/annotate/inst/doc/query.pdf,
vignettes/annotate/inst/doc/useDataPkgs.pdf,
vignettes/annotate/inst/doc/useHomology.pdf,
vignettes/annotate/inst/doc/useProbeInfo.pdf
vignetteTitles: Annotation Overview, HowTo: use chromosomal
information, Basic GO Usage, HowTo: Get HTML Output, HOWTO: Use
the online query tools, Using Data Packages, Using the homology
package, Using Affymetrix Probe Level Data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/annotate/inst/doc/annotate.R,
vignettes/annotate/inst/doc/chromLoc.R,
vignettes/annotate/inst/doc/GOusage.R,
vignettes/annotate/inst/doc/prettyOutput.R,
vignettes/annotate/inst/doc/query.R,
vignettes/annotate/inst/doc/useDataPkgs.R,
vignettes/annotate/inst/doc/useHomology.R,
vignettes/annotate/inst/doc/useProbeInfo.R
dependsOnMe: Agi4x44PreProcess, ChromHeatMap, GeneAnswers, geneplotter,
GSEABase, idiogram, macat, MLInterfaces, PCpheno, phenoTest,
PREDA, RpsiXML, safe, ScISI
importsMe: affycoretools, Category, categoryCompare, ChromHeatMap,
codelink, gCMAP, GeneAnswers, genefilter, GeneGroupAnalysis,
geneplotter, GlobalAncova, globaltest, GOstats, GSEABase, lumi,
methyAnalysis, methylumi, phenoTest, qpgraph, safe, ScISI,
splicegear, tigre
suggestsMe: BiocCaseStudies, biomaRt, geneplotter, GlobalAncova,
globaltest, GOstats, GSEAlm, maigesPack, MLP, oneChannelGUI,
puma, siggenes, tigre
Package: AnnotationDbi
Version: 1.20.7
Depends: R (>= 2.7.0), methods, utils, BiocGenerics (>= 0.1.13),
Biobase (>= 1.17.0)
Imports: methods, utils, DBI, RSQLite, BiocGenerics, Biobase, IRanges
Suggests: DBI (>= 0.2-4), RSQLite (>= 0.6-4), hgu95av2.db, GO.db,
org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit,
TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db,
seqnames.db, reactome.db, AnnotationForge
License: Artistic-2.0
Title: Annotation Database Interface
Description: Provides user interface and database connection code for
annotation data packages using SQLite data storage.
biocViews: Annotation, Infrastructure
Author: Herve Pages, Marc Carlson, Seth Falcon, Nianhua Li
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: 05c014c2b2b45e40d65706b09f1bb1a2
source.ver: src/contrib/AnnotationDbi_1.20.7.tar.gz
win.binary.ver: bin/windows/contrib/2.15/AnnotationDbi_1.20.7.zip
win64.binary.ver: bin/windows64/contrib/2.15/AnnotationDbi_1.20.7.zip
mac.binary.leopard.ver:
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vignettes: vignettes/AnnotationDbi/inst/doc/AnnotationDbi.pdf,
vignettes/AnnotationDbi/inst/doc/databaseTypes.pdf,
vignettes/AnnotationDbi/inst/doc/IntroToAnnotationPackages.pdf
vignetteTitles: How to use bimaps from the ".db" annotation packages,
databaseTypes.pdf, AnnotationDbi: Introduction To Bioconductor
Annotation Packages
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/AnnotationDbi/inst/doc/AnnotationDbi.R,
vignettes/AnnotationDbi/inst/doc/IntroToAnnotationPackages.R,
vignettes/AnnotationDbi/inst/doc/makeProbePackage.R,
vignettes/AnnotationDbi/inst/doc/NewSchema.R,
vignettes/AnnotationDbi/inst/doc/SQLForge.R
dependsOnMe: a4Base, a4Preproc, annotate, AnnotationForge,
AnnotationFuncs, attract, Category, categoryCompare,
ChromHeatMap, eisa, ExpressionView, GenomicFeatures,
GOFunction, goProfiles, MLP, OrganismDbi, PADOG, PAnnBuilder,
pathRender, PGSEA, Resourcerer, RpsiXML, topGO
importsMe: adSplit, affycoretools, annaffy, annotate, attract,
beadarray, BioNet, CancerMutationAnalysis, Category,
categoryCompare, ChIPpeakAnno, ChromHeatMap, clusterProfiler,
CoCiteStats, domainsignatures, DOSE, ExpressionView, FunciSNP,
genefilter, GeneGroupAnalysis, geneplotter, GGBase, GGtools,
GlobalAncova, globaltest, GOFunction, GOSemSim, goseq, GOstats,
goTools, graphite, GSEABase, Gviz, HTSanalyzeR, KEGGprofile,
lumi, methyAnalysis, methylumi, MiRaGE, OrganismDbi, PADOG,
PAnnBuilder, pcaGoPromoter, PCpheno, phenoTest, qpgraph,
ReactomePA, REDseq, safe, ScISI, SLGI, tigre, topGO,
VariantAnnotation, virtualArray
suggestsMe: BiocCaseStudies, BiocGenerics, GeneAnswers, GeneRegionScan,
MmPalateMiRNA, oneChannelGUI, sigPathway
Package: AnnotationForge
Version: 1.0.3
Depends: R (>= 2.7.0), methods, utils, BiocGenerics (>= 0.1.13),
Biobase (>= 1.17.0), AnnotationDbi (>= 1.19.15), org.Hs.eg.db
Imports: methods, utils, DBI, RSQLite, BiocGenerics, Biobase
Suggests: DBI (>= 0.2-4), RSQLite (>= 0.6-4), XML, RCurl, hgu95av2.db,
human.db0, affy, Homo.sapiens, hom.Hs.inp.db, GO.db
License: Artistic-2.0
Title: Code for Building Annotation Database Packages
Description: Provides code for generating Annotation packages and their
databases. Packages produced are intended to be used with
AnnotationDbi.
biocViews: Annotation, Infrastructure
Author: Marc Carlson, Herve Pages
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: 2a0080456452385248b864f8376e8977
source.ver: src/contrib/AnnotationForge_1.0.3.tar.gz
win.binary.ver: bin/windows/contrib/2.15/AnnotationForge_1.0.3.zip
win64.binary.ver: bin/windows64/contrib/2.15/AnnotationForge_1.0.3.zip
mac.binary.leopard.ver:
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vignettes: vignettes/AnnotationForge/inst/doc/makeProbePackage.pdf,
vignettes/AnnotationForge/inst/doc/NewSchema.pdf,
vignettes/AnnotationForge/inst/doc/SQLForge.pdf
vignetteTitles: Creating probe packages, Creating an annotation package
with a new database schema, SQLForge: An easy way to create a
new annotation package with a standard database schema.
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/AnnotationForge/inst/doc/makeProbePackage.R,
vignettes/AnnotationForge/inst/doc/NewSchema.R,
vignettes/AnnotationForge/inst/doc/SQLForge.R
importsMe: GOstats
suggestsMe: AnnotationDbi
Package: AnnotationFuncs
Version: 1.8.0
Depends: R (>= 2.7.0), AnnotationDbi
Suggests: org.Bt.eg.db, GO.db, org.Hs.eg.db, hom.Hs.inp.db
License: GPL-2
Title: Annotation translation functions
Description: Functions for handling translating between different
identifieres using the Biocore Data Team data-packages (e.g.
org.Bt.eg.db).
biocViews: AnnotationData, Software
Author: Stefan McKinnon Edwards <stefan.hoj-edwards@agrsci.dk>
Maintainer: Stefan McKinnon Edwards <stefan.hoj-edwards@agrsci.dk>
URL: http://www.iysik.com/index.php?page=annotation-functions
MD5sum: 83295b8f214366c259f012d053c0f798
source.ver: src/contrib/AnnotationFuncs_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/AnnotationFuncs_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/AnnotationFuncs_1.8.0.zip
mac.binary.leopard.ver:
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vignettes:
vignettes/AnnotationFuncs/inst/doc/AnnotationFuncsUserguide.pdf
vignetteTitles: Annotation mapping functions
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: annotationTools
Version: 1.32.0
Imports: Biobase, stats
License: GPL
Title: Annotate microarrays and perform cross-species gene expression
analyses using flat file databases.
Description: Functions to annotate microarrays, find orthologs, and
integrate heterogeneous gene expression profiles using
annotation and other molecular biology information available as
flat file database (plain text files).
biocViews: Microarray, Annotation
Author: Alexandre Kuhn <alexandre.m.kuhn@gmail.com>
Maintainer: Alexandre Kuhn <alexandre.m.kuhn@gmail.com>
MD5sum: 47a2f46e43050363afe95632de17dca3
source.ver: src/contrib/annotationTools_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/annotationTools_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/annotationTools_1.32.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/annotationTools/inst/doc/annotationTools.pdf
vignetteTitles: annotationTools Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/annotationTools/inst/doc/annotationTools.R
Package: anota
Version: 1.6.0
Depends: qvalue
Imports: multtest, qvalue
License: GPL-3
Title: ANalysis Of Translational Activity (ANOTA).
Description: Genome wide studies of translational control is emerging
as a tool to study verious biological conditions. The output
from such analysis is both the mRNA level (e.g. cytosolic mRNA
level) and the levl of mRNA actively involved in translation
(the actively translating mRNA level) for each mRNA. The
standard analysis of such data strives towards identifying
differential translational between two or more sample classes -
i.e. differences in actively translated mRNA levels that are
independent of underlying differences in cytosolic mRNA levels.
This package allows for such analysis using partial variances
and the random variance model. As 10s of thousands of mRNAs are
analyzed in parallell the library performs a number of tests to
assure that the data set is suitable for such analysis.
biocViews: GeneExpression, DifferentialExpression, Microarray,
HighThroughputSequencing
Author: Ola Larsson <ola.larsson@ki.se>, Nahum Sonenberg
<nahum.sonenberg@mcgill.ca>, Robert Nadon
<robert.nadon@mcgill.ca>
Maintainer: Ola Larsson <ola.larsson@ki.se>
MD5sum: 425d005789afaeeccd0f1380867e4aff
source.ver: src/contrib/anota_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/anota_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/anota_1.6.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/anota_1.6.0.tgz
vignettes: vignettes/anota/inst/doc/anota.pdf
vignetteTitles: ANalysis Of Translational Activity (anota)
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/anota/inst/doc/anota.R
Package: apComplex
Version: 2.24.0
Depends: R (>= 2.10), graph, RBGL
Imports: Rgraphviz, stats, org.Sc.sgd.db
License: LGPL
Title: Estimate protein complex membership using AP-MS protein data
Description: Functions to estimate a bipartite graph of protein complex
membership using AP-MS data.
biocViews: NetworkInference, MassSpectrometry, GraphsAndNetworks
Author: Denise Scholtens <dscholtens@northwestern.edu>
Maintainer: Denise Scholtens <dscholtens@northwestern.edu>
MD5sum: 4e6fa1f58f69569f643f6f4bad418b7b
source.ver: src/contrib/apComplex_2.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/apComplex_2.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/apComplex_2.24.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/apComplex/inst/doc/apComplex.pdf
vignetteTitles: apComplex
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/apComplex/inst/doc/apComplex.R
dependsOnMe: ScISI
suggestsMe: BiocCaseStudies
Package: aroma.light
Version: 1.28.0
Depends: R (>= 2.10.0), matrixStats (>= 0.5.3)
Imports: R.methodsS3 (>= 1.4.2)
Suggests: R.oo (>= 1.9.9), R.utils (>= 1.16.2), princurve (>= 1.1-11)
License: GPL (>= 2)
Title: Light-weight methods for normalization and visualization of
microarray data using only basic R data types
Description: Methods for microarray analysis that take basic data types
such as matrices and lists of vectors. These methods can be
used standalone, be utilized in other packages, or be wrapped
up in higher-level classes.
biocViews: Infrastructure, Microarray, OneChannel, TwoChannel,
MultiChannel, Visualization, Preprocessing
Author: Henrik Bengtsson <henrikb@braju.com>
Maintainer: Henrik Bengtsson <henrikb@braju.com>
URL: http://www.aroma-project.org/
MD5sum: 69dabbb219ddad3fbb1a8ece946956d8
source.ver: src/contrib/aroma.light_1.28.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/aroma.light_1.28.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/aroma.light_1.28.0.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: EDASeq
Package: ArrayExpress
Version: 1.18.0
Depends: R (>= 2.9.0), Biobase (>= 2.4.0)
Imports: XML, affy, limma
License: Artistic-2.0
Title: Access the ArrayExpress Microarray Database at EBI and build
Bioconductor data structures: ExpressionSet, AffyBatch,
NChannelSet
Description: Access the ArrayExpress Repository at EBI and build
Bioconductor data structures: ExpressionSet, AffyBatch,
NChannelSet
biocViews: Microarray, DataImport, OneChannel, TwoChannel
Author: Audrey Kauffmann, Ibrahim Emam
Maintainer: Ibrahim Emam <iemam@ebi.ac.uk>
MD5sum: 49e003ae79249d566d6174eb5517b2c6
source.ver: src/contrib/ArrayExpress_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ArrayExpress_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ArrayExpress_1.18.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ArrayExpress/inst/doc/ArrayExpress.pdf
vignetteTitles: ArrayExpress: Import and convert ArrayExpress data sets
into R object
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ArrayExpress/inst/doc/ArrayExpress.R
Package: ArrayExpressHTS
Version: 1.8.0
Depends: sampling, Rsamtools (>= 1.3.32), snow
Imports: Biobase, Biostrings, DESeq, GenomicRanges, Hmisc, IRanges,
R2HTML, RColorBrewer, Rsamtools, ShortRead, XML, biomaRt,
edgeR, grDevices, graphics, methods, rJava, stats, svMisc,
utils
LinkingTo: Rsamtools
License: Artistic License 2.0
Title: ArrayExpress High Throughput Sequencing Processing Pipeline
Description: RNA-Seq processing pipeline for public ArrayExpress
experiments or local datasets
biocViews: RNAseq, Sequencing, HighThroughputSequencing
Author: Angela Goncalves, Andrew Tikhonov
Maintainer: Angela Goncalves <filimon@ebi.ac.uk>, Andrew Tikhonov
<andrew@ebi.ac.uk>
MD5sum: 6b3eabc698e67f45d32088f8833d9555
source.ver: src/contrib/ArrayExpressHTS_1.8.0.tar.gz
mac.binary.leopard.ver:
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vignettes: vignettes/ArrayExpressHTS/inst/doc/ArrayExpressHTS.pdf
vignetteTitles: ArrayExpressHTS: RNA-Seq Pipeline for transcription
profiling experiments
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ArrayExpressHTS/inst/doc/ArrayExpressHTS.R
Package: arrayMvout
Version: 1.16.0
Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy,
lumi
Imports: simpleaffy, mdqc, affyContam,
Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata,
hgu133atagcdf
License: Artistic-2.0
Title: multivariate outlier detection for expression array QA
Description: This package supports the application of diverse quality
metrics to AffyBatch instances, summarizing these metrics via
PCA, and then performing parametric outlier detection on the
PCs to identify aberrant arrays with a fixed Type I error rate
biocViews: Infrastructure, Bioinformatics, Microarray, QualityControl
Author: Z. Gao, A. Asare, R. Wang, V. Carey
Maintainer: V. Carey <stvjc@channing.harvard.edu>
MD5sum: 47eb77a7982309573d7c947c4f992266
source.ver: src/contrib/arrayMvout_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/arrayMvout_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/arrayMvout_1.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/arrayMvout/inst/doc/arrayMvout-asdad.pdf,
vignettes/arrayMvout/inst/doc/arrayMvout-lkadas.pdf,
vignettes/arrayMvout/inst/doc/arrayMvout-lkda.pdf,
vignettes/arrayMvout/inst/doc/arrayMvout.pdf
vignetteTitles: arrayMvout-asdad.pdf, arrayMvout-lkadas.pdf,
arrayMvout-lkda.pdf, arrayMvout -- multivariate outlier
algorithm for expression arrays
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/arrayMvout/inst/doc/arrayMvout.R
Package: arrayQuality
Version: 1.36.0
Depends: R (>= 2.2.0)
Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray,
methods, RColorBrewer, stats, utils
Suggests: mclust, MEEBOdata, HEEBOdata
License: LGPL
Title: Assessing array quality on spotted arrays
Description: Functions for performing print-run and array level quality
assessment.
biocViews: Microarray,TwoChannel,QualityControl,Visualization
Author: Agnes Paquet and Jean Yee Hwa Yang <yeehwa@stat.berkeley.edu>
Maintainer: Agnes Paquet <paquetagnes@yahoo.com>
URL: http://arrays.ucsf.edu/
MD5sum: 51c331a456f32b31c34499ae9bb478f4
source.ver: src/contrib/arrayQuality_1.36.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/arrayQuality_1.36.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/arrayQuality_1.36.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/arrayQuality/inst/doc/
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
htmlDocs: vignettes/arrayQuality/inst/doc/basicQuality.html,
vignettes/arrayQuality/inst/doc/customQuality.html,
vignettes/arrayQuality/inst/doc/index.html,
vignettes/arrayQuality/inst/doc/print-runQC.html
Package: arrayQualityMetrics
Version: 3.14.0
Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, Cairo (>=
1.4-6), genefilter, graphics, grDevices, grid, Hmisc, hwriter,
lattice, latticeExtra, limma, methods, RColorBrewer, setRNG,
simpleaffy, stats, SVGAnnotation (>= 0.9-0), utils, vsn (>=
3.23.3), XML
Suggests: ALLMLL, CCl4
License: LGPL (>= 2)
Title: Quality metrics on microarray data sets
Description: This package generates microarray quality metrics reports
for data in Bioconductor microarray data containers
(ExpressionSet, NChannelSet, AffyBatch). Report contain both
general and platform-specific sections. Both one and two color
array platforms are supported.
biocViews: Microarray, QualityControl, OneChannel, TwoChannel,
ReportWriting
Author: Audrey Kauffmann, Wolfgang Huber
Maintainer: Audrey Kauffmann <akauffmann.bioinfo@gmail.com>
MD5sum: dd80d40e0831282d32675d80cc3646ac
source.ver: src/contrib/arrayQualityMetrics_3.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/arrayQualityMetrics_3.14.0.zip
win64.binary.ver:
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mac.binary.leopard.ver:
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vignettes: vignettes/arrayQualityMetrics/inst/doc/aqm.pdf,
vignettes/arrayQualityMetrics/inst/doc/arrayQualityMetrics.pdf
vignetteTitles: Advanced topics: Customizing arrayQualityMetrics
reports and programmatic processing of the output,
Introduction: microarray quality assessment with
arrayQualityMetrics
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/arrayQualityMetrics/inst/doc/aqm.R,
vignettes/arrayQualityMetrics/inst/doc/arrayQualityMetrics.R
Package: ArrayTools
Version: 1.18.0
Depends: R (>= 2.7.0), affy (>= 1.23.4), Biobase (>= 2.5.5), methods
Imports: affy, Biobase, graphics, grDevices, limma, methods, stats,
utils, xtable
Suggests: simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy,
gcrma, hugene10sttranscriptcluster.db
License: LGPL (>= 2.0)
Title: geneChip Analysis Package
Description: This package is designed to provide solutions for quality
assessment and to detect differentially expressed genes for the
Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST
arrays. The package generates comprehensive analysis reports in
HTML format. Hyperlinks on the report page will lead to a
series of QC plots, processed data, and differentially
expressed gene lists. Differentially expressed genes are
reported in tabular format with annotations hyperlinked to
online biological databases.
biocViews: Microarray, OneChannel, QualityControl, Preprocessing,
Statistics, DifferentialExpression, Annotation, ReportWriting,
Visualization
Author: Xiwei Wu, Arthur Li
Maintainer: Arthur Li <xueli@coh.org>
MD5sum: 691e6103836ddab3b4bca90950c8ae0f
source.ver: src/contrib/ArrayTools_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ArrayTools_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ArrayTools_1.18.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/ArrayTools_1.18.0.tgz
vignettes: vignettes/ArrayTools/inst/doc/ArrayTools.pdf
vignetteTitles: 1. Primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ArrayTools/inst/doc/ArrayTools.R
Package: ASEB
Version: 1.2.0
Depends: R (>= 2.8.0), methods
Imports: graphics, methods, utils
License: GPL (>= 3)
Archs: i386, x64
Title: Predict Acetylated Lysine Sites
Description: ASEB is an R package to predict lysine sites that can be
acetylated by a specific KAT-family.
biocViews: Proteomics
Author: Likun Wang <wanglikun@tsinghua.edu.cn> and Tingting Li
<litt@hsc.pku.edu.cn>.
Maintainer: Likun Wang <wanglikun@tsinghua.edu.cn>
MD5sum: f0e0b594657203e2e52bfb54d94cfce7
source.ver: src/contrib/ASEB_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ASEB_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ASEB_1.2.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ASEB_1.2.0.tgz
vignettes: vignettes/ASEB/inst/doc/ASEB.pdf
vignetteTitles: ASEB
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ASEB/inst/doc/ASEB.R
Package: attract
Version: 1.10.0
Depends: R (>= 2.10.0), AnnotationDbi, KEGG.db, limma, cluster,
GOstats, graphics, methods, stats
Imports: Biobase, AnnotationDbi, KEGG.db, limma, cluster, GOstats,
graphics, methods, stats
Suggests: illuminaHumanv1.db
License: LGPL (>= 2.0)
Title: Methods to Find the Gene Expression Modules that Represent the
Drivers of Kauffman's Attractor Landscape
Description: This package contains the functions to find the gene
expression modules that represent the drivers of Kauffman's
attractor landscape. The modules are the core attractor
pathways that discriminate between different cell types of
groups of interest. Each pathway has a set of synexpression
groups, which show transcriptionally-coordinated changes in
gene expression.
biocViews: Statistics, GeneExpression
Author: Jessica Mar
Maintainer: Jessica Mar <jess@jimmy.harvard.edu>
MD5sum: a55e0be79006dd997d05196322858119
source.ver: src/contrib/attract_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/attract_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/attract_1.10.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/attract/inst/doc/attract.pdf
vignetteTitles: Package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/attract/inst/doc/attract.R
Package: BAC
Version: 1.18.0
Depends: R (>= 2.10)
License: Artistic-2.0
Archs: i386, x64
Title: Bayesian Analysis of Chip-chip experiment
Description: This package uses a Bayesian hierarchical model to detect
enriched regions from ChIP-chip experiments
biocViews: Microarray,Transcription,Bioinformatics
Author: Raphael Gottardo
Maintainer: Raphael Gottardo <raph@stat.ubc.ca>
MD5sum: 391cb6a1daa2cb692e688c446c416d6d
source.ver: src/contrib/BAC_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BAC_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BAC_1.18.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BAC_1.18.0.tgz
vignettes: vignettes/BAC/inst/doc/BAC.pdf
vignetteTitles: 1. Primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BAC/inst/doc/BAC.R
Package: BayesPeak
Version: 1.10.0
Depends: R (>= 2.14), IRanges
Imports: IRanges, graphics
License: GPL (>= 2)
Archs: i386, x64
Title: Bayesian Analysis of ChIP-seq Data
Description: This package is an implementation of the BayesPeak
algorithm for peak-calling in ChIP-seq data.
biocViews: ChIPseq
Author: Christiana Spyrou, Jonathan Cairns, Rory Stark, Andy Lynch,
Simon Tavar\\'{e},
Maintainer: Jonathan Cairns <jmc200@cam.ac.uk>
MD5sum: 84e920f0e00bb920880d38938e9a067a
source.ver: src/contrib/BayesPeak_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BayesPeak_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BayesPeak_1.10.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/BayesPeak_1.10.0.tgz
vignettes: vignettes/BayesPeak/inst/doc/BayesPeak.pdf,
vignettes/BayesPeak/inst/doc/regionOFdiag.pdf
vignetteTitles: BayesPeak Vignette, regionOFdiag.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BayesPeak/inst/doc/BayesPeak.R
Package: baySeq
Version: 1.12.0
Depends: R (>= 2.3.0), methods
Suggests: snow, edgeR
License: GPL-3
Title: Empirical Bayesian analysis of patterns of differential
expression in count data
Description: This package identifies differential expression in
high-throughput 'count' data, such as that derived from
next-generation sequencing machines, calculating estimated
posterior likelihoods of differential expression (or more
complex hypotheses) via empirical Bayesian methods.
biocViews: Bioinformatics, HighThroughputSequencing,
DifferentialExpression, MultipleComparisons, SAGE
Author: Thomas J. Hardcastle
Maintainer: Thomas J. Hardcastle <tjh48@cam.ac.uk>
MD5sum: e473abf0576db5a7374276b0d9d12ca0
source.ver: src/contrib/baySeq_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/baySeq_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/baySeq_1.12.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/baySeq_1.12.0.tgz
vignettes: vignettes/baySeq/inst/doc/baySeq.pdf
vignetteTitles: baySeq
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/baySeq/inst/doc/baySeq.R
dependsOnMe: Rcade, segmentSeq
importsMe: segmentSeq
suggestsMe: oneChannelGUI
Package: BCRANK
Version: 1.20.0
Depends: methods
Imports: Biostrings
Suggests: seqLogo
License: GPL-2
Archs: i386, x64
Title: Predicting binding site consensus from ranked DNA sequences
Description: Functions and classes for de novo prediction of
transcription factor binding consensus by heuristic search
biocViews: MotifDiscovery, GeneRegulation
Author: Adam Ameur <Adam.Ameur@genpat.uu.se>
Maintainer: Adam Ameur <Adam.Ameur@genpat.uu.se>
MD5sum: 9eefe7c2e772c69181fb761ca4b5c144
source.ver: src/contrib/BCRANK_1.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BCRANK_1.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BCRANK_1.20.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/BCRANK_1.20.0.tgz
vignettes: vignettes/BCRANK/inst/doc/BCRANK_intro_fig1.pdf,
vignettes/BCRANK/inst/doc/BCRANK_intro_fig2.pdf,
vignettes/BCRANK/inst/doc/BCRANK.pdf
vignetteTitles: BCRANK_intro_fig1.pdf, BCRANK_intro_fig2.pdf, BCRANK
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BCRANK/inst/doc/BCRANK.R
Package: beadarray
Version: 2.8.1
Depends: R (>= 2.13.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8),
methods, ggplot2
Imports: BeadDataPackR, limma, AnnotationDbi, stats4, BiocGenerics,
reshape2
Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData,
illuminaHumanv3.db, gridExtra
License: GPL-2
Archs: i386, x64
Title: Quality assessment and low-level analysis for Illumina BeadArray
data
Description: The package is able to read bead-level data (raw TIFFs and
text files) output by BeadScan as well as bead-summary data
from BeadStudio. Methods for quality assessment and low-level
analysis are provided.
biocViews: Microarray, OneChannel, QualityControl, Preprocessing
Author: Mark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt
Ritchie
Maintainer: Mark Dunning <Mark.Dunning@cancer.org.uk>
MD5sum: 6a4bfbe9c665b3e211ae3f4fd6c63071
source.ver: src/contrib/beadarray_2.8.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/beadarray_2.8.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/beadarray_2.8.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/beadarray_2.8.1.tgz
vignettes: vignettes/beadarray/inst/doc/beadarray.pdf,
vignettes/beadarray/inst/doc/beadlevel.pdf,
vignettes/beadarray/inst/doc/beadsummary.pdf,
vignettes/beadarray/inst/doc/ImageProcessing.pdf
vignetteTitles: beadarray.pdf, beadlevel.pdf, beadsummary.pdf,
ImageProcessing.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/beadarray/inst/doc/beadarray.R,
vignettes/beadarray/inst/doc/beadlevel.R,
vignettes/beadarray/inst/doc/beadsummary.R,
vignettes/beadarray/inst/doc/ImageProcessing.R
importsMe: arrayQualityMetrics
suggestsMe: beadarraySNP, lumi
Package: beadarraySNP
Version: 1.24.0
Depends: methods, Biobase (>= 2.5.5), quantsmooth
Suggests: aCGH, affy, limma, snapCGH, beadarray, DNAcopy
License: GPL-2
Title: Normalization and reporting of Illumina SNP bead arrays
Description: Importing data from Illumina SNP experiments and
performing copy number calculations and reports.
biocViews: CopyNumberVariants, SNP, GeneticVariability, TwoChannel,
Preprocessing, DataImport
Author: Jan Oosting
Maintainer: Jan Oosting <j.oosting@lumc.nl>
MD5sum: c7d0df61bca38e8481900ed667323610
source.ver: src/contrib/beadarraySNP_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/beadarraySNP_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/beadarraySNP_1.24.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/beadarraySNP_1.24.0.tgz
vignettes: vignettes/beadarraySNP/inst/doc/beadarraySNP.pdf
vignetteTitles: beadarraySNP.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/beadarraySNP/inst/doc/beadarraySNP.R
Package: BeadDataPackR
Version: 1.10.0
License: GPL-2
Archs: i386, x64
Title: Compression of Illumina BeadArray data
Description: Provides functionality for the compression and
decompression of raw bead-level data from the Illumina
BeadArray platform
biocViews: Microarray
Author: Mike Smith, Andy Lynch
Maintainer: Mike Smith <mike.l.smith@cancer.org.uk>
MD5sum: c169f4248ef377c7b88e33bf71e11d6f
source.ver: src/contrib/BeadDataPackR_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BeadDataPackR_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BeadDataPackR_1.10.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/BeadDataPackR_1.10.0.tgz
vignettes: vignettes/BeadDataPackR/inst/doc/BeadDataPackR.pdf
vignetteTitles: BeadDataPackR.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BeadDataPackR/inst/doc/BeadDataPackR.R
importsMe: beadarray
Package: betr
Version: 1.14.0
Depends: R(>= 2.6.0)
Imports: Biobase (>= 2.5.5), limma, mvtnorm, methods, stats
Suggests: Biobase
License: LGPL
Title: Identify differentially expressed genes in microarray
time-course data
Description: The betr package implements the BETR (Bayesian Estimation
of Temporal Regulation) algorithm to identify differentially
expressed genes in microarray time-course data.
biocViews: Microarray, Bioinformatics, DifferentialExpression,
TimeCourse
Author: Martin Aryee
Maintainer: Martin Aryee <aryee@jhu.edu>
MD5sum: ee23b3e5b50afc61927186efab3fd996
source.ver: src/contrib/betr_1.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/betr_1.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/betr_1.14.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/betr_1.14.0.tgz
vignettes: vignettes/betr/inst/doc/betr.pdf
vignetteTitles: BETR Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/betr/inst/doc/betr.R
Package: bgafun
Version: 1.20.0
Depends: made4, seqinr,ade4
License: Artistic-2.0
Title: BGAfun A method to identify specifity determining residues in
protein families
Description: A method to identify specifity determining residues in
protein families using Between Group Analysis
biocViews: Bioinformatics,Classification
Author: Iain Wallace
Maintainer: Iain Wallace <iain.wallace@ucd.ie>
MD5sum: 33fa63edfe9cc6968abbeeb3cfa1b6b3
source.ver: src/contrib/bgafun_1.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/bgafun_1.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/bgafun_1.20.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/bgafun_1.20.0.tgz
vignettes: vignettes/bgafun/inst/doc/bgafun.pdf
vignetteTitles: bgafun.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/bgafun/inst/doc/bgafun.R
Package: BGmix
Version: 1.18.0
Depends: R (>= 2.3.1), KernSmooth
License: GPL-2
Title: Bayesian models for differential gene expression
Description: Fully Bayesian mixture models for differential gene
expression
biocViews: Microarray, DifferentialExpression, MultipleComparisons
Author: Alex Lewin, Natalia Bochkina
Maintainer: Alex Lewin <a.m.lewin@imperial.ac.uk>
MD5sum: 621c968387e61c2d20628449f5340983
source.ver: src/contrib/BGmix_1.18.0.tar.gz
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/BGmix_1.18.0.tgz
vignettes: vignettes/BGmix/inst/doc/BGmix.pdf
vignetteTitles: BGmix Tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BGmix/inst/doc/BGmix.R
Package: bgx
Version: 1.22.0
Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), gcrma (>= 2.4.1)
Suggests: affydata, hgu95av2cdf
License: GPL-2
Archs: i386, x64
Title: Bayesian Gene eXpression
Description: Bayesian integrated analysis of Affymetrix GeneChips
biocViews: Microarray, DifferentialExpression
Author: Ernest Turro, Graeme Ambler, Anne-Mette K Hein
Maintainer: Ernest Turro <ernest.turro@ic.ac.uk>
MD5sum: 5ddc4b6823ddce958f9822247e483b77
source.ver: src/contrib/bgx_1.22.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/bgx_1.22.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/bgx_1.22.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bgx_1.22.0.tgz
vignettes: vignettes/bgx/inst/doc/bgx.pdf
vignetteTitles: HowTo BGX
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/bgx/inst/doc/bgx.R
Package: BHC
Version: 1.10.0
License: GPL-3
Archs: i386, x64
Title: Bayesian Hierarchical Clustering
Description: The method performs bottom-up hierarchical clustering,
using a Dirichlet Process (infinite mixture) to model
uncertainty in the data and Bayesian model selection to decide
at each step which clusters to merge. This avoids several
limitations of traditional methods, for example how many
clusters there should be and how to choose a principled
distance metric. This implementation accepts multinomial (i.e.
discrete, with 2+ categories) or time-series data. This version
also includes a randomised algorithm which is more efficient
for larger data sets.
biocViews: Microarray, Clustering
Author: Rich Savage, Emma Cooke, Robert Darkins, Yang Xu
Maintainer: Rich Savage <r.s.savage@warwick.ac.uk>
MD5sum: 1a3b218e444a7b8f94659ec70ecf72ee
source.ver: src/contrib/BHC_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BHC_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BHC_1.10.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BHC_1.10.0.tgz
vignettes: vignettes/BHC/inst/doc/bhc.pdf
vignetteTitles: Bayesian Hierarchical Clustering
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BHC/inst/doc/bhc.R
Package: BicARE
Version: 1.16.0
Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase
License: GPL-2
Archs: i386, x64
Title: Biclustering Analysis and Results Exploration
Description: Biclustering Analysis and Results Exploration
biocViews: Microarray, Transcription, Bioinformatics, Clustering
Author: Pierre Gestraud
Maintainer: Pierre Gestraud <pierre.gestraud@curie.fr>
URL: http://bioinfo.curie.fr
MD5sum: fa6e0d850d00911fa955df05a29e9b6a
source.ver: src/contrib/BicARE_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BicARE_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BicARE_1.16.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/BicARE_1.16.0.tgz
vignettes: vignettes/BicARE/inst/doc/BicARE.pdf
vignetteTitles: BicARE
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BicARE/inst/doc/BicARE.R
Package: bigmemoryExtras
Version: 1.0.0
Depends: R (>= 2.12), bigmemory (>= 4.3)
Imports: bigmemory, methods, Biobase
Suggests: RUnit, BiocGenerics (>= 0.1.0)
OS_type: unix
License: Artistic-2.0
Title: An extension of the bigmemory package with added safety,
convenience, and a factor class.
Description: This package defines a "BigMatrix" ReferenceClass which
adds safety and convenience features to the
filebacked.big.matrix class from the bigmemory package.
BigMatrix protects against segfaults by monitoring and
gracefully restoring the connection to on-disk data and it also
protects against accidental data modification with a
filesystem-based permissions system. We provide utilities for
using BigMatrix-derived classes as assayData matrices within
the Biobase package's eSet family of classes. BigMatrix
provides some optimizations related to attaching to, and
indexing into, file-backed matrices with dimnames.
Additionally, the package provides a "BigMatrixFactor" class, a
file-backed matrix with factor properties.
biocViews: Infrastructure, DataRepresentation
Author: Peter M. Haverty
Maintainer: Peter M. Haverty <phaverty@gene.com>
MD5sum: 4fb351c4218f8240a6bd1aa0f8a42f93
source.ver: src/contrib/bigmemoryExtras_1.0.0.tar.gz
mac.binary.leopard.ver:
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vignettes: vignettes/bigmemoryExtras/inst/doc/bigmemoryExtras.pdf
vignetteTitles: bigmemoryExtras
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/bigmemoryExtras/inst/doc/bigmemoryExtras.R
importsMe: gCMAP
Package: Biobase
Version: 2.18.0
Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), utils
Imports: methods, BiocGenerics
Suggests: tools, tkWidgets, ALL
License: Artistic-2.0
Archs: i386, x64
Title: Biobase: Base functions for Bioconductor
Description: Functions that are needed by many other packages or which
replace R functions.
biocViews: Infrastructure, Bioinformatics
Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: 257ffbd8d658368656a1b6778fa38268
source.ver: src/contrib/Biobase_2.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Biobase_2.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Biobase_2.18.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Biobase/inst/doc/BiobaseDevelopment.pdf,
vignettes/Biobase/inst/doc/Bioconductor.pdf,
vignettes/Biobase/inst/doc/esApply.pdf,
vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf,
vignettes/Biobase/inst/doc/HowTo.pdf,
vignettes/Biobase/inst/doc/Qviews.pdf
vignetteTitles: Notes for eSet developers, Bioconductor Overview,
esApply Introduction, An introduction to Biobase and
ExpressionSets, Notes for writing introductory 'how to'
documents, quick views of eSet instances
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Biobase/inst/doc/BiobaseDevelopment.R,
vignettes/Biobase/inst/doc/Bioconductor.R,
vignettes/Biobase/inst/doc/esApply.R,
vignettes/Biobase/inst/doc/ExpressionSetIntroduction.R,
vignettes/Biobase/inst/doc/HowTo.R,
vignettes/Biobase/inst/doc/Qviews.R
dependsOnMe: a4Base, a4Core, ACME, affy, affycomp, affyContam,
affycoretools, affyPLM, affyQCReport, AGDEX, Agi4x44PreProcess,
altcdfenvs, annaffy, AnnotationDbi, AnnotationForge,
ArrayExpress, arrayMvout, ArrayTools, beadarray, beadarraySNP,
bgx, BicARE, BiocCaseStudies, BioMVCClass, BioNet, birta,
BrainStars, CAMERA, cancerclass, Category, categoryCompare,
cellHTS, cellHTS2, CGHbase, CGHcall, CGHregions, charm,
chroGPS, clippda, clusterStab, CMA, cn.farms, cn.mops,
codelink, convert, copa, ddCt, DESeq, DEXSeq, DFP, DSS, dualKS,
dyebias, easyRNASeq, EBarrays, EDASeq, eisa, ExiMiR, fabia,
factDesign, fastseg, flowClust, flowCore, flowWorkspace, frma,
gaga, GeneAnswers, GeneExpressionSignature, GeneMeta,
geneRecommender, GeneRegionScan, GeneSelectMMD, GeneSelector,
genoset, GEOquery, GOFunction, goProfiles, GOstats, GSEABase,
GSEAlm, GWASTools, hapFabia, HELP, hopach, HTqPCR, htSeqTools,
HybridMTest, idiogram, inSilicoDb, inSilicoMerging, isobar,
iterativeBMA, LMGene, lumi, macat, maDB, maSigPro, MergeMaid,
methyAnalysis, methylumi, Mfuzz, MiChip, minfi, MLInterfaces,
MmPalateMiRNA, MSnbase, Mulcom, multtest, NOISeq, NormqPCR,
nucleR, oligo, oneChannelGUI, OrderedList, OTUbase, OutlierD,
PADOG, PAnnBuilder, panp, pcaMethods, pcot2, pdInfoBuilder,
pdmclass, PGSEA, phenoTest, plgem, PLPE, prada, PREDA, PROMISE,
puma, qpcrNorm, R453Plus1Toolbox, RbcBook1, rbsurv, ReadqPCR,
reb, RefPlus, Resourcerer, rHVDM, Ringo, Risa, Rmagpie, rMAT,
RNAinteract, rnaSeqMap, RpsiXML, rqubic, RTopper, Rtreemix,
safe, SCAN.UPC, sigaR, siggenes, simpleaffy, SpeCond, spkTools,
TDARACNE, tigre, tilingArray, topGO, tspair, VegaMC, vsn,
waveTiling, webbioc, XDE
importsMe: ABarray, aCGH, adSplit, affy, affyILM, affyQCReport,
AgiMicroRna, annmap, annotate, AnnotationDbi, AnnotationForge,
annotationTools, ArrayExpressHTS, arrayQualityMetrics,
ArrayTools, attract, betr, bigmemoryExtras, biocViews,
BioSeqClass, BrainStars, bsseq, Category, categoryCompare,
CGHnormaliter, charm, ChIPXpress, ChromHeatMap,
ConsensusClusterPlus, crlmm, cycle, EBarrays, ecolitk, farms,
ffpe, flowCore, flowFlowJo, flowFP, flowMeans, flowQB,
flowStats, flowType, flowUtils, flowViz, flowWorkspace, frma,
frmaTools, gCMAP, gcrma, genefilter, GeneMeta, geneplotter,
geneRecommender, GeneRegionScan, GeneSelectMMD,
genomeIntervals, GenomicFeatures, GEOsubmission, GGBase, ggbio,
GGtools, girafe, globaltest, gmapR, GOFunction, GOstats,
GSEABase, GSRI, GSVA, Gviz, Harshlight, HEM, HiTC, hopach,
HTqPCR, IdMappingAnalysis, iFlow, imageHTS, lapmix,
LiquidAssociation, lumi, maanova, makecdfenv, maSigPro, mBPCR,
MCRestimate, metaArray, methyAnalysis, methylumi, MiChip,
MinimumDistance, MiPP, MmPalateMiRNA, multiscan, mzR, nucleR,
oligoClasses, OrderedList, PADOG, PAnnBuilder, panp,
pcaGoPromoter, PCpheno, plateCore, plier, ppiStats, prada,
PROMISE, puma, pvac, qpgraph, R453Plus1Toolbox, randPack,
ReadqPCR, RGalaxy, Rmagpie, rMAT, rols, rqubic, rSFFreader,
Rtreemix, safe, SAGx, ShortRead, simpleaffy, SLGI, SNPchip,
spade, spkTools, splicegear, synapter, TEQC, tigre, timecourse,
topGO, TSSi, twilight, VanillaICE, VariantAnnotation,
virtualArray, XDE, xmapcore
suggestsMe: annotate, betr, BiocCaseStudies, BiocGenerics, biocViews,
BSgenome, Category, DART, farms, genefilter, genefu,
geneplotter, GlobalAncova, globaltest, Heatplus, les, nem,
OSAT, pkgDepTools, ROC, survcomp, tkWidgets, TypeInfo, vbmp,
widgetTools
Package: BiocCaseStudies
Version: 1.20.0
Depends: tools, methods, utils, Biobase
Suggests: affy (>= 1.17.3), affyPLM (>= 1.15.1), affyQCReport (>=
1.17.0), ALL (>= 1.4.3), annaffy (>= 1.11.1), annotate (>=
1.17.3), AnnotationDbi (>= 1.1.6), apComplex (>= 2.5.0),
Biobase (>= 1.17.5), bioDist (>= 1.11.3), biocGraph (>= 1.1.1),
biomaRt (>= 1.13.5), CCl4 (>= 1.0.6), CLL (>= 1.2.4), Category
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hgu95av2.db, hgu95av2cdf (>= 2.0.0), hgu95av2probe (>= 2.0.0),
hopach (>= 1.13.0), KEGG.db (>= 2.0.2), kohonen (>= 2.0.2),
lattice (>= 0.17.2), latticeExtra (>= 0.3-1), limma (>=
2.13.1), MASS (>= 7.2-38), MLInterfaces (>= 1.13.17), multtest
(>= 1.19.0), org.Hs.eg.db (>= 2.0.2), ppiStats (>= 1.5.4),
randomForest (>= 4.5-20), RBGL (>= 1.15.6), RColorBrewer (>=
1.0-2), Rgraphviz (>= 1.17.11), vsn (>= 3.4.0), weaver (>=
1.5.0), xtable (>= 1.5-2), yeastExpData (>= 0.9.11)
License: Artistic-2.0
Title: BiocCaseStudies: Support for the Case Studies Monograph
Description: Software and data to support the case studies.
biocViews: Infrastructure, Bioinformatics
Author: R. Gentleman, W. Huber, F. Hahne, M. Morgan, S. Falcon
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: a00e75c9713d324c6bfc0971eb1687c3
source.ver: src/contrib/BiocCaseStudies_1.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BiocCaseStudies_1.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BiocCaseStudies_1.20.0.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: BiocGenerics
Version: 0.4.0
Depends: methods, graphics, stats
Imports: methods, graphics, stats
Suggests: Biobase, IRanges, GenomicRanges, AnnotationDbi, oligoClasses,
oligo, affyPLM, RUnit
License: Artistic-2.0
Title: Generic functions for Bioconductor
Description: S4 generic functions needed by many other Bioconductor
packages.
biocViews: Infrastructure
Author: The Bioconductor Dev Team
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: ae874c6b065d87ef8f0e16299070ab5a
source.ver: src/contrib/BiocGenerics_0.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BiocGenerics_0.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BiocGenerics_0.4.0.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: affy, affyPLM, altcdfenvs, AnnotationDbi, AnnotationForge,
beadarray, Biobase, Biostrings, BSgenome, bsseq, Category,
categoryCompare, ChIPpeakAnno, chipseq, ChIPseqR, ChromHeatMap,
cn.mops, codelink, cummeRbund, easyRNASeq, EDASeq, eisa, flowQ,
flowWorkspace, genomeIntervals, GenomicFeatures, GenomicRanges,
Genominator, genoset, GSEABase, gwascat, htSeqTools, IRanges,
KEGGSOAP, MEDIPS, minfi, MinimumDistance, MotIV, MSnbase,
nucleR, oligo, oligoClasses, PICS, R453Plus1Toolbox, REDseq,
Repitools, rMAT, rsbml, ShortRead, simpleaffy, TEQC, tigre,
TSSi
importsMe: affy, affyPLM, annmap, annotate, AnnotationDbi,
AnnotationForge, beadarray, Biobase, biocGraph, Biostrings,
biovizBase, Category, categoryCompare, cghMCR, ChIPpeakAnno,
chipseq, ChromHeatMap, cn.mops, codelink, crlmm, cummeRbund,
EDASeq, eisa, fastseg, ffpe, flowCore, flowFP, flowMerge,
flowQ, flowStats, frma, GenomicFeatures, GenomicRanges, GGBase,
ggbio, GGtools, graph, GSEABase, GSVA, Gviz, HTSeqGenie,
IRanges, LVSmiRNA, MEDIPS, methylumi, minfi, MinimumDistance,
MiRaGE, MotifDb, MotIV, nucleR, oligo, oligoClasses,
OrganismDbi, pcaMethods, PING, prada, R453Plus1Toolbox,
RCytoscape, REDseq, Repitools, RGalaxy, Ringo, rMAT, Rsamtools,
rsbml, rtracklayer, ShortRead, simpleaffy, SLGI, snpStats,
Streamer, tigre, triform, TSSi, VariantAnnotation,
VariantTools, XDE
suggestsMe: bigmemoryExtras, BiocInstaller, CellNOptR, ChIPXpress,
CNORfuzzy, DBChIP, gCMAP, GeneNetworkBuilder, GOstats,
inSilicoMerging, motifStack, Rcade, Rgraphviz
Package: biocGraph
Version: 1.20.0
Depends: Rgraphviz, graph
Imports: Rgraphviz, geneplotter, graph, BiocGenerics, methods
Suggests: fibroEset, geneplotter, hgu95av2.db
License: Artistic-2.0
Title: Graph examples and use cases in Bioinformatics
Description: This package provides examples and code that make use of
the different graph related packages produced by Bioconductor.
biocViews: NetworkVisualization, GraphsAndNetworks
Author: Li Long <li.long@isb-sib.ch>, Robert Gentleman
<rgentlem@fhcrc.org>, Seth Falcon <sethf@fhcrc.org> Florian
Hahne <fhahne@fhcrc.org>
Maintainer: Florian Hahne <florian.hahne@novartis.com>
MD5sum: 460d406131cee79d0033129261f4aefb
source.ver: src/contrib/biocGraph_1.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/biocGraph_1.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/biocGraph_1.20.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/biocGraph/inst/doc/biocGraph.pdf,
vignettes/biocGraph/inst/doc/layingOutPathways.pdf
vignetteTitles: Examples of plotting graphs Using Rgraphviz, HOWTO
layout pathways
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/biocGraph/inst/doc/biocGraph.R,
vignettes/biocGraph/inst/doc/layingOutPathways.R
suggestsMe: BiocCaseStudies
Package: BiocInstaller
Version: 1.8.3
Depends: R (>= 2.15.0)
Suggests: RUnit, BiocGenerics
License: Artistic-2.0
Title: Install/Update Bioconductor and CRAN Packages
Description: Installs/updates Bioconductor and CRAN packages
biocViews: Software
Author: Dan Tenenbaum and Biocore Team
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: c19dedfa043497076ecad08f6a78415b
source.ver: src/contrib/BiocInstaller_1.8.3.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BiocInstaller_1.8.3.zip
win64.binary.ver: bin/windows64/contrib/2.15/BiocInstaller_1.8.3.zip
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: affylmGUI
importsMe: affy, gcrma, oligoClasses, webbioc
suggestsMe: pkgDepTools
Package: biocViews
Version: 1.26.0
Depends: R (>= 2.4.0)
Imports: Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools,
utils, XML, RCurl, RUnit
Suggests: Biobase
License: Artistic-2.0
Title: Categorized views of R package repositories
Description: structures for vocabularies and narratives of views
biocViews: Infrastructure
Author: VJ Carey <stvjc@channing.harvard.edu>, BJ Harshfield
<rebjh@channing.harvard.edu>, S Falcon <sfalcon@fhcrc.org>
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
URL: http://www.bioconductor.org/packages/release/BiocViews.html
MD5sum: 42a8ab74075ac7bd36360fea33ed8ce5
source.ver: src/contrib/biocViews_1.26.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/biocViews_1.26.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/biocViews_1.26.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/biocViews/inst/doc/createReposHtml.pdf,
vignettes/biocViews/inst/doc/HOWTO-BCV.pdf
vignetteTitles: biocViews-CreateRepositoryHTML, biocViews-HOWTO
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/biocViews/inst/doc/createReposHtml.R,
vignettes/biocViews/inst/doc/HOWTO-BCV.R
Package: bioDist
Version: 1.30.0
Depends: R (>= 2.0), methods, Biobase,KernSmooth
Suggests: locfit
License: Artistic-2.0
Title: Different distance measures
Description: A collection of software tools for calculating distance
measures.
biocViews: Bioinformatics
Author: B. Ding, R. Gentleman and Vincent Carey
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: 87d77ba501dac6091f3c5e0e535c3abb
source.ver: src/contrib/bioDist_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/bioDist_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/bioDist_1.30.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/bioDist/inst/doc/bioDist.pdf
vignetteTitles: bioDist Introduction
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/bioDist/inst/doc/bioDist.R
dependsOnMe: flowQ
suggestsMe: BiocCaseStudies
Package: biomaRt
Version: 2.14.0
Depends: methods
Imports: utils, XML, RCurl
Suggests: annotate
License: Artistic-2.0
Title: Interface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase
and Gramene)
Description: In recent years a wealth of biological data has become
available in public data repositories. Easy access to these
valuable data resources and firm integration with data analysis
is needed for comprehensive bioinformatics data analysis.
biomaRt provides an interface to a growing collection of
databases implementing the BioMart software suite
(http://www.biomart.org). The package enables retrieval of
large amounts of data in a uniform way without the need to know
the underlying database schemas or write complex SQL queries.
Examples of BioMart databases are Ensembl, COSMIC, Uniprot,
HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These
major databases give biomaRt users direct access to a diverse
set of data and enable a wide range of powerful online queries
from gene annotation to database mining.
biocViews: Annotation
Author: Steffen Durinck <sdurinck@gmail.com>, Wolfgang Huber
<huber@ebi.ac.uk>
Maintainer: Steffen Durinck <sdurinck@gmail.com>
MD5sum: b428114e02b5f8d34ff541e86c7b0fd5
source.ver: src/contrib/biomaRt_2.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/biomaRt_2.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/biomaRt_2.14.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/biomaRt/inst/doc/biomaRt.pdf
vignetteTitles: The biomaRt users guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/biomaRt/inst/doc/biomaRt.R
dependsOnMe: ChIPpeakAnno, domainsignatures, easyRNASeq, gene2pathway,
genefu, GenomeGraphs, VegaMC
importsMe: affycoretools, ArrayExpressHTS, ChIPpeakAnno, DEXSeq,
GenomicFeatures, Gviz, HTSanalyzeR, IdMappingRetrieval,
methyAnalysis, phenoTest, R453Plus1Toolbox, RNAither
suggestsMe: BiocCaseStudies, GeneAnswers, GenomicFeatures, Genominator,
isobar, maDB, MiRaGE, oneChannelGUI, Rcade, ShortRead, SIM
Package: BioMVCClass
Version: 1.26.0
Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz
License: LGPL
Title: Model-View-Controller (MVC) Classes That Use Biobase
Description: Creates classes used in model-view-controller (MVC) design
biocViews: Visualization, Infrastructure, GraphsAndNetworks
Author: Elizabeth Whalen
Maintainer: Elizabeth Whalen <ewhalen@hsph.harvard.edu>
MD5sum: 6ac6df752b6c8028af0c8d29bdbfa590
source.ver: src/contrib/BioMVCClass_1.26.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BioMVCClass_1.26.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BioMVCClass_1.26.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/BioMVCClass/inst/doc/BioMVCClass.pdf
vignetteTitles: BioMVCClass
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BioMVCClass/inst/doc/BioMVCClass.R
Package: BioNet
Version: 1.16.0
Depends: R (>= 2.10.0), Biobase, graph, RBGL
Imports: igraph0, AnnotationDbi
Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma,
hgu95av2.db, XML
License: GPL (>= 2)
Title: Routines for the functional analysis of biological networks
Description: This package provides functions for the integrated
analysis of protein-protein interaction networks and the
detection of functional modules. Different datasets can be
integrated into the network by assigning p-values of
statistical tests to the nodes of the network. E.g. p-values
obtained from the differential expression of the genes from an
Affymetrix array are assigned to the nodes of the network. By
fitting a beta-uniform mixture model and calculating scores
from the p-values, overall scores of network regions can be
calculated and an integer linear programming algorithm
identifies the maximum scoring subnetwork.
biocViews: Microarray, DataImport, GraphsAndNetworks, NetworkAnalysis,
NetworkEnrichment, GeneExpression, DifferentialExpression
Author: Marcus Dittrich and Daniela Beisser
Maintainer: Marcus Dittrich
<marcus.dittrich@biozentrum.uni-wuerzburg.de>
URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/
MD5sum: be4610be34282c228c94733848cc1546
source.ver: src/contrib/BioNet_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BioNet_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BioNet_1.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/BioNet/inst/doc/bum1.pdf,
vignettes/BioNet/inst/doc/bum2.pdf,
vignettes/BioNet/inst/doc/cytoscape.pdf,
vignettes/BioNet/inst/doc/prec_recall_large.pdf,
vignettes/BioNet/inst/doc/prec_recall_small.pdf,
vignettes/BioNet/inst/doc/Tutorial-3dplot.pdf,
vignettes/BioNet/inst/doc/Tutorial.pdf
vignetteTitles: bum1.pdf, bum2.pdf, cytoscape.pdf,
prec_recall_large.pdf, prec_recall_small.pdf,
Tutorial-3dplot.pdf, BioNet Tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BioNet/inst/doc/Tutorial.R
importsMe: HTSanalyzeR
Package: BioSeqClass
Version: 1.16.0
Depends: R (>= 2.10), scatterplot3d
Imports: Biostrings, ipred, e1071, klaR, randomForest, class, tree,
nnet, rpart, party, foreign, Biobase, utils, stats, grDevices
Suggests: scatterplot3d
License: LGPL (>= 2.0)
Title: Classification for Biological Sequences
Description: Extracting Features from Biological Sequences and Building
Classification Model
biocViews: Classification
Author: Li Hong sysptm@gmail.com
Maintainer: Li Hong <sysptm@gmail.com>
MD5sum: df29825d9db5a7602a6055df62e99e37
source.ver: src/contrib/BioSeqClass_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BioSeqClass_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BioSeqClass_1.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/BioSeqClass/inst/doc/BioSeqClass.pdf,
vignettes/BioSeqClass/inst/doc/cvFFSClassify0005.pdf,
vignettes/BioSeqClass/inst/doc/FeatureSets16.pdf,
vignettes/BioSeqClass/inst/doc/workflow.pdf
vignetteTitles: Using the BioSeqClass Package, cvFFSClassify0005.pdf,
FeatureSets16.pdf, workflow.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BioSeqClass/inst/doc/BioSeqClass.R
Package: Biostrings
Version: 2.26.3
Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.1.2), IRanges (>=
1.15.37)
Imports: graphics, methods, stats, utils, BiocGenerics, IRanges
LinkingTo: IRanges
Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=
1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),
BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,
hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy,
affydata (>= 1.11.5), RUnit
Enhances: Rmpi
License: Artistic-2.0
Archs: i386, x64
Title: String objects representing biological sequences, and matching
algorithms
Description: Memory efficient string containers, string matching
algorithms, and other utilities, for fast manipulation of large
biological sequences or sets of sequences.
biocViews: SequenceMatching, Genetics, Sequencing, Infrastructure,
DataImport, DataRepresentation
Author: H. Pages, P. Aboyoun, R. Gentleman, and S. DebRoy
Maintainer: H. Pages <hpages@fhcrc.org>
MD5sum: 7c7c1eef1ccd2208fd54118422bc9d91
source.ver: src/contrib/Biostrings_2.26.3.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Biostrings_2.26.3.zip
win64.binary.ver: bin/windows64/contrib/2.15/Biostrings_2.26.3.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Biostrings/inst/doc/Biostrings2Classes.pdf,
vignettes/Biostrings/inst/doc/matchprobes.pdf,
vignettes/Biostrings/inst/doc/MultipleAlignments.pdf,
vignettes/Biostrings/inst/doc/PairwiseAlignments.pdf
vignetteTitles: A short presentation of the basic classes defined in
Biostrings 2, Handling probe sequence information, Multiple
Alignments, Pairwise Sequence Alignments
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Biostrings/inst/doc/Biostrings2Classes.R,
vignettes/Biostrings/inst/doc/matchprobes.R,
vignettes/Biostrings/inst/doc/MultipleAlignments.R,
vignettes/Biostrings/inst/doc/PairwiseAlignments.R
dependsOnMe: altcdfenvs, BRAIN, BSgenome, ChIPpeakAnno, ChIPsim,
CorMut, DECIPHER, deepSNV, easyRNASeq, GeneRegionScan, genomes,
iPAC, minfi, MotifDb, oneChannelGUI, PWMEnrich, qrqc,
R453Plus1Toolbox, REDseq, rGADEM, Rsamtools, rSFFreader,
SCAN.UPC, seqbias, ShortRead, waveTiling
importsMe: AffyCompatible, ArrayExpressHTS, BCRANK, BioSeqClass,
biovizBase, charm, ChIPpeakAnno, ChIPseqR, ChIPsim, DECIPHER,
gcrma, GeneRegionScan, GenomicFeatures, girafe, gmapR, Gviz,
gwascat, HiTC, HTSeqGenie, MEDIPS, MEDME, methVisual, microRNA,
motifRG, MotIV, oligo, oligoClasses, OTUbase, pdInfoBuilder,
qrqc, R453Plus1Toolbox, REDseq, rGADEM, Rolexa, Rsamtools,
rSFFreader, rtracklayer, ShortRead, VariantAnnotation,
VariantTools
suggestsMe: annotate, CSAR, exomeCopy, GenomicFeatures, GenomicRanges,
microRNA, MiRaGE, pcaGoPromoter, procoil
Package: biovizBase
Version: 1.6.2
Depends: R (>= 2.10), methods
Imports: methods, stats, grDevices, scales, Hmisc, RColorBrewer,
dichromat, BiocGenerics, IRanges, GenomicRanges, Biostrings,
Rsamtools, GenomicFeatures
Suggests: BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer
License: Artistic-2.0
Archs: i386, x64
Title: Basic graphic utilities for visualization of genomic data.
Description: The biovizBase package is designed to provide a set of
utilities, color schemes and conventions for genomic data. It
serves as the base for various high-level packages for
biological data visualization. This saves development effort
and encourages consistency.
biocViews: Infrastructure, Visualization, Bioinformatics, Preprocessing
Author: Tengfei Yin, Michael Lawrence, Dianne Cook
Maintainer: Tengfei Yin <yintengfei@gmail.com>
MD5sum: 2747e9a13a58dcc36ee213ad76582f5d
source.ver: src/contrib/biovizBase_1.6.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/biovizBase_1.6.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/biovizBase_1.6.2.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/biovizBase_1.6.2.tgz
vignettes: vignettes/biovizBase/inst/doc/intro.pdf,
vignettes/biovizBase/inst/doc/intro-shrinkageFun.pdf,
vignettes/biovizBase/inst/doc/intro-shrink-single.pdf
vignetteTitles: An Introduction to biovizBase, intro-shrinkageFun.pdf,
intro-shrink-single.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/biovizBase/inst/doc/intro.R
dependsOnMe: qrqc
importsMe: Gviz, qrqc
Package: birta
Version: 1.2.0
Depends: limma, MASS, R(>= 2.10), Biobase, methods
License: GPL (>= 2)
Archs: i386, x64
Title: Bayesian Inference of Regulation of Transcriptional Activity
Description: Expression levels of mRNA molecules are regulated by
different processes, comprising inhibition or activation by
transcription factors and post-transcriptional degradation by
microRNAs. birta (Bayesian Inference of Regulation of
Transcriptional Activity) uses the regulatory networks of TFs
and miRNAs together with mRNA and miRNA expression data to
predict switches in regulatory activity between two conditions.
A Bayesian network is used to model the regulatory structure
and Markov-Chain-Monte-Carlo is applied to sample the activity
states.
biocViews: Microarray, Sequencing, GeneExpression, Transcription,
Bioinformatics, GraphsAndNetworks
Author: Benedikt Zacher, Khalid Abnaof, Stephan Gade, Erfan Younesi,
Achim Tresch, Holger Froehlich
Maintainer: Benedikt Zacher <zacher@lmb.uni-muenchen.de>
MD5sum: 281f765d143412599f6ce32cad7b850c
source.ver: src/contrib/birta_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/birta_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/birta_1.2.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/birta_1.2.0.tgz
vignettes: vignettes/birta/inst/doc/birta.pdf
vignetteTitles: Bayesian Inference of Regulation of Transcriptional
Activity
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/birta/inst/doc/birta.R
Package: BitSeq
Version: 1.2.2
Depends: Rsamtools, zlibbioc
Imports: IRanges
LinkingTo: Rsamtools, zlibbioc
License: Artistic-2.0
Archs: i386, x64
Title: Transcript expression inference and differential expression
analysis for RNA-seq data
Description: The BitSeq package is targeted for transcript expression
analysis and differential expression analysis of RNA-seq data
in two stage process. In the first stage it uses Bayesian
inference methodology to infer expression of individual
transcripts from individual RNA-seq experiments. The second
stage of BitSeq embraces the differential expression analysis
of transcript expression. Providing expression estimates from
replicates of multiple conditions, Log-Normal model of the
estimates is used for inferring the condition mean transcript
expression and ranking the transcripts based on the likelihood
of differential expression.
biocViews: GeneExpression, DifferentialExpression,
HighThroughputSequencing, RNAseq
Author: Peter Glaus, Antti Honkela and Magnus Rattray
Maintainer: Peter Glaus <glaus@cs.man.ac.uk>
MD5sum: 85acf969f5f3ddded6caf5b393a7ea04
source.ver: src/contrib/BitSeq_1.2.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BitSeq_1.2.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/BitSeq_1.2.2.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/BitSeq_1.2.2.tgz
vignettes: vignettes/BitSeq/inst/doc/BitSeq.pdf
vignetteTitles: BitSeq User Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/BitSeq/inst/doc/BitSeq.R
Package: BRAIN
Version: 1.4.0
Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice
License: GPL-2
Title: Baffling Recursive Algorithm for Isotope distributioN
calculations
Description: Package for calculating aggregated isotopic distribution
and exact center-masses for chemical substances (in this
version composed of C, H, N, O and S). This is an
implementation of the BRAIN algorithm described in the paper by
J. Claesen, P. Dittwald, T. Burzykowski and D. Valkenborg.
biocViews: Bioinformatics, MassSpectrometry, Proteomics
Author: Piotr Dittwald, with contributions of Dirk Valkenborg and
Jurgen Claesen
Maintainer: Piotr Dittwald <piotr.dittwald@mimuw.edu.pl>
MD5sum: 4f4331ff03c725f707ffd580eb37f3b5
source.ver: src/contrib/BRAIN_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BRAIN_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BRAIN_1.4.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BRAIN_1.4.0.tgz
vignettes: vignettes/BRAIN/inst/doc/BRAIN-vignette.pdf
vignetteTitles: BRAIN Usage
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BRAIN/inst/doc/BRAIN-vignette.R
Package: BrainStars
Version: 1.2.0
Depends: RCurl, Biobase, methods
Imports: RJSONIO, Biobase
License: Artistic-2.0
Title: query gene expression data and plots from BrainStars (B*)
Description: This package can search and get gene expression data and
plots from BrainStars (B*). BrainStars is a quantitative
expression database of the adult mouse brain. The database has
genome-wide expression profile at 51 adult mouse CNS regions.
biocViews: Microarray, OneChannel, DataImport
Author: Itoshi NIKAIDO <dritoshi@gmail.com>
Maintainer: Itoshi NIKAIDO <dritoshi@gmail.com>
MD5sum: 1dce773fdd849fff860981889eeaac5c
source.ver: src/contrib/BrainStars_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BrainStars_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BrainStars_1.2.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/BrainStars/inst/doc/BrainStars.pdf
vignetteTitles: BrainStars
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BrainStars/inst/doc/BrainStars.R
Package: bridge
Version: 1.22.0
Depends: R (>= 1.9.0), rama
License: GPL (>= 2)
Archs: i386, x64
Title: Bayesian Robust Inference for Differential Gene Expression
Description: Test for differentially expressed genes with microarray
data. This package can be used with both cDNA microarrays or
Affymetrix chip. The packge fits a robust Bayesian hierarchical
model for testing for differential expression. Outliers are
modeled explicitly using a $t$-distribution. The model includes
an exchangeable prior for the variances which allow different
variances for the genes but still shrink extreme empirical
variances. Our model can be used for testing for differentially
expressed genes among multiple samples, and can distinguish
between the different possible patterns of differential
expression when there are three or more samples. Parameter
estimation is carried out using a novel version of Markov Chain
Monte Carlo that is appropriate when the model puts mass on
subspaces of the full parameter space.
biocViews: Microarray,OneChannel,TwoChannel,DifferentialExpression
Author: Raphael Gottardo
Maintainer: Raphael Gottardo <raph@stat.ubc.ca>
MD5sum: 2ea6f721a75103edf6fccf623ff2be48
source.ver: src/contrib/bridge_1.22.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/bridge_1.22.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/bridge_1.22.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/bridge_1.22.0.tgz
vignettes: vignettes/bridge/inst/doc/bridge.pdf
vignetteTitles: bridge Tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/bridge/inst/doc/bridge.R
Package: BSgenome
Version: 1.26.1
Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.1.2), IRanges (>=
1.13.6), GenomicRanges (>= 1.7.5), Biostrings (>= 2.23.3)
Suggests: RUnit, BSgenome.Celegans.UCSC.ce2 (>= 1.3.11),
BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.11),
SNPlocs.Hsapiens.dbSNP.20100427, hgu95av2probe, Biobase
License: Artistic-2.0
Title: Infrastructure for Biostrings-based genome data packages
Description: Infrastructure shared by all the Biostrings-based genome
data packages
biocViews: Genetics, Infrastructure, DataRepresentation,
SequenceMatching, Annotation, SNP
Author: Herve Pages
Maintainer: H. Pages <hpages@fhcrc.org>
MD5sum: c46bfe6388f351c7ee7a034e63fd784d
source.ver: src/contrib/BSgenome_1.26.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BSgenome_1.26.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/BSgenome_1.26.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/BSgenome_1.26.1.tgz
vignettes: vignettes/BSgenome/inst/doc/BSgenomeForge.pdf,
vignettes/BSgenome/inst/doc/GenomeSearching.pdf
vignetteTitles: How to forge a BSgenome data package, Efficient genome
searching with Biostrings and the BSgenome data packages
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BSgenome/inst/doc/BSgenomeForge.R,
vignettes/BSgenome/inst/doc/GenomeSearching.R
dependsOnMe: ChIPpeakAnno, chipseq, easyRNASeq, htSeqTools, MEDIPS,
REDseq, rGADEM
importsMe: charm, ChIPpeakAnno, chipseq, ggbio, girafe, Gviz, MEDIPS,
PING, R453Plus1Toolbox, Repitools, rtracklayer,
VariantAnnotation
suggestsMe: Biostrings, biovizBase, GeneRegionScan, GenomicFeatures,
GenomicRanges, MiRaGE, oneChannelGUI, Repitools, waveTiling
Package: bsseq
Version: 0.6.2
Depends: R (>= 2.15), methods, BiocGenerics, IRanges, GenomicRanges,
parallel, matrixStats
Imports: scales, stats, graphics, Biobase, locfit
Suggests: RUnit, bsseqData
License: Artistic-2.0
Title: Analyze, manage and store bisulfite sequencing data
Description: Tools for analyzing and visualizing bisulfite sequencing
data
biocViews: DNAMethylation
Author: Kasper Daniel Hansen
Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
MD5sum: b34a4cdf94079b0069fa6cf3805850bf
source.ver: src/contrib/bsseq_0.6.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/bsseq_0.6.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/bsseq_0.6.2.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bsseq_0.6.2.tgz
vignettes: vignettes/bsseq/inst/doc/bsseq_analysis.pdf,
vignettes/bsseq/inst/doc/bsseq.pdf
vignetteTitles: Analyzing WGBS with bsseq, The bsseq user's guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/bsseq/inst/doc/bsseq_analysis.R,
vignettes/bsseq/inst/doc/bsseq.R
Package: BufferedMatrix
Version: 1.22.0
Depends: R (>= 2.6.0), methods
License: LGPL (>= 2)
Archs: i386, x64
Title: A matrix data storage object held in temporary files
Description: A tabular style data object where most data is stored
outside main memory. A buffer is used to speed up access to
data.
biocViews: Infrastructure
Author: Benjamin Milo Bolstad <bmb@bmbolstad.com>
Maintainer: Benjamin Milo Bolstad <bmb@bmbolstad.com>
MD5sum: 37d5814a67dbc7883e1bedb9e8c9acf2
source.ver: src/contrib/BufferedMatrix_1.22.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BufferedMatrix_1.22.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BufferedMatrix_1.22.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/BufferedMatrix_1.22.0.tgz
vignettes: vignettes/BufferedMatrix/inst/doc/BufferedMatrix.pdf,
vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture1.pdf,
vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture2.pdf,
vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture3.pdf,
vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture4.pdf,
vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture5.pdf
vignetteTitles: BufferedMatrix: Introduction,
BufferedMatrixPicture1.pdf, BufferedMatrixPicture2.pdf,
BufferedMatrixPicture3.pdf, BufferedMatrixPicture4.pdf,
BufferedMatrixPicture5.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BufferedMatrix/inst/doc/BufferedMatrix.R
dependsOnMe: BufferedMatrixMethods
Package: BufferedMatrixMethods
Version: 1.22.0
Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods
LinkingTo: BufferedMatrix
Suggests: affyio, affy
License: GPL (>= 2)
Archs: i386, x64
Title: Microarray Data related methods that utlize BufferedMatrix
objects
Description: Microarray analysis methods that use BufferedMatrix
objects
biocViews: Infrastructure
Author: B. M. Bolstad <bmb@bmbolstad.com>
Maintainer: B. M. Bolstad <bmb@bmbolstad.com>
URL: http://www.bmbolstad.com
MD5sum: 48df2e667dd72e60cb7a7b5b241a8872
source.ver: src/contrib/BufferedMatrixMethods_1.22.0.tar.gz
win.binary.ver:
bin/windows/contrib/2.15/BufferedMatrixMethods_1.22.0.zip
win64.binary.ver:
bin/windows64/contrib/2.15/BufferedMatrixMethods_1.22.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/BufferedMatrixMethods_1.22.0.tgz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: BUS
Version: 1.14.0
Depends: R (>= 2.3.0), minet
Imports: stats
License: GPL-3
Archs: i386, x64
Title: Gene network reconstruction
Description: This package can be used to compute associations among
genes (gene-networks) or between genes and some external traits
(i.e. clinical).
biocViews: Preprocessing
Author: Yin Jin, Hesen Peng, Lei Wang, Raffaele Fronza, Yuanhua Liu and
Christine Nardini
Maintainer: Yuanhua Liu <liuyuanhua@picb.ac.cn>
MD5sum: 3724c24dac70c36eb8bb58962c1ada02
source.ver: src/contrib/BUS_1.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/BUS_1.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/BUS_1.14.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BUS_1.14.0.tgz
vignettes: vignettes/BUS/inst/doc/bus.pdf
vignetteTitles: bus.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/BUS/inst/doc/bus.R
Package: CALIB
Version: 1.24.0
Depends: R (>= 2.10), limma, methods
Imports: limma, methods, graphics, stats, utils
License: LGPL
Archs: i386, x64
Title: Calibration model for estimating absolute expression levels from
microarray data
Description: This package contains functions for normalizing spotted
microarray data, based on a physically motivated calibration
model. The model parameters and error distributions are
estimated from external control spikes.
biocViews: Microarray,TwoChannel,Preprocessing
Author: Hui Zhao, Kristof Engelen, Bart De Moor and Kathleen Marchal
Maintainer: Hui Zhao <hui.zhao@biw.kuleuven.be>
MD5sum: b87a23e79e4473ada38d6748b65a2198
source.ver: src/contrib/CALIB_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CALIB_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/CALIB_1.24.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/CALIB_1.24.0.tgz
vignettes: vignettes/CALIB/inst/doc/quickstart.pdf,
vignettes/CALIB/inst/doc/readme.pdf
vignetteTitles: CALIB Overview, readme.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CALIB/inst/doc/quickstart.R
Package: CAMERA
Version: 1.14.0
Depends: R (>= 2.1.0), methods, Biobase, xcms (>= 1.13.5), igraph
Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils,
Hmisc, igraph
Suggests: faahKO, RUnit
Enhances: Rmpi, snow
License: GPL (>= 2)
Archs: i386, x64
Title: Collection of annotation related methods for mass spectrometry
data
Description: Annotation of peaklists generated by xcms, rule based
annotation of isotopes and adducts, EIC correlation based
tagging of unknown adducts and fragments
biocViews: MassSpectrometry
Author: Carsten Kuhl, Ralf Tautenhahn, Steffen Neumann
{ckuhl|sneumann}@ipb-halle.de, rtautenh@scripps.edu
Maintainer: Carsten Kuhl <ckuhl@ipb-halle.de>
URL: http://msbi.ipb-halle.de/msbi/CAMERA/
MD5sum: 865ace52149237e62cf6e69be3c1bd9f
source.ver: src/contrib/CAMERA_1.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CAMERA_1.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/CAMERA_1.14.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/CAMERA_1.14.0.tgz
vignettes: vignettes/CAMERA/inst/doc/CAMERA.pdf
vignetteTitles: Molecule Identification with CAMERA
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CAMERA/inst/doc/CAMERA.R
Package: cancerclass
Version: 1.2.1
Depends: R (>= 2.10.1), Biobase, binom, methods, stats
Suggests: cancerdata
License: GPL 3
Archs: i386, x64
Title: Development and validation of diagnostic tests from
high-dimensional molecular data
Description: The classification protocol starts with a feature
selection step and continues with nearest-centroid
classification. The accurarcy of the predictor can be evaluated
using training and test set validation, leave-one-out
cross-validation or in a multiple random validation protocol.
Methods for calculation and visualization of continuous
prediction scores allow to balance sensitivity and specificity
and define a cutoff value according to clinical requirements.
biocViews: Cancer, Microarray, Classification, Visualization
Author: Jan Budczies, Daniel Kosztyla
Maintainer: Daniel Kosztyla <danielkossi@hotmail.com>
MD5sum: dfcffaf3a88afd7f490d35af520863be
source.ver: src/contrib/cancerclass_1.2.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/cancerclass_1.2.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/cancerclass_1.2.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/cancerclass_1.2.1.tgz
vignettes: vignettes/cancerclass/inst/doc/vignette_cancerclass.pdf
vignetteTitles: Cancerclass: An R package for development and
validation of diagnostic tests from high-dimensional molecular
data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/cancerclass/inst/doc/vignette_cancerclass.R
Package: CancerMutationAnalysis
Version: 1.2.1
Depends: R (>= 2.10.0), qvalue
Imports: AnnotationDbi, limma, methods, stats
Suggests: KEGG.db
License: GPL (>= 2) + file LICENSE
Archs: i386, x64
Title: Cancer mutation analysis
Description: This package implements gene and gene-set level analysis
methods for somatic mutation studies of cancer. The gene-level
methods distinguish between driver genes (which play an active
role in tumorigenesis) and passenger genes (which are mutated
in tumor samples, but have no role in tumorigenesis) and
incorporate a two-stage study design. The gene-set methods
implement a patient-oriented approach, which calculates
gene-set scores for each sample, then combines them across
samples; a gene-oriented approach which uses the Wilcoxon test
is also provided for comparison.
biocViews: Genetics, Bioinformatics, Software
Author: Giovanni Parmigiani, Simina M. Boca
Maintainer: Simina M. Boca <simina.boca@nih.gov>
MD5sum: 9a6fa2e56afe3c989fac4391b9be1905
source.ver: src/contrib/CancerMutationAnalysis_1.2.1.tar.gz
win.binary.ver:
bin/windows/contrib/2.15/CancerMutationAnalysis_1.2.1.zip
win64.binary.ver:
bin/windows64/contrib/2.15/CancerMutationAnalysis_1.2.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/CancerMutationAnalysis_1.2.1.tgz
vignettes:
vignettes/CancerMutationAnalysis/inst/doc/CancerMutationAnalysis.pdf
vignetteTitles: CancerMutationAnalysisTutorial
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Package: Category
Version: 2.24.0
Depends: BiocGenerics (>= 0.3.2), AnnotationDbi (>= 0.1.15), Biobase
(>= 2.17.8), methods
Imports: BiocGenerics, graph, methods, Biobase, AnnotationDbi, RBGL,
GSEABase (>= 1.19.3), genefilter, annotate (>= 1.15.6), stats,
utils
Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6),
hgu95av2.db, Matrix, KEGG.db, GO.db, SNPchip (>= 2.3.11),
geneplotter, limma, lattice, graph, Biobase, genefilter,
methods, RUnit, org.Sc.sgd.db, GOstats
License: Artistic-2.0
Title: Category Analysis
Description: A collection of tools for performing category analysis.
biocViews: Annotation, GO, Pathways, GeneSetEnrichment
Author: R. Gentleman with contributions from S. Falcon and D.Sarkar
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: a697c428c036065d7cb40f4636a47f15
source.ver: src/contrib/Category_2.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Category_2.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Category_2.24.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/Category_2.24.0.tgz
vignettes: vignettes/Category/inst/doc/Category.pdf,
vignettes/Category/inst/doc/ChromBand.pdf
vignetteTitles: Using Categories to Analyze Microarray Data, Using
Chromosome Bands as Categories
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Category/inst/doc/Category.R,
vignettes/Category/inst/doc/ChromBand.R
dependsOnMe: categoryCompare, eisa, GOstats, PCpheno
importsMe: categoryCompare, cellHTS2, gCMAP, GOstats, PCpheno,
phenoTest, ppiStats
suggestsMe: BiocCaseStudies, cellHTS, MmPalateMiRNA, qpgraph
Package: categoryCompare
Version: 1.2.0
Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8),
AnnotationDbi (>= 0.1.15), Category (>= 2.23.4)
Imports: BiocGenerics, Biobase, AnnotationDbi, hwriter, GSEABase,
Category, GOstats, annotate, colorspace, graph, RCytoscape (>=
1.5.11)
Suggests: methods, GSEABase, hwriter, colorspace, graph, GO.db,
KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy,
genefilter
License: GPL-2
Title: Meta-analysis of high-throughput experiments using feature
annotations
Description: Calculates significant annotations (categories) in each of
two (or more) feature (i.e. gene) lists, determines the overlap
between the annotations, and returns graphical and tabular data
about the significant annotations and which combinations of
feature lists the annotations were found to be significant.
Interactive exploration is facilitated through the use of
RCytoscape (heavily suggested).
biocViews: Bioinformatics, Annotation, GO, MultipleComparisons,
Pathways, GeneExpression
Author: Robert M. Flight <rflight79@gmail.com>
Maintainer: Robert M. Flight <rflight79@gmail.com>
SystemRequirements: Cytoscape (>= 2.8.0) (if used for visualization of
results, heavily suggested), CytoscapeRPC plugin (>= 1.8)
MD5sum: bf723461486857213fad9dba7f9ab213
source.ver: src/contrib/categoryCompare_1.2.0.tar.gz
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win64.binary.ver: bin/windows64/contrib/2.15/categoryCompare_1.2.0.zip
mac.binary.leopard.ver:
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vignettes:
vignettes/categoryCompare/inst/doc/categoryCompare_vignette.pdf
vignetteTitles: categoryCompare: High-throughput data meta-analysis
using gene annotations
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: cellGrowth
Version: 1.2.0
Depends: R (>= 2.12.0), locfit (>= 1.5-4)
Imports: lattice
License: Artistic-2.0
Title: Fitting cell population growth models
Description: This package provides functionalities for the fitting of
cell population growth models on experimental OD curves.
biocViews: CellBasedAssays, MicrotitrePlateAssay, DataImport,
Visualization, TimeCourse
Author: Julien Gagneur <gagneur@genzentrum.lmu.de>, Andreas Neudecker
<a.neudecker@arcor.de>
Maintainer: Julien Gagneur <gagneur@genzentrum.lmu.de>
MD5sum: ff03edf6efd6338c16659cffd5252501
source.ver: src/contrib/cellGrowth_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/cellGrowth_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/cellGrowth_1.2.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/cellGrowth/inst/doc/cellGrowth.pdf,
vignettes/cellGrowth/inst/doc/cellGrowth-platePlotex.pdf,
vignettes/cellGrowth/inst/doc/cellGrowth-plotex.pdf,
vignettes/cellGrowth/inst/doc/cellGrowth-welldatex.pdf
vignetteTitles: Overview of the cellGrowth package.,
cellGrowth-platePlotex.pdf, cellGrowth-plotex.pdf,
cellGrowth-welldatex.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/cellGrowth/inst/doc/cellGrowth.R
Package: cellHTS
Version: 1.28.0
Depends: R (>= 2.10), prada (>= 1.9.4), RColorBrewer, Biobase (>=
1.11.12), genefilter (>= 1.11.2)
Suggests: Category, GO.db, vsn (>= 2.0.35)
License: Artistic-2.0
Title: Analysis of cell-based screens
Description: Analysis of cell-based RNA interference screens
biocViews: CellBasedAssays, Visualization
Author: Wolfgang Huber <huber@ebi.ac.uk>, Ligia Bras <ligia@ebi.ac.uk>,
Michael Boutros <m.boutros@dkfz.de>
Maintainer: Ligia Bras <ligia@ebi.ac.uk>
URL: http://www.dkfz.de/signaling, http://www.ebi.ac.uk/huber
MD5sum: 9191b06d838f45b2f7a7582ed4d52a01
source.ver: src/contrib/cellHTS_1.28.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/cellHTS_1.28.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/cellHTS_1.28.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/cellHTS/inst/doc/cellhts.pdf,
vignettes/cellHTS/inst/doc/twoChannels.pdf,
vignettes/cellHTS/inst/doc/twoWay.pdf
vignetteTitles: Main vignette: End-to-end analysis of cell-based
screens, Supplement: multi-channel assays, Supplement: two-way
assays
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/cellHTS/inst/doc/cellhts.R,
vignettes/cellHTS/inst/doc/twoChannels.R,
vignettes/cellHTS/inst/doc/twoWay.R
suggestsMe: prada
Package: cellHTS2
Version: 2.22.0
Depends: R (>= 2.10), RColorBrewer, Biobase, methods, genefilter,
splots, vsn, hwriter, locfit, grid
Imports: prada, GSEABase, Category, stats4
License: Artistic-2.0
Title: Analysis of cell-based screens - revised version of cellHTS
Description: This package provides tools for the analysis of
high-throughput assays that were performed in 384-well
microtitre plate (or analogous) formats. The functionality
includes data import and management, normalisation, quality
assessment, replicate summarisation and statistical scoring. A
webpage that provides a detailed graphical overview over the
data and analysis results is produced. In our work, we have
applied the package to RNAi screens on fly and human cells, and
for screens of yeast libraries. See ?cellHTS2 for a brief
introduction.
biocViews: CellBasedAssays, Preprocessing, Visualization
Author: Ligia Bras, Wolfgang Huber <whuber@embl.de>, Michael Boutros
<m.boutros@dkfz.de>, Gregoire Pau <gpau@embl.de>, Florian Hahne
<florian.hahne@novartis.com>
Maintainer: Joseph Barry <joseph.barry@embl.de>
URL: http://www.dkfz.de/signaling, http://www.ebi.ac.uk/huber
MD5sum: 6c2b9145f32b99d94dfb1fa9b2a61eac
source.ver: src/contrib/cellHTS2_2.22.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/cellHTS2_2.22.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/cellHTS2_2.22.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/cellHTS2/inst/doc/cellhts2Complete.pdf,
vignettes/cellHTS2/inst/doc/cellhts2.pdf,
vignettes/cellHTS2/inst/doc/twoChannels.pdf,
vignettes/cellHTS2/inst/doc/twoWay.pdf
vignetteTitles: Main vignette (complete version): End-to-end analysis
of cell-based screens, Main vignette: End-to-end analysis of
cell-based screens, Supplement: multi-channel assays,
Supplement: enhancer-suppressor screens
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/cellHTS2/inst/doc/cellhts2Complete.R,
vignettes/cellHTS2/inst/doc/cellhts2.R,
vignettes/cellHTS2/inst/doc/twoChannels.R,
vignettes/cellHTS2/inst/doc/twoWay.R
dependsOnMe: coRNAi, imageHTS, staRank
importsMe: HTSanalyzeR, RNAinteract
Package: CellNOptR
Version: 1.4.0
Depends: R (>= 2.15.0), RBGL, graph, methods
Suggests: Rgraphviz,RUnit, BiocGenerics
Enhances: Rgraphviz
License: GPL-2
Archs: i386, x64
Title: Training of boolean logic models of signalling networks using
prior knowledge networks and perturbation data.
Description: This package does optimisation of boolean logic networks
of signalling pathways based on a previous knowledge network
and a set of data upon perturbation of the nodes in the
network.
biocViews: CellBasedAssays, CellBiology, Proteomics, Bioinformatics,
TimeCourse
Author: T.Cokelaer, F.Eduati, A.MacNamara, S.Schrier, C.Terfve
Maintainer: T.Cokelaer <cokelaer@ebi.ac.uk>
SystemRequirements: Graphviz version >= 2.2
MD5sum: 26ba2da9ff545690d17d20a9e34732d5
source.ver: src/contrib/CellNOptR_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CellNOptR_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/CellNOptR_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/CellNOptR/inst/doc/CellNOptR0_1flowchart.pdf,
vignettes/CellNOptR/inst/doc/CellNOptR-vignette.pdf,
vignettes/CellNOptR/inst/doc/Fig2.pdf,
vignettes/CellNOptR/inst/doc/Fig3.pdf,
vignettes/CellNOptR/inst/doc/Fig4.pdf,
vignettes/CellNOptR/inst/doc/Fig6.pdf,
vignettes/CellNOptR/inst/doc/Fig7.pdf
vignetteTitles: CellNOptR0_1flowchart.pdf, Main vignette:Playing with
networks using CellNOptR, Fig2.pdf, Fig3.pdf, Fig4.pdf,
Fig6.pdf, Fig7.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CellNOptR/inst/doc/CellNOptR-vignette.R
dependsOnMe: CNORdt, CNORfuzzy, CNORode
Package: CGEN
Version: 1.10.0
Depends: R (>= 2.10.1), survival, cluster
Suggests: cluster
License: GPL-2 + file LICENSE
Archs: i386, x64
Title: An R package for analysis of case-control studies in genetic
epidemiology
Description: An R package for analysis of case-control studies in
genetic epidemiology
biocViews: SNP, MultipleComparisons, Clustering
Author: Samsiddhi Bhattacharjee, Nilanjan Chatterjee and William
Wheeler
Maintainer: William Wheeler <wheelerb@imsweb.com>
MD5sum: e5d164a4257c42dcb4ce2f4c60f6bfd0
source.ver: src/contrib/CGEN_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CGEN_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/CGEN_1.10.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CGEN_1.10.0.tgz
vignettes: vignettes/CGEN/inst/doc/vignette.pdf
vignetteTitles: CGEN Vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/CGEN/inst/doc/vignette.R
Package: CGHbase
Version: 1.18.0
Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray
License: GPL
Title: CGHbase: Base functions and classes for arrayCGH data analysis.
Description: Contains functions and classes that are needed by arrayCGH
packages.
biocViews: Infrastructure, Microarray, CopyNumberVariants
Author: Sjoerd Vosse, Mark van de Wiel
Maintainer: Mark van de Wiel <mark.vdwiel@vumc.nl>
MD5sum: 9972d4a6fa7c463ef612c7578e0c16f4
source.ver: src/contrib/CGHbase_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CGHbase_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/CGHbase_1.18.0.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: CGHcall, CGHnormaliter, CGHregions, sigaR
importsMe: CGHnormaliter
Package: CGHcall
Version: 2.18.0
Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods,
Biobase, CGHbase (>= 1.15.1), snowfall
License: GPL (http://www.gnu.org/copyleft/gpl.html)
Title: Calling aberrations for array CGH tumor profiles.
Description: Calls aberrations for array CGH data using a six state
mixture model as well as several biological concepts that are
ignored by existing algorithms. Visualization of profiles is
also provided.
biocViews: Microarray,Preprocessing,Visualization
Author: Mark van de Wiel, Sjoerd Vosse
Maintainer: Mark van de Wiel <mark.vdwiel@vumc.nl>
MD5sum: c1b084a11dcd7e96e57bb1c4dd4e6daf
source.ver: src/contrib/CGHcall_2.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CGHcall_2.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/CGHcall_2.18.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/CGHcall/inst/doc/CGHcall.pdf
vignetteTitles: CGHcall
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CGHcall/inst/doc/CGHcall.R
dependsOnMe: CGHnormaliter
importsMe: CGHnormaliter
Package: cghMCR
Version: 1.16.0
Depends: methods, DNAcopy, CNTools, limma
Imports: BiocGenerics (>= 0.1.6), stats4
License: LGPL
Title: Find chromosome regions showing common gains/losses
Description: This package provides functions to identify genomic
regions of interests based on segmented copy number data from
multiple samples.
biocViews: Microarray, CopyNumberVariants
Author: J. Zhang and B. Feng
Maintainer: J. Zhang <jzhang@jimmy.harvard.edu>
MD5sum: 001090a495d9a23b28da26f551e241d8
source.ver: src/contrib/cghMCR_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/cghMCR_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/cghMCR_1.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/cghMCR/inst/doc/findMCR.pdf
vignetteTitles: cghMCR findMCR
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/cghMCR/inst/doc/findMCR.R
Package: CGHnormaliter
Version: 1.12.0
Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0)
Imports: Biobase, CGHbase, CGHcall, methods, stats, utils
License: GPL (>= 3)
Title: Normalization of array CGH data with imbalanced aberrations.
Description: Normalization and centralization of array comparative
genomic hybridization (aCGH) data. The algorithm uses an
iterative procedure that effectively eliminates the influence
of imbalanced copy numbers. This leads to a more reliable
assessment of copy number alterations (CNAs).
biocViews: Microarray, Preprocessing
Author: Bart P.P. van Houte, Thomas W. Binsl, Hannes Hettling
Maintainer: Bart P.P. van Houte <bvhoute@few.vu.nl>
MD5sum: 7e6ce3071ac12bef80b2673ac5ff8a4a
source.ver: src/contrib/CGHnormaliter_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CGHnormaliter_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/CGHnormaliter_1.12.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/CGHnormaliter/inst/doc/CGHnormaliter-method.pdf,
vignettes/CGHnormaliter/inst/doc/CGHnormaliter.pdf
vignetteTitles: CGHnormaliter-method.pdf, CGHnormaliter
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CGHnormaliter/inst/doc/CGHnormaliter.R
Package: CGHregions
Version: 1.16.0
Depends: R (>= 2.0.0), methods, Biobase, CGHbase
License: GPL (http://www.gnu.org/copyleft/gpl.html)
Title: Dimension Reduction for Array CGH Data with Minimal Information
Loss.
Description: Dimension Reduction for Array CGH Data with Minimal
Information Loss
biocViews: Microarray,CopyNumberVariants,Visualization
Author: Sjoerd Vosse & Mark van de Wiel
Maintainer: Sjoerd Vosse <info@vossewebdevelopment.nl>
MD5sum: 5fb7905ee95f84be91e8b7620b6335ca
source.ver: src/contrib/CGHregions_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CGHregions_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/CGHregions_1.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/CGHregions/inst/doc/CGHregions.pdf
vignetteTitles: CGHcall
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CGHregions/inst/doc/CGHregions.R
suggestsMe: ADaCGH2
Package: charm
Version: 2.4.0
Depends: R (>= 2.14.0), Biobase, SQN, fields, RColorBrewer, genefilter
Imports: BSgenome, Biobase, oligo (>= 1.11.31), oligoClasses(>=
1.17.39), ff, preprocessCore, methods, stats, Biostrings,
IRanges, siggenes, nor1mix, gtools, grDevices, graphics, utils,
limma, parallel, sva(>= 3.1.2)
Suggests: charmData, BSgenome.Hsapiens.UCSC.hg18, corpcor
License: LGPL (>= 2)
Title: Analysis of DNA methylation data from CHARM microarrays
Description: This package implements analysis tools for DNA methylation
data generated using Nimblegen microarrays and the McrBC
protocol. It finds differentially methylated regions between
samples, calculates percentage methylation estimates and
includes array quality assessment tools.
biocViews: Microarray, Bioinformatics, DNAMethylation
Author: Martin Aryee, Peter Murakami, Harris Jaffee, Rafael Irizarry
Maintainer: Peter Murakami <pmurakam@jhsph.edu>
MD5sum: 971f31b934e20f8de1eafa14e9af7e7a
source.ver: src/contrib/charm_2.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/charm_2.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/charm_2.4.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/charm_2.4.0.tgz
vignettes: vignettes/charm/inst/doc/charm.pdf
vignetteTitles: charm Vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/charm/inst/doc/charm.R
Package: ChemmineR
Version: 2.10.9
Depends: R (>= 2.10.0), methods
Imports: graphics, methods, stats, RCurl
License: Artistic-2.0
Title: Cheminformatics of Drug-like Small Molecule Data
Description: ChemmineR is a cheminformatics package for analyzing
drug-like small molecule data in R. Its latest version contains
functions for efficient processing of large numbers of
molecules, physicochemical/structural property predictions,
structural similarity searching, classification and clustering
of compound libraries with a wide spectrum of algorithms. In
addition, it offers visualization functions for compound
clustering results and chemical structures.
biocViews: MicrotitrePlateAssay, CellBasedAssays, Visualization,
Infrastructure, DataImport, Clustering, Bioinformatics,
Proteomics
Author: Y. Eddie Cao, Tyler Backman, Yan Wang, Thomas Girke
Maintainer: ChemmineR Team <see@url>
URL: http://manuals.bioinformatics.ucr.edu/home/chemminer
MD5sum: 49b5886bc340b9a4096c9f13d4448d84
source.ver: src/contrib/ChemmineR_2.10.9.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ChemmineR_2.10.9.zip
win64.binary.ver: bin/windows64/contrib/2.15/ChemmineR_2.10.9.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ChemmineR/inst/doc/ChemmineR.pdf
vignetteTitles: gpls Tutorial
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ChemmineR/inst/doc/ChemmineR.R
dependsOnMe: fmcsR
Package: ChIPpeakAnno
Version: 2.6.1
Depends: R (>= 2.10), grid,VennDiagram, BiocGenerics (>= 0.1.0),
biomaRt, multtest, IRanges, Biostrings, BSgenome,
BSgenome.Ecoli.NCBI.20080805, GO.db, org.Hs.eg.db, limma
Imports: gplots, BiocGenerics, biomaRt, multtest, IRanges, Biostrings,
BSgenome, GO.db, limma, AnnotationDbi
Suggests: reactome.db
License: GPL (>= 2)
Title: Batch annotation of the peaks identified from either ChIP-seq,
ChIP-chip experiments or any experiments resulted in large
number of chromosome ranges.
Description: The package includes functions to retrieve the sequences
around the peak, obtain enriched Gene Ontology (GO) terms, find
the nearest gene, exon, miRNA or custom features such as most
conserved elements and other transcription factor binding sites
supplied by users. Starting 2.0.5, new functions have been
added for finding the peaks with bi-directional promoters with
summary statistics (peaksNearBDP), for summarizing the
occurrence of motifs in peaks (summarizePatternInPeaks) and for
adding other IDs to annotated peaks or enrichedGO (addGeneIDs).
This package leverages the biomaRt, IRanges, Biostrings,
BSgenome, GO.db, multtest and stat packages
biocViews: Annotation, ChIPseq, ChIPchip
Author: Lihua Julie Zhu, Herve Pages, Claude Gazin, Nathan Lawson,
Jianhong Ou, Simon Lin, David Lapointe and Michael Green
Maintainer: Lihua Julie Zhu <julie.zhu@umassmed.edu>
MD5sum: 9f0cfbc091f6aba61e9c32ea095464fd
source.ver: src/contrib/ChIPpeakAnno_2.6.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ChIPpeakAnno_2.6.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/ChIPpeakAnno_2.6.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.pdf
vignetteTitles: ChIPpeakAnno Vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.R
dependsOnMe: REDseq
importsMe: FunciSNP, REDseq
suggestsMe: oneChannelGUI
Package: chipseq
Version: 1.8.0
Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.0), IRanges (>=
1.13.4), GenomicRanges (>= 1.7.7), BSgenome, ShortRead
Imports: methods, BiocGenerics, IRanges, BSgenome, GenomicRanges,
lattice, ShortRead, stats
Suggests: GenomicFeatures, BSgenome.Mmusculus.UCSC.mm9,
TxDb.Mmusculus.UCSC.mm9.knownGene
License: Artistic-2.0
Archs: i386, x64
Title: chipseq: A package for analyzing chipseq data
Description: Tools for helping process short read data for chipseq
experiments
biocViews: ChIPseq
Author: Deepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: af2ed54c45cef1b41b1a5113d5a000e1
source.ver: src/contrib/chipseq_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/chipseq_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/chipseq_1.8.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/chipseq/inst/doc/Workflow.pdf
vignetteTitles: A Sample ChIP-Seq analysis workflow
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/chipseq/inst/doc/Workflow.R
dependsOnMe: PING
importsMe: HTSeqGenie
suggestsMe: ggbio, oneChannelGUI
Package: ChIPseqR
Version: 1.12.0
Depends: R (>= 2.10.0), methods, BiocGenerics, ShortRead
Imports: Biostrings, fBasics, GenomicRanges, graphics, grDevices,
HilbertVis, IRanges, methods, ShortRead, stats, timsac, utils
License: GPL (>= 2)
Archs: i386, x64
Title: Identifying Protein Binding Sites in High-Throughput Sequencing
Data
Description: ChIPseqR identifies protein binding sites from ChIP-seq
and nucleosome positioning experiments. The model used to
describe binding events was developed to locate nucleosomes but
should flexible enough to handle other types of experiments as
well.
biocViews: ChIPseq, Bioinformatics, Infrastructure
Author: Peter Humburg
Maintainer: Peter Humburg <peter.humburg@well.ox.ac.uk>
MD5sum: ef90729990239b8000af74678aa5169a
source.ver: src/contrib/ChIPseqR_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ChIPseqR_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ChIPseqR_1.12.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ChIPseqR/inst/doc/Introduction.pdf
vignetteTitles: Introduction to ChIPseqR
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ChIPseqR/inst/doc/Introduction.R
Package: ChIPsim
Version: 1.12.0
Depends: Biostrings
Imports: IRanges, Biostrings, ShortRead, graphics, methods, stats,
utils
Suggests: actuar, zoo
License: GPL (>= 2)
Title: Simulation of ChIP-seq experiments
Description: A general framework for the simulation of ChIP-seq data.
Although currently focused on nucleosome positioning the
package is designed to support different types of experiments.
biocViews: Infrastructure, Bioinformatics, ChIPseq
Author: Peter Humburg
Maintainer: Peter Humburg <Peter.Humburg@well.ox.ac.uk>
MD5sum: c1806f8ec8f4521d6226711949a60c9f
source.ver: src/contrib/ChIPsim_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ChIPsim_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ChIPsim_1.12.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/ChIPsim_1.12.0.tgz
vignettes: vignettes/ChIPsim/inst/doc/ChIPsimIntro.pdf
vignetteTitles: Simulating ChIP-seq experiments
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ChIPsim/inst/doc/ChIPsimIntro.R
Package: ChIPXpress
Version: 1.0.0
Depends: R (>= 2.10), ChIPXpressData
Imports: Biobase, GEOquery, frma, affy, bigmemory, biganalytics
Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit,
BiocGenerics
License: GPL(>=2)
Title: ChIPXpress: enhanced transcription factor target gene
identification from ChIP-seq and ChIP-chip data using publicly
available gene expression profiles
Description: ChIPXpress takes as input predicted TF bound genes from
ChIPx data and uses a corresponding database of gene expression
profiles downloaded from NCBI GEO to rank the TF bound targets
in order of which gene is most likely to be functional TF
target.
biocViews: ChIPchip, ChIPseq, Bioinformatics
Author: George Wu
Maintainer: George Wu <gewu@jhsph.edu>
MD5sum: 3d86cb2df0a01b67584959af1e82df01
source.ver: src/contrib/ChIPXpress_1.0.0.tar.gz
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/ChIPXpress_1.0.0.tgz
vignettes: vignettes/ChIPXpress/inst/doc/ChIPXpress.pdf
vignetteTitles: ChIPXpress
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ChIPXpress/inst/doc/ChIPXpress.R
Package: chopsticks
Version: 1.22.4
Depends: R(>= 2.10.0), survival, methods
Suggests: hexbin
License: GPL-3
Archs: i386, x64
Title: The snp.matrix and X.snp.matrix classes
Description: Implements classes and methods for large-scale SNP
association studies
biocViews: Microarray, SNPsAndGeneticVariability, SNP,
GeneticVariability
Author: Hin-Tak Leung <htl10@users.sourceforge.net>
Maintainer: Hin-Tak Leung <htl10@users.sourceforge.net>
URL: http://outmodedbonsai.sourceforge.net/
MD5sum: c7b45011bba7b071705a75e6b7df0ff2
source.ver: src/contrib/chopsticks_1.22.4.tar.gz
win.binary.ver: bin/windows/contrib/2.15/chopsticks_1.22.4.zip
win64.binary.ver: bin/windows64/contrib/2.15/chopsticks_1.22.4.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/chopsticks_1.22.4.tgz
vignettes: vignettes/chopsticks/inst/doc/chopsticks-vignette.pdf,
vignettes/chopsticks/inst/doc/snpMatrix-4d.pdf,
vignettes/chopsticks/inst/doc/snpMatrix-paper-HumanHeridity2007.pdf,
vignettes/chopsticks/inst/doc/snpStatsBug_1.3.6_-vignette.pdf,
vignettes/chopsticks/inst/doc/snpStatsBug_1.5.4_-vignette.pdf,
vignettes/chopsticks/inst/doc/snpStatsBug-vignette.pdf
vignetteTitles: snpMatrix, snpMatrix-4d.pdf,
snpMatrix-paper-HumanHeridity2007.pdf,
snpStatsBug_1.3.6_-vignette.pdf,
snpStatsBug_1.5.4_-vignette.pdf, snpStatsBug-vignette.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/chopsticks/inst/doc/chopsticks-vignette.R
htmlDocs: vignettes/chopsticks/inst/doc/index.html
Package: chroGPS
Version: 1.0.1
Depends: R (>= 2.13.0), IRanges, methods, Biobase, MASS, graphics,
stats, rgl
Imports: graphics, cluster, DPpackage
Enhances: multicore
License: GPL (>=2)
Title: chroGPS: navigating through the epigenome
Description: We provide intuitive maps to visualize the association
between genetic elements, with emphasis on epigenetics. The
approach is based on Multi-Dimensional Scaling. We provide
several sensible distance metrics, and adjustment procedures to
remove systematic biases typically observed when merging data
obtained under different technologies or genetic backgrounds.
biocViews: Visualization, Clustering
Author: Oscar Reina, David Rossell
Maintainer: Oscar Reina <oscar.reina@irbbarcelona.org>
MD5sum: b1414755970affa9fa03bed8a203a321
source.ver: src/contrib/chroGPS_1.0.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/chroGPS_1.0.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/chroGPS_1.0.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/chroGPS_1.0.1.tgz
vignettes: vignettes/chroGPS/inst/doc/chroGPS.pdf
vignetteTitles: Manual for the chroGPS library
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/chroGPS/inst/doc/chroGPS.R
Package: ChromHeatMap
Version: 1.12.0
Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0),
AnnotationDbi (>= 1.4.0), hgu95av2.db
Imports: BiocGenerics, annotate, AnnotationDbi, Biobase (>= 2.17.8),
graphics, grDevices, methods, stats, IRanges, rtracklayer
Suggests: ALL
License: Artistic-2.0
Title: Heat map plotting by genome coordinate
Description: The ChromHeatMap package can be used to plot genome-wide
data (e.g. expression, CGH, SNP) along each strand of a given
chromosome as a heat map. The generated heat map can be used to
interactively identify probes and genes of interest.
biocViews: Visualization
Author: Tim F. Rayner
Maintainer: Tim F. Rayner <tfrayner@gmail.com>
MD5sum: 29fef3a98dd9f1412dd5eaf03ab2a90c
source.ver: src/contrib/ChromHeatMap_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ChromHeatMap_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ChromHeatMap_1.12.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/ChromHeatMap_1.12.0.tgz
vignettes: vignettes/ChromHeatMap/inst/doc/ChromHeatMap.pdf
vignetteTitles: Plotting expression data with ChromHeatMap
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ChromHeatMap/inst/doc/ChromHeatMap.R
Package: clippda
Version: 1.8.0
Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d,
graphics, grDevices, stats, utils, Biobase, tools, methods
License: GPL (>=2)
Title: A package for the clinical proteomic profiling data analysis
Description: Methods for the nalysis of data from clinical proteomic
profiling studies. The focus is on the studies of human
subjects, which are often observational case-control by design
and have technical replicates. A method for sample size
determination for planning these studies is proposed. It
incorporates routines for adjusting for the expected
heterogeneities and imbalances in the data and the
within-sample replicate correlations.
biocViews: Proteomics, OneChannel,
DataPreprocessing,Bioinformatics,DifferentialExpression,
MultipleComparisons, SampleSize
Author: Stephen Nyangoma
Maintainer: Stephen Nyangoma <s.o.nyangoma@bham.ac.uk>
URL: http://www.cancerstudies.bham.ac.uk/crctu/CLIPPDA.shtml
MD5sum: 8b19e25e97b5f33e6ec737f5ff3021dc
source.ver: src/contrib/clippda_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/clippda_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/clippda_1.8.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/clippda_1.8.0.tgz
vignettes: vignettes/clippda/inst/doc/clippda.pdf
vignetteTitles: Sample Size Calculation
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/clippda/inst/doc/clippda.R
Package: Clonality
Version: 1.6.0
Depends: R (>= 2.12.2), DNAcopy
Imports: DNAcopy, grDevices, graphics, stats, utils
Suggests: gdata, DNAcopy
License: GPL-3
Title: Clonality testing
Description: Statistical tests for clonality versus independence of
tumors from the same patient based on their LOH or genomewide
copy number profiles
biocViews: Microarray, CopyNumberVariants, Classification, aCGH
Author: Irina Ostrovnaya
Maintainer: Irina Ostrovnaya <ostrovni@mskcc.org>
MD5sum: 6e00c2bef18defc6e6f4954036c0da15
source.ver: src/contrib/Clonality_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Clonality_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Clonality_1.6.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/Clonality_1.6.0.tgz
vignettes: vignettes/Clonality/inst/doc/Clonality.pdf
vignetteTitles: Clonality
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Clonality/inst/doc/Clonality.R
Package: clst
Version: 1.6.0
Depends: R (>= 2.10)
Imports: ROC, lattice
Suggests: RUnit
License: GPL-3
Title: Classification by local similarity threshold
Description: Package for modified nearest-neighbor classification based
on calculation of a similarity threshold distinguishing
within-group from between-group comparisons.
biocViews: Classification
Author: Noah Hoffman
Maintainer: Noah Hoffman <ngh2@uw.edu>
MD5sum: 41225bfa61056a46788efb2ff7fe7b8a
source.ver: src/contrib/clst_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/clst_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/clst_1.6.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/clst_1.6.0.tgz
vignettes: vignettes/clst/inst/doc/clstDemo.pdf,
vignettes/clst/inst/doc/matchtypes.pdf
vignetteTitles: clst, matchtypes.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/clst/inst/doc/clstDemo.R
dependsOnMe: clstutils
Package: clstutils
Version: 1.6.0
Depends: R (>= 2.10), clst, rjson, ape
Imports: lattice, RSQLite
Suggests: RUnit, RSVGTipsDevice
License: GPL-3
Title: Tools for performing taxonomic assignment.
Description: Tools for performing taxonomic assignment based on
phylogeny using pplacer and clst.
biocViews: HighThroughputSequencing, Classification, Visualization,
QualityControl
Author: Noah Hoffman
Maintainer: Noah Hoffman <ngh2@uw.edu>
MD5sum: 1fa9524c5dcce06c63e6b693e423d742
source.ver: src/contrib/clstutils_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/clstutils_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/clstutils_1.6.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/clstutils_1.6.0.tgz
vignettes: vignettes/clstutils/inst/doc/pplacerDemo.pdf,
vignettes/clstutils/inst/doc/refSet.pdf
vignetteTitles: clst, clstutils
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/clstutils/inst/doc/pplacerDemo.R,
vignettes/clstutils/inst/doc/refSet.R
Package: clusterProfiler
Version: 1.6.0
Depends: R (>= 2.10), ggplot2
Imports: methods, stats4, DBI, plyr, AnnotationDbi, GO.db, KEGG.db,
org.Hs.eg.db, DOSE
Suggests: GOSemSim, ReactomePA
License: Artistic-2.0
Title: statistical analysis and visulization of functional profiles for
genes and gene clusters
Description: The package implements methods to analyze and visualize
functional profiles (GO and KEGG) of gene and gene clusters.
biocViews: Clustering, GO, Pathways, Visualization,
MultipleComparisons, GeneSetEnrichment
Author: Guangchuang Yu, Li-Gen Wang
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
URL: http://online.liebertpub.com/doi/abs/10.1089/omi.2011.0118
MD5sum: c9dbd755ae774f353eccbac05192f6c0
source.ver: src/contrib/clusterProfiler_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/clusterProfiler_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/clusterProfiler_1.6.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/clusterProfiler_1.6.0.tgz
vignettes:
vignettes/clusterProfiler/inst/doc/clusterProfiler_for_unsupported_organism.pdf,
vignettes/clusterProfiler/inst/doc/clusterProfiler.pdf,
vignettes/clusterProfiler/inst/doc/omics2012.pdf
vignetteTitles: clusterProfiler_for_unsupported_organism.pdf, An
introduction to clusterProfiler, omics2012.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/clusterProfiler/inst/doc/clusterProfiler.R
suggestsMe: DOSE, GOSemSim, ReactomePA
Package: clusterStab
Version: 1.30.0
Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods
Suggests: fibroEset, genefilter
License: Artistic-2.0
Title: Compute cluster stability scores for microarray data
Description: This package can be used to estimate the number of
clusters in a set of microarray data, as well as test the
stability of these clusters.
biocViews: Clustering
Author: James W. MacDonald, Debashis Ghosh, Mark Smolkin
Maintainer: James W. MacDonald <jmacdon@med.umich.edu>
MD5sum: 3106d9b02f81762848cbcb131ea3c3c4
source.ver: src/contrib/clusterStab_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/clusterStab_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/clusterStab_1.30.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/clusterStab_1.30.0.tgz
vignettes: vignettes/clusterStab/inst/doc/clusterStab.pdf
vignetteTitles: clusterStab Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/clusterStab/inst/doc/clusterStab.R
Package: CMA
Version: 1.16.0
Depends: R (>= 2.10), methods, stats, Biobase
Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics,
gbm, mgcv, corpcor, limma, st
License: GPL (>= 2)
Title: Synthesis of microarray-based classification
Description: This package provides a comprehensive collection of
various microarray-based classification algorithms both from
Machine Learning and Statistics. Variable Selection,
Hyperparameter tuning, Evaluation and Comparison can be
performed combined or stepwise in a user-friendly environment.
biocViews: Classification
Author: Martin Slawski <ms@cs.uni-sb.de>, Anne-Laure Boulesteix
<boulesteix@ibe.med.uni-muenchen.de>, Christoph Bernau
<bernau@ibe.med.uni-muenchen.de>.
Maintainer: Christoph Bernau <bernau@ibe.med.uni-muenchen.de>
MD5sum: 45d104b02bc435b6a2e537b98dec84c2
source.ver: src/contrib/CMA_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CMA_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/CMA_1.16.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CMA_1.16.0.tgz
vignettes: vignettes/CMA/inst/doc/CMA_vignette.pdf
vignetteTitles: CMA_vignette.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CMA/inst/doc/CMA_vignette.R
Package: CNAnorm
Version: 1.4.0
Depends: R (>= 2.10.1), DNAcopy, methods
Imports: methods
License: GPL-2
Archs: i386, x64
Title: A normalization method for Copy Number Aberration in cancer
samples
Description: Performs ratio, GC content correction and normalization of
data obtained using low coverage (one read every 100-10,000 bp)
high troughput sequencing. It performs a "discrete"
normalization looking for the ploidy of the genome. It will
also provide tumour content if at least two ploidy states can
be found.
biocViews: Bioinformatics, HighThroughputSequencing,
CopyNumberVariants, Sequencing, Cancer, Lung
Author: Stefano Berri <s.berri@leeds.ac.uk>, Henry M. Wood
<H.M.Wood@leeds.ac.uk>, Arief Gusnanto <a.gusnanto@leeds.ac.uk>
Maintainer: Stefano Berri <s.berri@leeds.ac.uk>
URL: http://www.r-project.org,
MD5sum: d6ec583d6b41b7a45c129e3702707a72
source.ver: src/contrib/CNAnorm_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CNAnorm_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/CNAnorm_1.4.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/CNAnorm_1.4.0.tgz
vignettes: vignettes/CNAnorm/inst/doc/CNAnorm.pdf
vignetteTitles: CNAnorm.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: cn.farms
Version: 1.6.0
Depends: R (>= 2.11), Biobase, methods, ff, oligoClasses, snowfall
Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice
Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5,
pd.genomewidesnp.6
License: LGPL (>= 2.0)
Archs: i386, x64
Title: cn.farms - Factor Analysis for copy number estimation
Description: This package implements the cn.FARMS algorithm for copy
number variation (CNV) analysis. cn.FARMS allows to analyze the
most common Affymetrix (250K-SNP6.0) array types, supports
high-performance computing using snow and ff.
biocViews: Microarray, Bioinformatics, CopyNumberVariants
Author: Andreas Mitterecker, Djork-Arne Clevert
Maintainer: Andreas Mitterecker <mitterecker@bioinf.jku.at>
URL: http://www.bioinf.jku.at/software/cnfarms/cnfarms.html
MD5sum: 60e0aa032af25d1b63abe8c98a00aa3d
source.ver: src/contrib/cn.farms_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/cn.farms_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/cn.farms_1.6.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/cn.farms_1.6.0.tgz
vignettes: vignettes/cn.farms/inst/doc/cn.farms.pdf
vignetteTitles: cn.farms: Manual for the R package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/cn.farms/inst/doc/cn.farms.R
Package: cn.mops
Version: 1.4.12
Depends: R (>= 2.12), BiocGenerics, Biobase, IRanges, GenomicRanges
Imports: methods, graphics, BiocGenerics, IRanges, Rsamtools,
Suggests: snow, DNAcopy
License: LGPL (>= 2.0)
Archs: i386, x64
Title: cn.mops - Mixture of Poissons for CNV detection in NGS data
Description: cn.mops (Copy Number estimation by a Mixture Of PoissonS)
is a data processing pipeline for copy number variations and
aberrations (CNVs and CNAs) from next generation sequencing
(NGS) data. The package supplies functions to convert BAM files
into read count matrices or genomic ranges objects, which are
the input objects for cn.mops. cn.mops models the depths of
coverage across samples at each genomic position. Therefore, it
does not suffer from read count biases along chromosomes. Using
a Bayesian approach, cn.mops decomposes read variations across
samples into integer copy numbers and noise by its mixture
components and Poisson distributions, respectively. cn.mops
guarantees a low FDR because wrong detections are indicated by
high noise and filtered out. cn.mops is very fast and written
in C++.
biocViews: HighThroughputSequencing, Sequencing, Bioinformatics,
CopyNumberVariants
Author: Guenter Klambauer
Maintainer: Guenter Klambauer <cn.mops@bioinf.jku.at>
URL: http://www.bioinf.jku.at/software/cnmops/cnmops.html
MD5sum: 524aeda2384b608617a0397fea197d75
source.ver: src/contrib/cn.mops_1.4.12.tar.gz
win.binary.ver: bin/windows/contrib/2.15/cn.mops_1.4.12.zip
win64.binary.ver: bin/windows64/contrib/2.15/cn.mops_1.4.12.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/cn.mops_1.4.12.tgz
vignettes: vignettes/cn.mops/inst/doc/cn.mops.pdf
vignetteTitles: cn.mops: Manual for the R package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/cn.mops/inst/doc/cn.mops.R
Package: CNORdt
Version: 1.0.0
Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind
License: GPL-2
Archs: i386, x64
Title: Add-on to CellNOptR: Discretized time treatments
Description: This add-on to the package CellNOptR handles time-course
data, as opposed to steady state data in CellNOptR. It scales
the simulation step to allow comparison and model fitting for
time-course data. Future versions will optimize delays and
strengths for each edge.
biocViews: CellBasedAssays, CellBiology, Proteomics, Bioinformatics,
TimeCourse
Author: A. MacNamara
Maintainer: A. MacNamara <aidan.macnamara@ebi.ac.uk>
MD5sum: 31d327e71e4ccf244ac3448d07a33625
source.ver: src/contrib/CNORdt_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CNORdt_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/CNORdt_1.0.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/CNORdt_1.0.0.tgz
vignettes: vignettes/CNORdt/inst/doc/CNORdt-vignette.pdf,
vignettes/CNORdt/inst/doc/CNORdt-vignette-plot.pdf
vignetteTitles: Using multiple time points to train logic models to
data, CNORdt-vignette-plot.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CNORdt/inst/doc/CNORdt-vignette.R
Package: CNORfuzzy
Version: 1.0.0
Depends: R (>= 2.15.0), CellNOptR (>= 1.3.29), nloptr (>= 0.8.5)
Suggests: xtable, Rgraphviz, RUnit, BiocGenerics
License: GPL-2
Title: Addon to CellNOptR: Fuzzy Logic
Description: This package is an extension to CellNOptR. It contains
additional functionality needed to simulate and train a prior
knowledge network to experimental data using constrained fuzzy
logic (cFL, rather than Boolean logic as is the case in
CellNOptR). Additionally, this package will contain functions
to use for the compilation of multiple optimization results
(either Boolean or cFL).
Author: M. Morris, T. Cokelaer
Maintainer: T. Cokelaer <cokelaer@ebi.ac.uk>
MD5sum: 8ecd008d76a6ed4ad3aa1dac8ec5056a
source.ver: src/contrib/CNORfuzzy_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CNORfuzzy_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/CNORfuzzy_1.0.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/CNORfuzzy_1.0.0.tgz
vignettes:
vignettes/CNORfuzzy/inst/doc/CNORfuzzy-vignette-FullAnalysis2.pdf,
vignettes/CNORfuzzy/inst/doc/CNORfuzzy-vignette-FullAnalysis3.pdf,
vignettes/CNORfuzzy/inst/doc/CNORfuzzy-vignette-FullAnalysis.pdf,
vignettes/CNORfuzzy/inst/doc/CNORfuzzy-vignette.pdf,
vignettes/CNORfuzzy/inst/doc/CNORfuzzy-vignette-plotMeanFuzzyFit.pdf,
vignettes/CNORfuzzy/inst/doc/tf1.pdf,
vignettes/CNORfuzzy/inst/doc/tf2.pdf
vignetteTitles: CNORfuzzy-vignette-FullAnalysis2.pdf,
CNORfuzzy-vignette-FullAnalysis3.pdf,
CNORfuzzy-vignette-FullAnalysis.pdf, Main vignette:Playing with
networks using CNORfuzzyl,
CNORfuzzy-vignette-plotMeanFuzzyFit.pdf, tf1.pdf, tf2.pdf
hasREADME: FALSE
hasNEWS: TRUE
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Rfiles: vignettes/CNORfuzzy/inst/doc/CNORfuzzy-vignette.R
Package: CNORode
Version: 1.0.0
Depends: CellNOptR, genalg
Enhances: MEIGOR
License: GPL-2
Archs: i386, x64
Title: ODE add-on to CellNOptR
Description: ODE add-on to CellNOptR
biocViews: CellBasedAssays, CellBiology, Proteomics, Bioinformatics,
TimeCourse
Author: David Henriques, Thomas Cokelaer
Maintainer: David Henriques <davidpcnet@hotmail.com>
MD5sum: f496815811d2fe0f0048b8739eb7e9cf
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vignettes: vignettes/CNORode/inst/doc/CNORode-vignette.pdf,
vignettes/CNORode/inst/doc/data_ToyModelMMB_FeddbackAnd.pdf
vignetteTitles: Main vignette:Playing with networks using CNORode,
data_ToyModelMMB_FeddbackAnd.pdf
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CNORode/inst/doc/CNORode-vignette.R
Package: CNTools
Version: 1.14.0
Depends: R (>= 2.10), methods, tools, stats, genefilter
License: LGPL
Archs: i386, x64
Title: Convert segment data into a region by sample matrix to allow for
other high level computational analyses.
Description: This package provides tools to convert the output of
segmentation analysis using DNAcopy to a matrix structure with
overlapping segments as rows and samples as columns so that
other computational analyses can be applied to segmented data
biocViews: Microarray, CopyNumberVariants
Author: Jianhua Zhang
Maintainer: J. Zhang <jzhang@jimmy.harvard.edu>
MD5sum: bca2952a88367a25c5a5d08dfb85818d
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vignettes: vignettes/CNTools/inst/doc/HowTo.pdf
vignetteTitles: NCTools HowTo
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hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CNTools/inst/doc/HowTo.R
dependsOnMe: cghMCR
Package: cnvGSA
Version: 1.2.0
Depends: methods, brglm
Suggests: cnvGSAdata, org.Hs.eg.db
License: LGPL
Title: Gene Set Analysis of (Rare) Copy Number Variants
Description: This package is intended to facilitate gene-set
association with rare CNVs in case-control studies.
biocViews: MultipleComparisons
Author: Daniele Merico <daniele.merico@gmail.com>; packaged by Robert
Ziman <rziman@gmail.com>
Maintainer: Robert Ziman <rziman@gmail.com>
MD5sum: 10c5357dc56e6ff216424857b311e823
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vignettes: vignettes/cnvGSA/inst/doc/cnvGSA-vignette.pdf
vignetteTitles: cnvGSA - Gene-Set Analysis of Rare Copy Number Variants
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/cnvGSA/inst/doc/cnvGSA-vignette.R
Package: CNVtools
Version: 1.52.0
Depends: R (>= 2.10), survival
License: GPL-3
Archs: i386, x64
Title: A package to test genetic association with CNV data
Description: This package is meant to facilitate the testing of Copy
Number Variant data for genetic association, typically in
case-control studies.
biocViews: GeneticVariability
Author: Chris Barnes <christopher.barnes@imperial.ac.uk> and Vincent
Plagnol <vincent.plagnol@cimr.cam.ac.uk>
Maintainer: Chris Barnes <christopher.barnes@imperial.ac.uk>
MD5sum: 31608963d07c36455cbd9d79e919f58d
source.ver: src/contrib/CNVtools_1.52.0.tar.gz
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mac.binary.leopard.ver:
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vignettes: vignettes/CNVtools/inst/doc/CNVtools-vignette.pdf
vignetteTitles: Copy Number Variation Tools
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CNVtools/inst/doc/CNVtools-vignette.R
Package: CoCiteStats
Version: 1.30.0
Depends: R (>= 2.0), org.Hs.eg.db
Imports: AnnotationDbi
License: CPL
Title: Different test statistics based on co-citation.
Description: A collection of software tools for dealing with
co-citation data.
biocViews: Bioinformatics
Author: B. Ding and R. Gentleman
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: 57b65a69c56c5f19091a6f895768e40a
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
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Package: codelink
Version: 1.26.0
Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>=
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Imports: BiocGenerics, annotate
Suggests: genefilter, parallel
License: GPL-2
Title: Manipulation of Codelink Bioarrays data.
Description: This packages allow reading into R of Codelink bioarray
data exported as text from the Codelink software. Also includes
some functions to ease the manipulation and pre-processing of
data, such in background correction and normalization.
biocViews: Microarray, OneChannel, DataImport, Preprocessing
Author: Diego Diez <diego10ruiz@gmail.com>
Maintainer: Diego Diez <diego10ruiz@gmail.com>
URL: http://www.kuicr.kyoto-u.ac.jp/~diez
MD5sum: 34c1c8cfdd7d0360d55d558f5c6dda48
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vignettes: vignettes/codelink/inst/doc/codelink.pdf,
vignettes/codelink/inst/doc/CodelinkSet.pdf
vignetteTitles: codelink, CodelinkSet
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/codelink/inst/doc/codelink.R,
vignettes/codelink/inst/doc/CodelinkSet.R
Package: CoGAPS
Version: 1.8.0
Depends: R (>= 2.9.0), R.utils (>= 1.2.4), gplots (>= 2.8.0)
Imports: graphics, grDevices, methods, stats, utils
License: GPL (== 2)
Title: Coordinated Gene Activity in Pattern Sets
Description: Coordinated Gene Activity in Pattern Sets (CoGAPS) infers
biological processes which are active in individual gene sets
from corresponding microarray measurements. CoGAPS achieves
this inference by combining a MCMC matrix decomposition
algorithm (GAPS) with a novel statistic inferring activity on
gene sets.
biocViews: GeneExpression, Microarray, Bioinformatics
Author: Elana J. Fertig
Maintainer: Elana J. Fertig <ejfertig@jhmi.edu>, Michael F. Ochs
<mfo@jhu.edu>
URL: http://www.cancerbiostats.onc.jhmi.edu/CoGAPS.cfm
SystemRequirements: GAPS-JAGS (==1.0.2)
MD5sum: baaac5dfe7ffa17d703c17fb29261481
source.ver: src/contrib/CoGAPS_1.8.0.tar.gz
vignettes: vignettes/CoGAPS/inst/doc/CoGAPSUsersManual.pdf
vignetteTitles: GAPS/CoGAPS Users Manual
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hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CoGAPS/inst/doc/CoGAPSUsersManual.R
Package: coGPS
Version: 1.2.0
Depends: R (>= 2.13.0)
Imports: graphics, grDevices
Suggests: limma
License: GPL-2
Title: cancer outlier Gene Profile Sets
Description: Gene Set Enrichment Analysis of P-value based statistics
for outlier gene detection in dataset merged from multiple
studies
biocViews: Microarray, Bioinformatics, DifferentialExpression
Author: Yingying Wei, Michael Ochs
Maintainer: Yingying Wei <ywei@jhsph.edu>
MD5sum: c94137678c6074bd74724af1312ef431
source.ver: src/contrib/coGPS_1.2.0.tar.gz
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vignettes: vignettes/coGPS/inst/doc/coGPS.pdf
vignetteTitles: coGPS
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/coGPS/inst/doc/coGPS.R
Package: ConsensusClusterPlus
Version: 1.10.0
Imports: Biobase, ALL, graphics, stats, utils
License: GPL version 2
Title: ConsensusClusterPlus
Description: algorithm for determining cluster count and membership by
stability evidence in unsupervised analysis
biocViews: Software, Bioinformatics, Clustering
Author: Matt Wilkerson
Maintainer: Matt Wilkerson <mwilkers@med.unc.edu>
MD5sum: 67573d9ad4e5a4fed7cb600733dce724
source.ver: src/contrib/ConsensusClusterPlus_1.10.0.tar.gz
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vignettes:
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vignetteTitles: ConsensusClusterPlus Tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: convert
Version: 1.34.0
Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray,
utils, methods
License: LGPL
Title: Convert Microarray Data Objects
Description: Define coerce methods for microarray data objects.
biocViews: Infrastructure, Microarray, TwoChannel
Author: Gordon Smyth <smyth@wehi.edu.au>, James Wettenhall
<wettenhall@wehi.edu.au>, Yee Hwa (Jean Yang)
<jean@biostat.ucsf.edu>, Martin Morgan
<mtmorgan@fhcrc.org>Martin Morgan
Maintainer: Yee Hwa (Jean) Yang <jean@biostat.ucsf.edu>
URL: http://bioinf.wehi.edu.au/limma/convert.html
MD5sum: 842a69a470e5dfc3203670b3f7fbba6b
source.ver: src/contrib/convert_1.34.0.tar.gz
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vignettes: vignettes/convert/inst/doc/convert.pdf
vignetteTitles: Converting Between Microarray Data Classes
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/convert/inst/doc/convert.R
htmlDocs: vignettes/convert/inst/doc/index.html
dependsOnMe: maigesPack, TurboNorm
suggestsMe: BiocCaseStudies, dyebias, OLIN
Package: copa
Version: 1.26.0
Depends: Biobase, methods
Suggests: colonCA
License: Artistic-2.0
Archs: i386, x64
Title: Functions to perform cancer outlier profile analysis.
Description: COPA is a method to find genes that undergo recurrent
fusion in a given cancer type by finding pairs of genes that
have mutually exclusive outlier profiles.
biocViews: OneChannel, TwoChannel, DifferentialExpression,
Visualization
Author: James W. MacDonald
Maintainer: James W. MacDonald <jmacdon@med.umich.edu>
MD5sum: 6dd60700c75cdc212007e6f00a0a6ac9
source.ver: src/contrib/copa_1.26.0.tar.gz
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vignettes: vignettes/copa/inst/doc/copa.pdf
vignetteTitles: copa Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/copa/inst/doc/copa.R
Package: Cormotif
Version: 1.4.0
Depends: R (>= 2.12.0), affy, limma
Imports: affy, graphics, grDevices
License: GPL-2
Title: Correlation Motif Fit
Description: It fits correlation motif model to multiple studies to
detect study specific differential expression patterns.
biocViews: Microarray, Bioinformatics, DifferentialExpression
Author: Hongkai Ji, Yingying Wei
Maintainer: Yingying Wei <ywei@jhsph.edu>
MD5sum: 4e82e6af2d3200a879714206a18c4a60
source.ver: src/contrib/Cormotif_1.4.0.tar.gz
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vignettes: vignettes/Cormotif/inst/doc/CormotifVignette.pdf
vignetteTitles: Cormotif Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Cormotif/inst/doc/CormotifVignette.R
Package: CorMut
Version: 1.0.0
Depends: methods, Biostrings, seqinr,igraph
License: GPL-2
Title: Detect the correlated mutations based on selection pressure
Description: CorMut provides functions for computing kaks for
individual sites or specific amino acids and detecting
correlated mutations among them. Two methods are provided for
detecting correlated mutations ,including conditional selection
pressure and mutual information. The computation consists of
two steps: First, the positive selection sites are detected;
Second, the mutation correlations are computed among the
positive selection sites. Note that the first step is optional.
Meanwhile, CorMut facilitates the comparison of the correlated
mutations between two conditions by the means of correlated
mutation network.
biocViews: Bioinformatics, Sequencing
Author: Zhenpeng Li, Yang Huang, Yabo Ouyang, Liying Ma
Maintainer: Zhenpeng Li<zpli21@gmail.com>
MD5sum: c5af394428e3f54a9b5f9c1da36c8d6b
source.ver: src/contrib/CorMut_1.0.0.tar.gz
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vignettes: vignettes/CorMut/inst/doc/CorMut.pdf
vignetteTitles: CorMut
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CorMut/inst/doc/CorMut.R
Package: coRNAi
Version: 1.8.0
Depends: R (>= 2.10), cellHTS2, limma, locfit
Imports: MASS, gplots, lattice, grDevices, graphics, stats
License: Artistic-2.0
Title: Analysis of co-knock-down RNAi data
Description: Analysis of combinatorial cell-based RNAi screens
biocViews: CellBasedAssays
Author: Elin Axelsson
Maintainer: Elin Axelsson <elin@ebi.ac.uk>
SystemRequirements: Graphviz
MD5sum: da4fcaf1487186a9113b8b9007133c1d
source.ver: src/contrib/coRNAi_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/coRNAi_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/coRNAi_1.8.0.zip
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vignettes: vignettes/coRNAi/inst/doc/coRNAi.pdf
vignetteTitles: coRNAi
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/coRNAi/inst/doc/coRNAi.R
Package: CORREP
Version: 1.24.0
Imports: e1071, stats
Suggests: cluster, MASS
License: GPL (>= 2)
Title: Multivariate Correlation Estimator and Statistical Inference
Procedures.
Description: Multivariate correlation estimation and statistical
inference. See package vignette.
biocViews: Bioinformatics, Microarray, Clustering, GraphsAndNetworks
Author: Dongxiao Zhu and Youjuan Li
Maintainer: Dongxiao Zhu <doz@stowers-institute.org>
MD5sum: c9ac04350fe6cb5dd4c8ac74a941bfb9
source.ver: src/contrib/CORREP_1.24.0.tar.gz
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win64.binary.ver: bin/windows64/contrib/2.15/CORREP_1.24.0.zip
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vignettes: vignettes/CORREP/inst/doc/CORREP.pdf
vignetteTitles: Multivariate Correlation Estimator
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CORREP/inst/doc/CORREP.R
Package: cosmoGUI
Version: 1.24.0
Depends: tkWidgets, cosmo
License: LGPL (>= 2)
Title: GUI for constructing constraint sets used by the cosmo package
Description: cosmoGUI allows the user to interactively define
constraint sets that can be used by the cosmo package to
supervise the search for shared motifs in a set of DNA
sequences. The constraints can be either adapted from a set of
commonly used templates or defined from scratch.
biocViews: SequenceMatching, GUI
Author: Fabian Gallusser, Oliver Bembom, and Sandrine Dudoit
Maintainer: Oliver Bembom <oliver.bembom@gmail.com>
URL: http://cosmoweb.berkeley.edu/intro.html,
http://www.bepress.com/ucbbiostat/paper209/
MD5sum: 366138e121e89fcecb598c165dd2fff6
source.ver: src/contrib/cosmoGUI_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/cosmoGUI_1.24.0.zip
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: cqn
Version: 1.4.0
Depends: R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore,
splines, quantreg
Imports: splines
Suggests: scales, edgeR
License: Artistic-2.0
Title: Conditional quantile normalization
Description: A normalization tool for RNA-Seq data, implementing the
conditional quantile normalization method.
biocViews: RNAseq, Preprocessing, DifferentialExpression
Author: Jean (Zhijin) Wu, Kasper Daniel Hansen
Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
MD5sum: ccc60f56455b047d7232facac725ba4d
source.ver: src/contrib/cqn_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/cqn_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/cqn_1.4.0.zip
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vignettes: vignettes/cqn/inst/doc/cqn.pdf
vignetteTitles: CQN (Conditional Quantile Normalization)
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/cqn/inst/doc/cqn.R
importsMe: tweeDEseq
Package: CRImage
Version: 1.6.1
Depends: EBImage, DNAcopy, aCGH
Imports: MASS, e1071, foreach, sgeostat
License: Artistic-2.0
Title: CRImage a package to classify cells and calculate tumour
cellularity
Description: CRImage provides functionality to process and analyze
images, in particular to classify cells in biological images.
Furthermore, in the context of tumor images, it provides
functionality to calculate tumour cellularity.
biocViews: CellBiology, Classification
Author: Henrik Failmezger <failmezger@mpipz.mpg.de>, Yinyin Yuan
<Yinyin.Yuan@cancer.org.uk>, Oscar Rueda
<oscar.rueda@cancer.org.uk>, Florian Markowetz
<Florian.Markowetz@cancer.org.uk>
Maintainer: Henrik Failmezger <failmezger@mpipz.mpg.de>, Yinyin Yuan
<Yinyin.Yuan@cancer.org.uk>
MD5sum: 45ebbc5726f0f45311cdc7adbe822d44
source.ver: src/contrib/CRImage_1.6.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CRImage_1.6.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/CRImage_1.6.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/CRImage/inst/doc/cellularity2.pdf,
vignettes/CRImage/inst/doc/CRImage.pdf,
vignettes/CRImage/inst/doc/labeledImage.pdf,
vignettes/CRImage/inst/doc/segmentedImage.pdf,
vignettes/CRImage/inst/doc/segmentedImageRaw.pdf
vignetteTitles: cellularity2.pdf, CRImage Manual, labeledImage.pdf,
segmentedImage.pdf, segmentedImageRaw.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CRImage/inst/doc/CRImage.R
Package: crlmm
Version: 1.16.9
Depends: R (>= 2.14.0), oligoClasses (>= 1.19.39), preprocessCore (>=
1.17.7)
Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
1.23.2), ellipse, genefilter (>= 1.37.1), mvtnorm, splines,
stats, SNPchip, utils, lattice, ff, foreach, RcppEigen
LinkingTo: preprocessCore (>= 1.17.7)
Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.4), GGdata, snpStats,
ellipse, RUnit
License: Artistic-2.0
Archs: i386, x64
Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0
arrays, as well as a copy number tool specific to 5.0, 6.0, and
Illumina platforms
biocViews: Microarray, Preprocessing, SNP, Bioinformatics,
CopyNumberVariants
Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
Ruczinski, Rafael A Irizarry
Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie
<mritchie@wehi.EDU.AU>
MD5sum: cf7411a6df6622feb7946461955dac5c
source.ver: src/contrib/crlmm_1.16.9.tar.gz
win.binary.ver: bin/windows/contrib/2.15/crlmm_1.16.9.zip
win64.binary.ver: bin/windows64/contrib/2.15/crlmm_1.16.9.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/crlmm_1.16.9.tgz
vignettes: vignettes/crlmm/inst/doc/AffyGW.pdf,
vignettes/crlmm/inst/doc/CopyNumberOverview.pdf,
vignettes/crlmm/inst/doc/genotyping.pdf,
vignettes/crlmm/inst/doc/gtypeDownstream.pdf,
vignettes/crlmm/inst/doc/IlluminaPreprocessCN.pdf,
vignettes/crlmm/inst/doc/Infrastructure.pdf
vignetteTitles: Copy number estimation, Overview of copy number
vignettes, crlmm Vignette - Genotyping, crlmm Vignette -
Downstream Analysis, Preprocessing and genotyping Illumina
arrays for copy number analysis, Infrastructure for copy number
analysis
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/crlmm/inst/doc/AffyGW.R,
vignettes/crlmm/inst/doc/CopyNumberOverview.R,
vignettes/crlmm/inst/doc/crlmmDownstream.R,
vignettes/crlmm/inst/doc/genotyping.R,
vignettes/crlmm/inst/doc/gtypeDownstream.R,
vignettes/crlmm/inst/doc/IlluminaPreprocessCN.R,
vignettes/crlmm/inst/doc/Infrastructure.R
importsMe: minfi, VanillaICE
suggestsMe: oligoClasses, SNPchip
Package: CSAR
Version: 1.10.0
Depends: R (>= 2.15.0), IRanges, GenomicRanges
Imports: stats, utils
Suggests: ShortRead, Biostrings
License: Artistic-2.0
Archs: i386, x64
Title: Statistical tools for the analysis of ChIP-seq data
Description: Statistical tools for ChIP-seq data analysis. The package
includes the statistical method described in Kaufmann et al.
(2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average
DNA fragment size subjected to sequencing into account, the
software calculates genomic single-nucleotide read-enrichment
values. After normalization, sample and control are compared
using a test based on the Poisson distribution. Test statistic
thresholds to control the false discovery rate are obtained
through random permutation.
biocViews: ChIPseq,Transcription,Genetics
Author: Jose M Muino
Maintainer: Jose M Muino <jose.muino@wur.nl>
MD5sum: 3cddb264f02bf01585ac1a7a49959fec
source.ver: src/contrib/CSAR_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/CSAR_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/CSAR_1.10.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CSAR_1.10.0.tgz
vignettes: vignettes/CSAR/inst/doc/CSAR.pdf
vignetteTitles: CSAR Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/CSAR/inst/doc/CSAR.R
importsMe: NarrowPeaks
suggestsMe: NarrowPeaks
Package: ctc
Version: 1.32.0
Depends: amap
License: GPL-2
Title: Cluster and Tree Conversion.
Description: Tools for export and import classification trees and
clusters to other programs
biocViews: Microarray, Clustering, Classification, DataImport,
Visualization
Author: Antoine Lucas <antoinelucas@gmail.com>, Laurent Gautier
<laurent@cbs.dtu.dk>
Maintainer: Antoine Lucas <antoinelucas@gmail.com>
URL: http://antoinelucas.free.fr/ctc
MD5sum: 004ec1bdf0c95016ce502ecbd020bd6a
source.ver: src/contrib/ctc_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ctc_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ctc_1.32.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ctc_1.32.0.tgz
vignettes: vignettes/ctc/inst/doc/ctc.pdf
vignetteTitles: Introduction to ctc
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ctc/inst/doc/ctc.R
Package: cummeRbund
Version: 2.0.0
Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2,
reshape2, fastcluster, rtracklayer, Gviz
Imports: methods, plyr, BiocGenerics
Suggests: cluster, plyr
License: Artistic-2.0
Title: Analysis, exploration, manipulation, and visualization of
Cufflinks high-throughput sequencing data.
Description: Allows for persistent storage, access, exploration, and
manipulation of Cufflinks high-throughput sequencing data. In
addition, provides numerous plotting functions for commonly
used visualizations.
biocViews: HighThroughputSequencing, HighThroughputSequencingData,
RNAseq, RNAseqData, GeneExpression, DifferentialExpression,
Infrastructure, DataImport, DataRepresentation, Visualization,
Bioinformatics, Clustering, MultipleComparisons, QualityControl
Author: L. Goff, C. Trapnell, D. Kelley
Maintainer: Loyal A. Goff <lgoff@csail.mit.edu>
MD5sum: b76bed64c322f27a706f627c2af8ee8c
source.ver: src/contrib/cummeRbund_2.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/cummeRbund_2.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/cummeRbund_2.0.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/cummeRbund_2.0.0.tgz
vignettes: vignettes/cummeRbund/inst/doc/cuffData_schema.pdf,
vignettes/cummeRbund/inst/doc/cummeRbund-example-workflow.pdf,
vignettes/cummeRbund/inst/doc/cummeRbund-manual.pdf,
vignettes/cummeRbund/inst/doc/ENCODE_SCV.pdf
vignetteTitles: cuffData_schema.pdf, Sample cummeRbund workflow,
CummeRbund User Guide, ENCODE_SCV.pdf
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/cummeRbund/inst/doc/cummeRbund-example-workflow.R,
vignettes/cummeRbund/inst/doc/cummeRbund-manual.R
suggestsMe: oneChannelGUI
Package: cycle
Version: 1.12.0
Depends: R (>= 2.10.0), Mfuzz
Imports: Biobase, stats
License: GPL-2
Title: Significance of periodic expression pattern in time-series data
Description: Package for assessing the statistical significance of
periodic expression based on Fourier analysis and comparison
with data generated by different background models
biocViews: Microarray, Bioinformatics,TimeCourse
Author: Matthias Futschik <mfutschik@ualg.pt>
Maintainer: Matthias Futschik <mfutschik@ualg.pt>
URL:
http://itb.biologie.hu-berlin.de/~futschik/software/R/cycle/index.html
MD5sum: cbcef5e4a02d260813f9f6120719ffb6
source.ver: src/contrib/cycle_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/cycle_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/cycle_1.12.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/cycle_1.12.0.tgz
vignettes: vignettes/cycle/inst/doc/cycle.pdf
vignetteTitles: Introduction to cycle
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/cycle/inst/doc/cycle.R
Package: daMA
Version: 1.30.0
Imports: MASS, stats
License: GPL (>= 2)
Title: Efficient design and analysis of factorial two-colour microarray
data
Description: This package contains functions for the efficient design
of factorial two-colour microarray experiments and for the
statistical analysis of factorial microarray data. Statistical
details are described in Bretz et al. (2003, submitted)
biocViews: Microarray, TwoChannel, Bioinformatics,
DifferentialExpression
Author: Jobst Landgrebe <jlandgr1@gwdg.de> and Frank Bretz
<bretz@bioinf.uni-hannover.de>
Maintainer: Jobst Landgrebe <jlandgr1@gwdg.de>
URL: http://www.microarrays.med.uni-goettingen.de
MD5sum: 79fb38ae5c4b737753dc7ee988e1ff19
source.ver: src/contrib/daMA_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/daMA_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/daMA_1.30.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/daMA_1.30.0.tgz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: DART
Version: 1.4.0
Depends: R (>= 2.10.0), igraph0
Suggests: breastCancerVDX, breastCancerMAINZ, Biobase
License: GPL-2
Title: Denoising Algorithm based on Relevance network Topology
Description: Denoising Algorithm based on Relevance network Topology
(DART) is an algorithm designed to evaluate the consistency of
prior information molecular signatures (e.g in-vitro
perturbation expression signatures) in independent molecular
data (e.g gene expression data sets). If consistent, a pruning
network strategy is then used to infer the activation status of
the molecular signature in individual samples.
biocViews: GeneExpression, DifferentialExpression, GraphsAndNetworks,
Pathways, Bioinformatics
Author: Yan Jiao, Katherine Lawler, Andrew E Teschendorff
Maintainer: Katherine Lawler <katherine.lawler@kcl.ac.uk>
MD5sum: 500d4317eef7c8afd5603a8a97ae788d
source.ver: src/contrib/DART_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DART_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DART_1.4.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DART_1.4.0.tgz
vignettes: vignettes/DART/inst/doc/DART.pdf
vignetteTitles: DART Tutorial
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DART/inst/doc/DART.R
Package: DAVIDQuery
Version: 1.18.0
Depends: RCurl (>= 1.4.0), utils
License: GPL-2
Title: Retrieval from the DAVID bioinformatics data resource into R
Description: Tools to retrieve data from DAVID, the Database for
Annotation, Visualization and Integrated Discovery
biocViews: Annotation
Author: Roger Day, Alex Lisovich
Maintainer: Roger Day <day01@pitt.edu>
MD5sum: 31f9af37515dd1afb3f481f7b6c3c8fa
source.ver: src/contrib/DAVIDQuery_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DAVIDQuery_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DAVIDQuery_1.18.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/DAVIDQuery_1.18.0.tgz
vignettes: vignettes/DAVIDQuery/inst/doc/DAVIDQuery.pdf
vignetteTitles: An R Package for retrieving data from DAVID into R
objects.
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DAVIDQuery/inst/doc/DAVIDQuery.R
importsMe: IdMappingRetrieval
Package: DBChIP
Version: 1.2.0
Depends: R (>= 2.15.0), edgeR, DESeq
Suggests: ShortRead, BiocGenerics
License: GPL (>= 2)
Title: Differential Binding of Transcription Factor with ChIP-seq
Description: DBChIP detects differentially bound sharp binding sites
across multiple conditions, with or without matching control
samples.
biocViews: ChIPseq, Sequencing, Transcription, Genetics, Bioinformatics
Author: Kun Liang
Maintainer: Kun Liang <kliang@stat.wisc.edu>
MD5sum: 2d0468c436fe43cb063118d6cd73fc89
source.ver: src/contrib/DBChIP_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DBChIP_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DBChIP_1.2.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/DBChIP_1.2.0.tgz
vignettes: vignettes/DBChIP/inst/doc/DBChIP.pdf
vignetteTitles: DBChIP
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DBChIP/inst/doc/DBChIP.R
Package: ddCt
Version: 1.12.0
Depends: R (>= 2.3.0), Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3),
xtable, lattice, methods
Suggests: RUnit
License: LGPL-3
Title: The ddCt Algorithm for the Analysis of Quantitative Real-Time
PCR (qRT-PCR)
Description: The Delta-Delta-Ct (ddCt) Algorithm is an approximation
method to determine relative gene expression with quantitative
real-time PCR (qRT-PCR) experiments. Compared to other
approaches, it requires no standard curve for each
primer-target pair, therefore reducing the working load and yet
returning accurate enough results as long as the assumptions of
the amplification efficiency hold. The ddCt package implements
a pipeline to collect, analyse and visualize qRT-PCR results,
for example those from TaqMan SDM software, mainly using the
ddCt method. The pipeline can be either invoked by a script in
command-line or through the API consisting of S4-Classes,
methods and functions.
biocViews: GeneExpression, DifferentialExpression,
MicrotitrePlateAssay, qPCR
Author: Jitao David Zhang, Rudolf Biczok and Markus Ruschhaupt
Maintainer: Jitao David Zhang <jitao_david.zhang@roche.com>
MD5sum: 12682eac96a1e55c1e5151b060f1954a
source.ver: src/contrib/ddCt_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ddCt_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ddCt_1.12.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ddCt_1.12.0.tgz
vignettes: vignettes/ddCt/inst/doc/rtPCR.pdf,
vignettes/ddCt/inst/doc/RT-PCR-Script-ddCt.pdf,
vignettes/ddCt/inst/doc/rtPCR-usage.pdf
vignetteTitles: Introduction to the ddCt method for qRT-PCR data
analysis: background,, algorithm and example, How to apply the
ddCt method, Analyse RT-PCR data with the end-to-end script in
ddCt package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ddCt/inst/doc/rtPCR.R,
vignettes/ddCt/inst/doc/RT-PCR-Script-ddCt.R,
vignettes/ddCt/inst/doc/rtPCR-usage.R
Package: ddgraph
Version: 1.2.0
Depends: graph, methods, Rcpp
Imports: bnlearn (>= 2.8), infotheo, gtools, pcalg, RColorBrewer,
plotrix, MASS
LinkingTo: Rcpp
Suggests: testthat, Rgraphviz, e1071, ROCR, testthat
License: GPL-3
Archs: i386, x64
Title: Distinguish direct and indirect interactions with Graphical
Modelling
Description: Distinguish direct from indirect interactions in gene
regulation and infer combinatorial code from highly correlated
variables such as transcription factor binding profiles. The
package implements the Neighbourhood Consistent PC algorithm
(NCPC) and draws Direct Dependence Graphs to represent
dependence structure around a target variable. The package also
provides a unified interface to other Graphical Modelling
(Bayesian Network) packages for distinguishing direct and
indirect interactions.
biocViews: Bioinformatics, GraphsAndNetworks
Author: Robert Stojnic
Maintainer: Robert Stojnic <robert.stojnic@gmail.com>
MD5sum: aedc12ac6861d8f9f709f11abd0b4faf
source.ver: src/contrib/ddgraph_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ddgraph_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ddgraph_1.2.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/ddgraph_1.2.0.tgz
vignettes: vignettes/ddgraph/inst/doc/ddgraph-cluster.pdf,
vignettes/ddgraph/inst/doc/ddgraph-ddgraph-plot.pdf,
vignettes/ddgraph/inst/doc/ddgraph.pdf
vignetteTitles: ddgraph-cluster.pdf, ddgraph-ddgraph-plot.pdf, Overview
of the 'ddgraph' package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ddgraph/inst/doc/ddgraph.R
Package: DECIPHER
Version: 1.4.0
Depends: R (>= 2.13.0), Biostrings (>= 2.16), RSQLite (>= 0.9),
IRanges, stats
Imports: Biostrings, RSQLite, IRanges, stats
LinkingTo: Biostrings, RSQLite, IRanges, stats
License: GPL-3
Archs: i386, x64
Title: Database Enabled Code for Ideal Probe Hybridization Employing R
Description: A toolset that assist in the design of hybridization
probes.
biocViews: Clustering, Genetics, Sequencing, Infrastructure,
DataImport, Visualization, Microarray, QualityControl
Author: Erik Wright
Maintainer: Erik Wright <DECIPHER@cae.wisc.edu>
MD5sum: e9d35cd8dc7f1d4de36caa3029394242
source.ver: src/contrib/DECIPHER_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DECIPHER_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DECIPHER_1.4.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/DECIPHER_1.4.0.tgz
vignettes: vignettes/DECIPHER/inst/doc/DECIPHERing.pdf,
vignettes/DECIPHER/inst/doc/DesignPrimers.pdf,
vignettes/DECIPHER/inst/doc/FindChimeras.pdf
vignetteTitles: Getting Started DECIPHERing, Design Group-Specific
Primers, Finding Chimeric Sequences
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DECIPHER/inst/doc/DECIPHERing.R,
vignettes/DECIPHER/inst/doc/DesignPrimers.R,
vignettes/DECIPHER/inst/doc/FindChimeras.R
Package: DeconRNASeq
Version: 1.0.0
Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid
License: GPL-2
Title: Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
Description: DeconSeq is an R package for deconvolution of
heterogeneous tissues based on mRNA-Seq data. It modeled
expression levels from heterogeneous cell populations in
mRNA-Seq as the weighted average of expression from different
constituting cell types and predicted cell type proportions of
single expression profiles.
biocViews: Bioinformatics, ExperimentData, RNAExpressionData
Author: Ting Gong <tinggong@gmail.com> Joseph D. Szustakowski
<joseph.szustakowski@novartis.com>
Maintainer: Ting Gong <tinggong@gmail.com>
MD5sum: 09fc3e9c499b8788552bca497a82541b
source.ver: src/contrib/DeconRNASeq_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DeconRNASeq_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DeconRNASeq_1.0.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/DeconRNASeq_1.0.0.tgz
vignettes: vignettes/DeconRNASeq/inst/doc/DeconRNASeq.pdf
vignetteTitles: DeconRNASeq Demo
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DeconRNASeq/inst/doc/DeconRNASeq.R
Package: DEDS
Version: 1.32.0
Depends: R (>= 1.7.0)
License: LGPL
Archs: i386, x64
Title: Differential Expression via Distance Summary for Microarray Data
Description: This library contains functions that calculate various
statistics of differential expression for microarray data,
including t statistics, fold change, F statistics, SAM,
moderated t and F statistics and B statistics. It also
implements a new methodology called DEDS (Differential
Expression via Distance Summary), which selects differentially
expressed genes by integrating and summarizing a set of
statistics using a weighted distance approach.
biocViews: Bioinformatics, Microarray, DifferentialExpression
Author: Yuanyuan Xiao <yxiao@itsa.ucsf.edu>, Jean Yee Hwa Yang
<jeany@maths.usyd.edu.au>.
Maintainer: Yuanyuan Xiao <yxiao@itsa.ucsf.edu>
MD5sum: eac2b9851e6a73366a4726ce5142b6b0
source.ver: src/contrib/DEDS_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DEDS_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DEDS_1.32.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DEDS_1.32.0.tgz
vignettes: vignettes/DEDS/inst/doc/DEDS.pdf
vignetteTitles: DEDS.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DEDS/inst/doc/DEDS.R
Package: deepSNV
Version: 1.4.0
Depends: R (>= 2.13.0), Rsamtools (>= 1.4.3), GenomicRanges, IRanges,
Biostrings, VGAM, methods, graphics
Imports: Rsamtools
LinkingTo: Rsamtools
License: GPL-3
Archs: i386, x64
Title: Detection of subclonal SNVs in deep sequencing experiments.
Description: This package provides provides a quantitative variant
caller for detecting subclonal mutations in ultra-deep (>=100x
coverage) sequencing experiments. It assumes a comparative
setup with a control experiment of the same loci and a
beta-binomial model to discriminate sequencing errors and
subclonal SNVs.
biocViews: GeneticVariability, SNP, Sequencing, Genetics, DataImport
Author: Moritz Gerstung and Niko Beerenwinkel
Maintainer: Moritz Gerstung <moritz.gerstung@sanger.ac.uk>
URL: http://www.cbg.ethz.ch/software/deepSNV
MD5sum: 80582a5a973643b3f8584ddfd2bc5b99
source.ver: src/contrib/deepSNV_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/deepSNV_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/deepSNV_1.4.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/deepSNV_1.4.0.tgz
vignettes: vignettes/deepSNV/inst/doc/deepSNV.pdf
vignetteTitles: An R package for detecting low frequency variants in
deep sequencing experiments
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/deepSNV/inst/doc/deepSNV.R
Package: DEGraph
Version: 1.10.0
Depends: R (>= 2.10.0), R.utils
Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL,
Rgraphviz, rrcov, NCIgraph
Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL,
rrcov, Rgraphviz, NCIgraph
License: GPL-3
Title: Two-sample tests on a graph
Description: DEGraph implements recent hypothesis testing methods which
directly assess whether a particular gene network is
differentially expressed between two conditions. This is to be
contrasted with the more classical two-step approaches which
first test individual genes, then test gene sets for enrichment
in differentially expressed genes. These recent methods take
into account the topology of the network to yield more powerful
detection procedures. DEGraph provides methods to easily test
all KEGG pathways for differential expression on any gene
expression data set and tools to visualize the results.
biocViews: Microarray, DifferentialExpression, GraphsAndNetworks,
NetworkAnalysis, NetworkEnrichment
Author: Laurent Jacob, Pierre Neuvial and Sandrine Dudoit
Maintainer: Laurent Jacob <laurent.jacob@gmail.com>
MD5sum: 6513411118526a0fdb65851025a3e060
source.ver: src/contrib/DEGraph_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DEGraph_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DEGraph_1.10.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/DEGraph_1.10.0.tgz
vignettes: vignettes/DEGraph/inst/doc/DEGraph.pdf
vignetteTitles: DEGraph: differential expression testing for gene
networks
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DEGraph/inst/doc/DEGraph.R
suggestsMe: graphite
Package: DEGseq
Version: 1.12.0
Depends: R (>= 2.8.0), qvalue, samr, methods
Imports: graphics, grDevices, methods, stats, utils
License: LGPL (>=2)
Archs: i386, x64
Title: Identify Differentially Expressed Genes from RNA-seq data
Description: DEGseq is an R package to identify differentially
expressed genes from RNA-Seq data.
biocViews: RNAseq, Preprocessing, GeneExpression,
DifferentialExpression
Author: Likun Wang <wanglikun@tsinghua.edu.cn> and Xi Wang
<wang-xi05@mails.tsinghua.edu.cn>.
Maintainer: Likun Wang <wanglikun@tsinghua.edu.cn>
MD5sum: 718ffede5346e8e29b3efb2154db1dbc
source.ver: src/contrib/DEGseq_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DEGseq_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DEGseq_1.12.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/DEGseq/inst/doc/DEGseq.pdf
vignetteTitles: DEGseq
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DEGseq/inst/doc/DEGseq.R
Package: DESeq
Version: 1.10.1
Depends: Biobase (>= 2.13.11), locfit, lattice
Imports: genefilter, geneplotter, methods, MASS, RColorBrewer
Suggests: pasilla (>= 0.2.10), vsn, gplots
License: GPL (>= 3)
Archs: i386, x64
Title: Differential gene expression analysis based on the negative
binomial distribution
Description: Estimate variance-mean dependence in count data from
high-throughput sequencing assays and test for differential
expression based on a model using the negative binomial
distribution
biocViews: HighThroughputSequencing, ChIPseq, RNAseq, SAGE,
DifferentialExpression
Author: Simon Anders, EMBL Heidelberg <sanders@fs.tum.de>
Maintainer: Simon Anders <sanders@fs.tum.de>
URL: http://www-huber.embl.de/users/anders/DESeq
MD5sum: 1b95f6c724fd3609c22f112bb9864685
source.ver: src/contrib/DESeq_1.10.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DESeq_1.10.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/DESeq_1.10.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/DESeq/inst/doc/DESeq.pdf,
vignettes/DESeq/inst/doc/vst.pdf
vignetteTitles: Analysing RNA-Seq data with the "DESeq" package,
vst.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DESeq/inst/doc/DESeq.R
dependsOnMe: DBChIP, easyRNASeq, gCMAP
importsMe: ArrayExpressHTS, DiffBind, EDASeq, rnaSeqMap
suggestsMe: DiffBind, EDASeq, GenomicRanges, oneChannelGUI
Package: DEXSeq
Version: 1.4.0
Depends: Biobase (>= 2.13.11)
Imports: biomaRt, hwriter, methods, stringr, statmod (>= 1.4.15)
Suggests: pasilla (>= 0.2.13)
Enhances: parallel
License: GPL (>= 3)
Title: Inference of differential exon usage in RNA-Seq
Description: The package is focused on finding differential exon usage
using RNA-seq exon counts between samples with different
experimental designs. It provides functions that allows the
user to make the necessary statistical tests based on a model
that uses the negative binomial distribution to estimate the
variance between biological replicates and generalized linear
models for testing. The package also provides functions for the
visualization and exploration of the results.
biocViews: HighThroughputSequencing, RNAseq, DifferentialExpression
Author: Simon Anders <sanders@fs.tum.de> and Alejandro Reyes
<alejandro.reyes@embl.de>, both at EMBL Heidelberg
Maintainer: Alejandro Reyes <alejandro.reyes@embl.de>
MD5sum: 0e679cf44416f27fb2718d74d3491afd
source.ver: src/contrib/DEXSeq_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DEXSeq_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DEXSeq_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/DEXSeq/inst/doc/DEXSeq.pdf
vignetteTitles: Analyzing RNA-seq data for differential exon usage with
the "DEXSeq" package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DEXSeq/inst/doc/DEXSeq.R
suggestsMe: GenomicRanges
Package: DFP
Version: 1.16.0
Depends: methods, Biobase (>= 2.5.5)
License: GPL-2
Title: Gene Selection
Description: This package provides a supervised technique able to
identify differentially expressed genes, based on the
construction of \emph{Fuzzy Patterns} (FPs). The Fuzzy Patterns
are built by means of applying 3 Membership Functions to
discretized gene expression values.
biocViews: Bioinformatics, Microarray, DifferentialExpression
Author: R. Alvarez-Gonzalez, D. Glez-Pena, F. Diaz, F. Fdez-Riverola
Maintainer: Rodrigo Alvarez-Glez <rodrigo.djv@uvigo.es>
MD5sum: 45319033c657ff3dff877cb15cfddc3c
source.ver: src/contrib/DFP_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DFP_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DFP_1.16.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DFP_1.16.0.tgz
vignettes: vignettes/DFP/inst/doc/DFP.pdf
vignetteTitles: Howto: Discriminat Fuzzy Pattern
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DFP/inst/doc/DFP.R
Package: DiffBind
Version: 1.4.2
Depends: R (>= 2.14.0), GenomicRanges
Imports: RColorBrewer, amap, edgeR (>= 2.3.58), gplots, DESeq,
grDevices, stats, utils, IRanges, zlibbioc
LinkingTo: Rsamtools
Suggests: DESeq
Enhances: rgl, parallel
License: Artistic-2.0
Archs: i386, x64
Title: Differential Binding Analysis of ChIP-Seq peak data
Description: Compute differentially bound sites from multiple ChIP-seq
experiments using affinity (quantitative) data. Also enables
occupancy (overlap) analysis and plotting functions.
biocViews: Bioinformatics, HighThroughputSequencing, ChIPseq
Author: Rory Stark<rory.stark@cancer.org.uk>, Gordon Brown
<gordon.brown@cancer.org.uk>
Maintainer: Rory Stark<rory.stark@cancer.org.uk>
MD5sum: 8f6a455a01d16cbfe3aea6196f685871
source.ver: src/contrib/DiffBind_1.4.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DiffBind_1.4.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/DiffBind_1.4.2.zip
mac.binary.leopard.ver:
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vignettes: vignettes/DiffBind/inst/doc/DiffBind.pdf
vignetteTitles: DiffBind User's Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DiffBind/inst/doc/DiffBind.R
Package: diffGeneAnalysis
Version: 1.40.0
Imports: graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils
License: GPL
Title: Performs differential gene expression Analysis
Description: Analyze microarray data
biocViews: Bioinformatics, Microarray, DifferentialExpression
Author: Choudary Jagarlamudi
Maintainer: Choudary Jagarlamudi <choudary.jagar@swosu.edu>
MD5sum: abfee77173137064a4e30768cb3604b7
source.ver: src/contrib/diffGeneAnalysis_1.40.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/diffGeneAnalysis_1.40.0.zip
win64.binary.ver:
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mac.binary.leopard.ver:
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vignettes: vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf
vignetteTitles: Documentation on diffGeneAnalysis
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.R
Package: DirichletMultinomial
Version: 1.0.0
Depends: IRanges
Imports: stats4, methods
Suggests: lattice, parallel, MASS, RColorBrewer, xtable
License: LGPL-3
Archs: i386, x64
Title: Dirichlet-Multinomial Mixture Model Machine Learning for
Microbiome Data
Description: Dirichlet-multinomial mixture models can be used to
describe variability in microbial metagenomic data. This
package is an interface to code originally made available by
Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as
discussed further in the man page for this package,
?DirichletMultinomial.
biocViews: HighThroughputSequencing, Clustering, Classification
Author: Martin Morgan <mtmorgan@fhcrc.org>
Maintainer: Martin Morgan <mtmorgan@fhcrc.org>
SystemRequirements: gsl
MD5sum: 6f35898c921260a6fce276e195a37f50
source.ver: src/contrib/DirichletMultinomial_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DirichletMultinomial_1.0.0.zip
win64.binary.ver:
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mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/DirichletMultinomial_1.0.0.tgz
vignettes:
vignettes/DirichletMultinomial/inst/doc/DirichletMultinomial.pdf
vignetteTitles: An introduction to DirichletMultinomial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: dks
Version: 1.4.0
Depends: R (>= 2.8)
Imports: cubature
License: GPL
Title: The double Kolmogorov-Smirnov package for evaluating multiple
testing procedures.
Description: The dks package consists of a set of diagnostic functions
for multiple testing methods. The functions can be used to
determine if the p-values produced by a multiple testing
procedure are correct. These functions are designed to be
applied to simulated data. The functions require the entire set
of p-values from multiple simulated studies, so that the joint
distribution can be evaluated.
biocViews: Bioinformatics,MultipleComparisons,QualityControl
Author: Jeffrey T. Leek <jleek@jhsph.edu>
Maintainer: Jeffrey T. Leek <jleek@jhsph.edu>
MD5sum: a21668c48848ef735e1fab9f8123b075
source.ver: src/contrib/dks_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/dks_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/dks_1.4.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/dks_1.4.0.tgz
vignettes: vignettes/dks/inst/doc/betas2.pdf,
vignettes/dks/inst/doc/dks.pdf
vignetteTitles: betas2.pdf, dksTutorial
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/dks/inst/doc/dks.R
Package: DNAcopy
Version: 1.32.0
License: GPL (>= 2)
Archs: i386, x64
Title: DNA copy number data analysis
Description: Segments DNA copy number data using circular binary
segmentation to detect regions with abnormal copy number
biocViews: Microarray, CopyNumberVariants
Author: Venkatraman E. Seshan, Adam Olshen
Maintainer: Venkatraman E. Seshan <seshanv@mskcc.org>
MD5sum: 9a32e8724e519de210fa4325e203ffcc
source.ver: src/contrib/DNAcopy_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DNAcopy_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DNAcopy_1.32.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/DNAcopy/inst/doc/DNAcopy.pdf
vignetteTitles: DNAcopy
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DNAcopy/inst/doc/DNAcopy.R
dependsOnMe: CGHcall, cghMCR, Clonality, CNAnorm, CRImage, snapCGH
importsMe: Clonality, cn.farms, GWASTools, MinimumDistance, Repitools,
snapCGH
suggestsMe: ADaCGH2, beadarraySNP, Clonality, cn.mops, fastseg,
genoset, Repitools
Package: domainsignatures
Version: 1.18.0
Depends: R (>= 2.4.0), KEGG.db, prada, biomaRt, methods
Imports: AnnotationDbi
License: Artistic-2.0
Title: Geneset enrichment based on InterPro domain signatures
Description: Find significantly enriched gene classifications in a list
of functionally undescribed genes based on their InterPro
domain structure.
biocViews: Annotation, Pathways, GeneSetEnrichment
Author: Florian Hahne, Tim Beissbarth
Maintainer: Florian Hahne <florian.hahne@novartis.com>
MD5sum: ccecdc26c4ca6d7f8a5cbdb9f9aae871
source.ver: src/contrib/domainsignatures_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/domainsignatures_1.18.0.zip
win64.binary.ver:
bin/windows64/contrib/2.15/domainsignatures_1.18.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/domainsignatures_1.18.0.tgz
vignettes: vignettes/domainsignatures/inst/doc/domainenrichment.pdf
vignetteTitles: Gene set enrichment using InterPro domain signatures
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/domainsignatures/inst/doc/domainenrichment.R
Package: DOSE
Version: 1.4.0
Depends: R (>= 2.10), ggplot2
Imports: methods, plyr, qvalue, stats4, AnnotationDbi, DO.db,
org.Hs.eg.db, igraph, scales, reshape2, graphics, GOSemSim
Suggests: clusterProfiler, ReactomePA
License: Artistic-2.0
Title: Disease Ontology Semantic and Enrichment analysis
Description: Implemented five methods proposed by Resnik, Schlicker,
Jiang, Lin and Wang respectively for measuring DO semantic
similarities, and hypergeometric test for enrichment analysis.
biocViews: Bioinformatics, Annotation
Author: Guangchuang Yu, Li-Gen Wang
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
MD5sum: ace5db23bd1a6102e801770b6c1800e4
source.ver: src/contrib/DOSE_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DOSE_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DOSE_1.4.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DOSE_1.4.0.tgz
vignettes: vignettes/DOSE/inst/doc/DOSE.pdf
vignetteTitles: An introduction to DOSE
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DOSE/inst/doc/DOSE.R
dependsOnMe: ReactomePA
importsMe: clusterProfiler
suggestsMe: GOSemSim
Package: DSS
Version: 1.0.0
Depends: Biobase, locfdr
Imports: methods
License: GPL
Title: Dispersion shrinakge for sequencing data.
Description: DSS is an R library performing the differential expression
analysis for RNA-seq count data. DSS implements a new
dispersion shrinkage method to estimate the gene-specific
biological variance. Extensive simulation results showed that
DSS performs favorabily compared to DESeq and edgeR when the
variation of biological variances is large.
biocViews: HighThroughputSequencing, RNAseq, ChIPseq,
DifferentialExpression
Author: Hao Wu <hao.wu@emory.edu>
Maintainer: Hao Wu <hao.wu@emory.edu>
MD5sum: 3e87e45f73915ff3741f490c11113039
source.ver: src/contrib/DSS_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DSS_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DSS_1.0.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DSS_1.0.0.tgz
vignettes: vignettes/DSS/inst/doc/DSS.pdf
vignetteTitles: Differential expression for RNA-seq data with
dispersion shrinkage
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DSS/inst/doc/DSS.R
Package: DTA
Version: 2.4.0
Depends: R (>= 2.10), LSD
Imports: scatterplot3d
License: Artistic-2.0
Title: Dynamic Transcriptome Analysis
Description: Dynamic Transcriptome Analysis (DTA) can monitor the
cellular response to perturbations with higher sensitivity and
temporal resolution than standard transcriptomics. The package
implements the underlying kinetic modeling approach capable of
the precise determination of synthesis- and decay rates from
individual microarray or RNAseq measurements.
biocViews: Microarray, DifferentialExpression, GeneExpression,
Transcription
Author: Bjoern Schwalb, Benedikt Zacher, Sebastian Duemcke, Achim
Tresch
Maintainer: Bjoern Schwalb <schwalb@lmb.uni-muenchen.de>
MD5sum: a12915d55af318da52f11b8a9b8bc5f6
source.ver: src/contrib/DTA_2.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DTA_2.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DTA_2.4.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DTA_2.4.0.tgz
vignettes: vignettes/DTA/inst/doc/DTA.pdf
vignetteTitles: A guide to Dynamic Transcriptome Analysis (DTA)
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/DTA/inst/doc/DTA.R
Package: dualKS
Version: 1.18.0
Depends: R (>= 2.6.0), Biobase (>= 1.15.0), affy, methods
License: LGPL (>= 2.0)
Title: Dual KS Discriminant Analysis and Classification
Description: This package implements a Kolmogorov Smirnov rank-sum
based algorithm for training (i.e. discriminant
analysis--identification of genes that discriminate between
classes) and classification of gene expression data sets. One
of the chief strengths of this approach is that it is amenable
to the "multiclass" problem. That is, it can discriminate
between more than 2 classes.
biocViews: Microarray, Bioinformatics
Author: Eric J. Kort, Yarong Yang
Maintainer: Eric J. Kort <eric.kort@vai.org>
MD5sum: ba95efef6f2ed7b3a34ddaa8dc8e7fc5
source.ver: src/contrib/dualKS_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/dualKS_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/dualKS_1.18.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/dualKS/inst/doc/dualKS.pdf
vignetteTitles: dualKS.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/dualKS/inst/doc/dualKS.R
Package: dyebias
Version: 1.16.0
Depends: R (>= 1.4.1), marray, Biobase
Suggests: limma, convert, GEOquery, dyebiasexamples, methods
License: GPL-3
Title: The GASSCO method for correcting for slide-dependent
gene-specific dye bias
Description: Many two-colour hybridizations suffer from a dye bias that
is both gene-specific and slide-specific. The former depends on
the content of the nucleotide used for labeling; the latter
depends on the labeling percentage. The slide-dependency was
hitherto not recognized, and made addressing the artefact
impossible. Given a reasonable number of dye-swapped pairs of
hybridizations, or of same vs. same hybridizations, both the
gene- and slide-biases can be estimated and corrected using the
GASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009),
doi:10.1038/msb.2009.21)
biocViews: Microarray, TwoChannel, QualityControl, Preprocessing
Author: Philip Lijnzaad and Thanasis Margaritis
Maintainer: Philip Lijnzaad <p.lijnzaad@umcutrecht.nl>
URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad
MD5sum: f4e809d85871d940726c24ed9dd1d593
source.ver: src/contrib/dyebias_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/dyebias_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/dyebias_1.16.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/dyebias_1.16.0.tgz
vignettes: vignettes/dyebias/inst/doc/dyebiasCompleteVignette.pdf,
vignettes/dyebias/inst/doc/dyebias-vignette.pdf,
vignettes/dyebias/inst/doc/gassco.pdf
vignetteTitles: dyebiasCompleteVignette.pdf, dye bias correction,
gassco.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/dyebias/inst/doc/dyebias-vignette.R
Package: DynDoc
Version: 1.36.0
Depends: methods, utils
Imports: methods
License: Artistic-2.0
Title: Dynamic document tools
Description: A set of functions to create and interact with dynamic
documents and vignettes.
biocViews: ReportWriting, Infrastructure
Author: R. Gentleman, Jeff Gentry
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: d4c647f134914d369e9587fb8d474f5a
source.ver: src/contrib/DynDoc_1.36.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/DynDoc_1.36.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/DynDoc_1.36.0.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: tkWidgets
Package: EasyqpcR
Version: 1.2.0
Imports: plyr, matrixStats, plotrix, gWidgetsRGtk2
Suggests: SLqPCR, qpcrNorm, qpcR, knitr
License: GPL (>=2)
Title: EasyqpcR for low-throughput real-time quantitative PCR data
analysis
Description: This package is based on the qBase algorithms published by
Hellemans et al. in 2007. The EasyqpcR package allows you to
import easily qPCR data files as described in the vignette.
Thereafter, you can calculate amplification efficiencies,
relative quantities and their standard errors, normalization
factors based on the best reference genes choosen (using the
SLqPCR package), and then the normalized relative quantities,
the NRQs scaled to your control and their standard errors. This
package has been created for low-throughput qPCR data analysis.
biocViews: qPCR, GeneExpression
Author: Le Pape Sylvain
Maintainer: Le Pape Sylvain <sylvain.le.pape@univ-poitiers.fr>
MD5sum: 23987219cbda1b3637681c763360a44f
source.ver: src/contrib/EasyqpcR_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/EasyqpcR_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/EasyqpcR_1.2.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/EasyqpcR/inst/doc/vignette_EasyqpcR.pdf
vignetteTitles: EasyqpcR
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/EasyqpcR/inst/doc/vignette_EasyqpcR.R
Package: easyRNASeq
Version: 1.4.2
Depends: graphics, methods, parallel, utils, genomeIntervals (>=
1.14.0), Biobase (>= 2.18.0), BiocGenerics (>= 0.4.0), biomaRt
(>= 2.14.0), edgeR (>= 3.0.0), Biostrings (>= 2.26.0), BSgenome
(>= 1.26.0), DESeq (>= 1.10.0), GenomicRanges (>= 1.10.0),
IRanges (>= 1.16.0), Rsamtools (>= 1.10.0), ShortRead (>=
1.16.0)
Suggests: BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), GenomicFeatures
(>= 1.10.0), RnaSeqTutorial (>= 0.0.10)
Enhances: edgeR, genomeIntervals, DESeq, ShortRead
License: Artistic-2.0
Title: Count summarization and normalization for RNA-Seq data.
Description: Calculates the coverage of high-throughput short-reads
against a genome of reference and summarizes it per feature of
interest (e.g. exon, gene, transcript). The data can be
normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.
biocViews: GeneExpression, RNAseq, Genetics, Preprocessing
Author: Nicolas Delhomme, Ismael Padioleau
Maintainer: Nicolas Delhomme <delhomme@embl.de>
MD5sum: 3743cc970388ee7d03df3ae67f7bcb2b
source.ver: src/contrib/easyRNASeq_1.4.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/easyRNASeq_1.4.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/easyRNASeq_1.4.2.zip
mac.binary.leopard.ver:
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vignettes: vignettes/easyRNASeq/inst/doc/easyRNASeq.pdf
vignetteTitles: RNA-Seq
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/easyRNASeq/inst/doc/easyRNASeq.R
Package: EBarrays
Version: 2.22.0
Depends: R (>= 1.8.0), Biobase, lattice, methods
Imports: Biobase, cluster, graphics, grDevices, lattice, methods, stats
License: GPL (>= 2)
Archs: i386, x64
Title: Unified Approach for Simultaneous Gene Clustering and
Differential Expression Identification
Description: EBarrays provides tools for the analysis of
replicated/unreplicated microarray data.
biocViews: Clustering, DifferentialExpression
Author: Ming Yuan, Michael Newton, Deepayan Sarkar and Christina
Kendziorski
Maintainer: Ming Yuan <myuan@isye.gatech.edu>
MD5sum: 7e79ce3957d58d26690c70dfc4ec6e8f
source.ver: src/contrib/EBarrays_2.22.0.tar.gz
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win64.binary.ver: bin/windows64/contrib/2.15/EBarrays_2.22.0.zip
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vignettes: vignettes/EBarrays/inst/doc/vignette.pdf
vignetteTitles: Introduction to EBarrays
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/EBarrays/inst/doc/vignette.R
dependsOnMe: EBcoexpress, gaga
suggestsMe: Category
Package: EBcoexpress
Version: 1.2.0
Depends: EBarrays, mclust, minqa
Suggests: graph, igraph, colorspace
License: GPL (>= 2)
Archs: i386, x64
Title: EBcoexpress for Differential Co-Expression Analysis
Description: An Empirical Bayesian Approach to Differential
Co-Expression Analysis at the Gene-Pair Level
Author: John A. Dawson
Maintainer: John A. Dawson <jadawson@wisc.edu>
MD5sum: 383f4789003dd40458ca63ea0bca5250
source.ver: src/contrib/EBcoexpress_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/EBcoexpress_1.2.0.zip
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vignettes: vignettes/EBcoexpress/inst/doc/EBcoexpressVignette.pdf
vignetteTitles: EBcoexpress Demo
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/EBcoexpress/inst/doc/EBcoexpressVignette.R
Package: EBImage
Version: 4.0.0
Imports: methods, graphics, stats, abind, utils, tiff, jpeg, png
License: LGPL
Archs: i386, x64
Title: Image processing toolbox for R
Description: EBImage is an R package which provides general purpose
functionality for the reading, writing, processing and analysis
of images. Furthermore, in the context of microscopy based
cellular assays, EBImage offers tools to transform the images,
segment cells and extract quantitative cellular descriptors.
biocViews: Visualization
Author: Gregoire Pau, Andrzej Oles, Mike Smith, Oleg Sklyar, Wolfgang
Huber
Maintainer: Gregoire Pau <paug@gene.com>
MD5sum: b0724cf73201a893c3d575880b019b41
source.ver: src/contrib/EBImage_4.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/EBImage_4.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/EBImage_4.0.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/EBImage/inst/doc/EBImage-introduction.pdf
vignetteTitles: Introduction to EBImage
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/EBImage/inst/doc/EBImage-installation.R,
vignettes/EBImage/inst/doc/EBImage-introduction.R
dependsOnMe: CRImage, imageHTS
suggestsMe: HilbertVis
Package: ecolitk
Version: 1.30.1
Depends: R (>= 2.10)
Imports: Biobase, graphics, methods
Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy
License: GPL (>= 2)
Title: Meta-data and tools for E. coli
Description: Meta-data and tools to work with E. coli. The tools are
mostly plotting functions to work with circular genomes. They
can used with other genomes/plasmids.
biocViews: Annotation, Visualization
Author: Laurent Gautier
Maintainer: Laurent Gautier <lgautier@gmail.com>
MD5sum: 1609b1cdcf2d60a02cc3962e1400f239
source.ver: src/contrib/ecolitk_1.30.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ecolitk_1.30.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/ecolitk_1.30.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ecolitk/inst/doc/ecolitk.pdf
vignetteTitles: ecolitk
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ecolitk/inst/doc/ecolitk.R
Package: EDASeq
Version: 1.4.0
Depends: BiocGenerics (>= 0.1.3), Biobase (>= 2.15.1), ShortRead (>=
1.11.42), Rsamtools (>= 1.5.75), aroma.light
Imports: methods, graphics, BiocGenerics, IRanges (>= 1.13.9), DESeq
Suggests: yeastRNASeq, leeBamViews, edgeR, DESeq
License: Artistic-2.0
Title: Exploratory Data Analysis and Normalization for RNA-Seq
Description: Numerical and graphical summaries of RNA-Seq read data.
Within-lane normalization procedures to adjust for GC-content
effect (or other gene-level effects) on read counts: loess
robust local regression, global-scaling, and full-quantile
normalization (Risso et al., 2011). Between-lane normalization
procedures to adjust for distributional differences between
lanes (e.g., sequencing depth): global-scaling and
full-quantile normalization (Bullard et al., 2010).
biocViews: HighThroughputSequencing, RNAseq, Preprocessing,
QualityControl, DifferentialExpression
Author: Davide Risso and Sandrine Dudoit
Maintainer: Davide Risso <risso.davide@gmail.com>
MD5sum: 8adcf448b3a092bbad445afc104e57ed
source.ver: src/contrib/EDASeq_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/EDASeq_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/EDASeq_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/EDASeq/inst/doc/EDASeq.pdf
vignetteTitles: EDASeq: Exploratory Data Analysis and Normalization for
RNA-Seq data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/EDASeq/inst/doc/EDASeq.R
suggestsMe: oneChannelGUI
Package: edgeR
Version: 3.0.8
Depends: R (>= 2.15.0), methods, limma
Suggests: MASS, statmod, splines, locfit, KernSmooth
License: GPL (>=2)
Archs: i386, x64
Title: Empirical analysis of digital gene expression data in R
Description: Differential expression analysis of RNA-seq and digital
gene expression profiles with biological replication. Uses
empirical Bayes estimation and exact tests based on the
negative binomial distribution. Also useful for differential
signal analysis with other types of genome-scale count data.
biocViews: Bioinformatics, DifferentialExpression, SAGE,
HighThroughputSequencing, RNAseq, ChIPseq
Author: Mark Robinson <mrobinson@wehi.edu.au>, Davis McCarthy
<dmccarthy@wehi.edu.au>, Yunshun Chen <yuchen@wehi.edu.au>,
Aaron Lun <alun@wehi.edu.au>, Gordon Smyth <smyth@wehi.edu.au>
Maintainer: Mark Robinson <mrobinson@wehi.edu.au>, Davis McCarthy
<dmccarthy@wehi.edu.au>, Yunshun Chen <yuchen@wehi.edu.au>,
Gordon Smyth <smyth@wehi.edu.au>
MD5sum: 838a554ee36938775df1c3ac5b4f3ce5
source.ver: src/contrib/edgeR_3.0.8.tar.gz
win.binary.ver: bin/windows/contrib/2.15/edgeR_3.0.8.zip
win64.binary.ver: bin/windows64/contrib/2.15/edgeR_3.0.8.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/edgeR_3.0.8.tgz
vignettes: vignettes/edgeR/inst/doc/edgeR.pdf,
vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
vignetteTitles: edgeR Vignette, edgeRUsersGuide.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/edgeR/inst/doc/edgeR.R
htmlDocs: vignettes/edgeR/inst/doc/index.html
dependsOnMe: DBChIP, easyRNASeq, manta
importsMe: ArrayExpressHTS, DiffBind, Repitools, rnaSeqMap, tweeDEseq
suggestsMe: baySeq, cqn, EDASeq, GenomicRanges, goseq, GSVA,
oneChannelGUI, Repitools
Package: eisa
Version: 1.10.0
Depends: BiocGenerics (>= 0.3.2), methods, isa2, Biobase (>= 2.17.8),
AnnotationDbi, Category (>= 2.23.4), genefilter, DBI
Imports: BiocGenerics
Suggests: igraph0 (>= 0.5.5), Matrix, GOstats, GO.db, KEGG.db, biclust,
MASS, xtable, ALL, hgu95av2.db, targetscan.Hs.eg.db,
org.Hs.eg.db
License: GPL (>= 2)
Title: Expression data analysis via the Iterative Signature Algorithm
Description: The Iterative Signature Algorithm (ISA) is a biclustering
method; it finds correlated blocks (transcription modules) in
gene expression (or other tabular) data. The ISA is capable of
finding overlapping modules and it is resilient to noise. This
package provides a convenient interface to the ISA, using
standard BioConductor data structures; and also contains
various visualization tools that can be used with other
biclustering algorithms.
biocViews: Classification, Visualization, Microarray, GeneExpression
Author: Gabor Csardi <csardi.gabor@gmail.com>
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
MD5sum: 28f8871e24fa818c97c69713e8c97e53
source.ver: src/contrib/eisa_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/eisa_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/eisa_1.10.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/eisa_1.10.0.tgz
vignettes: vignettes/eisa/inst/doc/EISA_biclust.pdf,
vignettes/eisa/inst/doc/EISA_tutorial.pdf,
vignettes/eisa/inst/doc/ISA_internals.pdf,
vignettes/eisa/inst/doc/tissues.pdf
vignetteTitles: The eisa and the biclust packages, The Iterative
Signature Algorithm for Gene Expression Data,
ISA_internals.pdf, tissues.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/eisa/inst/doc/EISA_biclust.R,
vignettes/eisa/inst/doc/EISA_tutorial.R
dependsOnMe: ExpressionView
importsMe: ExpressionView
Package: ENVISIONQuery
Version: 1.6.0
Depends: rJava, XML, utils
License: GPL-2
Title: Retrieval from the ENVISION bioinformatics data portal into R
Description: Tools to retrieve data from ENVISION, the Database for
Annotation, Visualization and Integrated Discovery portal
biocViews: Annotation
Author: Alex Lisovich, Roger Day
Maintainer: Alex Lisovich <all67@pitt.edu>, Roger Day <day01@pitt.edu>
MD5sum: 487d91db449cb0d260a350fb973c4750
source.ver: src/contrib/ENVISIONQuery_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ENVISIONQuery_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ENVISIONQuery_1.6.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ENVISIONQuery/inst/doc/ENVISIONQuery.pdf
vignetteTitles: An R Package for retrieving data from EnVision into R
objects.
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ENVISIONQuery/inst/doc/ENVISIONQuery.R
dependsOnMe: IdMappingRetrieval
importsMe: IdMappingRetrieval
Package: ExiMiR
Version: 2.0.0
Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.26.1), limma
Imports: affyio(>= 1.13.3), Biobase(>= 2.5.5), preprocessCore(>=
1.10.0)
License: GPL-2
Title: R functions for the normalization of Exiqon miRNA array data
Description: This package contains functions for reading raw data in
ImaGene TXT format obtained from Exiqon miRCURY LNA arrays,
annotating them with appropriate GAL files, and normalizing
them using a spike-in probe-based method. Other platforms and
data formats are also supported.
biocViews: Microarray, OneChannel, DualChannel, Preprocessing,
GeneExpression, Transcription
Author: Sylvain Gubian <DL.RSupport@pmi.com>, Alain Sewer
<DL.RSupport@pmi.com>, PMP SA
Maintainer: Sylvain Gubian <DL.RSupport@pmi.com>
MD5sum: b3c3530fdc67d3c8b66eb3bced24fbbc
source.ver: src/contrib/ExiMiR_2.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ExiMiR_2.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ExiMiR_2.0.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ExiMiR/inst/doc/ExiMiR-vignette.pdf
vignetteTitles: Description of ExiMiR
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/ExiMiR/inst/doc/ExiMiR-vignette.R
Package: exomeCopy
Version: 1.4.4
Depends: IRanges, GenomicRanges, Rsamtools
Imports: stats4, methods
Suggests: Biostrings
License: GPL (>= 2)
Archs: i386, x64
Title: Copy number variant detection from exome sequencing read depth
Description: Detection of copy number variants (CNV) from exome
sequencing samples, including unpaired samples. The package
implements a hidden Markov model which uses positional
covariates, such as background read depth and GC-content, to
simultaneously normalize and segment the samples into regions
of constant copy count.
biocViews: CopyNumberVariants, Sequencing, HighThroughputSequencing,
Genetics
Author: Michael Love
Maintainer: Michael Love <love@molgen.mpg.de>
MD5sum: e75e1aa6a99e8b79c4378ccfe8b25c07
source.ver: src/contrib/exomeCopy_1.4.4.tar.gz
win.binary.ver: bin/windows/contrib/2.15/exomeCopy_1.4.4.zip
win64.binary.ver: bin/windows64/contrib/2.15/exomeCopy_1.4.4.zip
mac.binary.leopard.ver:
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vignettes: vignettes/exomeCopy/inst/doc/exomeCopy.pdf
vignetteTitles: Copy number variant detection in exome sequencing data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/exomeCopy/inst/doc/exomeCopy.R
Package: explorase
Version: 1.22.0
Depends: R (>= 2.6.2)
Imports: limma, rggobi, RGtk2
Suggests: cairoDevice
License: GPL-2
Title: GUI for exploratory data analysis of systems biology data
Description: explore and analyze *omics data with R and GGobi
biocViews: Visualization,Microarray,GUI
Author: Michael Lawrence, Eun-kyung Lee, Dianne Cook, Jihong Kim,
Hogeun An, and Dongshin Kim
Maintainer: Michael Lawrence <mflawren@fhcrc.org>
URL: http://www.metnetdb.org/MetNet_exploRase.htm
MD5sum: 50ed0f32b753c3c46499c94342bd4c0f
source.ver: src/contrib/explorase_1.22.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/explorase_1.22.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/explorase_1.22.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/explorase/inst/doc/explorase.pdf
vignetteTitles: Introduction to exploRase
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/explorase/inst/doc/explorase.R
Package: ExpressionView
Version: 1.10.1
Depends: caTools, bitops, methods, isa2, eisa, GO.db, KEGG.db,
AnnotationDbi
Imports: methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi
Suggests: ALL, hgu95av2.db, biclust, affy
License: GPL (>= 2)
Archs: i386, x64
Title: Visualize biclusters identified in gene expression data
Description: ExpressionView visualizes possibly overlapping biclusters
in a gene expression matrix. It can use the result of the ISA
method (eisa package) or the algorithms in the biclust package
or others. The viewer itself was developed using Adobe Flex and
runs in a flash-enabled web browser.
biocViews: Classification, Visualization, Microarray, GeneExpression
Author: Andreas Luscher <andreas.luescher@a3.epfl.ch>
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
MD5sum: 41bc71f53839f3d43b0d9b3191f3d819
source.ver: src/contrib/ExpressionView_1.10.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ExpressionView_1.10.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/ExpressionView_1.10.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ExpressionView/inst/doc/ExpressionView.format.pdf,
vignettes/ExpressionView/inst/doc/ExpressionView.ordering.pdf,
vignettes/ExpressionView/inst/doc/ExpressionView.tutorial.pdf
vignetteTitles: ExpressionView file format, How the ordering algorithm
works, ExpressionView
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ExpressionView/inst/doc/ExpressionView.format.R,
vignettes/ExpressionView/inst/doc/ExpressionView.ordering.R,
vignettes/ExpressionView/inst/doc/ExpressionView.tutorial.R
Package: externalVector
Version: 1.24.0
Depends: R (>= 1.8.0), methods, stats
License: LGPL
Archs: i386, x64
Title: Vector objects for R with external storage
Description: Basic class definitions and generics for external pointer
based vector objects for R. A simple in-memory implementation
is also provided.
biocViews: Infrastructure
Author: Saikat DebRoy
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: c277848030d8a38bf03c2362123e1507
source.ver: src/contrib/externalVector_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/externalVector_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/externalVector_1.24.0.zip
mac.binary.leopard.ver:
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hasREADME: TRUE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: fabia
Version: 2.4.0
Depends: R (>= 2.8.0), Biobase
Imports: methods, graphics, grDevices, stats, utils
License: LGPL (>= 2.1)
Archs: i386, x64
Title: FABIA: Factor Analysis for Bicluster Acquisition
Description: Biclustering by "Factor Analysis for Bicluster
Acquisition" (FABIA). FABIA is a model-based technique for
biclustering, that is clustering rows and columns
simultaneously. Biclusters are found by factor analysis where
both the factors and the loading matrix are sparse. FABIA is a
multiplicative model that extracts linear dependencies between
samples and feature patterns. It captures realistic
non-Gaussian data distributions with heavy tails as observed in
gene expression measurements. FABIA utilizes well understood
model selection techniques like the EM algorithm and
variational approaches and is embedded into a Bayesian
framework. FABIA ranks biclusters according to their
information content and separates spurious biclusters from true
biclusters. The code is written in C.
biocViews: Bioinformatics, Statistics, Microarray,
DifferentialExpression, MultipleComparisons, Clustering,
Visualization
Author: Sepp Hochreiter <hochreit@bioinf.jku.at>
Maintainer: Sepp Hochreiter <hochreit@bioinf.jku.at>
URL: http://www.bioinf.jku.at/software/fabia/fabia.html
MD5sum: 52f7d5c5ee4962ead582bfbfed0b5910
source.ver: src/contrib/fabia_2.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/fabia_2.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/fabia_2.4.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/fabia_2.4.0.tgz
vignettes: vignettes/fabia/inst/doc/fabia.pdf
vignetteTitles: FABIA: Manual for the R package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/fabia/inst/doc/fabia.R
dependsOnMe: hapFabia
Package: factDesign
Version: 1.34.1
Depends: Biobase (>= 2.5.5)
Imports: stats
Suggests: affy, genefilter, multtest
License: LGPL
Title: Factorial designed microarray experiment analysis
Description: This package provides a set of tools for analyzing data
from a factorial designed microarray experiment, or any
microarray experiment for which a linear model is appropriate.
The functions can be used to evaluate tests of contrast of
biological interest and perform single outlier detection.
biocViews: Bioinformatics, Microarray, DifferentialExpression
Author: Denise Scholtens
Maintainer: Denise Scholtens <dscholtens@northwestern.edu>
MD5sum: cac052b9010f12c87b841c65651dc886
source.ver: src/contrib/factDesign_1.34.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/factDesign_1.34.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/factDesign_1.34.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/factDesign/inst/doc/factDesign.pdf
vignetteTitles: factDesign
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/factDesign/inst/doc/factDesign.R
Package: farms
Version: 1.10.0
Depends: R (>= 2.8), affy (>= 1.20.0), MASS, methods
Imports: affy, MASS, Biobase (>= 1.13.41), methods, graphics
Suggests: affydata, Biobase, utils
License: LGPL (>= 2.1)
Title: FARMS - Factor Analysis for Robust Microarray Summarization
Description: The package provides the summarization algorithm called
Factor Analysis for Robust Microarray Summarization (FARMS) and
a novel unsupervised feature selection criterion called
"I/NI-calls"
biocViews: GeneExpression, Microarray, Preprocessing, QualityControl
Author: Djork-Arne Clevert <okko@clevert.de>
Maintainer: Djork-Arne Clevert <okko@clevert.de>
URL: http://www.bioinf.jku.at/software/farms/farms.html
MD5sum: 07fcbfa81377110130883c5c7627cef2
source.ver: src/contrib/farms_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/farms_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/farms_1.10.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/farms/inst/doc/farms.pdf
vignetteTitles: Using farms
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/farms/inst/doc/farms.R
Package: fastseg
Version: 1.4.0
Depends: R (>= 2.13), GenomicRanges, Biobase
Imports: graphics, stats, IRanges, BiocGenerics
Suggests: DNAcopy, oligo
License: LGPL (>= 2.0)
Archs: i386, x64
Title: fastseg - a fast segmentation algorithm
Description: fastseg implements a very fast and efficient segmentation
algorithm. It has similar functionality as DNACopy (Olshen and
Venkatraman 2004), but is considerably faster and more
flexible. fastseg can segment data from DNA microarrays and
data from next generation sequencing for example to detect copy
number segments. Further it can segment data from RNA
microarrays like tiling arrays to identify transcripts. Most
generally, it can segment data given as a matrix or as a
vector. Various data formats can be used as input to fastseg
like expression set objects for microarrays or GRanges for
sequencing data. The segmentation criterion of fastseg is based
on a statistical test in a Bayesian framework, namely the cyber
t-test (Baldi 2001). The speed-up arises from the facts, that
sampling is not necessary in for fastseg and that a dynamic
programming approach is used for calculation of the segments'
first and higher order moments.
biocViews: Classification, CopyNumberVariants
Author: Guenter Klambauer
Maintainer: Guenter Klambauer <fastseg@bioinf.jku.at>
URL: http://www.bioinf.jku.at/software/fastseg/fastseg.html
MD5sum: aef828c88395c4be14b1c6cdb050731a
source.ver: src/contrib/fastseg_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/fastseg_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/fastseg_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/fastseg/inst/doc/fastseg.pdf
vignetteTitles: fastseg: Manual for the R package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/fastseg/inst/doc/fastseg.R
Package: fdrame
Version: 1.30.0
Imports: tcltk, graphics, grDevices, stats, utils
License: GPL (>= 2)
Archs: i386, x64
Title: FDR adjustments of Microarray Experiments (FDR-AME)
Description: This package contains two main functions. The first is
fdr.ma which takes normalized expression data array,
experimental design and computes adjusted p-values It returns
the fdr adjusted p-values and plots, according to the methods
described in (Reiner, Yekutieli and Benjamini 2002). The
second, is fdr.gui() which creates a simple graphic user
interface to access fdr.ma
biocViews: Microarray,DifferentialExpression,MultipleComparisons
Author: Yoav Benjamini, Effi Kenigsberg, Anat Reiner, Daniel Yekutieli
Maintainer: Effi Kenigsberg <effiken.fdrame@gmail.com>
MD5sum: 304bd77881502733851b72c7ba072e09
source.ver: src/contrib/fdrame_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/fdrame_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/fdrame_1.30.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/fdrame_1.30.0.tgz
vignettes: vignettes/fdrame/inst/doc/fdrame.pdf
vignetteTitles: Annotation Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/fdrame/inst/doc/fdrame.R
Package: ffpe
Version: 1.2.0
Depends: R (>= 2.10.0), TTR, methods
Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc
Suggests: genefilter, affy, ffpeExampleData
License: GPL (>2)
Title: Quality assessment and control for FFPE microarray expression
data
Description: Identify low-quality data using metrics developed for
expression data derived from Formalin-Fixed, Paraffin-Embedded
(FFPE) data. Also a function for making Concordance at the Top
plots (CAT-plots).
biocViews: Microarray, GeneExpression, QualityControl, Bioinformatics
Author: Levi Waldron
Maintainer: Levi Waldron <lwaldron@hsph.harvard.edu>
MD5sum: dd981105a231cd0b70f8d10ec4dbd65c
source.ver: src/contrib/ffpe_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ffpe_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ffpe_1.2.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ffpe_1.2.0.tgz
vignettes: vignettes/ffpe/inst/doc/ffpe.pdf
vignetteTitles: ffpe package user guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ffpe/inst/doc/ffpe.R
Package: flagme
Version: 1.14.0
Depends: gcspikelite, xcms
Imports: gplots, graphics, MASS, methods, SparseM, stats, utils
License: LGPL (>= 2)
Archs: i386, x64
Title: Analysis of Metabolomics GC/MS Data
Description: Fragment-level analysis of gas chromatography - mass
spectrometry metabolomics data
biocViews: Bioinformatics, DifferentialExpression, MassSpectrometry
Author: Mark Robinson <mrobinson@wehi.edu.au>
Maintainer: Mark Robinson <mrobinson@wehi.edu.au>
MD5sum: 13cc0667f87c50bdf8be58d3274ed030
source.ver: src/contrib/flagme_1.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flagme_1.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flagme_1.14.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flagme_1.14.0.tgz
vignettes: vignettes/flagme/inst/doc/flagme.pdf
vignetteTitles: Using flagme -- Fragment-level analysis of GCMS-based
metabolomics data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flagme/inst/doc/flagme.R
Package: flowClust
Version: 2.16.0
Depends: R(>= 2.5.0),BiocGenerics, methods, mnormt, ellipse, Biobase,
flowCore(>= 1.11.23)
Imports: stats4
Suggests: snowfall
Enhances: multicore
License: Artistic-2.0
Archs: i386, x64
Title: Clustering for Flow Cytometry
Description: Robust model-based clustering using a t-mixture model with
Box-Cox transformation. Note: users should have GSL installed.
Windows users: 'consult the README file available in the inst
directory of the source distribution for necessary
configuration instructions'.
biocViews: Clustering, Bioinformatics, Visualization, FlowCytometry
Author: Raphael Gottardo <raph@stat.ubc.ca>, Kenneth Lo
<c.lo@stat.ubc.ca>
Maintainer: Raphael Gottardo <raph@stat.ubc.ca>
MD5sum: 3e61455e37280bd874d4bc2568e7abc8
source.ver: src/contrib/flowClust_2.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowClust_2.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowClust_2.16.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flowClust_2.16.0.tgz
vignettes: vignettes/flowClust/inst/doc/flowClust.pdf
vignetteTitles: flowClust package
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowClust/inst/doc/flowClust.R
dependsOnMe: flowMerge
importsMe: flowPhyto, flowTrans, flowType
Package: flowCore
Version: 1.24.2
Depends: R (>= 2.10.0), Biobase, rrcov
Imports: Biobase, BiocGenerics (>= 0.1.14), feature, graph, graphics,
grDevices, MASS, methods, rrcov, stats, utils, stats4
Suggests: Rgraphviz, flowViz, ncdf
License: Artistic-2.0
Archs: i386, x64
Title: flowCore: Basic structures for flow cytometry data
Description: Provides S4 data structures and basic functions to deal
with flow cytometry data.
biocViews: Infrastructure, FlowCytometry, CellBasedAssays
Author: B. Ellis, P. Haaland, F. Hahne, N. Le Meur, N. Gopalakrishnan
Maintainer: M.Jiang <wjiang2@fhcrc.org>
MD5sum: 37f283cb8da9763d96177f375d5c13c8
source.ver: src/contrib/flowCore_1.24.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowCore_1.24.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowCore_1.24.2.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flowCore_1.24.2.tgz
vignettes: vignettes/flowCore/inst/doc/HowTo-flowCore.pdf
vignetteTitles: Basic Functions for Flow Cytometry Data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowCore/inst/doc/HowTo-flowCore.R
htmlDocs: vignettes/flowCore/inst/doc/fcs3.html
dependsOnMe: flowFP, flowMerge, flowStats, flowTrans, flowUtils,
flowViz, flowWorkspace, iFlow, ncdfFlow, plateCore
importsMe: flowFlowJo, flowFP, flowMeans, flowPhyto, flowQ, flowStats,
flowTrans, flowType, flowUtils, flowViz, flowWorkspace, iFlow,
plateCore, spade
suggestsMe: flowQB, RchyOptimyx
Package: flowFlowJo
Version: 1.16.0
Depends: R (>= 2.5.0), MASS,
Imports: flowCore, XML (>= 1.96), methods, Biobase
License: GPL (>=3)
Title: Tools for extracting information from a FlowJo workspace and
working with the data in the flowCore paradigm.
Description: FlowJo is a commercial GUI based software package from
TreeStar Inc. for the visualization and analysis of flow
cytometry data. One of the FlowJo standard export file types
is the "FlowJo Workspace". This is an XML document that
describes files and manipulations that have been performed in
the FlowJo GUI environment. This package can take apart the
FlowJo workspace and deliver the data into R in the flowCore
paradigm.
biocViews: FlowCytometry
Author: John J. Gosink <gosinkj@amgen.com>
Maintainer: John J. Gosink <gosinkj@amgen.com>
MD5sum: 6bef68fe8200c06cc5f57398ada53d36
source.ver: src/contrib/flowFlowJo_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowFlowJo_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowFlowJo_1.16.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flowFlowJo_1.16.0.tgz
vignettes: vignettes/flowFlowJo/inst/doc/flowFlowJo.pdf
vignetteTitles: Basic Functions for working with FlowJo
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowFlowJo/inst/doc/flowFlowJo.R
Package: flowFP
Version: 1.16.0
Depends: R (>= 2.10), flowCore, flowViz
Imports: Biobase, BiocGenerics (>= 0.1.6), flowCore, flowViz, graphics,
grDevices, methods, stats, stats4
Suggests: RUnit
License: Artistic-2.0
Archs: i386, x64
Title: Fingerprinting for Flow Cytometry
Description: Fingerprint generation of flow cytometry data, used to
facilitate the application of machine learning and datamining
tools for flow cytometry.
biocViews: Bioinformatics, FlowCytometry, CellBasedAssays, Clustering,
Visualization
Author: Herb Holyst <holyst@mail.med.upenn.edu>, Wade Rogers
<rogersw@mail.med.upenn.edu>
Maintainer: Herb Holyst <holyst@mail.med.upenn.edu>
MD5sum: 399ff943d5d3602d1cc201930642fc22
source.ver: src/contrib/flowFP_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowFP_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowFP_1.16.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flowFP_1.16.0.tgz
vignettes: vignettes/flowFP/inst/doc/flowFP_HowTo.pdf
vignetteTitles: Fingerprinting for Flow Cytometry
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowFP/inst/doc/flowFP_HowTo.R
Package: flowMeans
Version: 1.10.0
Depends: R (>= 2.10.0)
Imports: Biobase, graphics, grDevices, methods, rrcov, stats, feature,
flowCore
License: Artistic-2.0
Title: Non-parametric Flow Cytometry Data Gating
Description: Identifies cell populations in Flow Cytometry data using
non-parametric clustering and segmented-regression-based change
point detection. Note: R 2.11.0 or newer is required.
biocViews: Bioinformatics, FlowCytometry, CellBiology, Clustering,
Cancer, FlowCytData, StemCells, HIV
Author: Nima Aghaeepour
Maintainer: Nima Aghaeepour <naghaeep@bccrc.ca>
MD5sum: 0301d2eecb3e091545e9e739c450cfe0
source.ver: src/contrib/flowMeans_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowMeans_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowMeans_1.10.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flowMeans_1.10.0.tgz
vignettes: vignettes/flowMeans/inst/doc/flowMeans.pdf
vignetteTitles: flowMeans: Non-parametric Flow Cytometry Data Gating
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowMeans/inst/doc/flowMeans.R
importsMe: flowPhyto, flowType
Package: flowMerge
Version: 2.6.0
Depends: Rgraphviz, flowClust, flowCore,
methods,snow,foreach,graph,feature
Imports: rrcov, flowClust,flowCore, graphics, methods, rrcov, stats,
utils, BiocGenerics (>= 0.1.6)
Suggests: Rgraphviz
Enhances: doMC, multicore
License: Artistic-2.0
Title: Cluster Merging for Flow Cytometry Data
Description: Merging of mixture components for model-based automated
gating of flow cytometry data using the flowClust framework.
Note: users should have a working copy of flowClust 2.0
installed.
biocViews: Bioinformatics, Clustering, FlowCytometry
Author: Greg Finak <gfinak@fhcrc.org>, Raphael Gottardo
<rgottard@fhcrc.org>
Maintainer: Greg Finak <gfinak@fhcrc.org>
MD5sum: cf44b15180c5357663c5ef84f1c2c84f
source.ver: src/contrib/flowMerge_2.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowMerge_2.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowMerge_2.6.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flowMerge_2.6.0.tgz
vignettes: vignettes/flowMerge/inst/doc/flowMerge.pdf
vignetteTitles: flowMerge package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowMerge/inst/doc/flowMerge.R
importsMe: flowType
Package: flowPeaks
Version: 1.0.0
Depends: R (>= 2.12.0)
Enhances: flowCore
License: Artistic-1.0
Archs: i386, x64
Title: An R package for flow data clustering
Description: A fast and automatic clustering to classify the cells into
subpopulations based on finding the peaks from the overall
density function generated by K-means.
biocViews: Flow cytometry, Clustering, Gating, Bioinformatics
Author: Yongchao Ge<yongchao.ge@gmail.com>
Maintainer: Yongchao Ge<yongchao.ge@gmail.com>
MD5sum: 553b019842b10f0935363ab0a5e44103
source.ver: src/contrib/flowPeaks_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowPeaks_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowPeaks_1.0.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flowPeaks_1.0.0.tgz
vignettes: vignettes/flowPeaks/inst/doc/flowPeaks-guide.pdf
vignetteTitles: Tutorial of flowPeaks package
hasREADME: TRUE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowPeaks/inst/doc/flowPeaks-guide.R
Package: flowPhyto
Version: 1.10.0
Depends: R (>= 1.8.0)
Imports: caroline, flowClust, flowCore, flowMeans, TTR
Suggests: RPostgreSQL, zoo, maps, mapdata, plotrix
License: Artistic-2.0
Title: Methods for Continuous Flow Cytometry
Description: Automated Analysis of Continuous Flow Cytometry Data.
biocViews: FlowCytometry, DataImport, QualityControl, Classification,
Bioinformatics, Visualization, Clustering
Author: Francois Ribalet <ribalet@u.washington.edu> and David M.
Schruth <dschruth@u.washington.edu>
Maintainer: David M. Schruth <dschruth@u.washington.edu>
URL: http://seaflow.ocean.washington.edu
MD5sum: b88ad09435b240148ee89da13be80207
source.ver: src/contrib/flowPhyto_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowPhyto_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowPhyto_1.10.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flowPhyto_1.10.0.tgz
vignettes: vignettes/flowPhyto/inst/doc/flowPhyto.pdf
vignetteTitles: flowPhyto
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowPhyto/inst/doc/flowPhyto.R
Package: flowPlots
Version: 1.6.0
Depends: R (>= 2.13.0), methods
Suggests: vcd
License: Artistic-2.0
Title: flowPlots: analysis plots and data class for gated flow
cytometry data
Description: Graphical displays with embedded statistical tests for
gated ICS flow cytometry data, and a data class which stores
"stacked" data and has methods for computing summary measures
on stacked data, such as marginal and polyfunctional degree
data.
biocViews: FlowCytometry, CellBasedAssays, Visualization,
DataRepresentation
Author: N. Hawkins, S. Self
Maintainer: N. Hawkins <hawkins@fhcrc.org>
MD5sum: 6ad1ad117d0661c28483d652c484f21b
source.ver: src/contrib/flowPlots_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowPlots_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowPlots_1.6.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flowPlots_1.6.0.tgz
vignettes: vignettes/flowPlots/inst/doc/flowPlots.pdf
vignetteTitles: Plots with Embedded Tests for Gated Flow Cytometry Data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowPlots/inst/doc/flowPlots.R
Package: flowQ
Version: 1.18.0
Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.1.3), outliers,
lattice, flowViz, mvoutlier, bioDist, parody, RColorBrewer,
latticeExtra
Imports: methods, BiocGenerics, geneplotter, flowCore, flowViz, IRanges
Suggests: flowStats
License: Artistic-2.0
Title: Quality control for flow cytometry
Description: Provides quality control and quality assessment tools for
flow cytometry data.
biocViews: Infrastructure, FlowCytometry, CellBasedAssays
Author: R. Gentleman, F. Hahne, J. Kettman, N. Le Meur, N.
Gopalakrishnan
Maintainer: Mike Jiang <wjiang2@fhcrc.org>
SystemRequirements: ImageMagick
MD5sum: 98ecec21225c36367c4021672e0348ce
source.ver: src/contrib/flowQ_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowQ_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowQ_1.18.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flowQ_1.18.0.tgz
vignettes: vignettes/flowQ/inst/doc/DataQualityAssessment.pdf,
vignettes/flowQ/inst/doc/Extending-flowQ.pdf,
vignettes/flowQ/inst/doc/flowQStructure.pdf,
vignettes/flowQ/inst/doc/stainInfo.pdf
vignetteTitles: Data Quality Assesment for Ungated Flow Cytometry Data,
Basic Functions for Flow Cytometry Data, flowQStructure.pdf,
stainInfo.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowQ/inst/doc/DataQualityAssessment.R,
vignettes/flowQ/inst/doc/Extending-flowQ.R
Package: flowQB
Version: 1.0.1
Imports: Biobase, graphics,methods, flowCore,stats
Suggests: flowCore
License: Artistic-2.0
Title: Flow cytometer sensitivity-Automatic Q and B Calculations.
Description: flowQB is a fully automated R Bioconductor package to
calculate automatically the detector efficiency (Q), optical
background (B), and electronic noise.
biocViews: FlowCytometry
Author: Faysal El Khettabi
Maintainer: Faysal El Khettabi <faysal.el.khettabi@gmail.com>
MD5sum: 7d323d793463d59bb1f83a634997a280
source.ver: src/contrib/flowQB_1.0.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowQB_1.0.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowQB_1.0.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flowQB_1.0.1.tgz
vignettes: vignettes/flowQB/inst/doc/flowQB_Sweave_.pdf
vignetteTitles: flowQB package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowQB/inst/doc/flowQB_Sweave_.R
Package: flowStats
Version: 1.16.0
Depends: R (>= 2.10), flowCore (>= 1.10.0), fda (>= 2.2.6), mvoutlier,
cluster, flowWorkspace
Imports: BiocGenerics, MASS, flowViz, flowCore, fda (>= 2.2.6),
Biobase, methods, grDevices, graphics, stats, utils,
KernSmooth, lattice,compositions
Suggests: flowViz, xtable
Enhances: RBGL,ncdfFlow,graph
License: Artistic-2.0
Title: Statistical methods for the analysis of flow cytometry data
Description: Methods and functionality to analyse flow data that is
beyond the basic infrastructure provided by the flowCore
package.
biocViews: FlowCytometry, CellBasedAssays, Bioinformatics
Author: Florian Hahne, Nishant Gopalakrishnan, Alireza Hadj
Khodabakhshi, Chao-Jen Wong, Kyongryun Lee
Maintainer: Greg Finak <gfinak@fhcrc.org> and Mike Jiang
<wjiang2@fhcrc.org>
MD5sum: 707f4662ccc776f939b7389b7921e7f9
source.ver: src/contrib/flowStats_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowStats_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowStats_1.16.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flowStats_1.16.0.tgz
vignettes: vignettes/flowStats/inst/doc/GettingStartedWithFlowStats.pdf
vignetteTitles: flowStats Overview
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowStats/inst/doc/GettingStartedWithFlowStats.R
dependsOnMe: iFlow
importsMe: iFlow
suggestsMe: flowQ
Package: flowTrans
Version: 1.10.0
Depends: R (>= 2.11.0), flowCore, flowViz,flowClust
Imports: flowCore, methods, flowViz, stats, flowClust
License: Artistic-2.0
Title: Parameter Optimization for Flow Cytometry Data Transformation
Description: Profile maximum likelihood estimation of parameters for
flow cytometry data transformations.
biocViews: Bioinformatics, FlowCytometry
Author: Greg Finak <greg.finak@ircm.qc.ca>, Juan Manuel-Perez
<jperez@ircm.qc.ca>, Raphael Gottardo
<raphael.gottardo@ircm.qc.ca>
Maintainer: Greg Finak <greg.finak@ircm.qc.ca>
MD5sum: e74e8ea3ea961adf7234cc4536401b58
source.ver: src/contrib/flowTrans_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowTrans_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowTrans_1.10.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flowTrans_1.10.0.tgz
vignettes: vignettes/flowTrans/inst/doc/flowTrans.pdf
vignetteTitles: flowTrans package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowTrans/inst/doc/flowTrans.R
Package: flowType
Version: 1.4.0
Depends: R (>= 2.10)
Imports: Biobase, graphics, grDevices, methods, flowCore, flowMeans,
sfsmisc, rrcov, flowClust, flowMerge, stats
Suggests: xtable
License: Artistic-2.0
Title: Phenotyping Flow Cytometry Assays
Description: Phenotyping Flow Cytometry Assays using multidimentional
expantion of single dimentional partitions.
biocViews: FlowCytometry
Author: Nima Aghaeepour
Maintainer: Nima Aghaeepour <naghaeep@bccrc.ca>
MD5sum: 1b7178faf6514540b943ddb6af192489
source.ver: src/contrib/flowType_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowType_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowType_1.4.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/flowType_1.4.0.tgz
vignettes: vignettes/flowType/inst/doc/flowType.pdf
vignetteTitles: flowType package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowType/inst/doc/flowType.R
suggestsMe: RchyOptimyx
Package: flowUtils
Version: 1.18.0
Depends: R (>= 2.2.0), flowCore (>= 1.2.0)
Imports: Biobase, flowCore, graph, methods, RUnit, stats, utils, XML,
flowViz
Suggests: gatingMLData
License: Artistic-2.0
Title: Utilities for flow cytometry
Description: Provides utilities for flow cytometry data.
biocViews: Infrastructure, FlowCytometry, CellBasedAssays
Author: Gopalakrishnan N, F. Hahne, B. Ellis, R. Gentleman M.
Dalphin,N. Le Meur, B. Purcell.
Maintainer: Nishant Gopalakrishnan <ngopalak@fhcrc.org>
MD5sum: e4636950c739e63da1a3eef37d9bdd4c
source.ver: src/contrib/flowUtils_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowUtils_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowUtils_1.18.0.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: flowViz
Version: 1.22.0
Depends: R (>= 2.7.0), flowCore (>= 1.5.17), lattice, grDevices
Imports: stats4, Biobase, flowCore, graphics, grDevices, grid,
KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer,
stats, utils, hexbin,IDPmisc
Suggests: colorspace,RColorBrewer
License: Artistic-2.0
Title: Visualization for flow cytometry
Description: Provides visualization tools for flow cytometry data.
biocViews: Infrastructure, Flowcytometry, CellBasedAssays,
Visualization
Author: B. Ellis, R. Gentleman, F. Hahne, N. Le Meur, D. Sarkar
Maintainer: Mike Jiang <wjiang2@fhcrc.org>
MD5sum: 71837a890d4f2c5b666a3df0d66ad91b
source.ver: src/contrib/flowViz_1.22.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowViz_1.22.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowViz_1.22.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/flowViz/inst/doc/filters.pdf
vignetteTitles: Visualizing Gates with Flow Cytometry Data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowViz/inst/doc/filters.R
dependsOnMe: flowFP, flowQ, flowWorkspace, iFlow, plateCore
importsMe: flowFP, flowQ, flowStats, flowTrans, flowUtils, iFlow
suggestsMe: flowCore, flowStats, spade
Package: flowWorkspace
Version: 1.4.0
Depends: Cairo, BiocGenerics, methods, RBGL, graph, XML, flowCore,
flowViz, Biobase, IDPmisc, tools,hexbin
Imports: Biobase, XML, flowCore, graph, graphics, lattice, methods,
stats, stats4, utils
Suggests: testthat, flowWorkspaceData, Rgraphviz
Enhances: multicore,Rmpi,ncdfFlow
License: Artistic-2.0
Archs: i386, x64
Title: Import flowJo Workspaces into BioConductor and replicate flowJo
gating with flowCore
Description: This package is designed to facilitate comparison of
automated gating methods against manual gating done in flowJo.
This package allows you to import basic flowJo workspaces into
BioConductor and replicate the gating from flowJo using the
flowCore functionality. Gating hierarchies, groups of samples,
compensation, and transformation are performed so that the
output matches the flowJo analysis.
biocViews: FlowCytometry, DataImport, Preprocessing, DataRepresentation
Author: Greg Finak, Mike Jiang, Mose Andre
Maintainer: Greg Finak <gfinak@fhcrc.org>
MD5sum: 039ef031444868b8e18bf73d25fe5bea
source.ver: src/contrib/flowWorkspace_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/flowWorkspace_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/flowWorkspace_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/flowWorkspace/inst/doc/flowWorkspace.pdf
vignetteTitles: Importing flowJo Workspaces into R
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/flowWorkspace/inst/doc/flowWorkspace.R
dependsOnMe: flowStats
Package: fmcsR
Version: 1.0.5
Depends: R (>= 2.10.0), ChemmineR, methods
License: Artistic-2.0
Archs: i386, x64
Title: Flexible Maximum Common Substructure (FMCS) Searching
Description: The fmcsR package introduces an efficient maximum common
substructure (MCS) algorithms combined with a novel matching
strategy that allows for atom and/or bond mismatches in the
substructures shared among two small molecules. The resulting
flexible MCSs (FMCSs) are often larger than strict MCSs,
resulting in the identification of more common features in
their source structures, as well as a higher sensitivity in
finding compounds with weak structural similarities. The fmcsR
package provides several utilities to use the FMCS algorithm
for pairwise compound comparisons, structure similarity
searching and clustering.
biocViews: MicrotitrePlateAssay, CellBasedAssays, Visualization,
Infrastructure, DataImport, Clustering, Bioinformatics,
Proteomics
Author: Yan Wang, Tyler Backman, Kevin Horan, Thomas Girke
Maintainer: ChemmineR Team <see@url>
URL: http://manuals.bioinformatics.ucr.edu/home/chemminer
MD5sum: ba6ac14864e38e37a6c59abe837e743b
source.ver: src/contrib/fmcsR_1.0.5.tar.gz
win.binary.ver: bin/windows/contrib/2.15/fmcsR_1.0.5.zip
win64.binary.ver: bin/windows64/contrib/2.15/fmcsR_1.0.5.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/fmcsR_1.0.5.tgz
vignettes: vignettes/fmcsR/inst/doc/fmcsR.pdf
vignetteTitles: gpls Tutorial
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/fmcsR/inst/doc/fmcsR.R
Package: frma
Version: 1.10.0
Depends: R (>= 2.10.0), Biobase (>= 2.6.0)
Imports: Biobase, MASS, DBI, affy, methods, oligo, oligoClasses,
preprocessCore, utils, BiocGenerics
Suggests: hgu133afrmavecs, frmaExampleData
License: GPL (>= 2)
Title: Frozen RMA and Barcode
Description: Preprocessing and analysis for single microarrays and
microarray batches.
biocViews: Software, Microarray, Preprocessing
Author: Matthew N. McCall <mccallm@gmail.com>, Rafael A. Irizarry
<rafa@jhu.edu>, with contributions from Terry Therneau
Maintainer: Matthew N. McCall <mccallm@gmail.com>
URL: http://bioconductor.org
MD5sum: 5ae0ea9031403c123749f3f44c55eef0
source.ver: src/contrib/frma_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/frma_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/frma_1.10.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/frma_1.10.0.tgz
vignettes: vignettes/frma/inst/doc/frma.pdf
vignetteTitles: frma: Preprocessing for single arrays and array batches
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/frma/inst/doc/frma.R
importsMe: ChIPXpress
suggestsMe: frmaTools
Package: frmaTools
Version: 1.10.0
Depends: R (>= 2.10.0), affy
Imports: Biobase, DBI, methods, preprocessCore, stats, utils
Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM,
hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf,
hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData
License: GPL (>= 2)
Title: Frozen RMA Tools
Description: Tools for advanced use of the frma package.
biocViews: Software, Microarray, Preprocessing
Author: Matthew N. McCall <mccallm@gmail.com>, Rafael A. Irizarry
<rafa@jhu.edu>
Maintainer: Matthew N. McCall <mccallm@gmail.com>
URL: http://bioconductor.org
MD5sum: 0908301a5cc39327145314bcae874038
source.ver: src/contrib/frmaTools_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/frmaTools_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/frmaTools_1.10.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/frmaTools_1.10.0.tgz
vignettes: vignettes/frmaTools/inst/doc/frmaTools.pdf
vignetteTitles: frmaTools: Create packages containing the vectors used
by frma.
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/frmaTools/inst/doc/frmaTools.R
Package: FunciSNP
Version: 1.1.8
Depends: R (>= 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene,
FunciSNP.data
Imports: AnnotationDbi, IRanges, Rsamtools (>= 1.6.1), rtracklayer(>=
1.14.1), methods, ChIPpeakAnno (>= 2.2.0), GenomicRanges,
VariantAnnotation, plyr, org.Hs.eg.db, snpStats, ggplot2 (>=
0.9.0), reshape (>= 0.8.4), scales
Enhances: parallel
License: GPL-3
Title: Integrating Functional Non-coding Datasets with Genetic
Association Studies to Identify Candidate Regulatory SNPs
Description: FunciSNP integrates information from GWAS, 1000genomes and
chromatin feature to identify functional SNP in coding or
non-coding regions.
biocViews: Infrastructure, DataRepresentation, DataImport,
SequenceMatching, Annotation
Author: Simon G. Coetzee <simon@simoncoetzee.com> and Houtan Noushmehr,
PhD <houtan@usp.br>
Maintainer: Simon G. Coetzee <simon@simoncoetzee.com>
URL: http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/
MD5sum: dfd00cd07d05ef6d23f44ae386bf2911
source.ver: src/contrib/FunciSNP_1.1.8.tar.gz
win.binary.ver: bin/windows/contrib/2.15/FunciSNP_1.1.8.zip
win64.binary.ver: bin/windows64/contrib/2.15/FunciSNP_1.1.8.zip
mac.binary.leopard.ver:
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vignettes: vignettes/FunciSNP/inst/doc/FunciSNP_vignette.pdf,
vignettes/FunciSNP/inst/doc/UCSC_genomeviewer_glioma.pdf
vignetteTitles: FunciSNP Vignette, UCSC_genomeviewer_glioma.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/FunciSNP/inst/doc/FunciSNP_vignette.R
Package: gaga
Version: 2.4.0
Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv
Enhances: multicore
License: GPL (>= 2)
Archs: i386, x64
Title: GaGa hierarchical model for high-throughput data analysis
Description: Implements the GaGa model for high-throughput data
analysis, including differential expression analysis,
supervised gene clustering and classification. Additionally, it
performs sequential sample size calculations using the GaGa and
LNNGV models (the latter from EBarrays package).
biocViews:
OneChannel,MassSpectrometry,MultipleComparisons,DifferentialExpression,Classification
Author: David Rossell <rosselldavid@gmail.com>.
Maintainer: David Rossell <rosselldavid@gmail.com>
MD5sum: 90769a9303bd3ab636261439b3550ea8
source.ver: src/contrib/gaga_2.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/gaga_2.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/gaga_2.4.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gaga_2.4.0.tgz
vignettes: vignettes/gaga/inst/doc/gagamanual.pdf
vignetteTitles: Manual for the gaga library
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/gaga/inst/doc/gagamanual.R
Package: gage
Version: 2.8.0
Depends: R (>= 2.10), graph, multtest
Suggests: gageData, GO.db, GSEABase, KEGG.db, org.Hs.eg.db
License: GPL (>=2.0)
Title: Generally Applicable Gene-set Enrichment for Pathway Analysis
Description: GAGE is a published method for gene set or pathway
analysis. GAGE is generally applicable independent of
microarray data attributes including sample sizes, experimental
designs, microarray platforms, and other types of
heterogeneity, and consistently achieves superior performance
over other frequently used methods. In gage package, we provide
functions for basic GAGE analysis, result processing and
presentation. We have also built pipeline routines for of
multiple GAGE analyses in a batch, comparison between parallel
analyses, and combined analysis of heterogeneous data from
different sources/studies. In addition, we provide demo
microarray data and commonly used gene set data based on KEGG
pathways and GO terms. These funtions and data are also useful
for gene set analysis using other methods.
biocViews: Pathways, GO, DifferentialExpression, Microarray,
OneChannel, TwoChannel, RNAseq, Genetics, MultipleComparisons,
GeneSetEnrichment
Author: Weijun Luo
Maintainer: Weijun Luo <luo_weijun@yahoo.com>
URL: http://www.biomedcentral.com/1471-2105/10/161
MD5sum: ca598d0634c7351bf65763a00e108741
source.ver: src/contrib/gage_2.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/gage_2.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/gage_2.8.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gage_2.8.0.tgz
vignettes: vignettes/gage/inst/doc/gage.pdf
vignetteTitles: Generally Applicable Gene-set/Pathway Analysis
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/gage/inst/doc/gage.R
Package: gaggle
Version: 1.26.0
Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>=
0.4.17)
License: GPL version 2 or newer
Title: Broadcast data between R and Gaggle
Description: This package contains functions enabling data exchange
between R and Gaggle enabled bioinformatics software, including
Cytoscape, Firegoose and Gaggle Genome Browser.
biocViews: ConnectTools, NetworkVisualization, Annotation,
GraphsAndNetworks, DataImport
Author: Paul Shannon <pshannon@systemsbiology.org>
Maintainer: Christopher Bare <cbare@systemsbiology.org>
URL: http://gaggle.systemsbiology.net/docs/geese/r/
MD5sum: a8279a1307801fa331273d7d37795b57
source.ver: src/contrib/gaggle_1.26.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/gaggle_1.26.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/gaggle_1.26.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/gaggle_1.26.0.tgz
vignettes: vignettes/gaggle/inst/doc/gaggle.pdf
vignetteTitles: Gaggle Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/gaggle/inst/doc/gaggle.R
Package: gaia
Version: 2.2.0
Depends: R (>= 2.10)
License: GPL-2
Title: GAIA: An R package for genomic analysis of significant
chromosomal aberrations.
Description: This package allows to assess the statistical significance
of chromosomal aberrations.
biocViews: aCGH, CopyNumberVariants
Author: Sandro Morganella et al.
Maintainer: S. Morganella <morganellaalx@gmail.com>
MD5sum: a7966f7a030357fcaacdac8714f859c9
source.ver: src/contrib/gaia_2.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/gaia_2.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/gaia_2.2.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gaia_2.2.0.tgz
vignettes: vignettes/gaia/inst/doc/gaia.pdf
vignetteTitles: gaia
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/gaia/inst/doc/gaia.R
Package: gCMAP
Version: 1.1.7
Depends: methods, GSEABase, DESeq
Imports: Biobase, limma (>= 3.12.1), GSEAlm, Category, bigmemoryExtras
(>= 0.99.3), Matrix (>= 1.0.9), parallel, annotate, genefilter,
RColorBrewer, lattice, latticeExtra
Suggests: KEGG.db, reactome.db, RUnit, BiocGenerics, reshape
OS_type: unix
License: Artistic-2.0
Title: Tools for Connectivity Map-like analyses
Description: The gCMAP package provides a toolkit for comparing
differential gene expression profiles through gene set
enrichment analysis. Starting from normalized microarray or
RNA-seq gene expression values (stored in lists of
ExpressionSet and CountDataSet objects) the package performs
differential expression analysis using the limma or DESeq
packages. Supplying a simple list of gene identifiers, global
differential expression profiles or data from complete
experiments as input, users can use a unified set of several
well-known gene set enrichment analysis methods to retrieve
experiments with similar changes in gene expression. To take
into account the directionality of gene expression changes,
gCMAPQuery introduces the SignedGeneSet class, directly
extending GeneSet from the GSEABase package. To increase
performance of large queries, multiple gene sets are stored as
sparse incidence matrices within CMAPCollection eSets. gCMAP
offers implementations of 1. Fisher's exact test (Fisher, J R
Stat Soc, 1922) 2. The "connectivity map" method (Lamb et al,
Science, 2006) 3. Parametric and non-parametric t-statistic
summaries (Jiang & Gentleman, Bioinformatics, 2007) and 4.
Wilcoxon / Mann-Whitney rank sum statistics (Wilcoxon,
Biometrics Bulletin, 1945) as well as wrappers for the 5.
camera (Wu & Smyth, Nucleic Acid Res, 2012) 6. mroast and romer
(Wu et al, Bioinformatics, 2010) functions from the limma
package. All methods return CMAPResult objects, an S4 class
inheriting from AnnotatedDataFrame, containing enrichment
statistics as well as annotation data and providing simple
high-level summary plots.
biocViews: Bioinformatics, Microarray, Software, Pathways, Annotation
Author: Thomas Sandmann <sandmann.thomas@gene.com>, Richard Bourgon
<bourgon.richard@gene.com> and Sarah Kummerfeld
<kummerfeld.sarah@gene.com>
Maintainer: Thomas Sandmann <sandmann.thomas@gene.com>
MD5sum: 8c66e65e47e3ebe9fef671552273c4b0
source.ver: src/contrib/gCMAP_1.1.7.tar.gz
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gCMAP_1.1.7.tgz
vignettes: vignettes/gCMAP/inst/doc/diffExprAnalysis.pdf,
vignettes/gCMAP/inst/doc/gCMAP.pdf,
vignettes/gCMAP/inst/doc/keggReactome.pdf
vignetteTitles: main, main, main
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/gCMAP/inst/doc/diffExprAnalysis.R,
vignettes/gCMAP/inst/doc/gCMAP.R,
vignettes/gCMAP/inst/doc/keggReactome.R
Package: gcrma
Version: 2.30.0
Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats,
utils
Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), IRanges,
Biostrings (>= 2.11.32), splines, BiocInstaller
Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe
License: LGPL
Archs: i386, x64
Title: Background Adjustment Using Sequence Information
Description: Background adjustment using sequence information
biocViews: Microarray, OneChannel, Preprocessing
Author: Jean(ZHIJIN) Wu, Rafael Irizarry with contributions from James
MacDonald <jmacdon@med.umich.edu> Jeff Gentry
Maintainer: Z. Wu <zwu@stat.brown.edu>
MD5sum: 13a24a8182b435d538fc0abb67e47ebd
source.ver: src/contrib/gcrma_2.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/gcrma_2.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/gcrma_2.30.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/gcrma_2.30.0.tgz
vignettes: vignettes/gcrma/inst/doc/gcrma2.0.pdf
vignetteTitles: gcrma1.2
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/gcrma/inst/doc/gcrma2.0.R
dependsOnMe: affyILM, affyPLM, bgx, maskBAD, simpleaffy, webbioc
importsMe: affycoretools, simpleaffy, virtualArray
suggestsMe: AffyExpress, ArrayTools, BiocCaseStudies, panp
Package: genArise
Version: 1.34.0
Depends: R (>= 1.7.1), locfit, tkrplot, methods
Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable
License: file LICENSE
Title: Microarray Analysis tool
Description: genArise is an easy to use tool for dual color microarray
data. Its GUI-Tk based environment let any non-experienced user
performs a basic, but not simple, data analysis just following
a wizard. In addition it provides some tools for the developer.
biocViews: Microarray, TwoChannel, Preprocessing
Author: Ana Patricia Gomez Mayen <pgomez@ifc.unam.mx>,\\ Gustavo Corral
Guille <gcorral@ifc.unam.mx>, \\ Lina Riego Ruiz
<lriego@ifc.unam.mx>,\\ Gerardo Coello Coutino
<gcoello@ifc.unam.mx>
Maintainer: IFC Development Team <info-genarise@ifc.unam.mx>
URL: http://www.ifc.unam.mx/genarise
MD5sum: 8ca70f4c48247ecd1d2cc3bda26c754f
source.ver: src/contrib/genArise_1.34.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/genArise_1.34.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/genArise_1.34.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/genArise_1.34.0.tgz
vignettes: vignettes/genArise/inst/doc/genArise.pdf
vignetteTitles: genAriseGUI Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/genArise/inst/doc/genArise.R
Package: gene2pathway
Version: 2.12.0
Depends: R (>= 2.10.0), kernlab (>= 0.9), biomaRt (>= 1.12.1), KEGGSOAP
(>= 1.12.0), RBGL, AnnotationDbi,org.Dm.eg.db, keggorthology
(>= 2.0)
Imports: SSOAP, RCurl
Enhances: doMC
License: GPL (>= 2)
Title: Prediction of KEGG pathway membership for individual genes based
on InterPro domain signatures
Description: The package takes a list of genes and predicts to which
KEGG pathway each gene maps to. This is done by looking at the
InterPro domains of each gene. Each prediction is assigned a
confidence score. The package also allows to predict connected
component membership of genes within signaling pathways.
Separate models for each organism supported by KEGG can be
trained.
biocViews: Microarray, Classification, GraphsAndNetworks, Pathways,
NetworkEnrichment
Author: Holger Froehlich <frohlich@bit.uni-bonn.de>
Maintainer: Holger Froehlich <frohlich@bit.uni-bonn.de>
MD5sum: 048520597a77d10c57a787b3038013cf
source.ver: src/contrib/gene2pathway_2.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/gene2pathway_2.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/gene2pathway_2.12.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/gene2pathway/inst/doc/gene2pathway.pdf
vignetteTitles: gene2pathway
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/gene2pathway/inst/doc/gene2pathway.R
Package: GeneAnswers
Version: 1.16.0
Depends: R (>= 2.10.0), igraph0, RCurl, annotate, Biobase (>= 1.12.0),
methods, XML, RSQLite, MASS, rgl, Heatplus, RColorBrewer
Imports: graph, Rgraphviz, RBGL, annotate
Suggests: GO.db, KEGG.db, biomaRt, AnnotationDbi, org.Hs.eg.db,
org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db
License: LGPL (>= 2)
Title: Integrated Interpretation of Genes
Description: GeneAnswers provides an integrated tool for biological or
medical interpretation of the given one or more groups of genes
by means of statistical test.
biocViews: Infrastructure, DataRepresentation, Visualization,
GraphsAndNetworks
Author: Gang Feng, Pan Du, Tian Xia, Warren Kibbe and Simon Lin
Maintainer: Gang Feng <g-feng@northwestern.edu> , Pan Du
<dupan.mail@gmail.com> and Tian Xia <isutian@gmail.com>
MD5sum: a8b1a4bed91ee1a476fe47b1b3f04281
source.ver: src/contrib/GeneAnswers_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GeneAnswers_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GeneAnswers_1.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GeneAnswers/inst/doc/GeneAnswersCWAnnotation.pdf,
vignettes/GeneAnswers/inst/doc/geneAnswers.pdf,
vignettes/GeneAnswers/inst/doc/geneFunctionSummarize.pdf
vignetteTitles: GeneAnswers web-based visualization module,
GeneAnswers, Summarize gene annotations based on collective
ontology annotations
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GeneAnswers/inst/doc/GeneAnswersCWAnnotation.R,
vignettes/GeneAnswers/inst/doc/geneAnswers.R,
vignettes/GeneAnswers/inst/doc/geneFunctionSummarize.R
Package: GeneExpressionSignature
Version: 1.4.0
Depends: R (>= 2.13), Biobase, PGSEA
Suggests: apcluster,GEOquery
License: GPL-2
Title: Gene Expression Signature based Similarity Metric
Description: This package gives the implementations of the gene
expression signature and its distance to each. Gene expression
signature is represented as a list of genes whose expression is
correlated with a biological state of interest. And its
distance is defined using a nonparametric, rank-based
pattern-matching strategy based on the Kolmogorov-Smirnov
statistic. Gene expression signature and its distance can be
used to detect similarities among the signatures of drugs,
diseases, and biological states of interest.
biocViews: Bioinformatics, GeneExpression
Author: Yang Cao
Maintainer: Yang Cao <yiluheihei@gmail.com>, Fei Li
<pittacus@gmail.com>,Lu Han <hanl8910@gmail.com>
MD5sum: 319d8966b4f6c28aebdbfa4f0b8c2d51
source.ver: src/contrib/GeneExpressionSignature_1.4.0.tar.gz
win.binary.ver:
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win64.binary.ver:
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mac.binary.leopard.ver:
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vignettes:
vignettes/GeneExpressionSignature/inst/doc/GeneExpressionSignature.pdf
vignetteTitles: GeneExpressionSignature
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: genefilter
Version: 1.40.0
Imports: AnnotationDbi, annotate (>= 1.13.7), Biobase (>= 1.99.10),
graphics, methods, stats, survival
Suggests: Biobase (>= 1.99.10), class, hgu95av2.db, methods, tkWidgets,
ALL, ROC
License: Artistic-2.0
Archs: i386, x64
Title: genefilter: methods for filtering genes from microarray
experiments
Description: Some basic functions for filtering genes
biocViews: Bioinformatics, Microarray
Author: R. Gentleman, V. Carey, W. Huber, F. Hahne
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: 3bbb52c4acf1d83d58d45aa4b04397eb
source.ver: src/contrib/genefilter_1.40.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/genefilter_1.40.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/genefilter_1.40.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/genefilter/inst/doc/howtogenefilter.pdf,
vignettes/genefilter/inst/doc/howtogenefinder.pdf,
vignettes/genefilter/inst/doc/independent_filtering_plots.pdf
vignetteTitles: Using the genefilter function to filter genes from a
microarray dataset, How to find genes whose expression profile
is similar to that of specified genes, Diagnostic plots for
independent filtering
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/genefilter/inst/doc/howtogenefilter.R,
vignettes/genefilter/inst/doc/howtogenefinder.R,
vignettes/genefilter/inst/doc/independent_filtering_plots.R
dependsOnMe: a4Base, Agi4x44PreProcess, cellHTS, cellHTS2, charm,
CNTools, eisa, GeneMeta, MLInterfaces, simpleaffy
importsMe: affycoretools, affyQCReport, annmap, arrayQualityMetrics,
Category, crlmm, DESeq, gCMAP, GGBase, GSRI, methyAnalysis,
methylumi, phenoTest, Ringo, simpleaffy, tilingArray, XDE
suggestsMe: AffyExpress, annotate, ArrayTools, BiocCaseStudies, BioNet,
Category, categoryCompare, clusterStab, codelink, factDesign,
ffpe, GOstats, GSEAlm, GSVA, logicFS, lumi, MCRestimate, oligo,
oneChannelGUI, phyloseq, pvac, qpgraph, rtracklayer, siggenes,
topGO, VanillaICE, XDE
Package: genefu
Version: 1.8.0
Depends: R (>= 2.10), survcomp, mclust, biomaRt
Imports: amap
Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ,
breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT,
breastCancerNKI, rmeta, Biobase, xtable
License: Artistic-2.0
Title: Relevant Functions for Gene Expression Analysis, Especially in
Breast Cancer.
Description: Description: This package contains functions implementing
various tasks usually required by gene expression analysis,
especially in breast cancer studies: gene mapping between
different microarray platforms, identification of molecular
subtypes, implementation of published gene signatures, gene
selection, survival analysis, ...
biocViews: DifferentialExpression, GeneExpression, Visualization,
Clustering, Classification
Author: Benjamin Haibe-Kains, Markus Schroeder, Gianluca Bontempi,
Christos Sotiriou, John Quackenbush
Maintainer: Benjamin Haibe-Kains <bhaibeka@jimmy.harvard.edu>, Markus
Schroeder <mschroed@jimmy.harvard.edu>
URL: http://compbio.dfci.harvard.edu
MD5sum: d835843e4bce94d514911a91e2b82a57
source.ver: src/contrib/genefu_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/genefu_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/genefu_1.8.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/genefu/inst/doc/genefu.pdf
vignetteTitles: genefu An Introduction (HowTo)
hasREADME: TRUE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/genefu/inst/doc/genefu.R
Package: GeneGA
Version: 1.8.0
Depends: seqinr, hash, methods
License: GPL version 2
Title: Design gene based on both mRNA secondary structure and codon
usage bias using Genetic algorithm
Description: R based Genetic algorithm for gene expression optimization
by considering both mRNA secondary structure and codon usage
bias, GeneGA includes the information of highly expressed genes
of almost 200 genomes. Meanwhile, Vienna RNA Package is needed
to ensure GeneGA to function properly.
biocViews: GeneExpression
Author: Zhenpeng Li, Fei Li, Xiaochen Bo and Shengqi Wang
Maintainer: Zhenpeng Li <zpli21@gmail.com>
URL: http://www.tbi.univie.ac.at/~ivo/RNA/
MD5sum: 9ebfbb148f3a5b04cc5f23a206223eba
source.ver: src/contrib/GeneGA_1.8.0.tar.gz
mac.binary.leopard.ver:
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vignettes: vignettes/GeneGA/inst/doc/GeneGA.pdf
vignetteTitles: GeneGA
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GeneGA/inst/doc/GeneGA.R
Package: GeneGroupAnalysis
Version: 1.4.0
Depends: R (>= 2.10), MCMCpack, GO.db, breastCancerVDX,
rheumaticConditionWOLLBOLD, hgu133a.db, hgu133plus2.db
Imports: AnnotationDbi, annotate, tcltk
License: Artistic-2.0
Archs: i386, x64
Title: Gene Functional Class Analysis
Description: R package providing functions to peform gene-set
significance analysis over simple cross-sectional or time
series data designs.
biocViews: GeneExpression, DifferentialExpression, MultipleComparisons,
CrossSectional, TimeCourse
Author: Alejandro Quiroz-Zarate and John Quackenbush
Maintainer: Alejandro Quiroz-Zarate <aquiroz@hsph.harvard.edu>
URL: http://compbio.dfci.harvard.edu/
MD5sum: 378b3867ab1a93451ae09be732fb9049
source.ver: src/contrib/GeneGroupAnalysis_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GeneGroupAnalysis_1.4.0.zip
win64.binary.ver:
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mac.binary.leopard.ver:
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vignettes: vignettes/GeneGroupAnalysis/inst/doc/GeneGroupAnalysis.pdf
vignetteTitles: GeneGroupAnalysis: a package for performance assessment
and comparison for survival analysis
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GeneGroupAnalysis/inst/doc/GeneGroupAnalysis.R
Package: GeneMeta
Version: 1.30.1
Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter
Imports: methods, Biobase (>= 2.5.5)
Suggests: RColorBrewer
License: Artistic-2.0
Title: MetaAnalysis for High Throughput Experiments
Description: A collection of meta-analysis tools for analysing high
throughput experimental data
biocViews: Bioinformatics
Author: Lara Lusa <lusa@ifom-firc.it>, R. Gentleman, M. Ruschhaupt
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: 6c44d7454be47eea7e6d117f7aab0bb0
source.ver: src/contrib/GeneMeta_1.30.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GeneMeta_1.30.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/GeneMeta_1.30.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GeneMeta/inst/doc/GeneMeta.pdf
vignetteTitles: GeneMeta Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GeneMeta/inst/doc/GeneMeta.R
suggestsMe: genefu, XDE
Package: GeneNetworkBuilder
Version: 1.0.1
Depends: R (>= 2.15.1), Rcpp (>= 0.9.13), graph
Imports: plyr, graph
LinkingTo: Rcpp
Suggests: RUnit, BiocGenerics, Rgraphviz, XML, RCytoscape
License: GPL (>= 2)
Archs: i386, x64
Title: Build Regulatory Network from ChIP-chip/ChIP-seq and Expression
Data
Description: Appliation for discovering direct or indirect targets of
transcription factors using ChIP-chip or ChIP-seq, and
microarray or RNA-seq gene expression data. Inputting a list of
genes of potential targets of one TF from ChIP-chip or
ChIP-seq, and the gene expression results, GeneNetworkBuilder
generates a regulatory network of the TF.
biocViews: HighThroughputSequencing, Microarray, GraphsAndNetworks
Author: Jianhong Ou and Lihua Julie Zhu
Maintainer: Jianhong Ou <jianhong.ou@umassmed.edu>
MD5sum: e18243980ec2d371bcfd5470e6a85d60
source.ver: src/contrib/GeneNetworkBuilder_1.0.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GeneNetworkBuilder_1.0.1.zip
win64.binary.ver:
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mac.binary.leopard.ver:
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vignettes: vignettes/GeneNetworkBuilder/inst/doc/GeneNetworkBuilder.pdf
vignetteTitles: GeneNetworkBuilder Vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GeneNetworkBuilder/inst/doc/GeneNetworkBuilder.R
Package: geneplotter
Version: 1.36.0
Depends: R (>= 2.10),Biobase (>= 2.5.5), annotate, lattice
Imports: annotate, AnnotationDbi, Biobase (>= 2.5.5), graphics,
grDevices, grid, methods, RColorBrewer, stats, utils
Suggests: Biobase (>= 2.5.5), Rgraphviz, annotate, fibroEset,
hgu95av2.db, hu6800.db, hgu133a.db
License: Artistic-2.0
Title: Graphics related functions for Bioconductor
Description: Some basic functions for plotting genetic data
biocViews: Visualization
Author: R. Gentleman, Biocore
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: 94a3a993dcbc8facf2a77fb6e9753f50
source.ver: src/contrib/geneplotter_1.36.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/geneplotter_1.36.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/geneplotter_1.36.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/geneplotter/inst/doc/byChroms.pdf,
vignettes/geneplotter/inst/doc/visualize.pdf
vignetteTitles: How to assemble a chromLocation object, Visualization
of Microarray Data
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/geneplotter/inst/doc/byChroms.R,
vignettes/geneplotter/inst/doc/visualize.R
dependsOnMe: HMMcopy
importsMe: biocGraph, DESeq, flowQ, IsoGeneGUI, RNAinteract, RNAither
suggestsMe: BiocCaseStudies, biocGraph, Category, GOstats, maDB
Package: geneRecommender
Version: 1.30.0
Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods
Imports: Biobase, methods, stats
License: GPL (>= 2)
Title: A gene recommender algorithm to identify genes coexpressed with
a query set of genes
Description: This package contains a targeted clustering algorithm for
the analysis of microarray data. The algorithm can aid in the
discovery of new genes with similar functions to a given list
of genes already known to have closely related functions.
biocViews: Microarray, Clustering
Author: Gregory J. Hather <ghather@stat.berkeley.edu>, with
contributions from Art B. Owen <art@stat.stanford.edu> and
Terence P. Speed <terry@stat.berkeley.edu>
Maintainer: Greg Hather <ghather@stat.berkeley.edu>
MD5sum: a2d6d4b6166251bc05bb110749d9e65b
source.ver: src/contrib/geneRecommender_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/geneRecommender_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/geneRecommender_1.30.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/geneRecommender/inst/doc/geneRecommender.pdf
vignetteTitles: Using the geneRecommender Package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/geneRecommender/inst/doc/geneRecommender.R
Package: GeneRegionScan
Version: 1.14.0
Depends: methods, Biobase (>= 2.5.5), Biostrings
Imports: Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings
Suggests: BSgenome, affy, AnnotationDbi
License: GPL (>= 2)
Title: GeneRegionScan
Description: A package with focus on analysis of discrete regions of
the genome. This package is useful for investigation of one or
a few genes using Affymetrix data, since it will extract probe
level data using the Affymetrix Power Tools application and
wrap these data into a ProbeLevelSet. A ProbeLevelSet directly
extends the expressionSet, but includes additional information
about the sequence of each probe and the probe set it is
derived from. The package includes a number of functions used
for plotting these probe level data as a function of location
along sequences of mRNA-strands. This can be used for analysis
of variable splicing, and is especially well suited for use
with exon-array data.
biocViews: Microarray, DataImport, SNP, OneChannel, Visualization
Author: Lasse Folkersen, Diego Diez
Maintainer: Lasse Folkersen <lasse.folkersen@ki.se>
MD5sum: 4136888cd305c99919d039a085622e99
source.ver: src/contrib/GeneRegionScan_1.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GeneRegionScan_1.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GeneRegionScan_1.14.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GeneRegionScan/inst/doc/GeneRegionScan.pdf
vignetteTitles: GeneRegionScan
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GeneRegionScan/inst/doc/GeneRegionScan.R
Package: GeneSelectMMD
Version: 2.2.0
Depends: R (>= 2.13.2), Biobase
Imports: Biobase, MASS, graphics, stats, survival, limma
Suggests: ALL
License: GPL (>= 2)
Archs: i386, x64
Title: Gene selection based on the marginal distributions of gene
profiles that characterized by a mixture of three-component
multivariate distributions
Description: Gene selection based on a mixture of marginal
distributions
biocViews: Bioinformatics, DifferentialExpression
Author: Jarrett Morrow <remdj@channing.harvard.edu>, Weiliang Qiu
<stwxq@channing.harvard.edu>, Wenqing He <whe@stats.uwo.ca>,
Xiaogang Wang <stevenw@mathstat.yorku.ca>, Ross Lazarus
<ross.lazarus@channing.harvard.edu>.
Maintainer: Weiliang Qiu <stwxq@channing.harvard.edu>
MD5sum: a7df98bba98fa4379f0c4dd798b2fdc8
source.ver: src/contrib/GeneSelectMMD_2.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GeneSelectMMD_2.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GeneSelectMMD_2.2.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GeneSelectMMD/inst/doc/GS207runTimesSim1k.pdf,
vignettes/GeneSelectMMD/inst/doc/gsMMD.pdf
vignetteTitles: GS207runTimesSim1k.pdf, Gene Selection based on a
mixture of marginal distributions
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GeneSelectMMD/inst/doc/gsMMD.R
Package: GeneSelector
Version: 2.8.0
Depends: R (>= 2.5.1), methods, stats, Biobase
Imports: multtest, siggenes, samr, limma
Suggests: multtest, siggenes, samr, limma
License: GPL (>= 2)
Archs: i386, x64
Title: Stability and Aggregation of ranked gene lists
Description: The term 'GeneSelector' refers to a filter selecting those
genes which are consistently identified as differentially
expressed using various statistical procedures. 'Selected'
genes are those present at the top of the list in various
ranking methods (currently 14). In addition, the stability of
the findings can be taken into account in the final ranking by
examining perturbed versions of the original data set, e.g. by
leaving samples, swapping class labels, generating bootstrap
replicates or adding noise. Given multiple ranked lists, one
can use aggregation methods in order to find a synthesis.
biocViews: Statistics, DifferentialExpression
Author: Martin Slawski <ms@cs.uni-sb.de>, Anne-Laure Boulesteix
<boulesteix@ibe.med.uni-muenchen.de>.
Maintainer: Martin Slawski <ms@cs.uni-sb.de>
MD5sum: d67f9c2d3c3149e1eae260942957782e
source.ver: src/contrib/GeneSelector_2.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GeneSelector_2.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GeneSelector_2.8.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GeneSelector/inst/doc/GeneSelector.pdf
vignetteTitles: GeneSelector.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GeneSelector/inst/doc/GeneSelector.R
Package: GeneticsDesign
Version: 1.26.0
Imports: gmodels, graphics, gtools (>= 2.4.0), mvtnorm, stats
License: GPL-2
Title: Functions for designing genetics studies
Description: This package contains functions useful for designing
genetics studies, including power and sample-size calculations.
biocViews: Genetics
Author: Gregory Warnes <warnes@bst.rochester.edu> David Duffy
<davidD@qumr.edu.au>, Michael Man <michael.man@pfizer.com>
Weiliang Qiu <stwxq@channing.harvard.edu> Ross Lazarus
<ross.lazarus@channing.harvard.edu>
Maintainer: The R Genetics Project
<r-genetics-talk@lists.sourceforge.net>
MD5sum: d2f7eb2ad56fe30a9e725d50c6e417f8
source.ver: src/contrib/GeneticsDesign_1.26.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GeneticsDesign_1.26.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GeneticsDesign_1.26.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GeneticsDesign/inst/doc/GPC.pdf
vignetteTitles: Package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GeneticsDesign/inst/doc/GPC.R
Package: GeneticsPed
Version: 1.20.0
Depends: R (>= 2.4.0), gdata (>= 2.3.0), genetics (>= 1.3.0), MASS
Suggests: RUnit, gtools
License: LGPL (>= 2.1)
Archs: i386, x64
Title: Pedigree and genetic relationship functions
Description: Classes and methods for handling pedigree data. It also
includes functions to calculate genetic relationship measures
as relationship and inbreeding coefficients and other
utilities. Note that package is not yet stable. Use it with
care!
biocViews: Genetics
Author: Gregor Gorjanc and David A. Henderson <dnadave@comcast.net>,
with code contributions by Brian Kinghorn and Andrew Percy (see
file COPYING)
Maintainer: David Henderson <DNADavenator@GMail.Com>
URL: http://rgenetics.org
MD5sum: 836c6a7a1763853aa6642ab6899fc63e
source.ver: src/contrib/GeneticsPed_1.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GeneticsPed_1.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GeneticsPed_1.20.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GeneticsPed/inst/doc/geneticRelatedness.pdf,
vignettes/GeneticsPed/inst/doc/pedigreeHandling.pdf,
vignettes/GeneticsPed/inst/doc/quanGenAnimalModel.pdf
vignetteTitles: Calculation of genetic relatedness/relationship between
individuals in the pedigree, Pedigree handling, Quantitative
genetic (animal) model example in R
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/GeneticsPed/inst/doc/geneticRelatedness.R,
vignettes/GeneticsPed/inst/doc/pedigreeHandling.R,
vignettes/GeneticsPed/inst/doc/quanGenAnimalModel.R
Package: genoCN
Version: 1.10.0
Imports: graphics, stats, utils
License: GPL (>=2)
Archs: i386, x64
Title: genotyping and copy number study tools
Description: Simultaneous identification of copy number states and
genotype calls for regions of either copy number variations or
copy number aberrations
biocViews: Microarray, Genetics
Author: Wei Sun and ZhengZheng Tang
Maintainer: Wei Sun <wsun@bios.unc.edu>
MD5sum: 2a930ff589391326923dc9a56dcd42ae
source.ver: src/contrib/genoCN_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/genoCN_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/genoCN_1.10.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/genoCN/inst/doc/genoCN.pdf
vignetteTitles: add stuff
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/genoCN/inst/doc/genoCN.R
Package: GenomeGraphs
Version: 1.18.0
Depends: R (>= 2.10), methods, biomaRt, grid
License: Artistic-2.0
Title: Plotting genomic information from Ensembl
Description: Genomic data analyses requires integrated visualization of
known genomic information and new experimental data.
GenomeGraphs uses the biomaRt package to perform live
annotation queries to Ensembl and translates this to e.g.
gene/transcript structures in viewports of the grid graphics
package. This results in genomic information plotted together
with your data. Another strength of GenomeGraphs is to plot
different data types such as array CGH, gene expression,
sequencing and other data, together in one plot using the same
genome coordinate system.
biocViews: Visualization, Microarray
Author: Steffen Durinck <sdurinck@gmail.com>, James Bullard
<bullard@berkeley.edu>
Maintainer: Steffen Durinck <sdurinck@gmail.com>
MD5sum: 1e5eb419fb1d1c3251524f648ae44f7f
source.ver: src/contrib/GenomeGraphs_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GenomeGraphs_1.18.0.zip
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vignettes: vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf
vignetteTitles: The GenomeGraphs users guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GenomeGraphs/inst/doc/GenomeGraphs.R
dependsOnMe: Genominator, waveTiling
suggestsMe: rMAT
Package: genomeIntervals
Version: 1.14.0
Depends: R (>= 2.15.0), methods, intervals (>= 0.13.3), BiocGenerics
(>= 0.3.2)
Imports: methods, Biobase
License: Artistic-2.0
Title: Operations on genomic intervals
Description: This package defines classes for representing genomic
intervals and provides functions and methods for working with
these. Note: The package provides the basic infrastructure for
and is enhanced by the package 'girafe'.
biocViews: DataImport, Infrastructure, Genetics
Author: Julien Gagneur <gagneur@genzentrum.lmu.de>, Joern Toedling,
Richard Bourgon, Nicolas Delhomme
Maintainer: Julien Gagneur <gagneur@genzentrum.lmu.de>
MD5sum: 6c8e7ac7a71cc785e5c225647b343f44
source.ver: src/contrib/genomeIntervals_1.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/genomeIntervals_1.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/genomeIntervals_1.14.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/genomeIntervals/inst/doc/genomeIntervals.pdf
vignetteTitles: Overview of the genomeIntervals package.
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/genomeIntervals/inst/doc/genomeIntervals.R
dependsOnMe: easyRNASeq, girafe, HiTC
Package: genomes
Version: 2.4.0
Depends: R (>= 2.10), XML, RCurl, GenomicRanges, IRanges, Biostrings
License: Artistic-2.0
Title: Genome sequencing project metadata
Description: Collects genome sequencing project data from NCBI and the
ENA.
biocViews: Annotation, Genetics
Author: Chris Stubben
Maintainer: Chris Stubben <stubben@lanl.gov>
MD5sum: f3d65fb7d2ce23674b1be04acba9d921
source.ver: src/contrib/genomes_2.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/genomes_2.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/genomes_2.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/genomes/inst/doc/genome-tables.pdf
vignetteTitles: Introduction to genome projects
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/genomes/inst/doc/genome-tables.R
Package: GenomicFeatures
Version: 1.10.2
Depends: BiocGenerics (>= 0.1.0), IRanges (>= 1.15.35), GenomicRanges
(>= 1.9.66), AnnotationDbi (>= 1.19.36)
Imports: methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), BiocGenerics,
IRanges, GenomicRanges, Biostrings (>= 2.23.2), rtracklayer (>=
1.15.1), biomaRt, RCurl, utils, Biobase (>= 2.15.1)
Suggests: rtracklayer, biomaRt, org.Mm.eg.db, Biostrings, BSgenome,
BSgenome.Hsapiens.UCSC.hg18 (>= 1.3.14),
BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17),
BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>=
1.3.17), mirbase.db, FDb.UCSC.tRNAs,
TxDb.Hsapiens.UCSC.hg18.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), Rsamtools,
pasillaBamSubset (>= 0.0.5), RUnit
License: Artistic-2.0
Title: Tools for making and manipulating transcript centric annotations
Description: A set of tools and methods for making and manipulating
transcript centric annotations. With these tools the user can
easily download the genomic locations of the transcripts, exons
and cds of a given organism, from either the UCSC Genome
Browser or a BioMart database (more sources will be supported
in the future). This information is then stored in a local
database that keeps track of the relationship between
transcripts, exons, cds and genes. Flexible methods are
provided for extracting the desired features in a convenient
format.
biocViews: Genetics, Infrastructure, Annotation,
HighThroughputSequencing
Author: M. Carlson, H. Pages, P. Aboyoun, S. Falcon, M. Morgan, D.
Sarkar, M. Lawrence
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: 725df17052211788f6c5e6752676b412
source.ver: src/contrib/GenomicFeatures_1.10.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GenomicFeatures_1.10.2.zip
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mac.binary.leopard.ver:
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vignettes: vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf
vignetteTitles: Making and Utilizing TranscriptDb Objects
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GenomicFeatures/inst/doc/GenomicFeatures.R,
vignettes/GenomicFeatures/inst/doc/spliceGraph.R
dependsOnMe: OrganismDbi
importsMe: biovizBase, ggbio, gmapR, Gviz, HTSeqGenie, methyAnalysis,
VariantAnnotation, VariantTools
suggestsMe: Biostrings, chipseq, easyRNASeq, GenomicRanges, Gviz,
HTSeqGenie, MiRaGE, Rsamtools, ShortRead
Package: GenomicRanges
Version: 1.10.7
Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.12), IRanges (>=
1.15.42)
Imports: methods, utils, BiocGenerics, IRanges
LinkingTo: IRanges
Suggests: Biostrings (>= 2.25.3), Rsamtools (>= 1.9.21), BSgenome,
rtracklayer, GenomicFeatures, VariantAnnotation, edgeR, DESeq,
DEXSeq, EatonEtAlChIPseq (>= 0.0.3), leeBamViews, pasilla,
pasillaBamSubset, org.Sc.sgd.db,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
BSgenome.Scerevisiae.UCSC.sacCer2,
BSgenome.Dmelanogaster.UCSC.dm3, RUnit, digest
License: Artistic-2.0
Archs: i386, x64
Title: Representation and manipulation of genomic intervals
Description: The ability to efficiently store genomic annotations and
alignments is playing a central role when it comes to analyze
high-throughput sequencing data (a.k.a. NGS data). The package
defines general purpose containers for storing genomic
intervals as well as more specialized containers for storing
alignments against a reference genome.
biocViews: Genetics, Sequencing, HighThroughputSequencing, Annotation
Author: P. Aboyoun, H. Pages and M. Lawrence
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: c0cea669b165acc0e6498e0345e916c4
source.ver: src/contrib/GenomicRanges_1.10.7.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GenomicRanges_1.10.7.zip
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mac.binary.leopard.ver:
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vignettes:
vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.pdf,
vignettes/GenomicRanges/inst/doc/GenomicRangesUseCases.pdf,
vignettes/GenomicRanges/inst/doc/OverlapEncodings.pdf,
vignettes/GenomicRanges/inst/doc/summarizeOverlaps-modes.pdf,
vignettes/GenomicRanges/inst/doc/summarizeOverlaps.pdf
vignetteTitles: An Introduction to GenomicRanges, GenomicRanges Use
Cases, Overlap encodings, summarizeOverlaps-modes.pdf, Overview
of summarizeOverlaps
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GenomicRanges/inst/doc/GenomicRangesUseCases.R,
vignettes/GenomicRanges/inst/doc/OverlapEncodings.R,
vignettes/GenomicRanges/inst/doc/summarizeOverlaps.R
dependsOnMe: annmap, BSgenome, bsseq, chipseq, cn.mops, CSAR, deepSNV,
DiffBind, easyRNASeq, exomeCopy, fastseg, genomes,
GenomicFeatures, genoset, GGtools, gmapR, gwascat, htSeqTools,
minfi, PING, Rcade, Repitools, Rsamtools, rSFFreader,
rtracklayer, segmentSeq, seqbias, ShortRead, VariantAnnotation,
VariantTools
importsMe: ArrayExpressHTS, biovizBase, chipseq, ChIPseqR, FunciSNP,
GenomicFeatures, genoset, ggbio, gmapR, Gviz, HTSeqGenie,
methyAnalysis, MinimumDistance, NarrowPeaks, nucleR,
oligoClasses, PICS, Repitools, rnaSeqMap, Rsamtools,
rSFFreader, rtracklayer, segmentSeq, ShortRead, SNPchip,
VanillaICE, VariantTools, waveTiling
suggestsMe: BiocGenerics, IRanges, MiRaGE, NarrowPeaks, Repitools
Package: Genominator
Version: 1.12.0
Depends: R (>= 2.10), methods, RSQLite, DBI (>= 0.2-5), BiocGenerics
(>= 0.1.0), IRanges, GenomeGraphs
Imports: graphics, stats, utils
Suggests: biomaRt, ShortRead, yeastRNASeq
License: Artistic-2.0
Title: Analyze, manage and store genomic data
Description: Tools for storing, accessing, analyzing and visualizing
genomic data.
biocViews: Infrastructure
Author: James Bullard, Kasper Daniel Hansen
Maintainer: James Bullard <bullard@stat.berkeley.edu>
MD5sum: e53345554364e32d5cd8705b40485c8b
source.ver: src/contrib/Genominator_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Genominator_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Genominator_1.12.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Genominator/inst/doc/Genominator.pdf,
vignettes/Genominator/inst/doc/plotting.pdf,
vignettes/Genominator/inst/doc/withShortRead.pdf
vignetteTitles: The Genominator User Guide, Plotting with Genominator,
Working with the ShortRead Package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Genominator/inst/doc/Genominator.R,
vignettes/Genominator/inst/doc/plotting.R,
vignettes/Genominator/inst/doc/withShortRead.R
suggestsMe: oneChannelGUI
Package: genoset
Version: 1.10.1
Depends: R (>= 2.10), BiocGenerics (>= 0.1.6), Biobase (>= 2.15.1),
IRanges (>= 1.13.5), GenomicRanges
Imports: methods, graphics, GenomicRanges
Suggests: RUnit, DNAcopy, stats
Enhances: parallel
License: Artistic-2.0
Archs: i386, x64
Title: Provides classes similar to ExpressionSet for copy number
analysis
Description: Load, manipulate, and plot copynumber and BAF data.
GenoSet class extends eSet by adding a "locData" slot for a
RangedData or GRanegs object. This object contains feature
genome location data and provides for efficient subsetting on
genome location. CNSet and BAFSet extend GenoSet and require
assayData matrices for Copy Number (cn) or Log-R Ratio (lrr)
and B-Allele Frequency (baf) data. Implements and provides
convenience functions for processing of copy number and
B-Allele Frequency data.
biocViews: Infrastructure, DataRepresentation, Microarray, SNP,
CopyNumberVariants
Author: Peter M. Haverty
Maintainer: Peter M. Haverty <phaverty@gene.com>
MD5sum: f5867ab1dc2e5b58d03ba64de4d1257e
source.ver: src/contrib/genoset_1.10.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/genoset_1.10.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/genoset_1.10.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/genoset/inst/doc/genoset.pdf
vignetteTitles: genoset
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/genoset/inst/doc/genoset.R
dependsOnMe: VegaMC
importsMe: methyAnalysis
Package: GEOmetadb
Version: 1.18.0
Depends: GEOquery,RSQLite
License: Artistic-2.0
Title: A compilation of metadata from NCBI GEO
Description: The NCBI Gene Expression Omnibus (GEO) represents the
largest public repository of microarray data. However, finding
data of interest can be challenging using current tools.
GEOmetadb is an attempt to make access to the metadata
associated with samples, platforms, and datasets much more
feasible. This is accomplished by parsing all the NCBI GEO
metadata into a SQLite database that can be stored and queried
locally. GEOmetadb is simply a thin wrapper around the SQLite
database along with associated documentation. Finally, the
SQLite database is updated regularly as new data is added to
GEO and can be downloaded at will for the most up-to-date
metadata. GEOmetadb paper:
http://bioinformatics.oxfordjournals.org/cgi/content/short/24/23/2798
.
biocViews: Infrastructure
Author: Jack Zhu and Sean Davis
Maintainer: Jack Zhu <zhujack@mail.nih.gov>
URL: http://gbnci.abcc.ncifcrf.gov/geo/
MD5sum: 0db43d7953d44a75b352241b6ad20c8b
source.ver: src/contrib/GEOmetadb_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GEOmetadb_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GEOmetadb_1.18.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GEOmetadb/inst/doc/GEOmetadb_diagram.pdf,
vignettes/GEOmetadb/inst/doc/GEOmetadb.pdf
vignetteTitles: GEOmetadb_diagram.pdf, GEOmetadb
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GEOmetadb/inst/doc/GEOmetadb.R
Package: GEOquery
Version: 2.24.1
Depends: methods, Biobase
Imports: XML, RCurl
Suggests: limma, RUnit
License: GPL-2
Title: Get data from NCBI Gene Expression Omnibus (GEO)
Description: The NCBI Gene Expression Omnibus (GEO) is a public
repository of microarray data. Given the rich and varied
nature of this resource, it is only natural to want to apply
BioConductor tools to these data. GEOquery is the bridge
between GEO and BioConductor.
biocViews: Microarray, DataImport, OneChannel, TwoChannel, SAGE
Author: Sean Davis <sdavis2@mail.nih.gov>
Maintainer: Sean Davis <sdavis2@mail.nih.gov>
URL: http://watson.nci.nih.gov/~sdavis
MD5sum: 8deff757b1a4c675effab8917188c10d
source.ver: src/contrib/GEOquery_2.24.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GEOquery_2.24.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/GEOquery_2.24.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GEOquery/inst/doc/GEOquery.pdf
vignetteTitles: GEOquery
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GEOquery/inst/doc/GEOquery.R
importsMe: ChIPXpress, SRAdb, virtualArray
suggestsMe: dyebias, PGSEA
Package: GEOsubmission
Version: 1.10.0
Imports: affy, Biobase, utils
License: GPL (>= 2)
Title: Prepares microarray data for submission to GEO
Description: Helps to easily submit a microarray dataset and the
associated sample information to GEO by preparing a single file
for upload (direct deposit).
biocViews: Microarray
Author: Alexandre Kuhn <alexandre.m.kuhn@gmail.com>
Maintainer: Alexandre Kuhn <alexandre.m.kuhn@gmail.com>
MD5sum: cd66fee62236043fe89d34589a480628
source.ver: src/contrib/GEOsubmission_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GEOsubmission_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GEOsubmission_1.10.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GEOsubmission/inst/doc/GEOsubmission.pdf
vignetteTitles: GEOsubmission Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GEOsubmission/inst/doc/GEOsubmission.R
Package: GEWIST
Version: 1.2.0
Depends: R (>= 2.10), car
License: GPL-2
Title: Gene Environment Wide Interaction Search Threshold
Description: This 'GEWIST' package provides statistical tools to
efficiently optimize SNP prioritization for gene-gene and
gene-environment interactions.
biocViews: Bioinformatics, MultipleComparisons, BiologicalDomains,
Genetics
Author: Wei Q. Deng, Guillaume Pare
Maintainer: Wei Q. Deng <dengwq@mcmaster.ca>
MD5sum: 5af819424b4fefb8adc08ba1ef1a3e0b
source.ver: src/contrib/GEWIST_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GEWIST_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GEWIST_1.2.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GEWIST/inst/doc/GEWIST.pdf
vignetteTitles: GEWIST.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GEWIST/inst/doc/GEWIST.R
Package: GGBase
Version: 3.20.0
Depends: R (>= 2.14), methods, snpStats
Imports: limma, genefilter, Biobase, BiocGenerics, Matrix,
AnnotationDbi
License: Artistic-2.0
Title: GGBase infrastructure for genetics of gene expression package
GGtools
Description: infrastructure
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: 655d313e34843e6532d34e9f7c5c8f4a
source.ver: src/contrib/GGBase_3.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GGBase_3.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GGBase_3.20.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GGBase/inst/doc/ggbase.pdf
vignetteTitles: GGBase -- infrastructure for GGtools,, genetics of gene
expression
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GGBase/inst/doc/ggbase.R
dependsOnMe: GGtools
importsMe: qpgraph
Package: ggbio
Version: 1.6.6
Depends: methods, ggplot2 (>= 0.9.2)
Imports: methods, biovizBase(>= 1.5.9), reshape2, gtable, ggplot2(>=
0.9.2), BiocGenerics, Biobase, IRanges, GenomicRanges,
GenomicFeatures, Rsamtools, BSgenome, gridExtra, scales, plyr,
VariantAnnotation, Hmisc, rtracklayer
Suggests: BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, affyPLM, chipseq,
TxDb.Mmusculus.UCSC.mm9.knownGene, knitr
License: Artistic-2.0
Title: Static visualization for genomic data.
Description: The ggbio package extends and specializes the grammar of
graphics for biological data. The graphics are designed to
answer common scientific questions, in particular those often
asked of high throughput genomics data. All core Bioconductor
data structures are supported, where appropriate. The package
supports detailed views of particular genomic regions, as well
as genome-wide overviews. Supported overviews include ideograms
and grand linear views. High-level plots include sequence
fragment length, edge-linked interval to data view, mismatch
pileup, and several splicing summaries.
biocViews: Infrastructure, Visualization, Bioinformatics
Author: Tengfei Yin, Dianne Cook, Michael Lawrence
Maintainer: Tengfei Yin <yintengfei@gmail.com>
URL: http://tengfei.github.com/ggbio/
MD5sum: 89b73a756bf8379858aa7d14ef9bb02a
source.ver: src/contrib/ggbio_1.6.6.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ggbio_1.6.6.zip
win64.binary.ver: bin/windows64/contrib/2.15/ggbio_1.6.6.zip
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vignettes: vignettes/ggbio/inst/doc/ggbio.pdf
vignetteTitles: ggbio
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ggbio/inst/doc/autoplot.R,
vignettes/ggbio/inst/doc/chip-seq.R,
vignettes/ggbio/inst/doc/circular.R,
vignettes/ggbio/inst/doc/fake.R,
vignettes/ggbio/inst/doc/ggbio.R,
vignettes/ggbio/inst/doc/ideogram.R,
vignettes/ggbio/inst/doc/intro.R,
vignettes/ggbio/inst/doc/karyogram.R,
vignettes/ggbio/inst/doc/Manhattan.R,
vignettes/ggbio/inst/doc/mismatch.R,
vignettes/ggbio/inst/doc/rangeslinkedtodata.R,
vignettes/ggbio/inst/doc/tracks.R,
vignettes/ggbio/inst/doc/txdb.R
suggestsMe: gwascat
Package: GGtools
Version: 4.6.2
Depends: R (>= 2.14), stats4, GGBase (>= 3.19.7), IRanges,
GenomicRanges, Rsamtools
Imports: methods, utils, stats, BiocGenerics, snpStats, ff,
AnnotationDbi, Biobase, bit, VariantAnnotation
Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP.20111119
Enhances: MatrixEQTL
License: Artistic-2.0
Title: software and data for analyses in genetics of gene expression
Description: software and data for analyses in genetics of gene
expression
biocViews: Genetics, GeneExpression, GeneticVariability, SNP
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: bc707b416bad4184abdbfd7082cfaf10
source.ver: src/contrib/GGtools_4.6.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GGtools_4.6.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/GGtools_4.6.2.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GGtools/inst/doc/GGtools_2012.pdf
vignetteTitles: GGtools 2012: efficient tools for eQTL discovery
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GGtools/inst/doc/GGtools_2012.R
Package: girafe
Version: 1.10.1
Depends: R (>= 2.10.0), methods, IRanges (>= 1.3.53), Rsamtools,
ShortRead (>= 1.3.21), intervals (>= 0.13.1), genomeIntervals
(>= 1.7.3), grid
Imports: methods, Biobase, Biostrings, BSgenome, graphics, grDevices,
stats, utils, IRanges
Suggests: MASS, org.Mm.eg.db, RColorBrewer
Enhances: genomeIntervals
License: Artistic-2.0
Archs: i386, x64
Title: Genome Intervals and Read Alignments for Functional Exploration
Description: The package 'girafe' deals with the genome-level
representation of aligned reads from next-generation sequencing
data. It contains an object class for enabling a detailed
description of genome intervals with aligned reads and
functions for comparing, visualising, exporting and working
with such intervals and the aligned reads. As such, the package
interacts with and provides a link between the packages
ShortRead, IRanges and genomeIntervals.
biocViews: Sequencing, HighThroughputSequencing
Author: Joern Toedling, with contributions from Constance Ciaudo,
Olivier Voinnet, Edith Heard, Emmanuel Barillot, and Wolfgang
Huber
Maintainer: J. Toedling <j.toedling@imb-mainz.de>
MD5sum: c01b324a16c996fbfe68b2787508f619
source.ver: src/contrib/girafe_1.10.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/girafe_1.10.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/girafe_1.10.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/girafe_1.10.1.tgz
vignettes: vignettes/girafe/inst/doc/girafe.pdf
vignetteTitles: Genome intervals and read alignments for functional
exploration
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/girafe/inst/doc/girafe.R
dependsOnMe: HiTC
Package: GLAD
Version: 2.20.0
Depends: R (>= 2.10)
Suggests: aws, tcltk
License: GPL-2
Archs: i386, x64
Title: Gain and Loss Analysis of DNA
Description: Analysis of array CGH data : detection of breakpoints in
genomic profiles and assignment of a status (gain, normal or
loss) to each chromosomal regions identified.
biocViews: Microarray, CopyNumberVariants
Author: Philippe Hupe
Maintainer: Philippe Hupe <glad@curie.fr>
URL: http://bioinfo.curie.fr
SystemRequirements: gsl. Note: users should have GSL installed. Windows
users: 'consult the README file available in the inst directory
of the source distribution for necessary configuration
instructions'.
MD5sum: 2f4891c5cfd0600138ff1b022aba52df
source.ver: src/contrib/GLAD_2.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GLAD_2.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GLAD_2.20.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GLAD_2.20.0.tgz
vignettes: vignettes/GLAD/inst/doc/GLAD.pdf
vignetteTitles: GLAD
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GLAD/inst/doc/GLAD.R
dependsOnMe: ITALICS, MANOR
importsMe: ITALICS, MANOR, snapCGH
suggestsMe: ADaCGH2
Package: GlobalAncova
Version: 3.26.0
Depends: methods, corpcor, globaltest
Imports: annotate, AnnotationDbi
Suggests: Biobase, annotate, GO.db, KEGG.db, golubEsets, hu6800.db,
vsn, GSEABase, Rgraphviz
License: GPL (>= 2)
Archs: i386, x64
Title: Calculates a global test for differential gene expression
between groups
Description: We give the following arguments in support of the
GlobalAncova approach: After appropriate normalisation,
gene-expression-data appear rather symmetrical and outliers are
no real problem, so least squares should be rather robust.
ANCOVA with interaction yields saturated data modelling e.g.
different means per group and gene. Covariate adjustment can
help to correct for possible selection bias. Variance
homogeneity and uncorrelated residuals cannot be expected.
Application of ordinary least squares gives unbiased, but no
longer optimal estimates (Gauss-Markov-Aitken). Therefore,
using the classical F-test is inappropriate, due to
correlation. The test statistic however mirrors deviations from
the null hypothesis. In combination with a permutation
approach, empirical significance levels can be approximated.
Alternatively, an approximation yields asymptotic p-values.
This work was supported by the NGFN grant 01 GR 0459, BMBF,
Germany.
biocViews: Microarray, OneChannel, Bioinformatics,
DifferentialExpression, Pathways
Author: U. Mansmann, R. Meister, M. Hummel, R. Scheufele, with
contributions from S. Knueppel
Maintainer: Manuela Hummel <manuela.hummel@crg.eu>
MD5sum: 7b135f31e21927e49107920287fddbf5
source.ver: src/contrib/GlobalAncova_3.26.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GlobalAncova_3.26.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GlobalAncova_3.26.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/GlobalAncova_3.26.0.tgz
vignettes: vignettes/GlobalAncova/inst/doc/GlobalAncovaDecomp.pdf,
vignettes/GlobalAncova/inst/doc/GlobalAncova.pdf
vignetteTitles: GlobalAncovaDecomp.pdf, GlobalAncova.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GlobalAncova/inst/doc/GlobalAncovaDecomp.R,
vignettes/GlobalAncova/inst/doc/GlobalAncova.R
Package: globaltest
Version: 5.12.0
Depends: methods
Imports: Biobase (>= 2.5.5), survival, AnnotationDbi, annotate,
multtest, graphics
Suggests: vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db,
lungExpression, org.Hs.eg.db, annotate, Biobase (>= 2.5.5),
survival, GSEABase, penalized, gss, MASS, boot, rpart
License: GPL (>= 2)
Title: Testing groups of covariates/features for association with a
response variable, with applications to gene set testing
Description: The global test tests groups of covariates (or features)
for association with a response variable. This package
implements the test with diagnostic plots and multiple testing
utilities, along with several functions to facilitate the use
of this test for gene set testing of GO and KEGG terms.
biocViews: Microarray, OneChannel, Bioinformatics,
DifferentialExpression, GO, Pathways
Author: Jelle Goeman and Jan Oosting, with contributions by Livio Finos
and Aldo Solari
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>
URL: http://www.msbi.nl/goeman
MD5sum: 36957526c7ef9ca69931596b22f00a96
source.ver: src/contrib/globaltest_5.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/globaltest_5.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/globaltest_5.12.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/globaltest_5.12.0.tgz
vignettes: vignettes/globaltest/inst/doc/GlobalTest.pdf
vignetteTitles: Global Test
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/globaltest/inst/doc/GlobalTest_deprecated.R,
vignettes/globaltest/inst/doc/GlobalTest.R
dependsOnMe: GlobalAncova
importsMe: SIM
suggestsMe: topGO
Package: gmapR
Version: 1.0.0
Depends: R (>= 2.15.0), methods, GenomicRanges
Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15),
GenomicRanges, GenomicFeatures, Biostrings, VariantAnnotation,
tools, Biobase
Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Scerevisiae.UCSC.sacCer3, VariantAnnotation,
org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
BSgenome.Hsapiens.UCSC.hg19, LungCancerLines
License: Artistic-2.0
Title: Provides convenience methods to work with GMAP and GSNAP from
within R
Description: GSNAP and GMAP are a pair of tools to align short-read
data written by Tom Wu. This package provides convenience
methods to work with GMAP and GSNAP from within R. In addition,
it provides methods to tally alignment results on a
per-nucleotide basis using the bam_tally tool.
Author: Cory Barr, Thomas Wu, Michael Lawrence
Maintainer: Cory Barr <barr.cory@gene.com>
MD5sum: 0a8cd0a1ff17ec52c5665ceae6228a90
source.ver: src/contrib/gmapR_1.0.0.tar.gz
vignettes: vignettes/gmapR/inst/doc/gmapR.pdf
vignetteTitles: gmapR
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/gmapR/inst/doc/gmapR.R
dependsOnMe: HTSeqGenie
importsMe: VariantTools
Package: GOFunction
Version: 1.4.0
Depends: R (>= 2.11.0), methods, Biobase (>= 2.8.0), graph (>= 1.26.0),
Rgraphviz (>= 1.26.0), GO.db (>= 2.4.1), AnnotationDbi (>=
1.10.2), SparseM (>= 0.85)
Imports: methods, Biobase, graph, Rgraphviz, GO.db, AnnotationDbi,
SparseM
License: GPL (>= 2)
Title: GO-function: deriving biologcially relevant functions from
statistically significant functions
Description: The GO-function package provides a tool to address the
redundancy that result from the GO structure or multiple
annotation genes and derive biologically relevant functions
from the statistically significant functions based on some
intuitive assumption and statistical testing.
biocViews: GO, Pathways, Microarray, GeneSetEnrichment
Author: Jing Wang <jingwang.uestc@gmail.com>
Maintainer: Zheng Guo <guoz@ems.hrbmu.edu.cn>
MD5sum: 312ae67efb12ffe8b727f53478b44273
source.ver: src/contrib/GOFunction_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GOFunction_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GOFunction_1.4.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/GOFunction_1.4.0.tgz
vignettes: vignettes/GOFunction/inst/doc/GOFunction.pdf
vignetteTitles: GO-function
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GOFunction/inst/doc/GOFunction.R
Package: goProfiles
Version: 1.20.0
Depends: Biobase, AnnotationDbi, GO.db
Suggests: org.Hs.eg.db
License: GPL-2
Title: goProfiles: an R package for the statistical analysis of
functional profiles
Description: The package implements methods to compare lists of genes
based on comparing the corresponding 'functional profiles'.
biocViews: Microarray, GO
Author: Alex Sanchez, Jordi Ocana and Miquel Salicru
Maintainer: Alex Sanchez <asanchez@ub.edu>
MD5sum: 6b04464d9c10553a880adce884ca7e32
source.ver: src/contrib/goProfiles_1.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/goProfiles_1.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/goProfiles_1.20.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/goProfiles_1.20.0.tgz
vignettes: vignettes/goProfiles/inst/doc/goProfiles.pdf
vignetteTitles: goProfiles Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/goProfiles/inst/doc/goProfiles.R
Package: GOSemSim
Version: 1.16.1
Depends: R (>= 2.10), Rcpp
Imports: methods, AnnotationDbi, GO.db, org.Hs.eg.db
LinkingTo: Rcpp
Suggests: DOSE, clusterProfiler
License: GPL-2
Archs: i386, x64
Title: GO-terms Semantic Similarity Measures
Description: Implemented five methods proposed by Resnik, Schlicker,
Jiang, Lin and Wang respectively for estimating GO semantic
similarities. Support many species, including Anopheles,
Arabidopsis, Bovine, Canine, Chicken, Chimp, Coelicolor, E coli
strain K12 and Sakai, Fly, Human, Malaria, Mouse, Pig, Rhesus,
Rat, Worm, Xenopus, Yeast, and Zebrafish.
biocViews: GO, Clustering, Pathways, NetworkAnalysis
Author: Guangchuang Yu
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
URL: http://bioinformatics.oxfordjournals.org/content/26/7/976.full
MD5sum: bf4823b5f8d58a24aaf2d4f62e995edb
source.ver: src/contrib/GOSemSim_1.16.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GOSemSim_1.16.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/GOSemSim_1.16.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/GOSemSim_1.16.1.tgz
vignettes: vignettes/GOSemSim/inst/doc/GOSemSim.pdf
vignetteTitles: An introduction to GOSemSim
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GOSemSim/inst/doc/GOSemSim.R
importsMe: DOSE
suggestsMe: clusterProfiler, ReactomePA
Package: goseq
Version: 1.10.0
Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase
Imports: mgcv, graphics, stats, utils, AnnotationDbi
Suggests: GO.db, edgeR, org.Hs.eg.db
License: LGPL (>= 2)
Title: Gene Ontology analyser for RNA-seq and other length biased data
Description: Detects Gene Ontology and/or other user defined categories
which are over/under represented in RNA-seq data
biocViews: HighThroughputSequencingData, GO, GeneExpression,
Transcription, RNAseq
Author: Matthew Young
Maintainer: Matthew Young <myoung@wehi.edu.au>, Nadia Davidson
<nadia.davidson@mcri.edu.au>
MD5sum: 4568343d70df2b15964fbc3316d7676b
source.ver: src/contrib/goseq_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/goseq_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/goseq_1.10.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/goseq_1.10.0.tgz
vignettes: vignettes/goseq/inst/doc/goseq.pdf
vignetteTitles: goseq User's Guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/goseq/inst/doc/goseq.R
suggestsMe: oneChannelGUI
Package: GOstats
Version: 2.24.0
Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.3.26), graph
Imports: AnnotationDbi (>= 0.0.89), Biobase (>= 1.15.29), Category (>=
2.3.26), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), graph
(>= 1.15.15), methods, stats , AnnotationForge
Suggests: hgu95av2.db (>= 1.13.0), ALL, GO.db (>= 1.13.0), annotate,
multtest, genefilter, RColorBrewer, Rgraphviz, xtable, SparseM,
GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics
License: Artistic-2.0
Title: Tools for manipulating GO and microarrays.
Description: A set of tools for interacting with GO and microarray
data. A variety of basic manipulation tools for graphs,
hypothesis testing and other simple calculations.
biocViews: Bioinformatics, Annotation, GO, MultipleComparisons
Author: R. Gentleman and S. Falcon
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: 7530e5a062aa69555de8aaa00ac200a5
source.ver: src/contrib/GOstats_2.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GOstats_2.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GOstats_2.24.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/GOstats_2.24.0.tgz
vignettes:
vignettes/GOstats/inst/doc/GOstatsForUnsupportedOrganisms.pdf,
vignettes/GOstats/inst/doc/GOstatsHyperG.pdf,
vignettes/GOstats/inst/doc/GOvis.pdf
vignetteTitles: Hypergeometric tests for less common model organisms,
Hypergeometric Tests Using GOstats, Visualizing Data Using
GOstats
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GOstats/inst/doc/GOstatsHyperG.R,
vignettes/GOstats/inst/doc/GOvis.R
dependsOnMe: attract
importsMe: affycoretools, attract, categoryCompare
suggestsMe: BiocCaseStudies, Category, eisa, GSEAlm, HTSanalyzeR, MLP,
MmPalateMiRNA, oneChannelGUI, phenoDist, qpgraph, safe
Package: goTools
Version: 1.32.0
Depends: GO.db
Imports: AnnotationDbi, GO.db, graphics, grDevices
Suggests: hgu133a.db
License: GPL-2
Title: Functions for Gene Ontology database
Description: Wraper functions for description/comparison of oligo ID
list using Gene Ontology database
biocViews: Microarray,GO,Visualization
Author: Yee Hwa (Jean) Yang <jean@biostat.ucsf.edu>, Agnes Paquet
<paquetagnes@yahoo.com>
Maintainer: Agnes Paquet <paquetagnes@yahoo.com>
MD5sum: bf402f36354117cee1b0cc136a8464d8
source.ver: src/contrib/goTools_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/goTools_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/goTools_1.32.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/goTools_1.32.0.tgz
vignettes: vignettes/goTools/inst/doc/goTools.pdf
vignetteTitles: goTools overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/goTools/inst/doc/goTools.R
Package: gpls
Version: 1.30.0
Imports: stats
Suggests: MASS
License: Artistic-2.0
Title: Classification using generalized partial least squares
Description: Classification using generalized partial least squares for
two-group and multi-group (more than 2 group) classification.
biocViews: Bioinformatics, Classification, Microarray
Author: Beiying Ding
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: 6749928553dfd26d6c2de3c1847717d9
source.ver: src/contrib/gpls_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/gpls_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/gpls_1.30.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gpls_1.30.0.tgz
vignettes: vignettes/gpls/inst/doc/gpls.pdf
vignetteTitles: gpls Tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/gpls/inst/doc/gpls.R
suggestsMe: MCRestimate, MLInterfaces
Package: gprege
Version: 1.2.0
Depends: R (>= 2.8.0), gptk
Suggests: spam
License: AGPL-3
Title: Gaussian Process Ranking and Estimation of Gene Expression
time-series
Description: The gprege package implements the methodology described in
Kalaitzis & Lawrence (2011) "A simple approach to ranking
differentially expressed gene expression time-courses through
Gaussian process regression". The software fits two GPs with
the an RBF (+ noise diagonal) kernel on each profile. One GP
kernel is initialised wih a short lengthscale hyperparameter,
signal variance as the observed variance and a zero noise
variance. It is optimised via scaled conjugate gradients
(netlab). A second GP has fixed hyperparameters: zero
inverse-width, zero signal variance and noise variance as the
observed variance. The log-ratio of marginal likelihoods of the
two hypotheses acts as a score of differential expression for
the profile. Comparison via ROC curves is performed against
BATS (Angelini et.al, 2007). A detailed discussion of the
ranking approach and dataset used can be found in the paper
(http://www.biomedcentral.com/1471-2105/12/180).
biocViews: Microarray, Preprocessing, Bioinformatics,
DifferentialExpression, TimeCourse
Author: Alfredo A. Kalaitzis <alkalait@gmail.com>
Maintainer: Alfredo A. Kalaitzis <alkalait@gmail.com>
URL: http://staffwww.dcs.shef.ac.uk/people/A.Kalaitzis/
MD5sum: 367a3ccd7ab91b35a690575d421045b3
source.ver: src/contrib/gprege_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/gprege_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/gprege_1.2.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/gprege_1.2.0.tgz
vignettes: vignettes/gprege/inst/doc/gprege_quick.pdf
vignetteTitles: gprege Quick Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/gprege/inst/doc/gprege_quick.R
Package: graph
Version: 1.36.2
Depends: R (>= 2.10), methods
Imports: methods, stats, stats4, tools, utils, BiocGenerics (>= 0.1.11)
Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster
Enhances: Rgraphviz
License: Artistic-2.0
Archs: i386, x64
Title: graph: A package to handle graph data structures
Description: A package that implements some simple graph handling
capabilities.
biocViews: GraphsAndNetworks
Author: R. Gentleman, Elizabeth Whalen, W. Huber, S. Falcon
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: bf25376c51b9bb8fb67765c10bb6f765
source.ver: src/contrib/graph_1.36.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/graph_1.36.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/graph_1.36.2.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/graph_1.36.2.tgz
vignettes: vignettes/graph/inst/doc/clusterGraph.pdf,
vignettes/graph/inst/doc/graphAttributes.pdf,
vignettes/graph/inst/doc/GraphClass.pdf,
vignettes/graph/inst/doc/graph.pdf,
vignettes/graph/inst/doc/MultiGraphClass.pdf
vignetteTitles: clusterGraph and distGraph, Attributes for Graph
Objects, Graph Design, Graph, graphBAM and MultiGraph classes
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/graph/inst/doc/clusterGraph.R,
vignettes/graph/inst/doc/graphAttributes.R,
vignettes/graph/inst/doc/GraphClass.R,
vignettes/graph/inst/doc/graph.R,
vignettes/graph/inst/doc/MultiGraphClass.R
dependsOnMe: apComplex, biocGraph, BioMVCClass, BioNet, CellNOptR,
ddgraph, flowWorkspace, gage, gaggle, GeneNetworkBuilder,
GOFunction, GOstats, GraphAT, graphite, GSEABase, gwascat,
hyperdraw, hypergraph, KEGGgraph, maigesPack, NCIgraph, nem,
netresponse, pathRender, pkgDepTools, RbcBook1, RBGL, RBioinf,
RCytoscape, Rgraphviz, RpsiXML, Rtreemix, SRAdb, topGO
importsMe: biocGraph, biocViews, CAMERA, Category, categoryCompare,
DEGraph, flowCore, flowUtils, flowWorkspace, GeneAnswers,
GeneNetworkBuilder, GOFunction, GOstats, GraphAT, graphite,
GSEABase, HTSanalyzeR, KEGGgraph, keggorthology, NCIgraph, nem,
OrganismDbi, PCpheno, pkgDepTools, ppiStats, qpgraph,
RchyOptimyx, Rgraphviz, rsbml, Rtreemix, Streamer, topGO
suggestsMe: BiocCaseStudies, Category, categoryCompare, DEGraph,
EBcoexpress, ecolitk, MmPalateMiRNA, qpgraph, SPIA
Package: GraphAlignment
Version: 1.20.0
License: file LICENSE
Archs: i386, x64
Title: GraphAlignment
Description: Graph alignment is an extension package for the R
programming environment which provides functions for finding an
alignment between two networks based on link and node
similarity scores. (J. Berg and M. Laessig, "Cross-species
analysis of biological networks by Bayesian alignment", PNAS
103 (29), 10967-10972 (2006))
biocViews: GraphsAndNetworks, NetworkAnalysis
Author: Joern P. Meier <mail@ionflux.org>, Michal Kolar, Ville
Mustonen, Michael Laessig, and Johannes Berg.
Maintainer: Joern P. Meier <mail@ionflux.org>
URL: http://www.thp.uni-koeln.de/~berg/GraphAlignment/
MD5sum: 4c21615b1f2f837a88c275bbec81a390
source.ver: src/contrib/GraphAlignment_1.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GraphAlignment_1.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GraphAlignment_1.20.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GraphAlignment/inst/doc/align_principle2b1.pdf,
vignettes/GraphAlignment/inst/doc/align_principle2c1.pdf,
vignettes/GraphAlignment/inst/doc/align_principle_short1.pdf,
vignettes/GraphAlignment/inst/doc/a.pdf,
vignettes/GraphAlignment/inst/doc/binning-01a.pdf,
vignettes/GraphAlignment/inst/doc/GraphAlignment.pdf
vignetteTitles: align_principle2b1.pdf, align_principle2c1.pdf,
align_principle_short1.pdf, a.pdf, binning-01a.pdf,
GraphAlignment
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/GraphAlignment/inst/doc/GraphAlignment.R
Package: GraphAT
Version: 1.30.0
Depends: R (>= 2.10), graph, methods
Imports: graph, MCMCpack, methods, stats
License: LGPL
Title: Graph Theoretic Association Tests
Description: Functions and data used in Balasubramanian, et al. (2004)
biocViews: NetworkAnalysis, GraphsAndNetworks
Author: R. Balasubramanian, T. LaFramboise, D. Scholtens
Maintainer: Thomas LaFramboise <tlaframb@hsph.harvard.edu>
MD5sum: 0eea2a26fbe273097cb1d6a4612ae03f
source.ver: src/contrib/GraphAT_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GraphAT_1.30.0.zip
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: graphite
Version: 1.4.0
Depends: R (>= 2.10), graph
Imports: AnnotationDbi, graph, graphics, methods, org.Hs.eg.db, stats,
utils
Suggests: DEGraph (>= 1.4), hgu133plus2.db, RCytoscape (>= 1.6), SPIA
(>= 2.2), topologyGSA (>= 1.0)
License: AGPL-3
Title: GRAPH Interaction from pathway Topological Environment
Description: Graph objects from pathway topology derived from NCI,
KEGG, Biocarta and Reactome databases.
biocViews: Pathways, ConnectTools, GraphsAndNetworks
Author: Gabriele Sales <gabriele.sales@unipd.it>, Enrica Calura
<enrica.calura@gmail.com>, Chiara Romualdi
<chiara.romualdi@unipd.it>
Maintainer: Gabriele Sales <gabriele.sales@unipd.it>
MD5sum: b843bdd5db84a6a719336fd719bc3f0f
source.ver: src/contrib/graphite_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/graphite_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/graphite_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/graphite/inst/doc/graphite.pdf
vignetteTitles: GRAPH Interaction from pathway Topological Environment
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/graphite/inst/doc/graphite.R
Package: GRENITS
Version: 1.10.0
Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8),
ggplot2 (>= 0.9.0)
Imports: graphics, grDevices, reshape2, stats, utils
LinkingTo: Rcpp, RcppArmadillo
Suggests: network
License: GPL (>= 2)
Archs: i386, x64
Title: Gene Regulatory Network Inference Using Time Series
Description: The package offers four network inference statistical
models using Dynamic Bayesian Networks and Gibbs Variable
Selection: a linear interaction model, two linear interaction
models with added experimental noise (Gaussian and Student
distributed) for the case where replicates are available and a
non-linear interaction model.
biocViews: NetworkInference, GeneRegulation, TimeCourse,
GraphsAndNetworks
Author: Edward Morrissey
Maintainer: Edward Morrissey <edward.morrissey@gmail.com>
MD5sum: f608423bca1f467bd1572422125fcab4
source.ver: src/contrib/GRENITS_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GRENITS_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GRENITS_1.10.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GRENITS/inst/doc/GRENITS_package.pdf
vignetteTitles: GRENITS
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GRENITS/inst/doc/GRENITS_package.R
Package: GSEABase
Version: 1.20.2
Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8),
annotate, methods, graph
Imports: BiocGenerics, annotate, AnnotationDbi, Biobase, graph,
methods, XML
Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz
License: Artistic-2.0
Title: Gene set enrichment data structures and methods
Description: This package provides classes and methods to support Gene
Set Enrichment Analysis (GSEA).
biocViews: Infrastructure, Bioinformatics
Author: Martin Morgan, Seth Falcon, Robert Gentleman
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: 6eb22d9195f1d742afd9cb087031d179
source.ver: src/contrib/GSEABase_1.20.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GSEABase_1.20.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/GSEABase_1.20.2.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GSEABase/inst/doc/GSEABase.pdf
vignetteTitles: An introduction to GSEABase
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GSEABase/inst/doc/GSEABase.R
dependsOnMe: AGDEX, BicARE, gCMAP, GSVA, PROMISE
importsMe: Category, categoryCompare, cellHTS2, GSRI, GSVA,
HTSanalyzeR, PCpheno, phenoTest, PROMISE, ReportingTools
suggestsMe: BiocCaseStudies, categoryCompare, gage, GlobalAncova,
globaltest, GOstats, PGSEA, phenoTest
Package: GSEAlm
Version: 1.18.0
Depends: Biobase
Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db,
genefilter, GOstats, RColorBrewer
License: Artistic-2.0
Title: Linear Model Toolset for Gene Set Enrichment Analysis
Description: Models and methods for fitting linear models to gene
expression data, together with tools for computing and using
various regression diagnostics.
biocViews: Microarray, Bioinformatics
Author: Assaf Oron, Robert Gentleman (with contributions from S. Falcon
and Z. Jiang)
Maintainer: Assaf Oron <assaf@uw.edu>
MD5sum: 5918af9b11bc6ad26c64398bd760a746
source.ver: src/contrib/GSEAlm_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GSEAlm_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GSEAlm_1.18.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GSEAlm/inst/doc/GSEAlm.pdf
vignetteTitles: Linear models in GSEA
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GSEAlm/inst/doc/GSEAlm.R
importsMe: gCMAP
Package: GSRI
Version: 2.6.0
Depends: R (>= 2.14.2), fdrtool
Imports: methods, graphics, stats, utils, genefilter, Biobase,
GSEABase, les (>= 1.1.6)
Suggests: limma, hgu95av2.db
Enhances: multicore
License: GPL-3
Title: Gene Set Regulation Index
Description: The GSRI package estimates the number of differentially
expressed genes in gene sets, utilizing the concept of the Gene
Set Regulation Index (GSRI).
biocViews: Microarray, Transcription, DifferentialExpression, Genetics,
Bioinformatics
Author: Julian Gehring, Kilian Bartholome, Clemens Kreutz, Jens Timmer
Maintainer: Julian Gehring <julian.gehring@embl.de>
URL: http://julian-gehring.github.com/GSRI/
MD5sum: 833026887975f2a7e7bc834bb4a4b121
source.ver: src/contrib/GSRI_2.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GSRI_2.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/GSRI_2.6.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GSRI_2.6.0.tgz
vignettes: vignettes/GSRI/inst/doc/gsri.pdf
vignetteTitles: Introduction to the GSRI package: Estimating Regulatory
Effects utilizing the Gene Set Regulation Index
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/GSRI/inst/doc/gsri.R
Package: GSVA
Version: 1.6.6
Depends: R (>= 2.13.0), methods, GSEABase (>= 1.17.4)
Imports: methods, BiocGenerics, Biobase, GSEABase
Suggests: limma, RColorBrewer, genefilter, mclust, edgeR, GSVAdata
Enhances: snow, parallel
License: GPL (>= 2)
Archs: i386, x64
Title: Gene Set Variation Analysis for microarray and RNA-seq data
Description: Gene Set Variation Analysis (GSVA) is a non-parametric,
unsupervised method for estimating variation of gene set
enrichment through the samples of a expression data set. GSVA
performs a change in coordinate systems, transforming the data
from a gene by sample matrix to a gene-set by sample matrix,
thereby allowing the evaluation of pathway enrichment for each
sample. This new matrix of GSVA enrichment scores facilitates
applying standard analytical methods like functional
enrichment, survival analysis, clustering, CNV-pathway analysis
or cross-tissue pathway analysis, in a pathway-centric manner.
biocViews: Microarray, Pathways, GeneSetEnrichment
Author: Justin Guinney <justin.guinney@sagebase.org> (with
contributions from Robert Castelo <robert.castelo@upf.edu> and
Sonja Haenzelmann <sonjahaenzelmann@gmail.com>)
Maintainer: Justin Guinney <justin.guinney@sagebase.org>
URL: http://www.sagebase.org
MD5sum: cafb387a55ff0ea7929c4c5278f093ce
source.ver: src/contrib/GSVA_1.6.6.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GSVA_1.6.6.zip
win64.binary.ver: bin/windows64/contrib/2.15/GSVA_1.6.6.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GSVA_1.6.6.tgz
vignettes: vignettes/GSVA/inst/doc/GSVA.pdf
vignetteTitles: Gene Set Variation Analysis
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GSVA/inst/doc/GSVA.R
Package: Gviz
Version: 1.2.1
Depends: R (>= 2.10.0), methods, grid
Imports: IRanges (>= 1.13.19), rtracklayer (>= 1.15.5), lattice,
RColorBrewer, biomaRt (>= 2.11.0), GenomicRanges (>= 1.7.14),
AnnotationDbi (>= 1.17.11), Biobase (>= 2.15.3), BiocGenerics
(>= 0.1.4), GenomicFeatures (>= 1.9.7), BSgenome (>= 1.25.1),
Biostrings (>= 2.25.1), biovizBase (>= 1.5.7)
Suggests: xtable, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19
License: Artistic-2.0
Title: Plotting data and annotation information along genomic
coordinates
Description: Genomic data analyses requires integrated visualization of
known genomic information and new experimental data. Gviz uses
the biomaRt and the rtracklayer packages to perform live
annotation queries to Ensembl and UCSC and translates this to
e.g. gene/transcript structures in viewports of the grid
graphics package. This results in genomic information plotted
together with your data.
biocViews: Visualization, Microarray
Author: Florian Hahne, Steffen Durinck, Robert Ivanek, Arne Mueller,
Steve Lianoglou>
Maintainer: Florian Hahne <florian.hahne@novartis.com>
MD5sum: 24bb5af31cbc4195c274e8bd671c3751
source.ver: src/contrib/Gviz_1.2.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Gviz_1.2.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/Gviz_1.2.1.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Gviz_1.2.1.tgz
vignettes: vignettes/Gviz/inst/doc/Gviz.pdf,
vignettes/Gviz/inst/doc/ucsc1.pdf,
vignettes/Gviz/inst/doc/ucsc2.pdf
vignetteTitles: Gviz users guide, ucsc1.pdf, ucsc2.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Gviz/inst/doc/Gviz.R
dependsOnMe: cummeRbund
importsMe: methyAnalysis, PING
suggestsMe: gwascat
Package: gwascat
Version: 1.2.1
Depends: R (>= 2.14.0), methods, IRanges, GenomicRanges, snpStats,
graph, BiocGenerics
Imports: Biostrings
Suggests: DO.db, Gviz, ggbio, rtracklayer
Enhances: SNPlocs.Hsapiens.dbSNP.20111119, pd.genomewidesnp.6
License: Artistic-2.0
Title: representing and modeling data in the NHGRI GWAS catalog
Description: representing and modeling data in the NHGRI GWAS catalog
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: dbf9b89bf9f80086ba7c48fd6be0388b
source.ver: src/contrib/gwascat_1.2.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/gwascat_1.2.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/gwascat_1.2.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/gwascat/inst/doc/gwascat.pdf
vignetteTitles: gwascat -- exploring NHGRI GWAS catalog
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/gwascat/inst/doc/gwascat.R
Package: GWASTools
Version: 1.4.2
Depends: Biobase, ncdf, GWASExactHW, sandwich, gdsfmt
Imports: methods, DBI, RSQLite, DNAcopy, survival, lmtest, quantsmooth
Suggests: GWASdata, RUnit, SNPRelate, snpStats, VariantAnnotation
License: Artistic-2.0
Title: Tools for Genome Wide Association Studies
Description: Classes for storing very large GWAS data sets and
annotation, and functions for GWAS data cleaning and analysis.
biocViews: SNP, GeneticVariability, QualityControl, Microarray
Author: Stephanie M. Gogarten, Cathy Laurie, Tushar Bhangale, Matthew
P. Conomos, Cecelia Laurie, Caitlin McHugh, Ian Painter, Xiuwen
Zheng, Jess Shen, Rohit Swarnkar
Maintainer: Stephanie M. Gogarten <sdmorris@u.washington.edu>
MD5sum: 1f9a54055d2fae2992905f8fdb8d32ea
source.ver: src/contrib/GWASTools_1.4.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/GWASTools_1.4.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/GWASTools_1.4.2.zip
mac.binary.leopard.ver:
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vignettes: vignettes/GWASTools/inst/doc/Affymetrix.pdf,
vignettes/GWASTools/inst/doc/DataCleaning.pdf,
vignettes/GWASTools/inst/doc/Formats.pdf,
vignettes/GWASTools/inst/doc/VCF.pdf
vignetteTitles: Preparing Affymetrix Data, GWAS Data Cleaning, Data
formats in GWASTools, Converting VCF data for use in GWASTools
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/GWASTools/inst/doc/Affymetrix.R,
vignettes/GWASTools/inst/doc/DataCleaning.R,
vignettes/GWASTools/inst/doc/Formats.R,
vignettes/GWASTools/inst/doc/VCF.R
Package: hapFabia
Version: 1.0.6
Depends: R (>= 2.12.0), Biobase, fabia (>= 2.3.1)
Imports: methods, graphics, grDevices, stats, utils, KernSmooth
License: LGPL (>= 2.1)
Archs: i386, x64
Title: hapFabia: Identification of very short segments of identity by
descent (IBD) characterized by rare variants in large
sequencing data
Description: A package to identify very short IBD segments in large
sequencing data by FABIA biclustering. Two haplotypes are
identical by descent (IBD) if they share a segment that both
inherited from a common ancestor. Current IBD methods reliably
detect long IBD segments because many minor alleles in the
segment are concordant between the two haplotypes. However,
many cohort studies contain unrelated individuals which share
only short IBD segments. This package provides software to
identify short IBD segments in sequencing data. Knowledge of
short IBD segments are relevant for phasing of genotyping data,
association studies, and for population genetics, where they
shed light on the evolutionary history of humans. The package
supports VCF formats, is based on sparse matrix operations, and
provides visualization of haplotype clusters in different
formats.
biocViews: Genetics, GeneticVariability, SNP, Sequencing,
HighThroughputSequencing, Visualization, Clustering,
SequenceMatching, Homo_sapiens, Software
Author: Sepp Hochreiter <hochreit@bioinf.jku.at>
Maintainer: Sepp Hochreiter <hochreit@bioinf.jku.at>
URL: http://www.bioinf.jku.at/software/hapFabia/hapFabia.html
MD5sum: 8a078f2aa5f82b2f2bde86c338289f82
source.ver: src/contrib/hapFabia_1.0.6.tar.gz
win.binary.ver: bin/windows/contrib/2.15/hapFabia_1.0.6.zip
win64.binary.ver: bin/windows64/contrib/2.15/hapFabia_1.0.6.zip
mac.binary.leopard.ver:
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vignettes: vignettes/hapFabia/inst/doc/hapfabia.pdf
vignetteTitles: hapFabia: Manual for the R package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/hapFabia/inst/doc/hapfabia.R
Package: Harshlight
Version: 1.30.0
Depends: R (>= 2.10)
Imports: affy, altcdfenvs, Biobase, stats, utils
License: GPL (>= 2)
Archs: i386, x64
Title: A "corrective make-up" program for microarray chips
Description: The package is used to detect extended, diffuse and
compact blemishes on microarray chips. Harshlight automatically
marks the areas in a collection of chips (affybatch objects)
and a corrected AffyBatch object is returned, in which the
defected areas are substituted with NAs or the median of the
values of the same probe in the other chips in the collection.
The new version handle the substitute value as whole matrix to
solve the memory problem.
biocViews: Microarray, QualityControl, Preprocessing, AffymetrixChip,
ReportWriting
Author: Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkowski,
Marcelo O. Magnasco
Maintainer: Maurizio Pellegrino <mpellegri@berkeley.edu>
URL: http://asterion.rockefeller.edu/Harshlight/
MD5sum: 880e4c22d5297bc3782535c320c20838
source.ver: src/contrib/Harshlight_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Harshlight_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Harshlight_1.30.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Harshlight/inst/doc/Harshlight.pdf
vignetteTitles: Harshlight
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Harshlight/inst/doc/Harshlight.R
Package: Heatplus
Version: 2.4.0
Imports: graphics, grDevices, stats
Suggests: Biobase, hgu95av2.db, limma
License: GPL (>= 2)
Title: Heatmaps with row and/or column covariates and colored clusters
Description: Display a rectangular heatmap (intensity plot) of a data
matrix. By default, both samples (columns) and features (row)
of the matrix are sorted according to a hierarchical
clustering, and the corresponding dendrogram is plotted.
Optionally, panels with additional information about samples
and features can be added to the plot.
biocViews: Microarray, Visualization
Author: Alexander Ploner <Alexander.Ploner@ki.se>
Maintainer: Alexander Ploner <Alexander.Ploner@ki.se>
MD5sum: c71428fe38f6fa181635704c305935b6
source.ver: src/contrib/Heatplus_2.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Heatplus_2.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Heatplus_2.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Heatplus/inst/doc/annHeatmapCommentedSource.pdf,
vignettes/Heatplus/inst/doc/annHeatmap.pdf,
vignettes/Heatplus/inst/doc/oldHeatplus.pdf
vignetteTitles: Commented package source, Annotated and regular
heatmaps, Old functions (deprecated)
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Heatplus/inst/doc/annHeatmapCommentedSource.R,
vignettes/Heatplus/inst/doc/annHeatmap.R,
vignettes/Heatplus/inst/doc/oldHeatplus.R
dependsOnMe: GeneAnswers, phenoTest
Package: HELP
Version: 1.16.1
Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods
License: GPL (>= 2)
Title: Tools for HELP data analysis
Description: The package contains a modular pipeline for analysis of
HELP microarray data, and includes graphical and mathematical
tools with more general applications
biocViews: CpGIsland, DNAMethylation, Microarray, TwoChannel,
DataImport, QualityControl, Preprocessing, Visualization
Author: Reid F. Thompson <rthompso@aecom.yu.edu>, John M. Greally
<jgreally@aecom.yu.edu>, with contributions from Mark Reimers
<mreimers@vcu.edu>
Maintainer: Reid F. Thompson <rthompso@aecom.yu.edu>
MD5sum: 2bc77c138616f52637bd08719b33462d
source.ver: src/contrib/HELP_1.16.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/HELP_1.16.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/HELP_1.16.1.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HELP_1.16.1.tgz
vignettes: vignettes/HELP/inst/doc/HELP.pdf
vignetteTitles: 1. Primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HELP/inst/doc/HELP.R
Package: HEM
Version: 1.30.0
Depends: R (>= 2.1.0)
Imports: Biobase, grDevices, stats, utils
License: GPL (>= 2)
Archs: i386, x64
Title: Heterogeneous error model for identification of differentially
expressed genes under multiple conditions
Description: This package fits heterogeneous error models for analysis
of microarray data
biocViews: Microarray, DifferentialExpression, Bioinformatics
Author: HyungJun Cho <hcho@virginia.edu> and Jae K. Lee
<jaeklee@virginia.edu>
Maintainer: HyungJun Cho <hcho@virginia.edu>
URL:
http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/
MD5sum: 8724bedcde18ebcda3ddd94dd05fe7e1
source.ver: src/contrib/HEM_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/HEM_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/HEM_1.30.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HEM_1.30.0.tgz
vignettes: vignettes/HEM/inst/doc/HEM.pdf
vignetteTitles: HEM Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HEM/inst/doc/HEM.R
Package: HilbertVis
Version: 1.16.0
Depends: R (>= 2.6.0), grid, lattice
Suggests: IRanges, EBImage
License: GPL (>= 3)
Archs: i386, x64
Title: Hilbert curve visualization
Description: Functions to visualize long vectors of integer data by
means of Hilbert curves
biocViews: Visualization
Author: Simon Anders <sanders@fs.tum.de>
Maintainer: Simon Anders <sanders@fs.tum.de>
URL: http://www.ebi.ac.uk/~anders/hilbert
MD5sum: c01bec820963ab1678bea22d1e85c41b
source.ver: src/contrib/HilbertVis_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/HilbertVis_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/HilbertVis_1.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/HilbertVis/inst/doc/HilbertDisplay_GUI.pdf,
vignettes/HilbertVis/inst/doc/HilbertVis.pdf,
vignettes/HilbertVis/inst/doc/ThreeChTest.pdf
vignetteTitles: HilbertDisplay_GUI.pdf, Visualising very long data
vectors with the Hilbert curve, ThreeChTest.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HilbertVis/inst/doc/HilbertVis.R
dependsOnMe: HilbertVisGUI
importsMe: ChIPseqR
Package: HilbertVisGUI
Version: 1.16.0
Depends: R (>= 2.6.0), HilbertVis (>= 1.1.6)
Suggests: lattice, IRanges
License: GPL (>= 3)
Archs: i386, x64
Title: HilbertVisGUI
Description: An interactive tool to visualize long vectors of integer
data by means of Hilbert curves
biocViews: Visualization
Author: Simon Anders <sanders@fs.tum.de>
Maintainer: Simon Anders <sanders@fs.tum.de>
URL: http://www.ebi.ac.uk/~anders/hilbert
SystemRequirements: gtkmm-2.4
MD5sum: 39eef101ff3b3bd1551087004b7d453e
source.ver: src/contrib/HilbertVisGUI_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/HilbertVisGUI_1.16.0.zip
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vignettes: vignettes/HilbertVisGUI/inst/doc/HilbertVisGUI.pdf
vignetteTitles: See vignette in package HilbertVis
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: TRUE
hasLICENSE: FALSE
Rfiles: vignettes/HilbertVisGUI/inst/doc/HilbertVisGUI.R
Package: HiTC
Version: 1.2.0
Depends: R (>= 2.10.0), methods, girafe (>= 1.3.1), genomeIntervals (>=
1.7.1), RColorBrewer
Imports: methods, Biobase, Biostrings, graphics, grDevices, ShortRead
License: Artistic-2.0
Title: High Throughput Chromosome Conformation Capture analysis
Description: The HiTC package was developed to explore high-throughput
'C' data such as 5C or Hi-C.
biocViews: Sequencing, HighThroughputSequencing
Author: Nicolas Servant
Maintainer: Nicolas Servant <nicolas.servant@curie.fr>
MD5sum: 62fd8b518c55cf7d6f9236745f0efd25
source.ver: src/contrib/HiTC_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/HiTC_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/HiTC_1.2.0.zip
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vignettes: vignettes/HiTC/inst/doc/HiTC.pdf
vignetteTitles: Hight-Throughput Chromosome Conformation Capture
analysis
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HiTC/inst/doc/HiTC.R
Package: HMMcopy
Version: 1.0.0
Depends: R (>= 2.10.0), IRanges (>= 1.4.16), geneplotter (>= 1.24.0)
License: GPL-3
Archs: i386, x64
Title: Copy number prediction with correction for GC and mappability
bias for HTS data
Description: Corrects GC and mappability biases for readcounts (i.e.
coverage) in non-overlapping windows of fixed length for single
whole genome samples, yielding a rough estimate of copy number
for furthur analysis. Designed for rapid correction of high
coverage whole genome tumour and normal samples.
biocViews: Sequencing, Preprocessing, Visualization,
CopyNumberVariants, HighThroughputSequencing, Microarray
Author: Daniel Lai, Gavin Ha, Sohrab Shah
Maintainer: Daniel Lai <jujubix@cs.ubc.ca>, Gavin Ha <gha@bccrc.ca>,
Sohrab Shah <sshah@bccrc.ca>
MD5sum: d1c03c527febbfce6ec31815954042f5
source.ver: src/contrib/HMMcopy_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/HMMcopy_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/HMMcopy_1.0.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/HMMcopy/inst/doc/HMMcopy.pdf
vignetteTitles: HMMcopy
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HMMcopy/inst/doc/HMMcopy.R
Package: hopach
Version: 2.18.0
Depends: R (>= 2.11.0), cluster, Biobase, methods
Imports: Biobase, cluster, graphics, grDevices, methods, stats, utils
License: GPL (>= 2)
Archs: i386, x64
Title: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Description: The HOPACH clustering algorithm builds a hierarchical tree
of clusters by recursively partitioning a data set, while
ordering and possibly collapsing clusters at each level. The
algorithm uses the Mean/Median Split Silhouette (MSS) criteria
to identify the level of the tree with maximally homogeneous
clusters. It also runs the tree down to produce a final ordered
list of the elements. The non-parametric bootstrap allows one
to estimate the probability that each element belongs to each
cluster (fuzzy clustering).
biocViews: Clustering
Author: Katherine S. Pollard, with Mark J. van der Laan
<laan@stat.berkeley.edu> and Greg Wall
Maintainer: Katherine S. Pollard <katherine.pollard@gladstone.ucsf.edu>
URL: http://www.stat.berkeley.edu/~laan/, http://docpollard.org/
MD5sum: efcf3b7a3420b6e5c62ab8ec4ea5ab21
source.ver: src/contrib/hopach_2.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/hopach_2.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/hopach_2.18.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/hopach/inst/doc/bootplot.pdf,
vignettes/hopach/inst/doc/dplot.pdf,
vignettes/hopach/inst/doc/hopachManuscript.pdf,
vignettes/hopach/inst/doc/hopach.pdf,
vignettes/hopach/inst/doc/MSS.pdf
vignetteTitles: bootplot.pdf, dplot.pdf, hopachManuscript.pdf, hopach,
MSS.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/hopach/inst/doc/hopach.R
importsMe: phenoTest
suggestsMe: BiocCaseStudies
Package: hpar
Version: 1.0.1
Depends: R (>= 2.15)
Suggests: org.Hs.eg.db, GO.db, knitr
License: Artistic-2.0
Title: Human Protein Atlas in R
Description: A simple interface to and data from the Human Protein
Atlas project.
biocViews: Bioinformatics, Proteomics, Homo_sapiens, CellBiology
Author: Laurent Gatto
Maintainer: Laurent Gatto <lg390@cam.ac.uk>
MD5sum: c9c7173234320af0fce1849a3343093f
source.ver: src/contrib/hpar_1.0.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/hpar_1.0.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/hpar_1.0.1.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hpar_1.0.1.tgz
vignettes: vignettes/hpar/inst/doc/hpar.pdf
vignetteTitles: hpar
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/hpar/inst/doc/hpar.R
Package: HTqPCR
Version: 1.12.0
Depends: Biobase, RColorBrewer, limma
Imports: affy, Biobase, gplots, graphics, grDevices, limma, methods,
RColorBrewer, stats, stats4, utils
Suggests: statmod
License: Artistic-2.0
Title: Automated analysis of high-throughput qPCR data
Description: Analysis of Ct values from high throughput quantitative
real-time PCR (qPCR) assays across multiple conditions or
replicates. The input data can be from spatially-defined
formats such ABI TaqMan Low Density Arrays or OpenArray;
LightCycler from Roche Applied Science; the CFX plates from
Bio-Rad Laboratories; conventional 96- or 384-well plates; or
microfluidic devices such as the Dynamic Arrays from Fluidigm
Corporation. HTqPCR handles data loading, quality assessment,
normalization, visualization and parametric or non-parametric
testing for statistical significance in Ct values between
features (e.g. genes, microRNAs).
biocViews: MicrotitrePlateAssay, DifferentialExpression,
GeneExpression, DataImport, QualityControl, Preprocessing,
Bioinformatics, Visualization, MultipleComparisons, qPCR
Author: Heidi Dvinge, Paul Bertone
Maintainer: Heidi Dvinge <heidi@ebi.ac.uk>
URL: http://www.ebi.ac.uk/bertone/software
MD5sum: 73c267cc48f72d39f17c899f3edac536
source.ver: src/contrib/HTqPCR_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/HTqPCR_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/HTqPCR_1.12.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/HTqPCR/inst/doc/HTqPCR.pdf
vignetteTitles: qPCR analysis in R
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HTqPCR/inst/doc/HTqPCR.R
Package: HTSanalyzeR
Version: 2.10.0
Depends: R (>= 2.15), igraph0, methods
Imports: graph, igraph0, GSEABase, BioNet, cellHTS2, AnnotationDbi,
biomaRt, RankProd
Suggests: KEGG.db, GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db,
org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow
License: Artistic-2.0
Title: Gene set over-representation, enrichment and network analyses
for high-throughput screens
Description: This package provides classes and methods for gene set
over-representation, enrichment and network analyses on
high-throughput screens. The over-representation analysis is
performed based on hypergeometric tests. The enrichment
analysis is based on the GSEA algorithm (Subramanian et al.
PNAS 2005). The network analysis identifies enriched
subnetworks based on algorithms from the BioNet package
(Beisser et al., Bioinformatics 2010). A pipeline is also
specifically designed for cellHTS2 object to perform
integrative network analyses of high-throughput RNA
interference screens. The users can build their own analysis
pipeline for their own data set based on this package.
biocViews: CellBasedAssays, Bioinformatics, MultipleComparisons
Author: Xin Wang <Xin.Wang@cancer.org.uk>, Camille Terfve
<cdat2@cam.ac.uk>, John C. Rose <jcr53@cam.ac.uk>, Florian
Markowetz <Florian.Markowetz@cancer.org.uk>
Maintainer: Xin Wang <Xin.Wang@cancer.org.uk>
MD5sum: c596c41d5918d48ff962fa95c616be11
source.ver: src/contrib/HTSanalyzeR_2.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/HTSanalyzeR_2.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/HTSanalyzeR_2.10.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/HTSanalyzeR_2.10.0.tgz
vignettes: vignettes/HTSanalyzeR/inst/doc/Figure.pdf,
vignettes/HTSanalyzeR/inst/doc/HTSanalyzeR-Vignette.pdf
vignetteTitles: Figure.pdf, Main vignette:Gene set enrichment and
network analysis of high-throughput RNAi screen data using
HTSanalyzeR
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HTSanalyzeR/inst/doc/HTSanalyzeR-Vignette.R
importsMe: phenoTest
Package: HTSeqGenie
Version: 1.0.0
Depends: R (>= 2.15.0), ShortRead (>= 1.14.4), parallel, hwriter,
Cairo, tools, gmapR (>= 0.99.23), logging
Imports: BiocGenerics (>= 0.2.0), IRanges (>= 1.14.3), GenomicRanges
(>= 1.7.12), Rsamtools (>= 1.8.5), Biostrings (>= 2.24.1),
chipseq (>= 1.7.1), rtracklayer (>= 1.17.19), GenomicFeatures
(>= 1.9.31)
Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, GenomicFeatures,
LungCancerLines, org.Hs.eg.db
License: Artistic-2.0
Title: High-throughput sequencing data analysis pipeline.
Description: A software package to analyse high-throughput sequencing
experiments
Author: Gregoire Pau, Cory Barr, Jens Reeder, Michael Lawrence,
Jeremiah Degenhardt, Tom Wu, Melanie Huntley, Matt Brauer
Maintainer: Gregoire Pau <pau.gregoire@gene.com>
MD5sum: 6fa594d206683ba5de58b55c2d20e5c9
source.ver: src/contrib/HTSeqGenie_1.0.0.tar.gz
vignettes: vignettes/HTSeqGenie/inst/doc/HTSeqGenie.pdf
vignetteTitles: gmapR
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HTSeqGenie/inst/doc/HTSeqGenie.R
Package: htSeqTools
Version: 1.4.0
Depends: R (>= 2.12.2), methods, BiocGenerics (>= 0.1.0), Biobase,
IRanges, methods, MASS, BSgenome, GenomicRanges
Enhances: multicore
License: GPL (>=2)
Title: Quality Control, Visualization and Processing for
High-Throughput Sequencing data
Description: We provide efficient, easy-to-use tools for
High-Throughput Sequencing (ChIP-seq, RNAseq etc.). These
include MDS plots (analogues to PCA), detecting inefficient
immuno-precipitation or over-amplification artifacts, tools to
identify and test for genomic regions with large accumulation
of reads, and visualization of coverage profiles.
biocViews: HighThroughputSequencing,QualityControl
Author: Evarist Planet, Camille Stephan-Otto, Oscar Reina, Oscar
Flores, David Rossell
Maintainer: Oscar Reina <oscar.reina@irbbarcelona.org>
MD5sum: b6f26207649b369167875c0ea727fa94
source.ver: src/contrib/htSeqTools_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/htSeqTools_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/htSeqTools_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/htSeqTools/inst/doc/htSeqTools.pdf
vignetteTitles: Manual for the htSeqTools library
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/htSeqTools/inst/doc/htSeqTools.R
Package: HybridMTest
Version: 1.2.0
Depends: R (>= 2.9.0), Biobase, fdrtool, MASS, survival
Imports: stats
License: GPL Version 2 or later
Title: Hybrid Multiple Testing
Description: Performs hybrid multiple testing that incorporates method
selection and assumption evaluations into the analysis using
empirical Bayes probability (EBP) estimates obtained by
Grenander density estimation. For instance, for 3-group
comparison analysis, Hybrid Multiple testing considers EBPs as
weighted EBPs between F-test and H-test with EBPs from Shapiro
Wilk test of normality as weigth. Instead of just using EBPs
from F-test only or using H-test only, this methodology
combines both types of EBPs through EBPs from Shapiro Wilk test
of normality. This methodology uses then the law of total EBPs.
biocViews: GeneExpression, Genetics, Bioinformatics, Microarray
Author: Stan Pounds <stanley.pounds@stjude.org>, Demba Fofana
<demba.fofana@stjude.org>
Maintainer: Demba Fofana <demba.fofana@stjude.org>
MD5sum: 45a9cbf37e9a80c8aff4f1730115e07d
source.ver: src/contrib/HybridMTest_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/HybridMTest_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/HybridMTest_1.2.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/HybridMTest_1.2.0.tgz
vignettes: vignettes/HybridMTest/inst/doc/HybridMTest.pdf
vignetteTitles: Hybrid Multiple Testing
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/HybridMTest/inst/doc/HybridMTest.R
Package: hyperdraw
Version: 1.10.0
Depends: R (>= 2.9.0), methods, grid, graph, hypergraph, Rgraphviz
Imports: stats4
License: GPL (>= 2)
Title: Visualizing Hypergaphs
Description: Functions for visualizing hypergraphs.
biocViews: NetworkVisualization, GraphsAndNetworks
Author: Paul Murrell
Maintainer: Paul Murrell <p.murrell@auckland.ac.nz>
SystemRequirements: graphviz
MD5sum: b393a59e32a2d7d5def3dff627fd503f
source.ver: src/contrib/hyperdraw_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/hyperdraw_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/hyperdraw_1.10.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/hyperdraw/inst/doc/hyperdraw.pdf
vignetteTitles: Hyperdraw
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/hyperdraw/inst/doc/hyperdraw.R
Package: hypergraph
Version: 1.30.0
Depends: R (>= 2.1.0), methods, graph
License: Artistic-2.0
Title: A package providing hypergraph data structures
Description: A package that implements some simple capabilities for
representing and manipulating hypergraphs.
biocViews: GraphsAndNetworks
Author: Seth Falcon, Robert Gentleman
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: b2aa1392197faa55049c4e8adb4d93ee
source.ver: src/contrib/hypergraph_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/hypergraph_1.30.0.zip
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: altcdfenvs, hyperdraw, RpsiXML
Package: iASeq
Version: 1.2.0
Depends: R (>= 2.14.1)
Imports: graphics, grDevices
License: GPL-2
Title: iASeq: integrating multiple sequencing datasets for detecting
allele-specific events
Description: It fits correlation motif model to multiple RNAseq or
ChIPseq studies to improve detection of allele-specific events
and describe correlation patterns across studies.
biocViews: SNP, RNAseq, ChIPseq, Bioinformatics
Author: Yingying Wei, Hongkai Ji
Maintainer: Yingying Wei <ywei@jhsph.edu>
MD5sum: 5d57c79e8cdd710e5070fbb6d9fe418e
source.ver: src/contrib/iASeq_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/iASeq_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/iASeq_1.2.0.zip
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vignettes: vignettes/iASeq/inst/doc/iASeqVignette.pdf
vignetteTitles: iASeq Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/iASeq/inst/doc/iASeqVignette.R
Package: iBBiG
Version: 1.2.0
Depends: biclust
Imports: stats4,xtable,ade4
Suggests: methods
License: Artistic-2.0
Archs: i386, x64
Title: Iterative Binary Biclustering of Genesets
Description: iBBiG is a bi-clustering algorithm which is optimizes for
binary data analysis. We apply it to meta-gene set analysis of
large numbers of gene expression datasets. The iterative
algorithm extracts groups of phenotypes from multiple studies
that are associated with similar gene sets. iBBiG does not
require prior knowledge of the number or scale of clusters and
allows discovery of clusters with diverse sizes
biocViews: Clustering, Annotation, GeneSetEnrichment
Author: Daniel Gusenleitner, Aedin Culhane
Maintainer: Aedin Culhane <aedin@jimmy.harvard.edu>
URL: http://bcb.dfci.harvard.edu/~aedin/publications/
MD5sum: a78d604d83623d6f08839fa31e5c7e7c
source.ver: src/contrib/iBBiG_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/iBBiG_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/iBBiG_1.2.0.zip
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vignettes: vignettes/iBBiG/inst/doc/tutorial.pdf
vignetteTitles: iBBiG User Manual
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/iBBiG/inst/doc/tutorial.R
Package: ibh
Version: 1.6.0
Depends: simpIntLists
Suggests: yeastCC, stats
License: GPL (>= 2)
Title: Interaction Based Homogeneity for Evaluating Gene Lists
Description: This package contains methods for calculating Interaction
Based Homogeneity to evaluate fitness of gene lists to an
interaction network which is useful for evaluation of
clustering results and gene list analysis. BioGRID interactions
are used in the calculation. The user can also provide their
own interactions.
biocViews: QualityControl, DataImport, GraphsAndNetworks,
NetworkEnrichment
Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin Atalay.
Maintainer: Kircicegi Korkmaz <e102771@ceng.metu.edu.tr>
MD5sum: 494a7908468f187b804f18c95977b2ba
source.ver: src/contrib/ibh_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ibh_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ibh_1.6.0.zip
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vignettes: vignettes/ibh/inst/doc/ibh.pdf
vignetteTitles: ibh
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ibh/inst/doc/ibh.R
Package: Icens
Version: 1.30.0
Depends: survival
Imports: graphics
License: Artistic-2.0
Title: NPMLE for Censored and Truncated Data
Description: Many functions for computing the NPMLE for censored and
truncated data.
biocViews: Bioinformatics, Infrastructure
Author: R. Gentleman and Alain Vandal
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: ac1ce285046dd473fef924bab9f2d1e6
source.ver: src/contrib/Icens_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Icens_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Icens_1.30.0.zip
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: PROcess
importsMe: PROcess
Package: iChip
Version: 1.12.0
Depends: R (>= 2.10.0)
Imports: limma
License: GPL (>= 2)
Archs: i386, x64
Title: Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
Description: This package uses hidden Ising models to identify enriched
genomic regions in ChIP-chip data. It can be used to analyze
the data from multiple platforms (e.g., Affymetrix, Agilent,
and NimbleGen), and the data with single to multiple
replicates.
biocViews: ChIPchip, NimbleGen, Affymetrix, Agilent,Microarray,
Bioinformatics
Author: Qianxing Mo
Maintainer: Qianxing Mo <qmo@bcm.edu>
MD5sum: b0bc7730ffd848f3a54de85cdb048d96
source.ver: src/contrib/iChip_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/iChip_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/iChip_1.12.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/iChip/inst/doc/iChip.pdf
vignetteTitles: iChip
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/iChip/inst/doc/iChip.R
Package: idiogram
Version: 1.34.0
Depends: R (>= 2.10), methods, Biobase, annotate, plotrix
Suggests: hu6800.db, hgu95av2.db, golubEsets
License: GPL-2
Title: idiogram
Description: A package for plotting genomic data by chromosomal
location
biocViews: Visualization
Author: Karl J. Dykema <karl.dykema@vai.org>
Maintainer: Karl J. Dykema <karl.dykema@vai.org>
MD5sum: 5356025a6c22d553013101b3b14b2e14
source.ver: src/contrib/idiogram_1.34.0.tar.gz
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mac.binary.leopard.ver:
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vignettes: vignettes/idiogram/inst/doc/idiogram.pdf
vignetteTitles: HOWTO: idiogram
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/idiogram/inst/doc/idiogram.R
dependsOnMe: reb
Package: IdMappingAnalysis
Version: 1.2.1
Depends: R (>= 2.14), R.oo (>= 1.10.1), rChoiceDialogs
Imports: boot, mclust, RColorBrewer, Biobase
License: GPL-2
Title: ID Mapping Analysis
Description: Identifier mapping performance analysis
biocViews: Bioinformatics, Annotation, MultipleComparisons
Author: Alex Lisovich, Roger Day
Maintainer: Alex Lisovich <alex.lisovich@gmail.com>, Roger Day
<day01@pitt.edu>
MD5sum: 847750c422f160cbc38941c9c23594e7
source.ver: src/contrib/IdMappingAnalysis_1.2.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/IdMappingAnalysis_1.2.1.zip
win64.binary.ver:
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mac.binary.leopard.ver:
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vignettes: vignettes/IdMappingAnalysis/inst/doc/IdMappingAnalysis.pdf
vignetteTitles: Critically comparing identifier maps retrieved from
bioinformatics annotation resources.
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/IdMappingAnalysis/inst/doc/IdMappingAnalysis.R
Package: IdMappingRetrieval
Version: 1.4.0
Depends: R.oo, XML, RCurl, rChoiceDialogs, ENVISIONQuery
Imports: biomaRt, ENVISIONQuery, DAVIDQuery, AffyCompatible,
R.methodsS3, R.oo, utils
License: GPL-2
Title: ID Mapping Data Retrieval
Description: Data retrieval for identifier mapping performance analysis
biocViews: Bioinformatics, Annotation, MultipleComparisons
Author: Alex Lisovich, Roger Day
Maintainer: Alex Lisovich <all67@pitt.edu>, Roger Day <day01@pitt.edu>
MD5sum: 395bb70d48a75ddecd1338e23d8832d9
source.ver: src/contrib/IdMappingRetrieval_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/IdMappingRetrieval_1.4.0.zip
win64.binary.ver:
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mac.binary.leopard.ver:
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vignettes: vignettes/IdMappingRetrieval/inst/doc/IdMappingRetrieval.pdf
vignetteTitles: Collection and subsequent fast retrieval of identifier
mapping related information from various online sources.
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/IdMappingRetrieval/inst/doc/IdMappingRetrieval.R
Package: iFlow
Version: 2.10.0
Depends: R (>= 2.13.0), flowCore, flowViz, flowStats (>= 1.3.20)
Imports: Biobase, RGtk2, cairoDevice, flowCore, flowStats, flowViz,
grDevices, graphics, methods, utils
License: Artistic-2.0
Title: GUI based visualization for flow cytometry
Description: Tool to explore and visualize flow cytometry
biocViews: FlowCytometry, Bioinformatics, GUI
Author: Kyongryun Lee, Florian Hahne, Deepayan Sarkar
Maintainer: Kyongryun Lee <kyongryun.lee@gmail.com>
URL: http://www.hindawi.com/journals/abi/2009/103839.html
MD5sum: 96122598272bbf583a3facadecd6825b
source.ver: src/contrib/iFlow_2.10.0.tar.gz
mac.binary.leopard.ver:
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vignettes: vignettes/iFlow/inst/doc/iflow.pdf
vignetteTitles: How to iFlow
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/iFlow/inst/doc/iflow.R
Package: imageHTS
Version: 1.8.0
Depends: R (>= 2.9.0), EBImage (>= 3.99.17), cellHTS2 (>= 2.10.0)
Imports: tools, Biobase, hwriter, methods, vsn, stats, utils, e1071
Suggests: MASS
License: LGPL-2.1
Title: Analysis of high-throughput microscopy-based screens
Description: imageHTS is an R package dedicated to the analysis of
high-throughput microscopy-based screens. The package provides
a modular and extensible framework to segment cells, extract
quantitative cell features, predict cell types and browse
screen data through web interfaces. Designed to operate in
distributed environments, imageHTS provides a standardized
access to remote data and facilitates the dissemination of
high-throughput microscopy-based datasets.
biocViews: CellBasedAssays, Visualization, Preprocessing
Author: Gregoire Pau, Xian Zhang, Michael Boutros, Wolfgang Huber
Maintainer: Gregoire Pau <gregoire.pau@embl.de>
MD5sum: fdf7b446e023edca4561cca3d1918340
source.ver: src/contrib/imageHTS_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/imageHTS_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/imageHTS_1.8.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/imageHTS_1.8.0.tgz
vignettes: vignettes/imageHTS/inst/doc/imageHTS-introduction.pdf
vignetteTitles: Analysis of high-throughput microscopy-based screens
with imageHTS
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/imageHTS/inst/doc/imageHTS-introduction.R
dependsOnMe: phenoDist
Package: impute
Version: 1.32.0
Depends: R (>= 2.10)
License: GPL-2
Archs: i386, x64
Title: impute: Imputation for microarray data
Description: Imputation for microarray data (currently KNN only)
biocViews: Bioinformatics, Microarray
Author: Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan,
Gilbert Chu
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
MD5sum: 0964c072590885b349bc68dc295497ee
source.ver: src/contrib/impute_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/impute_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/impute_1.32.0.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: BioNet
Package: inSilicoDb
Version: 1.7.4
Depends: R (>= 2.11.0), rjson, Biobase
Imports: RCurl
Suggests: limma
License: GPL-2
Title: Access to the InSilico Database
Description: Access Human Affymetrix expert curated Gene Expression
Omnibus (GEO) datasets from the InSilico Database.
biocViews: Microarray, DataImport
Author: Jonatan Taminau <jtaminau@vub.ac.be>
Maintainer: Jonatan Taminau <jtaminau@vub.ac.be>, David Steenhoff
<davidsteenhoff@insilicodb.org>
URL: https://insilicodb.org
MD5sum: 513b496fdb6f09d87a8ab80e2dbbeba2
source.ver: src/contrib/inSilicoDb_1.7.4.tar.gz
win.binary.ver: bin/windows/contrib/2.15/inSilicoDb_1.7.4.zip
win64.binary.ver: bin/windows64/contrib/2.15/inSilicoDb_1.7.4.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/inSilicoDb_1.7.4.tgz
vignettes: vignettes/inSilicoDb/inst/doc/inSilicoDb.pdf
vignetteTitles: Using the inSilicoDb package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/inSilicoDb/inst/doc/inSilicoDb.R
suggestsMe: inSilicoMerging
Package: inSilicoMerging
Version: 1.2.3
Depends: R (>= 2.11.1), Biobase, DWD, limma
Imports: amap, moments
Suggests: BiocGenerics, inSilicoDb
License: GPL-2
Title: Collection of Merging Techniques for Gene Expression Data
Description: Collection of techniques to remove inter-study bias when
combining gene expression data originating from different
studies.
biocViews: Microarray
Author: Jonatan Taminau <jtaminau@vub.ac.be>, Stijn Meganck
<smeganck@vub.ac.be>, Cosmin Lazar <vlazar@vub.ac.be>
Maintainer: Jonatan Taminau <jtaminau@vub.ac.be>, Stijn Meganck
<smeganck@vub.ac.be>, Cosmin Lazar <vlazar@vub.ac.be>
URL: https://insilicodb.org/
MD5sum: 3ad0e3cc74013174a43011da5c2d8ec0
source.ver: src/contrib/inSilicoMerging_1.2.3.tar.gz
win.binary.ver: bin/windows/contrib/2.15/inSilicoMerging_1.2.3.zip
win64.binary.ver: bin/windows64/contrib/2.15/inSilicoMerging_1.2.3.zip
mac.binary.leopard.ver:
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vignettes: vignettes/inSilicoMerging/inst/doc/inSilicoMerging.pdf
vignetteTitles: Using the inSilicoMerging package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/inSilicoMerging/inst/doc/inSilicoMerging.R
Package: inveRsion
Version: 1.6.0
Depends: methods, haplo.stats
Imports: graphics, methods, utils
License: GPL (>= 2)
Archs: i386, x64
Title: Inversions in genotype data
Description: Package to find genetic inversions in genotype (SNP array)
data.
biocViews: Microarray, SNP
Author: Alejandro Caceres
Maintainer: Alejandro Caceres <acaceres@creal.cat>
MD5sum: 9feb21f975d085c4dc21be655b71dbca
source.ver: src/contrib/inveRsion_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/inveRsion_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/inveRsion_1.6.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/inveRsion/inst/doc/inveRsion.pdf,
vignettes/inveRsion/inst/doc/Manual.pdf
vignetteTitles: Quick start guide for inveRsion package, Manual.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/inveRsion/inst/doc/inveRsion.R
Package: iontree
Version: 1.4.0
Depends: methods, rJava, RSQLite, XML
Suggests: iontreeData
License: GPL-2
Title: Data management and analysis of ion trees from ion-trap mass
spectrometry
Description: Ion fragmentation provides structural information for
metabolite identification. This package provides utility
functions to manage and analyse MS2/MS3 fragmentation data from
ion trap mass spectrometry. It was designed for high throughput
metabolomics data with many biological samples and a large
numer of ion trees collected. Tests have been done with data
from low-resolution mass spectrometry but could be readily
extended to precursor ion based fragmentation data from high
resoultion mass spectrometry.
biocViews: Metabolomics, MassSpectrometry
Author: Mingshu Cao
Maintainer: Mingshu Cao <mingshu.cao@agresearch.co.nz>
MD5sum: 618ff3a2fc6f620efeed7d742164c71a
source.ver: src/contrib/iontree_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/iontree_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/iontree_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/iontree/inst/doc/iontree_doc.pdf
vignetteTitles: MSn
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/iontree/inst/doc/iontree_doc.R
Package: iPAC
Version: 1.0.0
Depends: R(>= 2.15),gdata, scatterplot3d, Biostrings, multtest
License: GPL-2
Title: Identification of Protein Amino acid Clustering
Description: iPAC is a novel tool to identify somatic amino acid
mutation clustering within proteins while taking into account
protein structure.
biocViews: Bioinformatics, Clustering, BiologicalDomains, Proteomics
Author: Gregory Ryslik, Hongyu Zhao
Maintainer: Gregory Ryslik <gregory.ryslik@yale.edu>
MD5sum: 64df228a3e89bdf1a2038d3e10ac873e
source.ver: src/contrib/iPAC_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/iPAC_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/iPAC_1.0.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iPAC_1.0.0.tgz
vignettes: vignettes/iPAC/inst/doc/iPAC.pdf
vignetteTitles: iPAC: identification of Protein Amino acid Mutations
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/iPAC/inst/doc/iPAC.R
Package: IPPD
Version: 1.6.0
Depends: R (>= 2.12.0), MASS, Matrix, XML, digest, bitops
Imports: methods, stats, graphics
License: GPL (version 2 or later)
Archs: i386, x64
Title: Isotopic peak pattern deconvolution for Protein Mass
Spectrometry by template matching
Description: The package provides functionality to extract isotopic
peak patterns from raw mass spectra. This is done by fitting a
large set of template basis functions to the raw spectrum using
either nonnegative least squares or least absolute deviation
fittting. The package offers a flexible function which tries to
estimate model parameters in a way tailored to the peak shapes
in the data. The package also provides functionality to process
LCMS runs.
biocViews: Proteomics
Author: Martin Slawski <ms@cs.uni-saarland.de>, Rene Hussong
<rene.hussong@uni.lu>, Matthias Hein <hein@cs.uni-saarland.de>
Maintainer: Martin Slawski <ms@cs.uni-saarland.de>
MD5sum: a44e1694684e996bbdca54ec6bb8a9b0
source.ver: src/contrib/IPPD_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/IPPD_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/IPPD_1.6.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/IPPD_1.6.0.tgz
vignettes: vignettes/IPPD/inst/doc/IPPD.pdf,
vignettes/IPPD/inst/doc/templatedetail.pdf,
vignettes/IPPD/inst/doc/templates.pdf
vignetteTitles: IPPD Manual, templatedetail.pdf, templates.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/IPPD/inst/doc/IPPD.R
Package: IRanges
Version: 1.16.6
Depends: R (>= 2.8.0), methods, utils, stats, BiocGenerics (>= 0.1.4)
Imports: methods, utils, stats, BiocGenerics, stats4
Suggests: GenomicRanges, RUnit
License: Artistic-2.0
Archs: i386, x64
Title: Infrastructure for manipulating intervals on sequences
Description: The package provides efficient low-level and highly
reusable S4 classes for storing ranges of integers, RLE vectors
(Run-Length Encoding), and, more generally, data that can be
organized sequentially (formally defined as Vector objects), as
well as views on these Vector objects. Efficient list-like
classes are also provided for storing big collections of
instances of the basic classes. All classes in the package use
consistent naming and share the same rich and consistent
"Vector API" as much as possible.
biocViews: Infrastructure, DataRepresentation
Author: H. Pages, P. Aboyoun and M. Lawrence
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: cb350d44ff25896567b127e3d02b7e36
source.ver: src/contrib/IRanges_1.16.6.tar.gz
win.binary.ver: bin/windows/contrib/2.15/IRanges_1.16.6.zip
win64.binary.ver: bin/windows64/contrib/2.15/IRanges_1.16.6.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/IRanges_1.16.6.tgz
vignettes: vignettes/IRanges/inst/doc/IRangesOverview.pdf,
vignettes/IRanges/inst/doc/RleTricks.pdf
vignetteTitles: An Introduction to IRanges, Rle Tips and Tricks
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/IRanges/inst/doc/IRangesOverview.R,
vignettes/IRanges/inst/doc/RleTricks.R
dependsOnMe: BayesPeak, Biostrings, BSgenome, bsseq, ChIPpeakAnno,
chipseq, chroGPS, cn.mops, CSAR, DECIPHER, deepSNV,
DirichletMultinomial, easyRNASeq, exomeCopy, genomes,
GenomicFeatures, GenomicRanges, Genominator, genoset, GGtools,
girafe, gwascat, HMMcopy, htSeqTools, methyAnalysis,
MinimumDistance, MotifDb, nucleR, oneChannelGUI, PING, r3Cseq,
rGADEM, rMAT, Rsamtools, segmentSeq, ShortRead, TEQC, triform,
VariantAnnotation, VariantTools, xmapcore
importsMe: annmap, AnnotationDbi, ArrayExpressHTS, BayesPeak,
Biostrings, biovizBase, BitSeq, charm, ChIPpeakAnno, chipseq,
ChIPseqR, ChIPsim, ChromHeatMap, cn.mops, DECIPHER, DiffBind,
EDASeq, fastseg, flowQ, FunciSNP, gcrma, GenomicFeatures,
GenomicRanges, ggbio, girafe, gmapR, Gviz, HTSeqGenie, MEDIPS,
methVisual, methyAnalysis, mosaics, motifRG, MotIV, MSnbase,
NarrowPeaks, nucleR, oligoClasses, OTUbase, pdInfoBuilder,
PICS, R453Plus1Toolbox, Rcade, REDseq, Repitools, rGADEM, rMAT,
rnaSeqMap, Rolexa, Rsamtools, rSFFreader, rtracklayer,
segmentSeq, ShortRead, triform, TSSi, VanillaICE,
VariantAnnotation, VariantTools, waveTiling
suggestsMe: BiocGenerics, HilbertVis, HilbertVisGUI, MiRaGE, Repitools,
SNPchip
Package: iSeq
Version: 1.10.0
Depends: R (>= 2.10.0)
License: GPL (>= 2)
Archs: i386, x64
Title: Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden
Ising Models
Description: This package uses Bayesian hidden Ising models to identify
IP-enriched genomic regions from ChIP-seq data. It can be used
to analyze ChIP-seq data with and without controls and
replicates.
biocViews: ChIPseq, HighThroughputSequencing, Bioinformatics
Author: Qianxing Mo
Maintainer: Qianxing Mo <qmo@bcm.edu>
MD5sum: 741ab42e8c9d3e4da1e90413f66e3111
source.ver: src/contrib/iSeq_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/iSeq_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/iSeq_1.10.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iSeq_1.10.0.tgz
vignettes: vignettes/iSeq/inst/doc/iSeq.pdf
vignetteTitles: iSeq
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/iSeq/inst/doc/iSeq.R
Package: isobar
Version: 1.4.0
Depends: R (>= 2.10.0), Biobase, stats, methods, plyr
Imports: distr
Suggests: MSnbase, OrgMassSpecR, XML, biomaRt, ggplot2, Hmisc, RJSONIO
License: LGPL-2
Title: Analysis and quantitation of isobarically tagged MSMS proteomics
data
Description: isobar provides methods for preprocessing, normalization,
and report generation for the analysis of quantitative mass
spectrometry proteomics data labeled with isobaric tags, such
as iTRAQ and TMT.
biocViews: Proteomics, MassSpectrometry, Bioinformatics,
MultipleComparisons, QualityControl
Author: Florian P Breitwieser <fbreitwieser@cemm.oeaw.ac.at> and
Jacques Colinge <jcolinge@cemm.oeaw.ac.at>, with contributions
from Xavier Robin <xavier.robin@unige.ch>
Maintainer: Florian P Breitwieser <fbreitwieser@cemm.oeaw.ac.at>
URL: http://bioinformatics.cemm.oeaw.ac.at
MD5sum: c2afab27ab6bb80e0044efb486432480
source.ver: src/contrib/isobar_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/isobar_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/isobar_1.4.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/isobar_1.4.0.tgz
vignettes: vignettes/isobar/inst/doc/isobar-devel.pdf,
vignettes/isobar/inst/doc/isobar.pdf
vignetteTitles: Isobar for developers, Isobar Usage
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/isobar/inst/doc/isobar-devel.R,
vignettes/isobar/inst/doc/isobar.R
Package: IsoGeneGUI
Version: 1.14.0
Depends: tcltk, tkrplot, IsoGene
Imports: multtest, relimp, WriteXLS,gdata, RColorBrewer, geneplotter
Suggests: RUnit
License: GPL-2
Title: A graphical user interface to conduct a dose-response analysis
of microarray data
Description: The IsoGene Graphical User Interface (IsoGene-GUI) is a
user friendly interface of the IsoGene package which is aimed
to identify for genes with a monotonic trend in the expression
levels with respect to the increasing doses using several test
statistics: global likelihood ratio test (E2), Bartholomew
1961, Barlow et al. 1972 and Robertson et al. 1988), Williams
(1971, 1972), Marcus (1976), the M (Hu et al. 2005) and the
modified M (Lin et al. 2007). The p-values of the global
likelihood ratio test (E2) are obtained using the excat
distribution and permutation. The other four test statistics
are obtained using permutation . Several p-values adjustment
are provided: Bonferroni, Holm (1979), Hochberg (1988), and
Sidak procedures for controlling the family-wise Type I error
rate (FWER), and BH (Benjamini and Hochberg 1995) and BY
(Benjamini and Yekutieli 2001) procedures are used for
controlling the FDR. the inference is based on resampling
methods, which control the False Discovery Rate (FDR) (both
permutations (Ge et al., 2003) and the Significance Analysis of
Microarrays (SAM), Tusher et al., 2001).
biocViews: Microarray, DifferentialExpression, GUI
Author: Setia Pramana, Dan Lin, Philippe Haldermans, Tobias Verbeke
Maintainer: Setia Pramana <setia.pramana@ki.se>
URL: http://www.ibiostat.be/software/IsoGeneGUI/index.html
MD5sum: f99f837c4a0c80f05565600b6e464eee
source.ver: src/contrib/IsoGeneGUI_1.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/IsoGeneGUI_1.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/IsoGeneGUI_1.14.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/IsoGeneGUI_1.14.0.tgz
vignettes: vignettes/IsoGeneGUI/inst/doc/IsoGeneGUI.pdf
vignetteTitles: IsoGeneGUI Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/IsoGeneGUI/inst/doc/IsoGeneGUI.R
Package: ITALICS
Version: 2.18.0
Depends: R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser,
pd.mapping50k.xba240
Imports: affxparser, DBI, GLAD, oligo, oligoClasses, stats
Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp
License: GPL-2
Title: ITALICS
Description: A Method to normalize of Affymetrix GeneChip Human Mapping
100K and 500K set
biocViews: Microarray, CopyNumberVariants
Author: Guillem Rigaill, Philippe Hupe
Maintainer: Guillem Rigaill <italics@curie.fr>
URL: http://bioinfo.curie.fr
MD5sum: 010a14d39f7b2764a2926b283b8ece8d
source.ver: src/contrib/ITALICS_2.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ITALICS_2.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ITALICS_2.18.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/ITALICS_2.18.0.tgz
vignettes: vignettes/ITALICS/inst/doc/ITALICS-006.pdf,
vignettes/ITALICS/inst/doc/ITALICS.pdf
vignetteTitles: ITALICS-006.pdf, ITALICS
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ITALICS/inst/doc/ITALICS.R
Package: iterativeBMA
Version: 1.16.0
Depends: BMA, leaps, Biobase (>= 2.5.5)
License: GPL (>= 2)
Title: The Iterative Bayesian Model Averaging (BMA) algorithm
Description: The iterative Bayesian Model Averaging (BMA) algorithm is
a variable selection and classification algorithm with an
application of classifying 2-class microarray samples, as
described in Yeung, Bumgarner and Raftery (Bioinformatics 2005,
21: 2394-2402).
biocViews: Microarray, Bioinformatics, Classification
Author: Ka Yee Yeung, University of Washington, Seattle, WA, with
contributions from Adrian Raftery and Ian Painter
Maintainer: Ka Yee Yeung <kayee@u.washington.edu>
URL: http://faculty.washington.edu/kayee/research.html
MD5sum: 0afd20fa6e09a5bee3fecba33c7718a6
source.ver: src/contrib/iterativeBMA_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/iterativeBMA_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/iterativeBMA_1.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/iterativeBMA/inst/doc/iterativeBMA.pdf
vignetteTitles: The Iterative Bayesian Model Averaging Algorithm
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/iterativeBMA/inst/doc/iterativeBMA.R
Package: iterativeBMAsurv
Version: 1.16.0
Depends: BMA, leaps, survival, splines
Imports: graphics, grDevices, stats, survival, utils
License: GPL (>= 2)
Title: The Iterative Bayesian Model Averaging (BMA) Algorithm For
Survival Analysis
Description: The iterative Bayesian Model Averaging (BMA) algorithm for
survival analysis is a variable selection method for applying
survival analysis to microarray data.
biocViews: Microarray, Bioinformatics
Author: Amalia Annest, University of Washington, Tacoma, WA Ka Yee
Yeung, University of Washington, Seattle, WA
Maintainer: Ka Yee Yeung <kayee@u.washington.edu>
URL: http://expression.washington.edu/ibmasurv/protected
MD5sum: b73f372f396853862b31deb07e7152d0
source.ver: src/contrib/iterativeBMAsurv_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/iterativeBMAsurv_1.16.0.zip
win64.binary.ver:
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mac.binary.leopard.ver:
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vignettes: vignettes/iterativeBMAsurv/inst/doc/iterativeBMAsurv.pdf
vignetteTitles: The Iterative Bayesian Model Averaging Algorithm For
Survival Analysis
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/iterativeBMAsurv/inst/doc/iterativeBMAsurv.R
Package: joda
Version: 1.6.0
Depends: R (>= 2.0), bgmm, RBGL
License: GPL (>= 2)
Title: JODA algorithm for quantifying gene deregulation using knowledge
Description: Package 'joda' implements three steps of an algorithm
called JODA. The algorithm computes gene deregulation scores.
For each gene, its deregulation score reflects how strongly an
effect of a certain regulator's perturbation on this gene
differs between two different cell populations. The algorithm
utilizes regulator knockdown expression data as well as
knowledge about signaling pathways in which the regulators are
involved (formalized in a simple matrix model).
biocViews: Microarray, Pathways, GraphsAndNetworks, Statistics,
NetworkInference
Author: Ewa Szczurek
Maintainer: Ewa Szczurek <szczurek@molgen.mpg.de>
URL: http://www.bioconductor.org
MD5sum: 25b170ce4a4a3d2dd369caa6ee9e892e
source.ver: src/contrib/joda_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/joda_1.6.0.zip
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vignettes: vignettes/joda/inst/doc/JodaVignette.pdf
vignetteTitles: Introduction to joda
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/joda/inst/doc/JodaVignette.R
Package: KCsmart
Version: 2.16.0
Depends: methods, siggenes, multtest, KernSmooth
Enhances: Biobase, CGHbase
License: GPL-3
Title: Multi sample aCGH analysis package using kernel convolution
Description: Multi sample aCGH analysis package using kernel
convolution
biocViews: CopyNumberVariants, Visualization, aCGH, Microarray
Author: Jorma de Ronde, Christiaan Klijn, Arno Velds
Maintainer: Jorma de Ronde <j.d.ronde@nki.nl>
MD5sum: c74f2d0234ab4c75f3e51d02f415e1f1
source.ver: src/contrib/KCsmart_2.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/KCsmart_2.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/KCsmart_2.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/KCsmart/inst/doc/KCS.pdf
vignetteTitles: KCsmart example session
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/KCsmart/inst/doc/KCS.R
Package: KEGGgraph
Version: 1.14.0
Depends: R (>= 2.10), methods, XML (>= 2.3-0), graph
Imports: methods, XML, graph
Suggests: Rgraphviz, RBGL, RUnit, RColorBrewer, KEGG.db, org.Hs.eg.db,
hgu133plus2.db, SPIA
License: GPL (>= 2)
Title: KEGGgraph: A graph approach to KEGG PATHWAY in R and
Bioconductor
Description: KEGGGraph is an interface between KEGG pathway and graph
object as well as a collection of tools to analyze, dissect and
visualize these graphs. It parses the regularly updated KGML
(KEGG XML) files into graph models maintaining all essential
pathway attributes. The package offers functionalities
including parsing, graph operation, visualization and etc.
biocViews: Pathways, GraphsAndNetworks, NetworkVisualization
Author: Jitao David Zhang
Maintainer: Jitao David Zhang <jitao_david.zhang@roche.com>
URL: http://www.nextbiomotif.com
MD5sum: 7fad1b40037731dd38b1f8b9a51fee3d
source.ver: src/contrib/KEGGgraph_1.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/KEGGgraph_1.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/KEGGgraph_1.14.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/KEGGgraph/inst/doc/KEGGgraphApp.pdf,
vignettes/KEGGgraph/inst/doc/KEGGgraph.pdf
vignetteTitles: KEGGgraph: Application Examples, KEGGgraph: graph
approach to KEGG PATHWAY
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/KEGGgraph/inst/doc/KEGGgraphApp.R,
vignettes/KEGGgraph/inst/doc/KEGGgraph.R
importsMe: DEGraph, NCIgraph
suggestsMe: DEGraph, SPIA
Package: keggorthology
Version: 2.10.0
Depends: R (>= 2.5.0),stats,graph,hgu95av2.db
Imports: AnnotationDbi,graph,DBI, graph, grDevices, methods, stats,
tools, utils
Suggests: RBGL,ALL
License: Artistic-2.0
Title: graph support for KO, KEGG Orthology
Description: graphical representation of the Feb 2010 KEGG Orthology.
The KEGG orthology is a set of pathway IDs that are not to be
confused with the KEGG ortholog IDs.
biocViews: Pathways, GraphsAndNetworks, NetworkVisualization
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: 62a2082d257b4a5477992df3f18b4580
source.ver: src/contrib/keggorthology_2.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/keggorthology_2.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/keggorthology_2.10.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/keggorthology/inst/doc/keggorth.pdf
vignetteTitles: keggorthology overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/keggorthology/inst/doc/keggorth.R
dependsOnMe: gene2pathway
suggestsMe: MLInterfaces
Package: KEGGprofile
Version: 1.0.0
Depends: XML, png, TeachingDemos, KEGG.db
Imports: AnnotationDbi
License: GPL (>= 2)
Title: An annotation and visualization package for multi-types and
multi-groups expression data in KEGG pathway
Description: KEGGprofile is an annotation and visualization tool which
integrated the expression profiles and the function annotation
in KEGG pathway maps. The multi-types and multi-groups
expression data can be visualized in one pathway map.
KEGGprofile facilitated more detailed analysis about the
specific function changes inner pathway or temporal
correlations in different genes and samples.
biocViews: Pathways
Author: Shilin Zhao
Maintainer: Shilin Zhao <zhaoshilin@gmail.com>
MD5sum: 1fc59a59c4fa1dec4b375399fa1bc86e
source.ver: src/contrib/KEGGprofile_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/KEGGprofile_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/KEGGprofile_1.0.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/KEGGprofile/inst/doc/KEGGprofile.pdf
vignetteTitles: KEGGprofile: Application Examples
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/KEGGprofile/inst/doc/KEGGprofile.R
Package: KEGGSOAP
Version: 1.32.1
Depends: methods, BiocGenerics
Imports: XML, RCurl, SSOAP (>= 0.2-2), XMLSchema
Suggests: RUnit
License: BSD
Title: Client-side SOAP access KEGG
Description: A package that provides a client interface to the KEGG
SOAP server
biocViews: Annotation, Pathways, ConnectTools
Author: J. Zhang and R. Gentleman
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: d609596ea0c04ca66087c133d1bdfaf7
source.ver: src/contrib/KEGGSOAP_1.32.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/KEGGSOAP_1.32.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/KEGGSOAP_1.32.1.zip
mac.binary.leopard.ver:
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hasREADME: TRUE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: gene2pathway
Package: lapmix
Version: 1.24.0
Depends: R (>= 2.6.0),stats
Imports: Biobase, graphics, grDevices, methods, stats, tools, utils
License: GPL (>= 2)
Title: Laplace Mixture Model in Microarray Experiments
Description: Laplace mixture modelling of microarray experiments. A
hierarchical Bayesian approach is used, and the hyperparameters
are estimated using empirical Bayes. The main purpose is to
identify differentially expressed genes.
biocViews: Bioinformatics, Microarray, OneChannel,
DifferentialExpression
Author: Yann Ruffieux, contributions from Debjani Bhowmick, Anthony C.
Davison, and Darlene R. Goldstein
Maintainer: Yann Ruffieux <yann.ruffieux@epfl.ch>
URL: http://www.r-project.org, http://www.bioconductor.org,
http://stat.epfl.ch
MD5sum: dea2902dd6d9348df61d812ca3fca5ad
source.ver: src/contrib/lapmix_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/lapmix_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/lapmix_1.24.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/lapmix/inst/doc/lapmix-example.pdf
vignetteTitles: lapmix example
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/lapmix/inst/doc/lapmix-example.R
Package: LBE
Version: 1.26.0
Depends: stats
Imports: graphics, grDevices, methods, stats, utils
Suggests: qvalue
License: GPL-2
Title: Estimation of the false discovery rate.
Description: LBE is an efficient procedure for estimating the
proportion of true null hypotheses, the false discovery rate
(and so the q-values) in the framework of estimating procedures
based on the marginal distribution of the p-values without
assumption for the alternative hypothesis.
biocViews: Bioinformatics, MultipleComparisons
Author: Cyril Dalmasso
Maintainer: Cyril Dalmasso <dalmasso@vjf.inserm.fr>
MD5sum: 1921ab8b122a05bb93f291e6d9f42c53
source.ver: src/contrib/LBE_1.26.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/LBE_1.26.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/LBE_1.26.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LBE_1.26.0.tgz
vignettes: vignettes/LBE/inst/doc/LBE.pdf
vignetteTitles: LBE Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/LBE/inst/doc/LBE.R
Package: les
Version: 1.8.0
Depends: R (>= 2.13.2), methods, graphics, fdrtool
Imports: boot, gplots, RColorBrewer
Suggests: Biobase, limma
Enhances: multicore
License: GPL-3
Title: Identifying Differential Effects in Tiling Microarray Data
Description: The 'les' package estimates Loci of Enhanced Significance
(LES) in tiling microarray data. These are regions of
regulation such as found in differential transcription,
CHiP-chip, or DNA modification analysis. The package provides a
universal framework suitable for identifying differential
effects in tiling microarray data sets, and is independent of
the underlying statistics at the level of single probes.
biocViews: Microarray, Bioinformatics, DifferentialExpression,
ChIPchip, DNAMethylation, Transcription
Author: Julian Gehring, Clemens Kreutz, Jens Timmer
Maintainer: Julian Gehring <julian.gehring@embl.de>
URL: http://julian-gehring.github.com/les/
MD5sum: 6f6bf27f65dd87fe958bbdd77c502d04
source.ver: src/contrib/les_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/les_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/les_1.8.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/les_1.8.0.tgz
vignettes: vignettes/les/inst/doc/les.pdf
vignetteTitles: Introduction to the les package: Identifying
Differential Effects in Tiling Microarray Data with the Loci of
Enhanced Significance Framework
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/les/inst/doc/les.R
importsMe: GSRI
Package: limma
Version: 3.14.4
Depends: R (>= 2.3.0), methods
Suggests: affy, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn
License: GPL (>=2)
Archs: i386, x64
Title: Linear Models for Microarray Data
Description: Data analysis, linear models and differential expression
for microarray data.
biocViews: Microarray, OneChannel, TwoChannel, DataImport,
QualityControl, Preprocessing, Bioinformatics,
DifferentialExpression, MultipleComparisons, TimeCourse
Author: Gordon Smyth with contributions from Matthew Ritchie, Jeremy
Silver, James Wettenhall, Natalie Thorne, Mette Langaas, Egil
Ferkingstad, Marcus Davy, Francois Pepin, Dongseok Choi, Davis
McCarthy, Di Wu, Alicia Oshlack, Carolyn de Graaf, Yifang Hu,
Wei Shi and Belinda Phipson.
Maintainer: Gordon Smyth <smyth@wehi.edu.au>
URL: http://bioinf.wehi.edu.au/limma
MD5sum: 1586bf14613a0c080fc0e8ba192dedb6
source.ver: src/contrib/limma_3.14.4.tar.gz
win.binary.ver: bin/windows/contrib/2.15/limma_3.14.4.zip
win64.binary.ver: bin/windows64/contrib/2.15/limma_3.14.4.zip
mac.binary.leopard.ver:
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vignettes: vignettes/limma/inst/doc/limma.pdf,
vignettes/limma/inst/doc/usersguide.pdf
vignetteTitles: Limma Vignette, usersguide.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/limma/inst/doc/limma.R
htmlDocs: vignettes/limma/inst/doc/index.html
dependsOnMe: a4Base, AffyExpress, affylmGUI, Agi4x44PreProcess,
attract, birta, CALIB, cghMCR, ChIPpeakAnno, codelink, convert,
Cormotif, coRNAi, edgeR, ExiMiR, HTqPCR, inSilicoMerging,
limmaGUI, lmdme, maDB, maigesPack, marray, MmPalateMiRNA, nem,
PADOG, qpcrNorm, Ringo, snapCGH, TurboNorm
importsMe: affycoretools, ArrayExpress, arrayQuality,
arrayQualityMetrics, ArrayTools, attract, beadarray, betr,
CALIB, CancerMutationAnalysis, charm, ChIPpeakAnno, explorase,
gCMAP, GeneSelectMMD, GeneSelector, GGBase, HTqPCR, iChip,
maSigPro, minfi, MmPalateMiRNA, OLIN, PADOG, phenoTest, Ringo,
RNAinteract, RNAither, RTopper, snapCGH, SSPA, timecourse,
tweeDEseq, vsn
suggestsMe: ABarray, beadarraySNP, BiocCaseStudies, BioNet, Category,
categoryCompare, CMA, coGPS, dyebias, GeneSelector, GEOquery,
GSRI, GSVA, Heatplus, inSilicoDb, les, lumi, methylumi, MLP,
oligo, oneChannelGUI, PGSEA, plw, PREDA, puma, Rcade, RTopper,
rtracklayer, virtualArray
Package: limmaGUI
Version: 1.34.0
Depends: limma, tcltk
Suggests: statmod, R2HTML, xtable, tkrplot
License: LGPL
Title: GUI for limma package
Description: A Graphical User Interface for the limma Microarray
package
biocViews: Microarray, TwoChannel, DataImport, QualityControl,
Preprocessing, Bioinformatics, DifferentialExpression,
MultipleComparisons, GUI
Author: James Wettenhall Division of Genetics and Bioinformatics, WEHI
Maintainer: Keith Satterley <keith@wehi.edu.au>
URL: http://bioinf.wehi.edu.au/limmaGUI/
MD5sum: 5ab7710025eb35d8da4f2a5a364b3a94
source.ver: src/contrib/limmaGUI_1.34.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/limmaGUI_1.34.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/limmaGUI_1.34.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/limmaGUI/inst/doc/extract.pdf,
vignettes/limmaGUI/inst/doc/limmaGUI.pdf,
vignettes/limmaGUI/inst/doc/LinModIntro.pdf
vignetteTitles: Extracting limma objects from limmaGUI files, limmaGUI
Vignette, LinModIntro.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/limmaGUI/inst/doc/extract.R,
vignettes/limmaGUI/inst/doc/limmaGUI.R
htmlDocs: vignettes/limmaGUI/inst/doc/about.html,
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vignettes/limmaGUI/inst/doc/index.html,
vignettes/limmaGUI/inst/doc/InputFiles.html,
vignettes/limmaGUI/inst/doc/lgDevel.html,
vignettes/limmaGUI/inst/doc/windowsFocus.html
Package: LiquidAssociation
Version: 1.12.0
Depends: geepack, methods, yeastCC, org.Sc.sgd.db
Imports: Biobase, graphics, grDevices, methods, stats
License: GPL (>=3)
Title: LiquidAssociation
Description: The package contains functions for calculate direct and
model-based estimators for liquid association. It also provides
functions for testing the existence of liquid association given
a gene triplet data.
biocViews: Pathways, GeneExpression, CellBiology, Genetics,
NetworkAnalysis, TimeCourse
Author: Yen-Yi Ho <yho@jhsph.edu>
Maintainer: Yen-Yi Ho <yho@jhsph.edu>
MD5sum: 7bbac13304945a7ce494e87fb4bf5d84
source.ver: src/contrib/LiquidAssociation_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/LiquidAssociation_1.12.0.zip
win64.binary.ver:
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mac.binary.leopard.ver:
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vignettes: vignettes/LiquidAssociation/inst/doc/LiquidAssociation.pdf
vignetteTitles: LiquidAssociation Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/LiquidAssociation/inst/doc/LiquidAssociation.R
Package: lmdme
Version: 1.0.0
Depends: R (>= 2.14.1), methods, limma, pls
Imports: stats
Suggests: stemHypoxia
Enhances: parallel
License: GPL (>=2)
Title: Linear Model decomposition for Designed Multivariate Experiments
Description: linear ANOVA decomposition of Multivariate Designed
Experiments implementation based on limma lmFit. Features: i)
Flexible formula type interface, ii) Fast limma based
implementation, iii) p and F values over deflacted coefficients
and iv) ploting functions for PCA and PLS
biocViews: Microarray, OneChannel, TwoChannel, Bioinformatics,
Visualization, AssayDomains, DifferentialExpression,
ExperimentData, Cancer
Author: Cristobal Fresno and Elmer A. Fernandez
Maintainer: Cristobal Fresno <cristobalfresno@gmail.com>
URL: http://200.45.112.41/bdmg/?page_id=38
MD5sum: 3e366a217504abcff70850e1d1dd1f81
source.ver: src/contrib/lmdme_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/lmdme_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/lmdme_1.0.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/lmdme_1.0.0.tgz
vignettes: vignettes/lmdme/inst/doc/lmdme-vignette.pdf
vignetteTitles: lmdme: linear model framework for PCA/PLS analysis of
ANOVA decomposition on Designed Multivariate Experiments in R
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/lmdme/inst/doc/lmdme-vignette.R
Package: LMGene
Version: 2.14.0
Depends: R (>= 2.10.0), Biobase (>= 2.5.5), multtest, survival, affy
Suggests: affydata
License: LGPL
Title: LMGene Software for Data Transformation and Identification of
Differentially Expressed Genes in Gene Expression Arrays
Description: LMGene package for analysis of microarray data using a
linear model and glog data transformation
biocViews: Microarray, Bioinformatics, DifferentialExpression,
Preprocessing
Author: David Rocke, Geun Cheol Lee, John Tillinghast, Blythe
Durbin-Johnson, and Shiquan Wu
Maintainer: Blythe Durbin-Johnson <bpdurbin@ucdavis.edu>
URL: http://dmrocke.ucdavis.edu/software.html
MD5sum: 8d60bc5ae232d6dbc01f9ba5ab2941bb
source.ver: src/contrib/LMGene_2.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/LMGene_2.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/LMGene_2.14.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/LMGene/inst/doc/LMGene.pdf
vignetteTitles: LMGene User's Guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/LMGene/inst/doc/LMGene.R
Package: logicFS
Version: 1.28.1
Depends: LogicReg, mcbiopi
Suggests: genefilter, siggenes
License: LGPL (>= 2)
Title: Identification of SNP Interactions
Description: Identification of interactions between binary variables
using Logic Regression. Can, e.g., be used to find interesting
SNP interactions. Contains also a bagging version of logic
regression for classification.
biocViews: SNP, Classification, Genetics
Author: Holger Schwender
Maintainer: Holger Schwender <holger.schw@gmx.de>
MD5sum: 4f7818ffc0a1aefd8fb140fd5f97adee
source.ver: src/contrib/logicFS_1.28.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/logicFS_1.28.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/logicFS_1.28.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/logicFS/inst/doc/logicFS.pdf
vignetteTitles: logicFS Manual
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/logicFS/inst/doc/logicFS.R
Package: logitT
Version: 1.16.0
Depends: affy
Suggests: SpikeInSubset
License: GPL (>= 2)
Archs: i386, x64
Title: logit-t Package
Description: The logitT library implements the Logit-t algorithm
introduced in --A high performance test of differential gene
expression for oligonucleotide arrays-- by William J Lemon,
Sandya Liyanarachchi and Ming You for use with Affymetrix data
stored in an AffyBatch object in R.
biocViews: Microarray, DifferentialExpression
Author: Tobias Guennel <tguennel@vcu.edu>
Maintainer: Tobias Guennel <tguennel@vcu.edu>
URL: http://www.bioconductor.org
MD5sum: 63bd3f1eb9d61f4313ea5d56eda1e1df
source.ver: src/contrib/logitT_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/logitT_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/logitT_1.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/logitT/inst/doc/logitT.pdf
vignetteTitles: logitT primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/logitT/inst/doc/logitT.R
Package: lol
Version: 1.6.0
Depends: penalized, Matrix
Imports: Matrix, penalized, graphics, grDevices, stats
License: GPL-2
Title: Lots Of Lasso
Description: Various optimization methods for Lasso inference with
matrix warpper
Author: Yinyin Yuan
Maintainer: Yinyin Yuan <yy341@cam.ac.uk>
MD5sum: cd56d0955249060d0bc163022e34e5d5
source.ver: src/contrib/lol_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/lol_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/lol_1.6.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/lol_1.6.0.tgz
vignettes: vignettes/lol/inst/doc/lol.pdf
vignetteTitles: An introduction to the lol package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/lol/inst/doc/lol.R
Package: LPE
Version: 1.32.0
Depends: R (>= 2.10)
Imports: stats
License: LGPL
Title: Methods for analyzing microarray data using Local Pooled Error
(LPE) method
Description: This LPE library is used to do significance analysis of
microarray data with small number of replicates. It uses
resampling based FDR adjustment, and gives less conservative
results than traditional 'BH' or 'BY' procedures. Data accepted
is raw data in txt format from MAS4, MAS5 or dChip. Data can
also be supplied after normalization. LPE library is primarily
used for analyzing data between two conditions. To use it for
paired data, see LPEP library. For using LPE in multiple
conditions, use HEM library.
biocViews: Microarray, Bioinformatics, DifferentialExpression
Author: Nitin Jain <emailnitinjain@gmail.com>, Michael O'Connell
<michaelo@warath.com>, Jae K. Lee <jaeklee@virginia.edu>.
Includes R source code contributed by HyungJun Cho
<hcho@virginia.edu>
Maintainer: Nitin Jain <emailnitinjain@gmail.com>
URL: http://www.r-project.org,
http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/,
http://sourceforge.net/projects/r-lpe/
MD5sum: 6707dcb05f8cdb698ee9b09f3b2c1004
source.ver: src/contrib/LPE_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/LPE_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/LPE_1.32.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LPE_1.32.0.tgz
vignettes: vignettes/LPE/inst/doc/LPE.pdf
vignetteTitles: LPE test for microarray data with small number of
replicates
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/LPE/inst/doc/LPE.R
dependsOnMe: LPEadj, PLPE
importsMe: LPEadj
suggestsMe: ABarray
Package: LPEadj
Version: 1.18.0
Depends: LPE
Imports: LPE, stats
License: LGPL
Title: A correction of the local pooled error (LPE) method to replace
the asymptotic variance adjustment with an unbiased adjustment
based on sample size.
Description: Two options are added to the LPE algorithm. The original
LPE method sets all variances below the max variance in the
ordered distribution of variances to the maximum variance. in
LPEadj this option is turned off by default. The second option
is to use a variance adjustment based on sample size rather
than pi/2. By default the LPEadj uses the sample size based
variance adjustment.
biocViews: Microarray, Bioinformatics, Proteomics
Author: Carl Murie <carl.murie@mcgill.ca>, Robert Nadon
<robert.nadon@mcgill.ca>
Maintainer: Carl Murie <carl.murie@mcgill.ca>
MD5sum: c135ea6ab5f52865dc956a13a52884aa
source.ver: src/contrib/LPEadj_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/LPEadj_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/LPEadj_1.18.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/LPEadj_1.18.0.tgz
vignettes: vignettes/LPEadj/inst/doc/LPEadj.pdf
vignetteTitles: LPEadj test for microarray data with small number of
replicates
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/LPEadj/inst/doc/LPEadj.R
Package: lumi
Version: 2.10.0
Depends: R (>= 2.10), Biobase (>= 2.5.5), nleqslv
Imports: affy (>= 1.23.4), methylumi (>= 2.3.2), annotate, Biobase (>=
2.5.5), lattice, mgcv (>= 1.4-0), hdrcde, KernSmooth,
preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics,
stats, stats4, methods
Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db,
lumiHumanIDMapping, genefilter, RColorBrewer
License: LGPL (>= 2)
Title: BeadArray Specific Methods for Illumina Methylation and
Expression Microarrays
Description: The lumi package provides an integrated solution for the
Illumina microarray data analysis. It includes functions of
Illumina BeadStudio (GenomeStudio) data input, quality control,
BeadArray-specific variance stabilization, normalization and
gene annotation at the probe level. It also includes the
functions of processing Illumina methylation microarrays,
especially Illumina Infinium methylation microarrays.
biocViews: Microarray, OneChannel, Preprocessing, DNAMethylation,
QualityControl, TwoChannel
Author: Pan Du, Richard Bourgon, Gang Feng, Simon Lin
Maintainer: Pan Du <dupan.mail@gmail.com>
MD5sum: f1cd8a3c17c448efb5a5237062e100cd
source.ver: src/contrib/lumi_2.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/lumi_2.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/lumi_2.10.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/lumi_2.10.0.tgz
vignettes: vignettes/lumi/inst/doc/Bioc2007_lumi_presentation.pdf,
vignettes/lumi/inst/doc/IlluminaAnnotation.pdf,
vignettes/lumi/inst/doc/lumi.pdf,
vignettes/lumi/inst/doc/lumi_VST_evaluation.pdf,
vignettes/lumi/inst/doc/methylationAnalysis.pdf
vignetteTitles: Bioc2007_lumi_presentation.pdf, Resolve the
inconsistency of Illumina identifiers through nuID, Using lumi
A package processing Illumina Microarray, Evaluation of VST
algorithm in lumi package, Analyze Illumina Infinium
methylation microarray data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/lumi/inst/doc/IlluminaAnnotation.R,
vignettes/lumi/inst/doc/lumi.R,
vignettes/lumi/inst/doc/lumi_VST_evaluation.R,
vignettes/lumi/inst/doc/methylationAnalysis.R
dependsOnMe: arrayMvout
importsMe: ffpe, methyAnalysis
suggestsMe: beadarray, methylumi, tigre, virtualArray
Package: LVSmiRNA
Version: 1.8.0
Depends: R (>= 2.10), Biobase,quantreg,splines,MASS,limma,affy,methods,
SparseM, vsn
Imports: BiocGenerics, stats4
Enhances: multicore,snow, Rmpi
License: GPL-2
Archs: i386, x64
Title: LVS normalization for Agilent miRNA data
Description: Normalization of Agilent miRNA arrays.
biocViews: Microarray,AgilentChip,OneChannel,Preprocessing
Author: Stefano Calza, Suo Chen, Yudi Pawitam
Maintainer: Stefano Calza <stefano.calza@biostatistics.it>
MD5sum: 34800cb974d531b793d691d8e07b14dd
source.ver: src/contrib/LVSmiRNA_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/LVSmiRNA_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/LVSmiRNA_1.8.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/LVSmiRNA_1.8.0.tgz
vignettes: vignettes/LVSmiRNA/inst/doc/LVSmiRNA.pdf
vignetteTitles: LVSmiRNA
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/LVSmiRNA/inst/doc/LVSmiRNA.R
Package: maanova
Version: 1.28.0
Depends: R (>= 2.10)
Imports: Biobase, graphics, grDevices, methods, stats, utils
Suggests: qvalue, snow
Enhances: Rmpi
License: GPL (>= 2)
Archs: i386, x64
Title: Tools for analyzing Micro Array experiments
Description: Analysis of N-dye Micro Array experiment using mixed model
effect. Containing analysis of variance, permutation and
bootstrap, cluster and consensus tree.
biocViews: Microarray, DifferentialExpression, Clustering
Author: Hao Wu, modified by Hyuna Yang and Keith Sheppard with ideas
from Gary Churchill, Katie Kerr and Xiangqin Cui.
Maintainer: Keith Sheppard <keith.sheppard@jax.org>
URL: http://research.jax.org/faculty/churchill
MD5sum: 111e616ea8d448adadadfc95309707bb
source.ver: src/contrib/maanova_1.28.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/maanova_1.28.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/maanova_1.28.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/maanova/inst/doc/abf1fig.pdf,
vignettes/maanova/inst/doc/hckidney.pdf,
vignettes/maanova/inst/doc/maanova.pdf,
vignettes/maanova/inst/doc/vgprofile.pdf
vignetteTitles: abf1fig.pdf, hckidney.pdf, R/maanova HowTo,
vgprofile.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/maanova/inst/doc/maanova.R
Package: macat
Version: 1.32.0
Depends: Biobase, annotate
Suggests: hgu95av2.db, stjudem
License: Artistic-2.0
Title: MicroArray Chromosome Analysis Tool
Description: This library contains functions to investigate links
between differential gene expression and the chromosomal
localization of the genes. MACAT is motivated by the common
observation of phenomena involving large chromosomal regions in
tumor cells. MACAT is the implementation of a statistical
approach for identifying significantly differentially expressed
chromosome regions. The functions have been tested on a
publicly available data set about acute lymphoblastic leukemia
(Yeoh et al.Cancer Cell 2002), which is provided in the library
'stjudem'.
biocViews: Microarray, DifferentialExpression, Visualization
Author: Benjamin Georgi, Matthias Heinig, Stefan Roepcke, Sebastian
Schmeier, Joern Toedling
Maintainer: Joern Toedling <j.toedling@imb-mainz.de>
MD5sum: 416903b83d43f0e83b17249e1a4d23ce
source.ver: src/contrib/macat_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/macat_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/macat_1.32.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/macat_1.32.0.tgz
vignettes: vignettes/macat/inst/doc/chrom6TkNN.pdf,
vignettes/macat/inst/doc/chrom6T.pdf,
vignettes/macat/inst/doc/evalkNN6.pdf,
vignettes/macat/inst/doc/macat.pdf,
vignettes/macat/inst/doc/Slidingchrom6s3.pdf
vignetteTitles: chrom6TkNN.pdf, chrom6T.pdf, evalkNN6.pdf, MicroArray
Chromosome Analysis Tool, Slidingchrom6s3.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/macat/inst/doc/macat.R
Package: maCorrPlot
Version: 1.28.0
Depends: lattice
Imports: graphics, grDevices, lattice, stats
License: GPL (>= 2)
Title: Visualize artificial correlation in microarray data
Description: Graphically displays correlation in microarray data that
is due to insufficient normalization
biocViews: Microarray, Preprocessing, Visualization
Author: Alexander Ploner <Alexander.Ploner@ki.se>
Maintainer: Alexander Ploner <Alexander.Ploner@ki.se>
URL:
http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15799785
MD5sum: 6ae3166555f50731a85215bc4c0befac
source.ver: src/contrib/maCorrPlot_1.28.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/maCorrPlot_1.28.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/maCorrPlot_1.28.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/maCorrPlot/inst/doc/maCorrPlot.pdf
vignetteTitles: maCorrPlot Introduction
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/maCorrPlot/inst/doc/maCorrPlot.R
Package: maDB
Version: 1.30.0
Depends: R (>= 2.6.0), Biobase (>= 2.5.5), affy (>= 1.23.4), pgUtils
(>= 1.23.2), limma (>= 1.8.0), methods
Suggests: annaffy (>= 1.6.2), biomaRt (>= 1.8.2), geneplotter
License: LGPL (>= 2)
Title: Microarray database and utility functions for microarray data
analysis.
Description: maDB allows to create a simple microarray database to
store microarray experiments and annotation data into it.
Affymetrix GeneChip expression values as well as values from
two color microarrays can be stored into the database. Whole
experiments or subsets from a experiment (or also values for a
subset of genes in a subset of microarrays) can be fetched back
to R. Additionally maDB provides different utility functions
for the microarray data analysis like functions to draw MA
plots or volcano plots with the data points color coded
according to the local point density or functions that allow a
replicate handling of miroarrays.
biocViews: Microarray,TwoChannel,OneChannel,Visualization
Author: Johannes Rainer <johannes.rainer@i-med.ac.at>
Maintainer: Johannes Rainer <johannes.rainer@i-med.ac.at>
MD5sum: 2ab7ecb3c8f8489fce0aee755a1742bc
source.ver: src/contrib/maDB_1.30.0.tar.gz
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/maDB_1.30.0.tgz
vignettes: vignettes/maDB/inst/doc/maDB-015.pdf,
vignettes/maDB/inst/doc/maDB-016.pdf,
vignettes/maDB/inst/doc/maDB.pdf
vignetteTitles: maDB-015.pdf, maDB-016.pdf, maDB.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: made4
Version: 1.32.0
Depends: ade4, RColorBrewer,gplots,scatterplot3d
Suggests: affy
License: Artistic-2.0
Title: Multivariate analysis of microarray data using ADE4
Description: Multivariate data analysis and graphical display of
microarray data. Functions include between group analysis and
coinertia analysis. It contains functions that require ADE4.
biocViews: Bioinformatics, Clustering, Classification,
MultipleComparisons
Author: Aedin Culhane
Maintainer: Aedin Culhane <Aedin@jimmy.harvard.edu>
URL: http://www.hsph.harvard.edu/researchers/aculhane.html
MD5sum: 5d59b706329d45f41e7672fd0c205d5e
source.ver: src/contrib/made4_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/made4_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/made4_1.32.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/made4/inst/doc/html3D.pdf,
vignettes/made4/inst/doc/introduction.pdf
vignetteTitles: html3D.pdf, introduction.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/made4/inst/doc/introduction.R
dependsOnMe: bgafun
Package: maigesPack
Version: 1.22.0
Depends: R (>= 2.10), convert, graph, limma, marray, methods
Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML,
rgl, som
License: GPL (>= 2)
Archs: i386, x64
Title: Functions to handle cDNA microarray data, including several
methods of data analysis
Description: This package uses functions of various other packages
together with other functions in a coordinated way to handle
and analyse cDNA microarray data
biocViews: Microarray, TwoChannel, Preprocessing, ConnectTools,
DifferentialExpression, Clustering, Classification,
GraphsAndNetworks
Author: Gustavo H. Esteves <gesteves@gmail.com>, with contributions
from Roberto Hirata Jr <hirata@ime.usp.br>, E. Jordao Neves
<neves@ime.usp.br>, Elier B. Cristo <elier@ime.usp.br>, Ana C.
Simoes <anakqui@ime.usp.br> and Lucas Fahham
<fahham@linux.ime.usp.br>
Maintainer: Gustavo H. Esteves <gesteves@gmail.com>
URL: http://www.maiges.org/en/software/
MD5sum: f1847469b9cd838a0e811113424fa180
source.ver: src/contrib/maigesPack_1.22.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/maigesPack_1.22.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/maigesPack_1.22.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/maigesPack/inst/doc/maigesPack_tutorial.pdf
vignetteTitles: maigesPack Tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/maigesPack/inst/doc/maigesPack_tutorial.R
Package: makecdfenv
Version: 1.36.0
Depends: R (>= 2.6.0), methods
Imports: Biobase, affy, methods, stats, utils, zlibbioc
License: GPL (>= 2)
Archs: i386, x64
Title: CDF Environment Maker
Description: This package has two functions. One reads a Affymetrix
chip description file (CDF) and creates a hash table
environment containing the location/probe set membership
mapping. The other creates a package that automatically loads
that environment.
biocViews: OneChannel, DataImport, Preprocessing
Author: Rafael A. Irizarry <rafa@jhu.edu>, Laurent Gautier
<laurent@cbs.dtu.dk>, Wolfgang Huber
<w.huber@dkfz-heidelberg.de>, Ben Bolstad <bmb@bmbolstad.com>
Maintainer: James W. MacDonald <jmacdon@med.umich.edu>
MD5sum: c24082bfa9e64e8934b4e7c5fec60af3
source.ver: src/contrib/makecdfenv_1.36.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/makecdfenv_1.36.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/makecdfenv_1.36.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/makecdfenv/inst/doc/makecdfenv.pdf
vignetteTitles: makecdfenv primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/makecdfenv/inst/doc/makecdfenv.R
dependsOnMe: altcdfenvs
Package: MANOR
Version: 1.30.0
Depends: R (>= 2.10), GLAD
Imports: GLAD, graphics, grDevices, stats, utils
License: GPL-2
Archs: i386, x64
Title: CGH Micro-Array NORmalization
Description: Importation, normalization, visualization, and quality
control functions to correct identified sources of variability
in array-CGH experiments.
biocViews: Microarray, TwoChannel, DataImport, QualityControl,
Preprocessing, CopyNumberVariants
Author: Pierre Neuvial <pierre.neuvial@gmail.com>, Philippe Hupe
<philippe.hupe@curie.fr>
Maintainer: Pierre Neuvial <pierre.neuvial@gmail.com>
URL: http://bioinfo.curie.fr/projects/manor/index.html
MD5sum: 4ae766ea1dffe4e7f09b180fd7f9d421
source.ver: src/contrib/MANOR_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MANOR_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MANOR_1.30.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/MANOR/inst/doc/MANOR.pdf
vignetteTitles: MANOR overview
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MANOR/inst/doc/MANOR.R
htmlDocs: vignettes/MANOR/inst/doc/index.html
Package: manta
Version: 1.4.0
Depends: R (>= 1.8.0), methods, edgeR (>= 2.5.13)
Imports: Hmisc, caroline(>= 0.6.6)
Suggests: RSQLite, plotrix
License: Artistic-2.0
Title: Microbial Assemblage Normalized Transcript Analysis
Description: Tools for robust comparative metatranscriptomics.
biocViews: DifferentialExpression, RNAseq, Genetics, GeneExpression,
Bioinformatics, HighThroughputSequencing, QualityControl,
DataImport, Visualization
Author: David M. Schruth <dschruth@uw.edu> and Adrian Marchetti
<amarchetti@unc.edu>
Maintainer: David M. Schruth <dschruth@uw.edu>
URL: http://manta.ocean.washington.edu/
MD5sum: a025bb361ab997311fe1d6663c4acc10
source.ver: src/contrib/manta_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/manta_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/manta_1.4.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/manta_1.4.0.tgz
vignettes: vignettes/manta/inst/doc/manta.pdf
vignetteTitles: manta
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/manta/inst/doc/manta.R
Package: MantelCorr
Version: 1.28.0
Depends: R (>= 2.10)
Imports: stats
License: GPL (>= 2)
Title: Compute Mantel Cluster Correlations
Description: Computes Mantel cluster correlations from a (p x n)
numeric data matrix (e.g. microarray gene-expression data).
biocViews: Bioinformatics, Clustering
Author: Brian Steinmeyer and William Shannon
Maintainer: Brian Steinmeyer <steinmeb@ilya.wustl.edu>
MD5sum: 8b92ae9f81d24ff399d8354bfd31d443
source.ver: src/contrib/MantelCorr_1.28.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MantelCorr_1.28.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MantelCorr_1.28.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/MantelCorr/inst/doc/MantelCorrVignette.pdf
vignetteTitles: MantelCorrVignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MantelCorr/inst/doc/MantelCorrVignette.R
Package: marray
Version: 1.36.0
Depends: R (>= 2.10.0), limma, methods
Suggests: tkWidgets
License: LGPL
Title: Exploratory analysis for two-color spotted microarray data
Description: Class definitions for two-color spotted microarray data.
Fuctions for data input, diagnostic plots, normalization and
quality checking.
biocViews: Microarray, TwoChannel, Preprocessing
Author: Yee Hwa (Jean) Yang <jeany@maths.usyd.edu.au> with
contributions from Agnes Paquet and Sandrine Dudoit.
Maintainer: Yee Hwa (Jean) Yang <jean@biostat.ucsf.edu>
URL: http://www.maths.usyd.edu.au/u/jeany/
MD5sum: b1e405d59a2700942c441a67aa9b46cd
source.ver: src/contrib/marray_1.36.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/marray_1.36.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/marray_1.36.0.zip
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vignettes: vignettes/marray/inst/doc/ExampleHTML.pdf,
vignettes/marray/inst/doc/marrayClasses.pdf,
vignettes/marray/inst/doc/marrayClassesShort.pdf,
vignettes/marray/inst/doc/marrayInput.pdf,
vignettes/marray/inst/doc/marrayNorm.pdf,
vignettes/marray/inst/doc/marray.pdf,
vignettes/marray/inst/doc/marrayPlots.pdf,
vignettes/marray/inst/doc/widget1.pdf
vignetteTitles: ExampleHTML.pdf, marrayClasses Overview, marrayClasses
Tutorial (short), marrayInput Introduction, marray
Normalization, marray Overview, marrayPlots Overview,
widget1.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/marray/inst/doc/marrayClasses.R,
vignettes/marray/inst/doc/marrayClassesShort.R,
vignettes/marray/inst/doc/marrayInput.R,
vignettes/marray/inst/doc/marrayNorm.R,
vignettes/marray/inst/doc/marrayPlots.R,
vignettes/marray/inst/doc/marray.R
dependsOnMe: CGHbase, convert, dyebias, maigesPack, nnNorm, OLIN,
stepNorm, TurboNorm
importsMe: arrayQuality, nnNorm, OLIN, OLINgui, sigaR, stepNorm,
timecourse
suggestsMe: Agi4x44PreProcess, DEGraph, Mfuzz
Package: maSigPro
Version: 1.30.0
Depends: R (>= 2.3.1), stats, Biobase
Imports: Biobase, graphics, grDevices, limma, Mfuzz, stats, utils
License: GPL (>= 2)
Title: Significant Gene Expression Profile Differences in Time Course
Microarray Data
Description: maSigPro is a regression based approach to find genes for
which there are significant gene expression profile differences
between experimental groups in time course microarray
experiments.
biocViews: Microarray, DifferentialExpression, TimeCourse
Author: Ana Conesa <aconesa@cipf.es>, Maria Jose Nueda <mj.nueda@ua.es>
Maintainer: Maria Jose Nueda <mj.nueda@ua.es>
URL: http://bioinfo.cipf.es/
MD5sum: ec770eac34bb24fe38a581313d2dc6d4
source.ver: src/contrib/maSigPro_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/maSigPro_1.30.0.zip
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mac.binary.leopard.ver:
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vignettes: vignettes/maSigPro/inst/doc/maSigPro-tutorial.pdf,
vignettes/maSigPro/inst/doc/PLOTGROUPS.pdf,
vignettes/maSigPro/inst/doc/PLOTPROFILES.pdf
vignetteTitles: maSigPro User's Guide, PLOTGROUPS.pdf, PLOTPROFILES.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/maSigPro/inst/doc/maSigPro-tutorial.R
suggestsMe: oneChannelGUI
Package: maskBAD
Version: 1.2.0
Depends: R (>= 2.10), gcrma (>= 2.27.1), affy
Suggests: hgu95av2probe
License: GPL version 2 or newer
Title: Masking probes with binding affinity differences
Description: Package includes functions to analyze and mask microarray
expression data.
Author: Michael Dannemann <michael_dannemann@eva.mpg.de>
Maintainer: Michael Dannemann <michael_dannemann@eva.mpg.de>
MD5sum: 891e46b431e2adabf72d3e1c31a7faa5
source.ver: src/contrib/maskBAD_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/maskBAD_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/maskBAD_1.2.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/maskBAD/inst/doc/maskBAD.pdf
vignetteTitles: Package maskBAD
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/maskBAD/inst/doc/maskBAD.R
Package: MassArray
Version: 1.10.0
Depends: R (>= 2.10.0), methods
Imports: graphics, grDevices, methods, stats, utils
License: GPL (>=2)
Title: Analytical Tools for MassArray Data
Description: This package is designed for the import, quality control,
analysis, and visualization of methylation data generated using
Sequenom's MassArray platform. The tools herein contain a
highly detailed amplicon prediction for optimal assay design.
Also included are quality control measures of data, such as
primer dimer and bisulfite conversion efficiency estimation.
Methylation data are calculated using the same algorithms
contained in the EpiTyper software package. Additionally,
automatic SNP-detection can be used to flag potentially
confounded data from specific CG sites. Visualization includes
barplots of methylation data as well as UCSC Genome
Browser-compatible BED tracks. Multiple assays can be
positionally combined for integrated analysis.
biocViews: DNAMethylation, SNP, MassSpectrometry, Genetics, DataImport,
Visualization
Author: Reid F. Thompson <rthompso@aecom.yu.edu>, John M. Greally
<jgreally@aecom.yu.edu>
Maintainer: Reid F. Thompson <rthompso@aecom.yu.edu>
MD5sum: eb4b4bccba149dd1bb2706ee5a8a2e91
source.ver: src/contrib/MassArray_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MassArray_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MassArray_1.10.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/MassArray/inst/doc/conversion.pdf,
vignettes/MassArray/inst/doc/MassArray.pdf
vignetteTitles: conversion.pdf, 1. Primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MassArray/inst/doc/MassArray.R
Package: MassSpecWavelet
Version: 1.24.0
Depends: waveslim
Suggests: xcms, caTools
License: LGPL (>= 2)
Archs: i386, x64
Title: Mass spectrum processing by wavelet-based algorithms
Description: Processing Mass Spectrometry spectrum by using wavelet
based algorithm
biocViews: MassSpectrometry, Proteomics
Author: Pan Du, Warren Kibbe, Simon Lin
Maintainer: Pan Du <dupan@northwestern.edu>
MD5sum: 25aabf5a70717b880d0af44feffb352a
source.ver: src/contrib/MassSpecWavelet_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MassSpecWavelet_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MassSpecWavelet_1.24.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/MassSpecWavelet/inst/doc/MassSpecWavelet.pdf
vignetteTitles: MassSpecWavelet
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MassSpecWavelet/inst/doc/MassSpecWavelet.R
suggestsMe: xcms
Package: matchBox
Version: 1.0.0
Depends: R (>= 2.8.0)
License: Artistic-2.0
Title: Utilities to compute, compare, and plot the agreement between
ordered vectors of features (ie. distinct genomic experiments).
The package includes Correspondence-At-the-TOP (CAT) analysis.
Description: The matchBox package enables comparing ranked vectors of
features, merging multiple datasets, removing redundant
features, using CAT-plots and Venn diagrams, and computing
statistical significance.
biocViews: Software, Annotation, Microarray, MultipleComparisons,
Visualization
Author: Luigi Marchionni <marchion@jhu.edu>, Anuj Gupta <Anuj Gupta
<agupta52@jhu.edu>
Maintainer: Luigi Marchionni <marchion@jhu.edu>, Anuj Gupta <Anuj Gupta
<agupta52@jhu.edu>
MD5sum: a159d3526485e6082817d1d7052b516a
source.ver: src/contrib/matchBox_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/matchBox_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/matchBox_1.0.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/matchBox/inst/doc/matchBox.pdf
vignetteTitles: Working with the matchBox package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/matchBox/inst/doc/matchBox.R
Package: MBCB
Version: 1.12.0
Depends: R (>= 2.9.0), tcltk, tcltk2
Imports: preprocessCore, stats, utils
License: GPL (>= 2)
Title: MBCB (Model-based Background Correction for Beadarray)
Description: This package provides a model-based background correction
method, which incorporates the negative control beads to
pre-process Illumina BeadArray data.
biocViews: Microarray, Preprocessing
Author: Yang Xie <Yang.Xie@UTSouthwestern.edu>
Maintainer: Jeff Allen <Jeffrey.Allen@UTSouthwestern.edu>
URL: http://www.utsouthwestern.edu
MD5sum: b3afc59686153498bee60e52961cff72
source.ver: src/contrib/MBCB_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MBCB_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MBCB_1.12.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MBCB_1.12.0.tgz
vignettes: vignettes/MBCB/inst/doc/MBCB.pdf
vignetteTitles: MBCB
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MBCB/inst/doc/MBCB.R
Package: mBPCR
Version: 1.12.0
Depends: oligoClasses, SNPchip
Imports: Biobase
Suggests: xtable
License: GPL (>= 2)
Title: Bayesian Piecewise Constant Regression for DNA copy number
estimation
Description: Estimates the DNA copy number profile using mBPCR to
detect regions with copy number changes
biocViews: aCGH, SNP, Microarray, CopyNumberVariants, Bioinformatics
Author: P.M.V. Rancoita <paola.rancoita@gmail.com>, with contributions
from M. Hutter <marcus.hutter@anu.edu.au>
Maintainer: P.M.V. Rancoita <paola.rancoita@gmail.com>
URL: http://www.idsia.ch/~paola/mBPCR
MD5sum: 9e301d6a30c44f6a6892483580857c2c
source.ver: src/contrib/mBPCR_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/mBPCR_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/mBPCR_1.12.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/mBPCR/inst/doc/mBPCR.pdf
vignetteTitles: mBPCR
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/mBPCR/inst/doc/mBPCR.R
Package: mcaGUI
Version: 1.6.0
Depends: lattice, MASS, proto, foreign, gWidgets(>= 0.0-36),
gWidgetsRGtk2(>= 0.0-53), OTUbase, vegan, bpca
Enhances: iplots, reshape, ggplot2, cairoDevice, OTUbase
License: GPL (>= 2)
Title: Microbial Community Analysis GUI
Description: Microbial community analysis GUI for R using gWidgets.
biocViews: GUI, Visualization, Bioinformatics, Clustering, Sequencing
Author: Wade K. Copeland, Vandhana Krishnan, Daniel Beck, Matt Settles,
James Foster, Kyu-Chul Cho, Mitch Day, Roxana Hickey, Ursel
M.E. Schutte, Xia Zhou, Chris Williams, Larry J. Forney, Zaid
Abdo, Poor Man's GUI (PMG) base code by John Verzani with
contributions by Yvonnick Noel
Maintainer: Wade K. Copeland <wade@kingcopeland.com>
URL: http://www.ibest.uidaho.edu/ibest/index.php
MD5sum: 3072aff15847feb23bddbb5aa949ce58
source.ver: src/contrib/mcaGUI_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/mcaGUI_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/mcaGUI_1.6.0.zip
mac.binary.leopard.ver:
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vignettes:
vignettes/mcaGUI/inst/doc/An_Introduction_and_User_Guide_for_mcaGUI.pdf
vignetteTitles: An_Introduction_and_User_Guide_for_mcaGUI.pdf
hasREADME: TRUE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: MCRestimate
Version: 2.14.0
Depends: R (>= 2.7.2), golubEsets (>= 1.4.6)
Imports: e1071 (>= 1.5-12), pamr (>= 1.22), randomForest (>= 3.9-6),
RColorBrewer (>= 0.1-3), Biobase (>= 2.5.5), graphics,
grDevices, stats, utils
Suggests: xtable (>= 1.2-1), ROC (>= 1.8.0), genefilter (>= 1.12.0),
gpls (>= 1.6.0)
License: GPL (>= 2)
Title: Misclassification error estimation with cross-validation
Description: This package includes a function for combining
preprocessing and classification methods to calculate
misclassification errors
biocViews: Bioinformatics, Classification
Author: Marc Johannes, Markus Ruschhaupt, Holger Froehlich, Ulrich
Mansmann, Andreas Buness, Patrick Warnat, Wolfgang Huber, Axel
Benner, Tim Beissbarth
Maintainer: Marc Johannes <m.johannes@dkfz.de>
MD5sum: 92772cd9ad8d0b6a7ce24ab655de0417
source.ver: src/contrib/MCRestimate_2.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MCRestimate_2.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MCRestimate_2.14.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/MCRestimate/inst/doc/UsingMCRestimate.pdf
vignetteTitles: HOW TO use MCRestimate
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MCRestimate/inst/doc/UsingMCRestimate.R
Package: mdqc
Version: 1.20.0
Depends: R (>= 2.2.1), cluster, MASS
License: LGPL (>= 2)
Title: Mahalanobis Distance Quality Control for microarrays
Description: MDQC is a multivariate quality assessment method for
microarrays based on quality control (QC) reports. The
Mahalanobis distance of an array's quality attributes is used
to measure the similarity of the quality of that array against
the quality of the other arrays. Then, arrays with unusually
high distances can be flagged as potentially low-quality.
biocViews: Microarray, QualityControl
Author: Justin Harrington
Maintainer: Gabriela Cohen-Freue <gcohen@mrl.ubc.ca>
MD5sum: 2dfde48bee9eeefcc3866057bc6e6f12
source.ver: src/contrib/mdqc_1.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/mdqc_1.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/mdqc_1.20.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mdqc_1.20.0.tgz
vignettes: vignettes/mdqc/inst/doc/mdqcvignette.pdf
vignetteTitles: Introduction to MDQC
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/mdqc/inst/doc/mdqcvignette.R
importsMe: arrayMvout
Package: MeasurementError.cor
Version: 1.30.0
License: LGPL
Title: Measurement Error model estimate for correlation coefficient
Description: Two-stage measurement error model for correlation
estimation with smaller bias than the usual sample correlation
biocViews: Bioinformatics
Author: Beiying Ding
Maintainer: Beiying Ding <bding@amgen.com>
MD5sum: ff4cbd68dc0c7b3a754b927c3c6bb643
source.ver: src/contrib/MeasurementError.cor_1.30.0.tar.gz
win.binary.ver:
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win64.binary.ver:
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mac.binary.leopard.ver:
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vignettes:
vignettes/MeasurementError.cor/inst/doc/MeasurementError.cor.pdf
vignetteTitles: MeasurementError.cor Tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: MEDIPS
Version: 1.8.0
Depends: R (>= 2.12.0), BiocGenerics (>= 0.1.3), BSgenome
Imports: methods, BiocGenerics, Biostrings, BSgenome, graphics, gtools,
IRanges, stats, utils
Suggests: BSgenome.Hsapiens.UCSC.hg19
License: GPL (>=2)
Archs: i386, x64
Title: MeDIP-Seq data analysis
Description: MEDIPS was developed for analyzing data derived from
methylated DNA immunoprecipitation (MeDIP) experiments followed
by sequencing (MeDIP-Seq). Nevertheless, functionalities like
the quality controls may be applied to other types of
sequencing data (e.g. ChIP-Seq). MEDIPS adresses several
aspects in the context of MeDIP-Seq data analysis.
biocViews: Sequencing, DNAMethylation, CpGIsland,
DifferentialExpression, HighThroughputSequencing, ChIPseq,
Preprocessing, QualityControl, Visualization, Methylseq
Author: Lukas Chavez, Joern Dietrich
Maintainer: Lukas Chavez <chavez@molgen.mpg.de>
MD5sum: ac88cdeb476f76506c9aebbb30812288
source.ver: src/contrib/MEDIPS_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MEDIPS_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MEDIPS_1.8.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/MEDIPS/inst/doc/MEDIPS.pdf
vignetteTitles: MEDIPS
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MEDIPS/inst/doc/MEDIPS.R
Package: MEDME
Version: 1.18.0
Depends: R (>= 2.15), grDevices, graphics, methods, stats, utils
Imports: Biostrings, MASS, drc
Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9
License: GPL (>= 2)
Archs: i386, x64
Title: Modelling Experimental Data from MeDIP Enrichment
Description: Description: MEDME allows the prediction of absolute and
relative methylation levels based on measures obtained by
MeDIP-microarray experiments
biocViews: Microarray, CpGIsland, DNAMethylation
Author: Mattia Pelizzola and Annette Molinaro
Maintainer: Mattia Pelizzola <mattia.pelizzola@gmail.com>
MD5sum: 53f7ded7a0dba349f408b5bd7d50d38c
source.ver: src/contrib/MEDME_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MEDME_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MEDME_1.18.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/MEDME/inst/doc/MEDME.pdf
vignetteTitles: MEDME.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MEDME/inst/doc/MEDME.R
Package: MergeMaid
Version: 2.30.0
Depends: R (>= 2.10.0), survival, Biobase, MASS, methods
License: GPL (>= 2)
Title: Merge Maid
Description: The functions in this R extension are intended for
cross-study comparison of gene expression array data. Required
from the user is gene expression matrices, their corresponding
gene-id vectors and other useful information, and they could be
'list','matrix', or 'ExpressionSet'. The main function is
'mergeExprs' which transforms the input objects into data in
the merged format, such that common genes in different datasets
can be easily found. And the function 'intcor' calculate the
correlation coefficients. Other functions use the output from
'modelOutcome' to graphically display the results and
cross-validate associations of gene expression data with
survival.
biocViews: Microarray, DifferentialExpression, Visualization
Author: Xiaogang Zhong <zhong@ams.jhu.edu> Leslie Cope <cope@jhu.edu>
Elizabeth Garrett <esg@jhu.edu> Giovanni Parmigiani
<gp@jhu.edu>
Maintainer: Xiaogang Zhong <zhong@ams.jhu.edu>
URL: http://astor.som.jhmi.edu/MergeMaid
MD5sum: dec227a3688fac6fe484d2722e401c9f
source.ver: src/contrib/MergeMaid_2.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MergeMaid_2.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MergeMaid_2.30.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/MergeMaid/inst/doc/MergeMaid.pdf
vignetteTitles: MergeMaid primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MergeMaid/inst/doc/MergeMaid.R
importsMe: metaArray, XDE
suggestsMe: oneChannelGUI
Package: metaArray
Version: 1.36.0
Imports: Biobase, MergeMaid, graphics, stats
License: LGPL-2
Archs: i386, x64
Title: Integration of Microarray Data for Meta-analysis
Description: 1) Data transformation for meta-analysis of microarray
Data: Transformation of gene expression data to signed
probability scale (MCMC/EM methods) 2) Combined differential
expression on raw scale: Weighted Z-score after stabilizing
mean-variance relation within platform
biocViews: Microarray, Bioinformatics, DifferentialExpression
Author: Debashis Ghosh <ghoshd@psu.edu> Hyungwon Choi
<hyung_won_choi@nuhs.edu.sg>
Maintainer: Hyungwon Choi <hyung_won_choi@nuhs.edu.sg>
MD5sum: 90680bc0b3a860e8acc4dd3824db3148
source.ver: src/contrib/metaArray_1.36.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/metaArray_1.36.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/metaArray_1.36.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/metaArray/inst/doc/metaArray.pdf
vignetteTitles: metaArray Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/metaArray/inst/doc/metaArray.R
suggestsMe: oneChannelGUI
Package: metahdep
Version: 1.16.0
Depends: R (>= 2.10), methods
Suggests: affyPLM
License: GPL-3
Archs: i386, x64
Title: Hierarchical Dependence in Meta-Analysis
Description: Tools for meta-analysis in the presence of hierarchical
(and/or sampling) dependence, including with gene expression
studies
biocViews: Microarray, Bioinformatics, DifferentialExpression
Author: John R. Stevens, Gabriel Nicholas
Maintainer: John R. Stevens <john.r.stevens@usu.edu>
MD5sum: 4635f23d52793a5834b555e02938b880
source.ver: src/contrib/metahdep_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/metahdep_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/metahdep_1.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/metahdep/inst/doc/metahdep.pdf
vignetteTitles: metahdep Primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/metahdep/inst/doc/metahdep.R
Package: methVisual
Version: 1.10.0
Depends: R (>= 2.11.0), Biostrings(>= 2.4.8), plotrix,gsubfn,
grid,sqldf
Imports: Biostrings, ca, graphics, grDevices, grid, gridBase, IRanges,
stats, utils
License: GPL (>= 2)
Title: Methods for visualization and statistics on DNA methylation data
Description: The package 'methVisual' allows the visualization of DNA
methylation data after bisulfite sequencing.
biocViews: Bioinformatics, DNAMethylation, Clustering, Classification
Author: A. Zackay, C. Steinhoff
Maintainer: Arie Zackay <arie.zackay@mail.huji.ac.il>
MD5sum: 77e46515182dbb940622c943c3154183
source.ver: src/contrib/methVisual_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/methVisual_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/methVisual_1.10.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/methVisual/inst/doc/methVisual.pdf
vignetteTitles: Introduction to methVisual
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/methVisual/inst/doc/methVisual.R
Package: methyAnalysis
Version: 1.0.0
Depends: R (>= 2.10), grid, IRanges, Biobase (>= 2.5.5), org.Hs.eg.db
Imports: lumi, methylumi, Gviz, genoset, GenomicRanges, IRanges,
rtracklayer, GenomicFeatures, annotate, Biobase (>= 2.5.5),
AnnotationDbi, genefilter, biomaRt, methods
Suggests: IlluminaHumanMethylation450k.db,
TxDb.Hsapiens.UCSC.hg19.knownGene
License: Artistic-2.0
Title: DNA methylation data analysis and visualization
Description: The methyAnalysis package aims for the DNA methylation
data analysis and visualization. A new class is defined to keep
the chromosome location information together with the data. The
current version of the package mainly focus on analyzing the
Illumina Infinium methylation array data, but most methods can
be generalized to other methylation array or sequencing data.
biocViews: Microarray, DNAMethylation, Visualization
Author: Pan Du, Richard Bourgon
Maintainer: Pan Du <dupan.mail@gmail.com>
MD5sum: 24a2e2bdb3b1153d96521a35744d9f62
source.ver: src/contrib/methyAnalysis_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/methyAnalysis_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/methyAnalysis_1.0.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/methyAnalysis_1.0.0.tgz
vignettes: vignettes/methyAnalysis/inst/doc/methyAnalysis.pdf
vignetteTitles: An Introduction to the methyAnalysis package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/methyAnalysis/inst/doc/methyAnalysis.R
Package: methylumi
Version: 2.4.0
Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2
Imports: Biobase, graphics, lattice, annotate, genefilter,
AnnotationDbi, stats4, BiocGenerics
Suggests: lumi, lattice, limma, xtable, IlluminaHumanMethylation27k.db
(>= 1.4.4), IlluminaHumanMethylation450k.db, SQN, MASS,
matrixStats, parallel
License: GPL-2
Title: Handle Illumina methylation data
Description: This package provides classes for holding and manipulating
Illumina methylation data. Based on eSet, it can contain MIAME
information, sample information, feature information, and
multiple matrices of data. An "intelligent" import function,
methylumiR can read the Illumina text files and create a
MethyLumiSet. methylumIDAT can directly read raw IDAT files
from HumanMethylation27 and HumanMethylation450 microarrays.
Normalization, background correction, and quality control
features for GoldenGate, Infinium, and Infinium HD arrays are
also included.
biocViews: DNAMethylation, TwoChannel, Preprocessing, QualityControl,
CpGIsland
Author: Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla
Maintainer: Sean Davis <sdavis2@mail.nih.gov>
MD5sum: 7360576a19ced4f94995b4a787694a53
source.ver: src/contrib/methylumi_2.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/methylumi_2.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/methylumi_2.4.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/methylumi_2.4.0.tgz
vignettes: vignettes/methylumi/inst/doc/methylumi.pdf
vignetteTitles: An Introduction to the methylumi package
hasREADME: TRUE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/methylumi/inst/doc/methylumi.R
importsMe: ffpe, lumi, methyAnalysis
Package: Mfuzz
Version: 2.16.1
Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071
Imports: tcltk, tkWidgets
Suggests: marray
License: GPL-2
Title: Soft clustering of time series gene expression data
Description: Package for noise-robust soft clustering of gene
expression time-series data (including a graphical user
interface)
biocViews: Microarray, Clustering, TimeCourse, Preprocessing,
Visualization
Author: Matthias Futschik <mfutschik@ualg.pt>
Maintainer: Matthias Futschik <mfutschik@ualg.pt>
URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/
MD5sum: fae6f79b0d1fc85fb9dcdf1b5648776b
source.ver: src/contrib/Mfuzz_2.16.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Mfuzz_2.16.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/Mfuzz_2.16.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/Mfuzz_2.16.1.tgz
vignettes: vignettes/Mfuzz/inst/doc/MfuzzguiScreenshot.pdf,
vignettes/Mfuzz/inst/doc/Mfuzz.pdf,
vignettes/Mfuzz/inst/doc/yeasttable3.pdf
vignetteTitles: MfuzzguiScreenshot.pdf, Introduction to Mfuzz,
yeasttable3.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Mfuzz/inst/doc/Mfuzz.R
dependsOnMe: cycle
importsMe: maSigPro
Package: mgsa
Version: 1.6.0
Depends: R (>= 2.9.0), methods, gplots
Imports: gplots, graphics, stats, utils
Suggests: DBI, RSQLite, GO.db
License: Artistic-2.0
Archs: i386, x64
Title: Model-based gene set analysis
Description: Model-based Gene Set Analysis (MGSA) is a Bayesian
modeling approach for gene set enrichment. The package mgsa
implements MGSA and tools to use MGSA together with the Gene
Ontology.
biocViews: Pathways, GO, GeneSetEnrichment
Author: Sebastian Bauer <Sebastian.Bauer@charite.de>, Julien Gagneur
<gagneur@genzentrum.lmu.de>
Maintainer: Sebastian Bauer <Sebastian.Bauer@charite.de>
MD5sum: 487822e9ec8ea974ed41d3a8ba63d17d
source.ver: src/contrib/mgsa_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/mgsa_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/mgsa_1.6.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mgsa_1.6.0.tgz
vignettes: vignettes/mgsa/inst/doc/mgsa.pdf
vignetteTitles: Overview of the mgsa package.
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/mgsa/inst/doc/mgsa.R
Package: MiChip
Version: 1.12.0
Depends: R (>= 2.3.0), Biobase
Imports: Biobase
License: GPL (>= 2)
Title: MiChip Parsing and Summarizing Functions
Description: This package takes the MiChip miRNA microarray .grp
scanner output files and parses these out, providing summary
and plotting functions to analyse MiChip hybridizations. A set
of hybridizations is packaged into an ExpressionSet allowing it
to be used by other BioConductor packages.
biocViews: Microarray, Preprocessing
Author: Jonathon Blake <blake@embl.de>
Maintainer: Jonathon Blake <blake@embl.de>
MD5sum: 4db67b3207869418b213cc4abce27ead
source.ver: src/contrib/MiChip_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MiChip_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MiChip_1.12.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/MiChip_1.12.0.tgz
vignettes: vignettes/MiChip/inst/doc/MiChip.pdf
vignetteTitles: MiChip miRNA Microarray Processing
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MiChip/inst/doc/MiChip.R
Package: microRNA
Version: 1.16.0
Depends: R (>= 2.10)
Imports: Biostrings (>= 2.11.32)
Suggests: Biostrings (>= 2.11.32)
Enhances: Rlibstree
License: Artistic-2.0
Title: Data and functions for dealing with microRNAs
Description: Different data resources for microRNAs and some functions
for manipulating them.
biocViews: Infrastructure, SequenceAnnotation, SequenceMatching
Author: R. Gentleman, S. Falcon
Maintainer: "James F. Reid" <james.reid@ifom-ieo-campus.it>
MD5sum: bc4280b3d0fc9acc14f9e3e9664d375e
source.ver: src/contrib/microRNA_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/microRNA_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/microRNA_1.16.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/microRNA_1.16.0.tgz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: MmPalateMiRNA, rtracklayer
Package: minet
Version: 3.12.0
Depends: infotheo
License: file LICENSE
Archs: i386, x64
Title: Mutual Information NETworks
Description: This package implements various algorithms for inferring
mutual information networks from data.
biocViews: Microarray, GraphsAndNetworks, NetworkAnalysis,
NetworkInference
Author: Patrick E. Meyer, Frederic Lafitte, Gianluca Bontempi
Maintainer: Patrick E. Meyer <software@meyerp.com>
URL: http://minet.meyerp.com
MD5sum: 65b5df351fe5cf71ed1b5582132c4c28
source.ver: src/contrib/minet_3.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/minet_3.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/minet_3.12.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/minet_3.12.0.tgz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
dependsOnMe: BUS, netresponse
suggestsMe: predictionet
Package: minfi
Version: 1.4.0
Depends: methods, BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8),
lattice, reshape, GenomicRanges, Biostrings, utils
Imports: BiocGenerics, beanplot, RColorBrewer, nor1mix, siggenes,
limma, preprocessCore, crlmm, matrixStats, mclust
Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), minfiData
(>= 0.2.0), RUnit
License: Artistic-2.0
Title: Analyze Illumina's 450k methylation arrays
Description: Tools for analyzing and visualizing Illumina's 450k array
data
biocViews: DNAMethylation, Microarray, TwoChannel, DataImport,
Preprocessing, QualityControl
Author: Kasper Daniel Hansen, Martin Aryee
Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
MD5sum: 2155ef1da26c026e7b34fc24679b9085
source.ver: src/contrib/minfi_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/minfi_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/minfi_1.4.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/minfi_1.4.0.tgz
vignettes: vignettes/minfi/inst/doc/minfi.pdf
vignetteTitles: Minfi Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/minfi/inst/doc/minfi.R
Package: MinimumDistance
Version: 1.2.4
Depends: R (>= 2.14), BiocGenerics (>= 0.3.2), IRanges (>= 1.13.30)
Imports: methods, DNAcopy, utils, msm, lattice, BiocGenerics,
VanillaICE (>= 1.19.23), ff, SNPchip (>= 2.3.10), Biobase (>=
2.17.8), foreach, oligoClasses (>= 1.19.34), GenomicRanges
Suggests: human610quadv1bCrlmm, RUnit
Enhances: snow, doSNOW
License: Artistic-2.0
Title: A package for de novo CNV detection in case-parent trios
Description: Analysis of de novo copy number variants in trios from
high-dimensional genotyping platforms
biocViews: Microarray, SNP, Bioinformatics, CopyNumberVariants
Author: Robert B Scharpf, Moiz Bootwalla, and Ingo Ruczinski
Maintainer: Robert B Scharpf <rscharpf@jhsph.edu>
MD5sum: 16802f4297ad3d00938b11e7a8340b24
source.ver: src/contrib/MinimumDistance_1.2.4.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MinimumDistance_1.2.4.zip
win64.binary.ver: bin/windows64/contrib/2.15/MinimumDistance_1.2.4.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/MinimumDistance_1.2.4.tgz
vignettes: vignettes/MinimumDistance/inst/doc/MinimumDistance.pdf
vignetteTitles: Detection of de novo copy number alterations in
case-parent trios
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MinimumDistance/inst/doc/MinimumDistance.R
Package: MiPP
Version: 1.30.0
Depends: R (>= 2.4)
Imports: Biobase, e1071, MASS, stats
License: GPL (>= 2)
Title: Misclassification Penalized Posterior Classification
Description: This package finds optimal sets of genes that seperate
samples into two or more classes.
biocViews: Microarray, Classification
Author: HyungJun Cho <hj4cho@korea.ac.kr>, Sukwoo Kim
<s4kim@korea.ac.kr>, Mat Soukup <soukup@fda.gov>, and Jae K.
Lee <jaeklee@virginia.edu>
Maintainer: Sukwoo Kim <s4kim@korea.ac.kr>
URL:
http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/
MD5sum: 73d94a55c1f34d616235772b80ac78f9
source.ver: src/contrib/MiPP_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MiPP_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MiPP_1.30.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MiPP_1.30.0.tgz
vignettes: vignettes/MiPP/inst/doc/MiPP.pdf
vignetteTitles: MiPP Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MiPP/inst/doc/MiPP.R
Package: MiRaGE
Version: 1.0.0
Depends: R (>= 2.12.1), Biobase(>= 2.16.0)
Imports: AnnotationDbi, BiocGenerics
Suggests: seqinr (>= 3.0.3), biomaRt (>= 2.6.0), GenomicFeatures (>=
1.8.1), Biostrings (>= 2.24.1), BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm9, miRNATarget, humanStemCell,
IRanges , GenomicRanges (>= 1.8.3), BSgenome,
beadarrayExampleData
License: GPL
Title: MiRNA Ranking by Gene Expression
Description: The package contains functions for inferece of target gene
regulation by miRNA, based on only target gene expression
profile.
biocViews: Microarray, GeneExpression, RNAseq, RNAseqData,
HighThroughputSequencingData, Sequencing, SAGE
Author: Y-h. Taguchi <tag@granular.com>
Maintainer: Y-h. Taguchi <tag@granular.com>
MD5sum: 48b4acb3c24585fc85957b34ac38eda7
source.ver: src/contrib/MiRaGE_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MiRaGE_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MiRaGE_1.0.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/MiRaGE_1.0.0.tgz
vignettes: vignettes/MiRaGE/inst/doc/MiRaGE.pdf
vignetteTitles: How to use MiRaGE Package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MiRaGE/inst/doc/MiRaGE.R
Package: miRNApath
Version: 1.18.0
Depends: methods, R(>= 2.7.0)
License: LGPL-2.1
Title: miRNApath: Pathway Enrichment for miRNA Expression Data
Description: This package provides pathway enrichment techniques for
miRNA expression data. Specifically, the set of methods handles
the many-to-many relationship between miRNAs and the multiple
genes they are predicted to target (and thus affect.) It also
handles the gene-to-pathway relationships separately. Both
steps are designed to preserve the additive effects of miRNAs
on genes, many miRNAs affecting one gene, one miRNA affecting
multiple genes, or many miRNAs affecting many genes.
biocViews: Annotation, Pathways, DifferentialExpression,
NetworkEnrichment, miRNA
Author: James M. Ward <jmw86069@gmail.com> with contributions from
Yunling Shi, Cindy Richards, John P. Cogswell
Maintainer: James M. Ward <jmw86069@gmail.com>
MD5sum: 1ef3291851b9d45cf2b1c440495c0944
source.ver: src/contrib/miRNApath_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/miRNApath_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/miRNApath_1.18.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/miRNApath_1.18.0.tgz
vignettes: vignettes/miRNApath/inst/doc/miRNApath.pdf
vignetteTitles: miRNApath: Pathway Enrichment for miRNA Expression Data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/miRNApath/inst/doc/miRNApath.R
Package: MLInterfaces
Version: 1.38.1
Depends: R (>= 2.9), Biobase, MASS, methods, genefilter, rpart, rda,
annotate, cluster, sfsmisc
Imports: mboost, gdata, pls
Suggests: class, e1071, ipred, randomForest, gpls, pamr, rpart, MASS,
nnet, ALL, gbm, mlbench, hgu95av2.db, som, RColorBrewer,
hu6800.db, lattice, caret (>= 5.07), golubEsets, ada,
keggorthology, kernlab, gbm, mboost, sfsmisc, party
Enhances: parallel
License: LGPL
Title: Uniform interfaces to R machine learning procedures for data in
Bioconductor containers
Description: Uniform interfaces to machine learning code for data in
Bioconductor containers
biocViews: Bioinformatics, Classification, Clustering
Author: Vince Carey <stvjc@channing.harvard.edu>, Robert Gentleman,
Jess Mar, and contributions from Jason Vertrees
<jv@cs.dartmouth.edu> and Laurent Gatto <lg390@cam.ac.uk>
Maintainer: V. Carey <stvjc@channing.harvard.edu>
MD5sum: 0fa16ef7e6bd7009b26031a268b283a0
source.ver: src/contrib/MLInterfaces_1.38.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MLInterfaces_1.38.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/MLInterfaces_1.38.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/MLInterfaces_1.38.1.tgz
vignettes: vignettes/MLInterfaces/inst/doc/MLint_devel.pdf,
vignettes/MLInterfaces/inst/doc/MLInterfaces.pdf,
vignettes/MLInterfaces/inst/doc/MLprac2_2.pdf,
vignettes/MLInterfaces/inst/doc/xvalComputerClusters.pdf
vignetteTitles: MLInterfaces devel for schema-based MLearn,
MLInterfaces Primer, A machine learning tutorial: applications
of the Bioconductor MLInterfaces package to expression and
ChIP-Seq data, MLInterfaces Computer Cluster
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MLInterfaces/inst/doc/MLint_devel.R,
vignettes/MLInterfaces/inst/doc/MLInterfaces.R,
vignettes/MLInterfaces/inst/doc/MLprac2_2.R,
vignettes/MLInterfaces/inst/doc/xvalComputerClusters.R
dependsOnMe: a4Classif
suggestsMe: BiocCaseStudies
Package: MLP
Version: 1.6.0
Depends: AnnotationDbi, affy, plotrix, gplots, gmodels, gdata, gtools
Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Cf.eg.db, KEGG.db, annotate, Rgraphviz, GOstats, limma,
mouse4302.db, reactome.db
License: GPL-3
Title: MLP
Description: Mean Log P Analysis
biocViews: Genetics
Author: Nandini Raghavan, Tobias Verbeke, An De Bondt with
contributions by Javier Cabrera, Dhammika Amaratunga, Tine
Casneuf and Willem Ligtenberg
Maintainer: Tobias Verbeke <tobias.verbeke@openanalytics.eu>
MD5sum: b3ebe9abcbff9b0cae6c88cb85dded03
source.ver: src/contrib/MLP_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MLP_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MLP_1.6.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MLP_1.6.0.tgz
vignettes: vignettes/MLP/inst/doc/UsingMLP.pdf
vignetteTitles: UsingMLP
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MLP/inst/doc/UsingMLP.R
suggestsMe: a4
Package: MmPalateMiRNA
Version: 1.6.0
Depends: R (>= 2.13.0), methods, Biobase, xtable, limma, statmod,
lattice, vsn
Imports: limma, lattice, Biobase
Suggests: GOstats, graph, Category, org.Mm.eg.db, microRNA,
targetscan.Mm.eg.db, RSQLite, DBI, AnnotationDbi, clValid,
class, cluster, multtest, RColorBrewer, latticeExtra
License: LGPL-3
Title: Murine Palate miRNA Expression Analysis
Description: R package compendium for the analysis of murine palate
miRNA two-color expression data.
biocViews: Microarray, TwoChannel, Bioinformatics, QualityControl,
Preprocessing, DifferentialExpression, MultipleComparisons,
Clustering, GO, Pathways, ReportWriting, SequenceMatching
Author: Guy Brock <guy.brock@louisville.edu>, Partha Mukhopadhyay
<p0mukh01@louisville.edu>, Vasyl Pihur
<vasyl.pihur@louisville.edu>, Robert M. Greene
<Dr.Bob.Greene@gmail.com>, and M. Michele Pisano
<mmpisa01@louisville.edu>
Maintainer: Guy Brock <guy.brock@louisville.edu>
MD5sum: d2a6eb3d4c877c86605debe186b9ebe5
source.ver: src/contrib/MmPalateMiRNA_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MmPalateMiRNA_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MmPalateMiRNA_1.6.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/MmPalateMiRNA_1.6.0.tgz
vignettes: vignettes/MmPalateMiRNA/inst/doc/MmPalateMiRNA.pdf
vignetteTitles: Palate miRNA Analysis
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MmPalateMiRNA/inst/doc/MmPalateMiRNA.R
Package: mosaics
Version: 1.6.0
Depends: R (>= 2.11.1), methods, graphics, Rcpp
Imports: MASS, splines, lattice, IRanges
LinkingTo: Rcpp
Suggests: mosaicsExample
Enhances: parallel
License: GPL (>= 2)
Archs: i386, x64
Title: MOSAiCS (MOdel-based one and two Sample Analysis and Inference
for ChIP-Seq)
Description: This package provides functions for fitting MOSAiCS, a
statistical framework to analyze one-sample or two-sample
ChIP-seq data.
biocViews: ChIPseq, Sequencing, Transcription, Genetics, Bioinformatics
Author: Dongjun Chung, Pei Fen Kuan, Sunduz Keles
Maintainer: Dongjun Chung <chungdon@stat.wisc.edu>
URL: http://groups.google.com/group/mosaics_user_group
SystemRequirements: Perl
MD5sum: d3ecbfe9ab430254a1ebe3c15a63e2d7
source.ver: src/contrib/mosaics_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/mosaics_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/mosaics_1.6.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/mosaics/inst/doc/Figure4a.pdf,
vignettes/mosaics/inst/doc/Figure4b.pdf,
vignettes/mosaics/inst/doc/Figure5a.pdf,
vignettes/mosaics/inst/doc/Figure5b.pdf,
vignettes/mosaics/inst/doc/Figure5c.pdf,
vignettes/mosaics/inst/doc/Figure5d.pdf,
vignettes/mosaics/inst/doc/GOF_matchLow.pdf,
vignettes/mosaics/inst/doc/GOF_rMOM.pdf,
vignettes/mosaics/inst/doc/mosaics-example.pdf
vignetteTitles: Figure4a.pdf, Figure4b.pdf, Figure5a.pdf, Figure5b.pdf,
Figure5c.pdf, Figure5d.pdf, GOF_matchLow.pdf, GOF_rMOM.pdf,
MOSAiCS
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/mosaics/inst/doc/mosaics-example.R
Package: MotifDb
Version: 1.0.0
Depends: R (>= 2.15.0), methods, IRanges, Biostrings
Imports: BiocGenerics, rtracklayer
Suggests: RUnit, MotIV, seqLogo
License: Artistic-2.0
Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
Description: More than 2000 annotated position frequency matrices from
five public source, for multiple organisms
biocViews: GenomicSequence, MotifAnnotation
Author: Paul Shannon
Maintainer: Paul Shannon <pshannon@fhcrc.org>
MD5sum: 6c23b6bfac7a679134b7ff4371ac36dc
source.ver: src/contrib/MotifDb_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MotifDb_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MotifDb_1.0.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/MotifDb/inst/doc/MotifDb.pdf
vignetteTitles: MotifDb Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MotifDb/inst/doc/MotifDb.R
Package: motifRG
Version: 1.2.0
Depends: R (>= 2.10)
Imports: Biostrings, IRanges, seqLogo, parallel, methods, grid,graphics
License: Artistic-2.0
Title: A package for discriminative motif discovery, designed for high
throughput sequencing dataset
Description: Tools for discriminative motif discovery using regression
methods
biocViews: Transcription, MotifDiscovery
Author: Zizhen Yao
Maintainer: Zizhen Yao <yzizhen@fhcrc.org>
MD5sum: 99d4aaad97edb2d3d45e70e0161a9bd3
source.ver: src/contrib/motifRG_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/motifRG_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/motifRG_1.2.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/motifRG/inst/doc/motifRG.pdf
vignetteTitles: motifRG: regression-based discriminative motif
discovery
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/motifRG/inst/doc/motifRG.R
Package: motifStack
Version: 1.0.4
Depends: R (>= 2.15.1), methods, grImport
Imports: grImport, grid, XML
Suggests: RUnit, BiocGenerics, MotIV
License: GPL (>= 2)
Title: Plot stacked logos for single or multiple DNA, RNA and amino
acid sequence
Description: The motifStack package is designed for graphic
representation of multiple motifs with different similarity
scores. It works with both DNA/RNA sequence motif and amino
acid sequence motif. In addition, it provides the flexibility
for users to customize the graphic parameters such as the font
type and symbol colors.
biocViews: SequenceMatching, GenomicsSequence, Visualization
Author: Jianhong Ou, Michael Brodsky, Scot Wolfe and Lihua Julie Zhu
Maintainer: Jianhong Ou <jianhong.ou@umassmed.edu>
MD5sum: 8933648d829df9b43097a430acac2377
source.ver: src/contrib/motifStack_1.0.4.tar.gz
win.binary.ver: bin/windows/contrib/2.15/motifStack_1.0.4.zip
win64.binary.ver: bin/windows64/contrib/2.15/motifStack_1.0.4.zip
mac.binary.leopard.ver:
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vignettes: vignettes/motifStack/inst/doc/motifStack.pdf
vignetteTitles: motifStack Vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/motifStack/inst/doc/motifStack.R
Package: MotIV
Version: 1.14.0
Depends: R (>= 2.10), BiocGenerics (>= 0.1.0)
Imports: graphics, grid, methods, BiocGenerics, IRanges (>= 1.13.5),
Biostrings (>= 1.24.0), lattice, rGADEM, stats, utils
Suggests: rtracklayer
License: GPL-2
Archs: i386, x64
Title: Motif Identification and Validation
Description: This package makes use of STAMP for comparing a set of
motifs to a given database (e.g. JASPAR). It can also be used
to visualize motifs, motif distributions, modules and filter
motifs.
biocViews: Microarray, ChIPchip, ChIPseq, GenomicSequence,
MotifAnnotation
Author: Eloi Mercier, Raphael Gottardo
Maintainer: Eloi Mercier <emercier@chibi.ubc.ca>, Raphael Gottardo
<rgottard@fhcrc.org>
MD5sum: 454b28721a332a5a98192c11a6d8b9c5
source.ver: src/contrib/MotIV_1.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MotIV_1.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MotIV_1.14.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/MotIV/inst/doc/MotIV.pdf
vignetteTitles: The MotIV users guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MotIV/inst/doc/MotIV.R
suggestsMe: MotifDb, motifStack
Package: MSnbase
Version: 1.6.2
Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.3), Biobase (>=
2.15.2), ggplot2, mzR
Imports: plyr, IRanges, preprocessCore, vsn, grid, reshape2, stats4,
affy
Suggests: testthat, zoo, knitr, rols, Rdisop
Enhances: foreach, doMC, parallel
License: Artistic-2.0
Title: MSnbase: Base Functions and Classes for MS-based Proteomics
Description: Basic plotting, data manipulation and processing of
MS-based Proteomics data
biocViews: Infrastructure, Bioinformatics, Proteomics, MassSpectrometry
Author: Laurent Gatto <lg390@cam.ac.uk> with contributions from
Guangchuang Yu <guangchuangyu@gmail.com>
Maintainer: Laurent Gatto <lg390@cam.ac.uk>
MD5sum: e0a6599f48af7ce2d40446d3c2c9c1cf
source.ver: src/contrib/MSnbase_1.6.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MSnbase_1.6.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/MSnbase_1.6.2.zip
mac.binary.leopard.ver:
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vignettes: vignettes/MSnbase/inst/doc/itraqchem.pdf,
vignettes/MSnbase/inst/doc/MSnbase-demo.pdf,
vignettes/MSnbase/inst/doc/MSnbase-development.pdf,
vignettes/MSnbase/inst/doc/MSnbase-io.pdf,
vignettes/MSnbase/inst/doc/plotMzDelta-pride12011.pdf
vignetteTitles: itraqchem.pdf, Base Functions and Classes for MS-based
Proteomics, MSnbase development, MSnbase IO capabilities,
plotMzDelta-pride12011.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MSnbase/inst/doc/MSnbase-demo.R,
vignettes/MSnbase/inst/doc/MSnbase-development.R,
vignettes/MSnbase/inst/doc/MSnbase-io.R
dependsOnMe: synapter
suggestsMe: isobar
Package: Mulcom
Version: 1.8.0
Depends: R (>= 2.10), fields, Biobase
Imports: graphics, grDevices, stats, methods
License: GPL-2
Archs: i386, x64
Title: Calculates Mulcom test
Description: Identification of differentially expressed genes and false
discovery rate (FDR) calculation by Multiple Comparison test
biocViews: Statistics, MultipleComparisons, Microarray,
DifferentialExpression, GeneExpression
Author: Claudio Isella
Maintainer: Claudio Isella <claudio.isella@ircc.it>
MD5sum: 8be6b3edc8c72bf715866d309432e7aa
source.ver: src/contrib/Mulcom_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Mulcom_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Mulcom_1.8.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Mulcom/inst/doc/MulcomVignette.pdf
vignetteTitles: Mulcom Manual
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Mulcom/inst/doc/MulcomVignette.R
Package: multiscan
Version: 1.18.0
Depends: R (>= 2.3.0)
Imports: Biobase, utils
License: GPL (>= 2)
Archs: i386, x64
Title: R package for combining multiple scans
Description: Estimates gene expressions from several laser scans of the
same microarray
biocViews: Microarray, Preprocessing
Author: Mizanur Khondoker <mizanur.khondoker@ed.ac.uk>, Chris Glasbey,
Bruce Worton.
Maintainer: Mizanur Khondoker <mizanur.khondoker@ed.ac.uk>
MD5sum: 5e1d96439e475de18d2a65d464f6bdca
source.ver: src/contrib/multiscan_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/multiscan_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/multiscan_1.18.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/multiscan/inst/doc/multiscan.pdf
vignetteTitles: An R Package for Estimating Gene Expressions using
Multiple Scans
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/multiscan/inst/doc/multiscan.R
Package: multtest
Version: 2.14.0
Depends: R (>= 2.10), methods, Biobase
Imports: survival, MASS, stats4
Suggests: snow
License: LGPL
Archs: i386, x64
Title: Resampling-based multiple hypothesis testing
Description: Non-parametric bootstrap and permutation resampling-based
multiple testing procedures (including empirical Bayes methods)
for controlling the family-wise error rate (FWER), generalized
family-wise error rate (gFWER), tail probability of the
proportion of false positives (TPPFP), and false discovery rate
(FDR). Several choices of bootstrap-based null distribution
are implemented (centered, centered and scaled,
quantile-transformed). Single-step and step-wise methods are
available. Tests based on a variety of t- and F-statistics
(including t-statistics based on regression parameters from
linear and survival models as well as those based on
correlation parameters) are included. When probing hypotheses
with t-statistics, users may also select a potentially faster
null distribution which is multivariate normal with mean zero
and variance covariance matrix derived from the vector
influence function. Results are reported in terms of adjusted
p-values, confidence regions and test statistic cutoffs. The
procedures are directly applicable to identifying
differentially expressed genes in DNA microarray experiments.
biocViews: Microarray, DifferentialExpression, MultipleComparisons
Author: Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra
Taylor, Sandrine Dudoit
Maintainer: Katherine S. Pollard <kpollard@gladstone.ucsf.edu>
MD5sum: 2cbfe12636fc0865e8fc3fe56272fa5f
source.ver: src/contrib/multtest_2.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/multtest_2.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/multtest_2.14.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/multtest/inst/doc/MTPALL.pdf,
vignettes/multtest/inst/doc/MTP.pdf,
vignettes/multtest/inst/doc/multtest.pdf
vignetteTitles: MTPALL.pdf, MTP.pdf, multtest.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: a4Base, aCGH, BicARE, ChIPpeakAnno, gage, iPAC, KCsmart,
LMGene, PREDA, REDseq, SAGx, siggenes, webbioc
importsMe: ABarray, aCGH, adSplit, anota, ChIPpeakAnno, GeneSelector,
globaltest, IsoGeneGUI, OCplus, phyloseq, REDseq, RTopper,
synapter, webbioc
suggestsMe: annaffy, BiocCaseStudies, ecolitk, factDesign,
GeneSelector, GOstats, GSEAlm, maigesPack, MmPalateMiRNA,
oneChannelGUI, pcot2, safe, SSPA, topGO, xcms
Package: MVCClass
Version: 1.32.0
Depends: R (>= 2.1.0), methods
License: LGPL
Title: Model-View-Controller (MVC) Classes
Description: Creates classes used in model-view-controller (MVC) design
biocViews: Visualization, Infrastructure, GraphsAndNetworks
Author: Elizabeth Whalen
Maintainer: Elizabeth Whalen <ewhalen@hsph.harvard.edu>
MD5sum: d929e3a7dd3a4754a6389ae87c8b0cf7
source.ver: src/contrib/MVCClass_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/MVCClass_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/MVCClass_1.32.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/MVCClass/inst/doc/MVCClass.pdf
vignetteTitles: MVCClass
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/MVCClass/inst/doc/MVCClass.R
dependsOnMe: BioMVCClass
Package: mzR
Version: 1.4.7
Depends: Rcpp (>= 0.10.3), methods, utils
Imports: Biobase
LinkingTo: Rcpp
Suggests: msdata (>= 0.1.9), RUnit, faahKO
License: Artistic-2.0
Archs: i386, x64
Title: parser for netCDF, mzXML, mzData and mzML files (mass
spectrometry data)
Description: mzR provides a unified API to the common file formats and
parsers available for mass spectrometry data. It comes with a
wrapper for the ISB random access parser for mass spectrometry
mzXML, mzData and mzML files. The package contains the original
code written by the ISB, and a subset of the proteowizard
library for mzML. The netCDF reading code has previously been
used in XCMS.
biocViews: Infrastructure, Bioinformatics, DataImport, Proteomics,
Metabolomics, MassSpectrometry
Author: Bernd Fischer, Steffen Neumann, Laurent Gatto
Maintainer: Bernd Fischer <bernd.fischer@embl.de>, Steffen Neumann
<sneumann@ipb-halle.de>, Laurent Gatto <lg390@cam.ac.uk>
SystemRequirements: GNU make, NetCDF, zlib
MD5sum: 9890c907c767e81709abd5268a3c2eb6
source.ver: src/contrib/mzR_1.4.7.tar.gz
win.binary.ver: bin/windows/contrib/2.15/mzR_1.4.7.zip
win64.binary.ver: bin/windows64/contrib/2.15/mzR_1.4.7.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mzR_1.4.7.tgz
vignettes: vignettes/mzR/inst/doc/mzR.pdf
vignetteTitles: mzR,, Ramp,, mzXML,, mzData,, mzML
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/mzR/inst/doc/mzR.R
dependsOnMe: MSnbase, TargetSearch, xcms
Package: NarrowPeaks
Version: 1.2.0
Depends: R (>= 2.10.0), splines
Imports: GenomicRanges, IRanges, fda, CSAR
Suggests: rtracklayer, GenomicRanges, CSAR
License: Artistic-2.0
Archs: i386, x64
Title: Functional Principal Component Analysis to Narrow Down
Transcription Factor Binding Site Candidates
Description: The package processes data in wiggle track format (WIG)
commonly produced by several ChIP-seq data analysis tools by
applying functional version of principal component analysis
(FPCA) over a set of selected candidate enriched regions. This
is done in order to shorten the genomic locations accounting
for a given proportion of variation among the enrichment-score
profiles. It allows the user to discriminate between binding
regions in close proximity to each other and to narrow down the
length of the putative transcription factor binding sites while
preserving the information present in the variability of the
dataset and capturing major sources of variation.
biocViews: Visualization, ChIPseq, Transcription, Genetics
Author: Pedro Madrigal <pm@engineering.com>, with contributions from
Pawel Krajewski <pkra@igr.poznan.pl>
Maintainer: Pedro Madrigal <pm@engineering.com>
MD5sum: 284ddff63b3733ca9c2d848fafda315c
source.ver: src/contrib/NarrowPeaks_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/NarrowPeaks_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/NarrowPeaks_1.2.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/NarrowPeaks/inst/doc/NarrowPeaks.pdf
vignetteTitles: NarrowPeaks Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/NarrowPeaks/inst/doc/NarrowPeaks.R
Package: ncdfFlow
Version: 1.4.3
Depends: R (>= 2.14.0), flowCore
Imports: Biobase,flowCore,flowViz,methods
License: Artistic-2.0
Title: ncdfFlow: A package that provides ncdf based storage for flow
cytometry data.
Description: Provides netCDF storage based methods and functions for
manipulation of flow cytometry data.
biocViews: FlowCytometry
Author: Mike Jiang,Greg Finak,N. Gopalakrishnan
Maintainer: M. Jiang <wjiang2@fhcrc.org>
SystemRequirements: netcdf 4.0.1, hdf5
MD5sum: c1eb7ca1817369c5f94b89b6b63c9340
source.ver: src/contrib/ncdfFlow_1.4.3.tar.gz
mac.binary.leopard.ver:
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vignettes: vignettes/ncdfFlow/inst/doc/ncdfFlow.pdf
vignetteTitles: Basic Functions for Flow Cytometry Data
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ncdfFlow/inst/doc/ncdfFlow.R
Package: NCIgraph
Version: 1.6.0
Depends: graph, R (>= 2.10.0)
Imports: graph, KEGGgraph, methods, RBGL, RCytoscape, R.methodsS3
Suggests: Rgraphviz
Enhances: DEGraph
License: GPL-3
Title: Pathways from the NCI Pathways Database
Description: Provides various methods to load the pathways from the NCI
Pathways Database in R graph objects and to re-format them.
biocViews: Pathways, GraphsAndNetworks
Author: Laurent Jacob
Maintainer: Laurent Jacob <laurent.jacob@gmail.com>
MD5sum: 7b391fc3851573659b5164c2c48d718a
source.ver: src/contrib/NCIgraph_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/NCIgraph_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/NCIgraph_1.6.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/NCIgraph/inst/doc/NCIgraph.pdf
vignetteTitles: NCIgraph: networks from the NCI pathway integrated
database as graphNEL objects.
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/NCIgraph/inst/doc/NCIgraph.R
importsMe: DEGraph
suggestsMe: DEGraph
Package: nem
Version: 2.34.0
Depends: R (>= 2.0), e1071 (>= 1.5), graph (>= 1.24), plotrix, limma,
cluster (>= 1.11), statmod, Hmisc, Rgraphviz
Imports: boot, e1071, graph, graphics, grDevices, methods, RBGL (>=
1.8.1), RColorBrewer, stats, utils, Rgraphviz
Suggests: Biobase (>= 1.10)
Enhances: doMC, Rglpk
License: GPL (>= 2)
Archs: i386, x64
Title: Nested Effects Models to reconstruct phenotypic hierarchies
Description: The package 'nem' allows to reconstruct features of
pathways from the nested structure of perturbation effects. It
takes as input (1.) a set of pathway components, which were
perturbed, and (2.) high-dimensional phenotypic readout of
these perturbations (e.g. gene expression, protein expression).
The output is a directed graph representing the phenotypic
hierarchy.
biocViews: Microarray, Bioinformatics, GraphsAndNetworks, Pathways
Author: Holger Froehlich, Florian Markowetz, Achim Tresch, Theresa
Niederberger, Christian Bender, Matthias Maneck, Claudio
Lottaz, Tim Beissbarth
Maintainer: Holger Froehlich <frohlich@bit.uni-bonn.de>
URL: http://www.bioconductor.org
MD5sum: bfd7efdac177dfb78edbae0261ef6d83
source.ver: src/contrib/nem_2.34.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/nem_2.34.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/nem_2.34.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/nem_2.34.0.tgz
vignettes: vignettes/nem/inst/doc/markowetz-thesis-2006.pdf,
vignettes/nem/inst/doc/nem.pdf
vignetteTitles: markowetz-thesis-2006.pdf, Nested Effects Models - An
example in Drosophila immune response
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/nem/inst/doc/nem.R
Package: netresponse
Version: 1.10.0
Depends: R (>= 2.15.0), dmt, igraph0, ggplot2, graph, mclust, methods,
minet, parallel, qvalue, RColorBrewer, reshape, Rgraphviz
License: GPL (>=2)
Archs: i386, x64
Title: NetResponse: functional network analysis
Description: Algorithms for functional network analysis. Includes an
implementation of a variational Dirichlet process Gaussian
mixture model for nonparametric mixture modeling.
biocViews: CellBiology, Clustering, GeneExpression, Genetics,
NetworkAnalysis, GraphsAndNetworks, DifferentialExpression,
Microarray, Transcription
Author: Leo Lahti, Olli-Pekka Huovilainen, Antonio Gusmao and Juuso
Parkkinen
Maintainer: Leo Lahti <leo.lahti@iki.fi>
URL: http://netpro.r-forge.r-project.org/
MD5sum: e34a2d9d8d9a7ce5095a796615754b1e
source.ver: src/contrib/netresponse_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/netresponse_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/netresponse_1.10.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/netresponse/inst/doc/netresponse.pdf
vignetteTitles: netresponse
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/netresponse/inst/doc/netresponse.R
Package: networkBMA
Version: 1.0.0
Depends: R (>= 2.15.0), stats, utils, BMA
License: GPL (>= 2)
Title: Regression-based network inference using Bayesian Model
Averaging
Description: An extension of Bayesian Model Averaging (BMA) for network
construction using time series gene expression data. Includes
assessment functions and sample test data.
Author: Chris Fraley, Ka Yee Yeung, Adrian Raftery (with contributions
from Kenneth Lo and Chad Young)
Maintainer: Chris Fraley <fraley@stat.washington.edu>
MD5sum: 0eb68b2920ffc09f9c52b01f6156c05a
source.ver: src/contrib/networkBMA_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/networkBMA_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/networkBMA_1.0.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/networkBMA/inst/doc/networkBMA.pdf,
vignettes/networkBMA/inst/doc/prc.pdf,
vignettes/networkBMA/inst/doc/roc.pdf
vignetteTitles: networkBMA, prc.pdf, roc.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/networkBMA/inst/doc/networkBMA.R
Package: nnNorm
Version: 2.22.0
Depends: R(>= 2.2.0), marray
Imports: graphics, grDevices, marray, methods, nnet, stats
License: LGPL
Title: Spatial and intensity based normalization of cDNA microarray
data based on robust neural nets
Description: This package allows to detect and correct for spatial and
intensity biases with two-channel microarray data. The
normalization method implemented in this package is based on
robust neural networks fitting.
biocViews: Microarray, TwoChannel, Preprocessing
Author: Adi Laurentiu Tarca <atarca@med.wayne.edu>
Maintainer: Adi Laurentiu Tarca <atarca@med.wayne.edu>
URL: http://bioinformaticsprb.med.wayne.edu/tarca/
MD5sum: 6e28948c63eb2ae4b1136ac7dc0bccd2
source.ver: src/contrib/nnNorm_2.22.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/nnNorm_2.22.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/nnNorm_2.22.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/nnNorm/inst/doc/nnNormGuide.pdf,
vignettes/nnNorm/inst/doc/nnNorm.pdf
vignetteTitles: nnNormGuide.pdf, nnNorm Tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/nnNorm/inst/doc/nnNorm.R
Package: NOISeq
Version: 1.1.5
Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11)
License: Artistic-2.0
Title: Exploratory analysis and differential expression for RNA-seq
data
Description: Analysis of RNA-seq expression data or other similar kind
of data. Exploratory plots to evualuate saturation, count
distribution, expression per chromosome, type of detected
features, features length, etc. Differential expression between
two experimental conditions with no parametric assumptions.
biocViews: Bioinformatics, RNAseq, DifferentialExpression,
Visualization, HighThroughputSequencing
Author: Sonia Tarazona, Pedro Furio-Tari, Alberto Ferrer and Ana Conesa
Maintainer: Sonia Tarazona <starazona@cipf.es>
MD5sum: 190784c277c4a7aa45a7bfc7b38234f7
source.ver: src/contrib/NOISeq_1.1.5.tar.gz
win.binary.ver: bin/windows/contrib/2.15/NOISeq_1.1.5.zip
win64.binary.ver: bin/windows64/contrib/2.15/NOISeq_1.1.5.zip
mac.binary.leopard.ver:
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vignettes: vignettes/NOISeq/inst/doc/NOISeq.pdf
vignetteTitles: NOISeq User's Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/NOISeq/inst/doc/NOISeq.R
Package: NormqPCR
Version: 1.4.0
Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR
Imports: ReadqPCR
License: LGPL-3
Title: Functions for normalisation of RT-qPCR data
Description: Functions for the selection of optimal reference genes and
the normalisation of real-time quantitative PCR data.
biocViews: MicrotitrePlateAssay, GeneExpression, qPCR
Author: Matthias Kohl, James Perkins
Maintainer: James Perkins <j.perkins@ucl.ac.uk>
URL: www.bioconductor.org/packages/release/bioc/html/NormqPCR.html
MD5sum: 33999a4c69f90fdd23c9859837e5b133
source.ver: src/contrib/NormqPCR_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/NormqPCR_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/NormqPCR_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/NormqPCR/inst/doc/NormqPCR.pdf
vignetteTitles: NormqPCR: Functions for normalisation of RT-qPCR data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/NormqPCR/inst/doc/NormqPCR.R
Package: NTW
Version: 1.8.0
Depends: R (>= 2.3.0)
Imports: mvtnorm, stats, utils
License: GPL-2
Title: Predict gene network using an Ordinary Differential Equation
(ODE) based method
Description: This package predicts the gene-gene interaction network
and identifies the direct transcriptional targets of the
perturbation using an ODE (Ordinary Differential Equation)
based method.
biocViews: Preprocessing
Author: Wei Xiao, Yin Jin, Darong Lai, Xinyi Yang, Yuanhua Liu,
Christine Nardini
Maintainer: Yuanhua Liu <liuyuanhua@picb.ac.cn>
MD5sum: c23fb57ab88ac5cf0bde2a1f8c993f1a
source.ver: src/contrib/NTW_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/NTW_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/NTW_1.8.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/NTW_1.8.0.tgz
vignettes: vignettes/NTW/inst/doc/NTW.pdf
vignetteTitles: NTW vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/NTW/inst/doc/NTW.R
Package: nucleR
Version: 1.6.0
Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Biobase
(>= 2.15.1), ShortRead, parallel
Imports: methods, BiocGenerics, IRanges, Biobase, ShortRead,
GenomicRanges, stats
Enhances: htSeqTools
License: LGPL (>= 3)
Title: Nucleosome positioning package for R
Description: Nucleosome positioning for Tiling Arrays and Next
Generation Sequencing Experiments
biocViews: ChIPseq, Microarray, Sequencing, Genetics,
HighThroughputSequencing
Author: Oscar Flores, David Rossell
Maintainer: Oscar Flores <oflores@mmb.pcb.ub.es>
MD5sum: 21fd9d2d71f7d58a5667e2ee9da00ecc
source.ver: src/contrib/nucleR_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/nucleR_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/nucleR_1.6.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/nucleR/inst/doc/nucleR.pdf
vignetteTitles: Quick analysis of nucleosome positioning experiments
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/nucleR/inst/doc/nucleR.R
Package: nudge
Version: 1.24.0
Imports: stats
License: GPL-2
Title: Normal Uniform Differential Gene Expression detection
Description: Package for normalizing microarray data in single and
multiple replicate experiments and fitting a normal-uniform
mixture to detect differentially expressed genes in the cases
where the two samples are being compared directly or indirectly
(via a common reference sample)
biocViews: Microarray, TwoChannel, DifferentialExpression
Author: N. Dean <nemad@stat.washington.edu> and A. E. Raftery
<raftery@stat.washington.edu>
Maintainer: N. Dean <nemad@stat.washington.edu>
MD5sum: 5e97dd07e8eee406fc585f71786bce7b
source.ver: src/contrib/nudge_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/nudge_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/nudge_1.24.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/nudge/inst/doc/nudge.vignette.pdf,
vignettes/nudge/inst/doc/nvignplot1.pdf,
vignettes/nudge/inst/doc/nvignplot2.pdf,
vignettes/nudge/inst/doc/nvignplot3.pdf,
vignettes/nudge/inst/doc/nvignplot4.pdf
vignetteTitles: nudge Overview, nvignplot1.pdf, nvignplot2.pdf,
nvignplot3.pdf, nvignplot4.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/nudge/inst/doc/nudge.vignette.R
Package: NuPoP
Version: 1.8.0
Depends: R (>= 2.10)
License: GPL-2
Archs: i386, x64
Title: An R package for nucleosome positioning prediction
Description: NuPoP is an R package for Nucleosome Positioning
Prediction.This package is built upon a duration hidden Markov
model proposed in Xi et al, 2010; Wang et al, 2008. The core of
the package was written in Fotran. In addition to the R
package, a stand-alone Fortran software tool is also available
at http://nucleosome.stats.northwestern.edu.
biocViews: Genetics,Visualization,Classification
Author: Ji-Ping Wang <jzwang@northwestern.edu>; Liqun Xi
<lxi700@northwestern.edu>
Maintainer: Ji-Ping Wang<jzwang@northwestern.edu>
MD5sum: 5e415bc57603f2fb1d711d5232ca98cf
source.ver: src/contrib/NuPoP_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/NuPoP_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/NuPoP_1.8.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/NuPoP_1.8.0.tgz
vignettes: vignettes/NuPoP/inst/doc/NuPoP-intro.pdf,
vignettes/NuPoP/inst/doc/NuPoP-manual.pdf
vignetteTitles: An R package for Nucleosome positioning prediction,
NuPoP-manual.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/NuPoP/inst/doc/NuPoP-intro.R
Package: occugene
Version: 1.18.0
Depends: R (>= 2.0.0)
License: GPL (>= 2)
Title: Functions for Multinomial Occupancy Distribution
Description: Statistical tools for building random mutagenesis
libraries for prokaryotes. The package has functions for
handling the occupancy distribution for a multinomial and for
estimating the number of essential genes in random transposon
mutagenesis libraries.
biocViews: Bioinformatics,Annotation,Pathways
Author: Oliver Will <oliverrreader@gmail.com>
Maintainer: Oliver Will <oliverrreader@gmail.com>
MD5sum: d2f8dfb7a98feddae574b6531ac56b78
source.ver: src/contrib/occugene_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/occugene_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/occugene_1.18.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/occugene/inst/doc/occugene.pdf
vignetteTitles: occugene
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/occugene/inst/doc/occugene.R
Package: OCplus
Version: 1.32.0
Depends: R (>= 2.1.0), akima
Imports: multtest (>= 1.7.3), graphics, grDevices, stats
License: LGPL
Title: Operating characteristics plus sample size and local fdr for
microarray experiments
Description: This package allows to characterize the operating
characteristics of a microarray experiment, i.e. the trade-off
between false discovery rate and the power to detect truly
regulated genes. The package includes tools both for planned
experiments (for sample size assessment) and for already
collected data (identification of differentially expressed
genes).
biocViews: Microarray, Bioinformatics, DifferentialExpression,
MultipleComparisons
Author: Yudi Pawitan <Yudi.Pawitan@ki.se> and Alexander Ploner
<Alexander.Ploner@ki.se>
Maintainer: Alexander Ploner <Alexander.Ploner@ki.se>
MD5sum: 5136e7c19d48c12c3bfe61ad455e5f79
source.ver: src/contrib/OCplus_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/OCplus_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/OCplus_1.32.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/OCplus/inst/doc/OCplus.pdf
vignetteTitles: OCplus Introduction
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/OCplus/inst/doc/OCplus.R
Package: oligo
Version: 1.22.0
Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>=
1.19.43), Biobase (>= 2.17.8)
Imports: affyio (>= 1.25.0), affxparser (>= 1.29.11), Biostrings (>=
2.25.12), BiocGenerics (>= 0.3.2), DBI (>= 0.2-5), ff,
graphics, methods, preprocessCore (>= 1.19.0), splines, stats,
stats4, utils, zlibbioc
LinkingTo: preprocessCore
Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.huex.1.0.st.v2,
pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex,
genefilter, limma, RColorBrewer, oligoData, RUnit
Enhances: ff, doMC, doMPI
License: LGPL (>= 2)
Archs: i386, x64
Title: Preprocessing tools for oligonucleotide arrays.
Description: A package to analyze oligonucleotide arrays
(expression/SNP/tiling/exon) at probe-level. It currently
supports Affymetrix (CEL files) and NimbleGen arrays (XYS
files).
biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP,
DifferentialExpression, ExonArray, GeneExpression,
Bioinformatics, DataImport
Author: Benilton Carvalho and Rafael Irizarry. Contributors: Ben
Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim
MacDonald, Matt Settles
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
MD5sum: 3acc50248812d0826780caf817954157
source.ver: src/contrib/oligo_1.22.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/oligo_1.22.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/oligo_1.22.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/oligo/inst/doc/primer.pdf
vignetteTitles: oligo - Primer
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/oligo/inst/doc/primer.R,
vignettes/oligo/inst/doc/V1Overview.R,
vignettes/oligo/inst/doc/V2NExpression.R,
vignettes/oligo/inst/doc/V3AffySnpGenotype.R,
vignettes/oligo/inst/doc/V4Experimental.R,
vignettes/oligo/inst/doc/V5ExonGene.R
dependsOnMe: ITALICS, pdInfoBuilder, SCAN.UPC, waveTiling
importsMe: charm, cn.farms, frma, ITALICS
suggestsMe: BiocGenerics, fastseg, frmaTools
Package: oligoClasses
Version: 1.20.0
Depends: R (>= 2.14), BiocGenerics (>= 0.3.2)
Imports: BiocGenerics, Biobase (>= 2.17.8), methods, graphics, IRanges
(>= 1.13.30), GenomicRanges, Biostrings (>= 2.23.6), affyio (>=
1.23.2), ff, foreach, BiocInstaller, utils
Suggests: RSQLite, hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6,
pd.genomewidesnp.5, pd.mapping50k.hind240,
pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp,
genomewidesnp6Crlmm, genomewidesnp5Crlmm, crlmm, SNPchip,
VanillaICE, RUnit, human370v1cCrlmm
Enhances: doMC, doMPI, doSNOW, doParallel, doRedis
License: GPL (>= 2)
Title: Classes for high-throughput arrays supported by oligo and crlmm
Description: This package contains class definitions, validity checks,
and initialization methods for classes used by the oligo and
crlmm packages.
biocViews: Infrastructure
Author: Benilton Carvalho and Robert Scharpf
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk> and
Robert Scharpf <rscharpf@jhsph.edu>
MD5sum: 5fde29b3b98293471a78bace36a0d4b0
source.ver: src/contrib/oligoClasses_1.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/oligoClasses_1.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/oligoClasses_1.20.0.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: cn.farms, crlmm, mBPCR, oligo, waveTiling
importsMe: frma, ITALICS, MinimumDistance, SNPchip, VanillaICE
suggestsMe: BiocGenerics
Package: OLIN
Version: 1.36.0
Depends: R (>= 2.10), methods, locfit, marray
Imports: graphics, grDevices, limma, marray, methods, stats
Suggests: convert
License: GPL-2
Title: Optimized local intensity-dependent normalisation of two-color
microarrays
Description: Functions for normalisation of two-color microarrays by
optimised local regression and for detection of artefacts in
microarray data
biocViews: Microarray, TwoChannel, QualityControl, Preprocessing,
Visualization
Author: Matthias Futschik <mfutschik@ualg.pt>
Maintainer: Matthias Futschik <mfutschik@ualg.pt>
URL:
http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/index.html
MD5sum: 69c5ffe946069ae878dbd8be0f4782e5
source.ver: src/contrib/OLIN_1.36.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/OLIN_1.36.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/OLIN_1.36.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OLIN_1.36.0.tgz
vignettes: vignettes/OLIN/inst/doc/OLIN.pdf
vignetteTitles: Introduction to OLIN
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/OLIN/inst/doc/OLIN.R
dependsOnMe: OLINgui
importsMe: OLINgui
suggestsMe: maigesPack
Package: OLINgui
Version: 1.32.1
Depends: R (>= 2.0.0), OLIN (>= 1.4.0)
Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools
License: GPL-2
Title: Graphical user interface for OLIN
Description: Graphical user interface for the OLIN package
biocViews: Microarray, TwoChannel, QualityControl, Preprocessing,
Visualization
Author: Matthias Futschik <mfutschik@ualg.pt>
Maintainer: Matthias Futschik <mfutschik@ualg.pt>
URL:
http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/index.html
MD5sum: 68bf48b1fcb0def62c23811203d5e5e8
source.ver: src/contrib/OLINgui_1.32.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/OLINgui_1.32.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/OLINgui_1.32.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/OLINgui/inst/doc/OLINgui.pdf,
vignettes/OLINgui/inst/doc/OLINguiScreenshot.pdf
vignetteTitles: Introduction to OLINgui, OLINguiScreenshot.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/OLINgui/inst/doc/OLINgui.R
Package: oneChannelGUI
Version: 1.24.0
Depends: Biobase, affylmGUI, tkWidgets, IRanges, Rsamtools, Biostrings,
siggenes
Suggests: annotate, genefilter, maSigPro, pamr, pdmclass, ChIPpeakAnno,
chipseq, BSgenome, Rgraphviz, affy ,annaffy, affyPLM, multtest,
ssize, sizepower, RankProd, org.Hs.eg.db, org.Mm.eg.db,
org.Rn.eg.db, edgeR, metaArray, MergeMaid, biomaRt,
GenomeGraphs,AffyCompatible, rtracklayer, Genominator, EDASeq,
limma, DESeq, goseq, hugene10sttranscriptcluster.db,
mogene10sttranscriptcluster.db, ragene10sttranscriptcluster.db,
GOstats, AnnotationDbi, preprocessCore, baySeq,
HuExExonProbesetLocation, MoExExonProbesetLocation,
RaExExonProbesetLocation, snow, RmiR, RmiR.Hs.miRNA,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,
BSgenome.Rnorvegicus.UCSC.rn4, R.utils, cummeRbund
License: Artistic-2.0
Title: A graphical interface designed to facilitate analysis of
microarrays and miRNA/RNA-seq data on laptops.
Description: This package was developed to simplify the use of
Bioconductor tools for beginners having limited or no
experience in writing R code. This library provides a graphical
interface for microarray gene and exon level analysis as well
as miRNA/mRNA-seq data analysis.
biocViews: HighThroughputSequencing, RNAseq, Microarray, OneChannel,
DataImport, QualityControl, Preprocessing, Statistics,
DifferentialExpression, GUI, MultipleComparisons
Author: Raffale A Calogero, Bioinformatics and Genomics Unit, Molecular
Biotechnology Center, Torino (Italy)
Maintainer: Raffaele A Calogero <raffaele.calogero@unito.it>
URL: http://www.bioinformatica.unito.it/oneChannelGUI/
MD5sum: f14113fa0fc8d5aeaf9e839470975f81
source.ver: src/contrib/oneChannelGUI_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/oneChannelGUI_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/oneChannelGUI_1.24.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/oneChannelGUI_1.24.0.tgz
vignettes: vignettes/oneChannelGUI/inst/doc/Exon-level.analysis.pdf,
vignettes/oneChannelGUI/inst/doc/fignew42.pdf,
vignettes/oneChannelGUI/inst/doc/gene-level.analysis.pdf,
vignettes/oneChannelGUI/inst/doc/install.pdf,
vignettes/oneChannelGUI/inst/doc/RNAseq.pdf,
vignettes/oneChannelGUI/inst/doc/standAloneFunctions.pdf
vignetteTitles: oneChannelGUI microarray exon-level data analysis
overview, fignew42.pdf, oneChannelGUI microarray gene-level
data analysis overview, oneChannelGUI Installation,
oneChannelGUI miRNA and RNA-seq data analysis overview,
oneChannelGUI Stand Alone Functions
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/oneChannelGUI/inst/doc/Exon-level.analysis.R,
vignettes/oneChannelGUI/inst/doc/gene-level.analysis.R,
vignettes/oneChannelGUI/inst/doc/install.R,
vignettes/oneChannelGUI/inst/doc/RNAseq.R,
vignettes/oneChannelGUI/inst/doc/standAloneFunctions.R
Package: ontoCAT
Version: 1.10.0
Depends: rJava, methods
License: Apache License 2.0
Title: Ontology traversal and search
Description: The ontoCAT R package provides a simple interface to
ontologies described in widely used standard formats, stored
locally in the filesystem or accessible online. The full
version of ontoCAT R package also supports searching for
ontology terms across multiple ontologies and in major ontology
repositories, as well as a number of advanced ontology
navigation functions: www.ontocat.org/wiki/r
biocViews: Classification, DataRepresentation
Author: Natalja Kurbatova, Tomasz Adamusiak, Pavel Kurnosov, Morris
Swertz, Misha Kapushevsky
Maintainer: Natalja Kurbatova <natalja@ebi.ac.uk>
MD5sum: 4032518261701043e93c6458cd309a8e
source.ver: src/contrib/ontoCAT_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ontoCAT_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ontoCAT_1.10.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/ontoCAT_1.10.0.tgz
vignettes: vignettes/ontoCAT/inst/doc/ontoCAT.pdf
vignetteTitles: ontoCAT package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/ontoCAT/inst/doc/ontoCAT.R
Package: OrderedList
Version: 1.30.0
Depends: R (>= 2.1.0), Biobase (>= 1.5.12), twilight (>= 1.9.2),
methods
Imports: Biobase, graphics, methods, stats, twilight
License: GPL (>= 2)
Title: Similarities of Ordered Gene Lists
Description: Detection of similarities between ordered lists of genes.
Thereby, either simple lists can be compared or gene expression
data can be used to deduce the lists. Significance of
similarities is evaluated by shuffling lists or by resampling
in microarray data, respectively.
biocViews: Microarray, DifferentialExpression, MultipleComparisons
Author: Xinan Yang, Stefanie Scheid, Claudio Lottaz
Maintainer: Claudio Lottaz <Claudio.Lottaz@klinik.uni-regensburg.de>
URL: http://compdiag.molgen.mpg.de/software/index.shtml
MD5sum: dccdf89ec7c4cd10f8612de63342aa4d
source.ver: src/contrib/OrderedList_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/OrderedList_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/OrderedList_1.30.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/OrderedList_1.30.0.tgz
vignettes: vignettes/OrderedList/inst/doc/bcb_logo.pdf,
vignettes/OrderedList/inst/doc/tr_2006_01.pdf
vignetteTitles: bcb_logo.pdf, Similarities of Ordered Gene Lists
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/OrderedList/inst/doc/tr_2006_01.R
Package: OrganismDbi
Version: 1.0.3
Depends: R (>= 2.14.0), methods, AnnotationDbi (>= 1.16.10),
GenomicFeatures
Imports: BiocGenerics, graph, RBGL, AnnotationDbi
Suggests: Homo.sapiens, Rattus.norvegicus, RUnit
License: Artistic-2.0
Title: Software to enable the smooth interfacing of different database
packages.
Description: The package enables a simple unified interface to several
annotation packages each of which has its own schema by taking
advantage of the fact that each of these packages implements a
select methods.
biocViews: AnnotationData, Infrastructure
Author: Marc Carlson, Herve Pages, Martin Morgan, Valerie Obenchain
Maintainer: Biocore Data Team <maintainer@bioconductor.org>
MD5sum: aaf0ed8a361467c80349b376dfba064c
source.ver: src/contrib/OrganismDbi_1.0.3.tar.gz
win.binary.ver: bin/windows/contrib/2.15/OrganismDbi_1.0.3.zip
win64.binary.ver: bin/windows64/contrib/2.15/OrganismDbi_1.0.3.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/OrganismDbi_1.0.3.tgz
vignettes: vignettes/OrganismDbi/inst/doc/OrganismDbi.pdf
vignetteTitles: OrganismDbi: A meta framework for Annotation Packages
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/OrganismDbi/inst/doc/OrganismDbi.R
Package: OSAT
Version: 1.6.0
Depends: methods,stats
Suggests: xtable, Biobase
License: Artistic-2.0
Title: OSAT: Optimal Sample Assignment Tool
Description: A sizable genomics study such as microarray often involves
the use of multiple batches (groups) of experiment due to
practical complication. To minimize batch effects, a careful
experiment design should ensure the even distribution of
biological groups and confounding factors across batches. OSAT
(Optimal Sample Assignment Tool) is developed to facilitate the
allocation of collected samples to different batches. With
minimum steps, it produces setup that optimizes the even
distribution of samples in groups of biological interest into
different batches, reducing the confounding or correlation
between batches and the biological variables of interest. It
can also optimize the even distribution of confounding factors
across batches. Our tool can handle challenging instances where
incomplete and unbalanced sample collections are involved as
well as ideal balanced RCBD. OSAT provides a number of
predefined layout for some of the most commonly used genomics
platform.
biocViews: Bioinformatics, DataRepresentation, Visualization, Design,
QualityControl
Author: Li Yan
Maintainer: Li Yan <li.yan@roswellpark.org>
MD5sum: 9f59187f299a07deb39632bdb789474a
source.ver: src/contrib/OSAT_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/OSAT_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/OSAT_1.6.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OSAT_1.6.0.tgz
vignettes: vignettes/OSAT/inst/doc/gSetupBlock.pdf,
vignettes/OSAT/inst/doc/gSetupOptimal.pdf,
vignettes/OSAT/inst/doc/Meth450_Tracking_Sheet_onepage.pdf,
vignettes/OSAT/inst/doc/OSAT.pdf,
vignettes/OSAT/inst/doc/paired.pdf,
vignettes/OSAT/inst/doc/random.pdf
vignetteTitles: gSetupBlock.pdf, gSetupOptimal.pdf,
Meth450_Tracking_Sheet_onepage.pdf, An introduction to OSAT,
paired.pdf, random.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/OSAT/inst/doc/OSAT.R
Package: OTUbase
Version: 1.8.0
Depends: R (>= 2.9.0), methods, ShortRead (>= 1.4.0), Biobase, vegan
Imports: Biostrings, ShortRead, IRanges
License: Artistic-2.0
Title: Provides structure and functions for the analysis of OTU data
Description: Provides a platform for Operational Taxonomic Unit based
analysis
biocViews: Bioinformatics, HighThroughputSequencingData, DataImport
Author: Daniel Beck, Matt Settles, and James A. Foster
Maintainer: Daniel Beck <danlbek@gmail.com>
MD5sum: 6c68e316e741e951c25dcf8cb05dc54a
source.ver: src/contrib/OTUbase_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/OTUbase_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/OTUbase_1.8.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/OTUbase_1.8.0.tgz
vignettes: vignettes/OTUbase/inst/doc/Introduction_to_OTUbase.pdf
vignetteTitles: An introduction to OTUbase
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/OTUbase/inst/doc/Introduction_to_OTUbase.R
dependsOnMe: mcaGUI
Package: OutlierD
Version: 1.22.0
Depends: R (>= 2.3.0), Biobase, quantreg
License: GPL (>= 2)
Title: Outlier detection using quantile regression on the M-A
scatterplots of high-throughput data
Description: This package detects outliers using quantile regression on
the M-A scatterplots of high-throughput data.
biocViews: Microarray, Bioinformatics
Author: HyungJun Cho <hj4cho@korea.ac.kr>
Maintainer: Sukwoo Kim <s4kim@korea.ac.kr>
URL: http://www.korea.ac.kr/~stat2242/
MD5sum: 37ac6251b9bd6b48cff9ec0e35d274b1
source.ver: src/contrib/OutlierD_1.22.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/OutlierD_1.22.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/OutlierD_1.22.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/OutlierD_1.22.0.tgz
vignettes: vignettes/OutlierD/inst/doc/OutlierD.pdf
vignetteTitles: Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/OutlierD/inst/doc/OutlierD.R
Package: PADOG
Version: 1.0.0
Depends: R (>= 2.14.0), KEGGdzPathwaysGEO, graphics, limma,
AnnotationDbi, Biobase, methods, nlme, GSA,KEGG.db
Imports: graphics, limma, hgu133plus2.db, hgu133a.db, KEGG.db,
AnnotationDbi, Biobase, methods, nlme
Suggests: parallel
License: GPL (>= 2)
Title: Pathway Analysis with Down-weighting of Overlapping Genes
(PADOG)
Description: This package implements a general purpose gene set
analysis method called PADOG that downplays the importance of
genes that apear often accross the sets of genes to be
analyzed. The package provides also a benchmark for gene set
analysis methods in terms of sensitivity and ranking using 24
public datasets from KEGGdzPathwaysGEO package.
biocViews: Microarray, OneChannel, TwoChannel, Bioinformatics
Author: Adi Laurentiu Tarca <atarca@med.wayne.edu>
Maintainer: Adi Laurentiu Tarca <atarca@med.wayne.edu>
MD5sum: 70f6f8799fbfa17eb1f4f9648b20abeb
source.ver: src/contrib/PADOG_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/PADOG_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/PADOG_1.0.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PADOG_1.0.0.tgz
vignettes: vignettes/PADOG/inst/doc/PADOG.pdf
vignetteTitles: PADOG
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/PADOG/inst/doc/PADOG.R
Package: PAnnBuilder
Version: 1.22.0
Depends: R (>= 2.7.0), methods, utils, RSQLite, Biobase (>= 1.17.0),
AnnotationDbi (>= 1.3.12)
Imports: methods, utils, Biobase, DBI, RSQLite, AnnotationDbi
Suggests: org.Hs.ipi.db
License: LGPL (>= 2.0)
Title: Protein annotation data package builder
Description: Processing annotation data from public data repositories
and building protein-centric annotation data packages.
biocViews: Annotation, Proteomics
Author: Li Hong lihong@sibs.ac.cn
Maintainer: Li Hong <sysptm@gmail.com>
URL: http://www.biosino.org/PAnnBuilder
MD5sum: d774401106a0cd7ec53ddd53788566fb
source.ver: src/contrib/PAnnBuilder_1.22.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/PAnnBuilder_1.22.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/PAnnBuilder_1.22.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/PAnnBuilder_1.22.0.tgz
vignettes: vignettes/PAnnBuilder/inst/doc/fulltext.pdf,
vignettes/PAnnBuilder/inst/doc/PAnnBuilder.pdf
vignetteTitles: fulltext.pdf, Using the PAnnBuilder Package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/PAnnBuilder/inst/doc/PAnnBuilder.R
Package: panp
Version: 1.28.1
Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5)
Imports: Biobase, methods, stats, utils
Suggests: gcrma
License: GPL (>= 2)
Title: Presence-Absence Calls from Negative Strand Matching Probesets
Description: A function to make gene presence/absence calls based on
distance from negative strand matching probesets (NSMP) which
are derived from Affymetrix annotation. PANP is applied after
gene expression values are created, and therefore can be used
after any preprocessing method such as MAS5 or GCRMA, or
PM-only methods like RMA. NSMP sets have been established for
the HGU133A and HGU133-Plus-2.0 chipsets to date.
biocViews: Infrastructure
Author: Peter Warren
Maintainer: Peter Warren <peter.warren@verizon.net>
MD5sum: 383afa151a48581e5fc0662681aa1d9f
source.ver: src/contrib/panp_1.28.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/panp_1.28.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/panp_1.28.1.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/panp_1.28.1.tgz
vignettes: vignettes/panp/inst/doc/panp.pdf
vignetteTitles: gene presence/absence calls
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/panp/inst/doc/panp.R
Package: PANR
Version: 1.4.0
Depends: R (>= 2.14), igraph
Imports: graphics, grDevices, MASS, methods, pvclust, stats, utils
Suggests: snow, RedeR
License: Artistic-2.0
Title: Posterior association networks and functional modules inferred
from rich phenotypes of gene perturbations
Description: This package provides S4 classes and methods for inferring
functional gene networks with edges encoding posterior beliefs
of gene association types and nodes encoding perturbation
effects.
biocViews: NetworkInference, NetworkVisualization, GraphsAndNetworks,
Clustering, CellBasedAssays
Author: Xin Wang <Xin.Wang@cancer.org.uk>
Maintainer: Xin Wang <Xin.Wang@cancer.org.uk>
MD5sum: 50b21fe6905ac0c72cebaa4f6bffb5fc
source.ver: src/contrib/PANR_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/PANR_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/PANR_1.4.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PANR_1.4.0.tgz
vignettes: vignettes/PANR/inst/doc/fullPAN.pdf,
vignettes/PANR/inst/doc/PANR-Vignette.pdf,
vignettes/PANR/inst/doc/pvmodule.pdf,
vignettes/PANR/inst/doc/sigmod.pdf
vignetteTitles: fullPAN.pdf, Main vignette:Posterior association
network and enriched functional gene modules inferred from rich
phenotypes of gene perturbations, pvmodule.pdf, sigmod.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/PANR/inst/doc/PANR-Vignette.R,
vignettes/PANR/inst/doc/PAN-Vignette.R
suggestsMe: RedeR
Package: parody
Version: 1.16.0
Depends: R (>= 2.5.0), methods, tools, utils
License: Artistic-2.0
Title: Parametric And Resistant Outlier DYtection
Description: routines for univariate and multivariate outlier detection
with a focus on parametric methods, but support for some
methods based on resistant statistics
biocViews: Bioinformatics, MultipleComparisons
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: VJ Carey <stvjc@channing.harvard.edu>
MD5sum: f9d450191e15a7ed2b06694d5c865c22
source.ver: src/contrib/parody_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/parody_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/parody_1.16.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/parody_1.16.0.tgz
vignettes: vignettes/parody/inst/doc/parody.pdf
vignetteTitles: parody: parametric and resistant outlier detection
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/parody/inst/doc/parody.R
dependsOnMe: arrayMvout, flowQ
Package: pathRender
Version: 1.26.0
Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods
Suggests: ALL, hgu95av2.db
License: LGPL
Title: Render molecular pathways
Description: build graphs from pathway databases, render them by
Rgraphviz
biocViews: GraphsAndNetworks, Pathways, NetworkVisualization
Author: Li Long <lilong@isb-sib.ch>
Maintainer: Li Long <lilong@isb-sib.ch>
URL: http://www.bioconductor.org
MD5sum: 568f93542efcdccd8282d3fb4ba7bee8
source.ver: src/contrib/pathRender_1.26.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/pathRender_1.26.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/pathRender_1.26.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/pathRender_1.26.0.tgz
vignettes: vignettes/pathRender/inst/doc/pathRender.pdf,
vignettes/pathRender/inst/doc/plotExG.pdf
vignetteTitles: pathRender overview, pathway graphs colored by
expression map
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/pathRender/inst/doc/pathRender.R,
vignettes/pathRender/inst/doc/plotExG.R
Package: pcaGoPromoter
Version: 1.2.0
Depends: R (>= 2.14.0) , ellipse
Imports: Biobase (>= 2.10.0) , AnnotationDbi
Suggests: Rgraphviz, GO.db, hgu133plus2.db, mouse4302.db, rat2302.db,
hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db,
Biostrings, pcaGoPromoter.Hs.hg19, pcaGoPromoter.Mm.mm9,
pcaGoPromoter.Rn.rn4, serumStimulation, parallel
License: GPL (>= 2)
Title: pcaGoPromoter is used to analyze DNA micro array data
Description: This package contains functions to ease the analyses of
DNA micro arrays. It utilizes principal component analysis as
the initial multivariate analysis, followed by functional
interpretation of the principal component dimensions with
overrepresentation analysis for GO terms and regulatory
interpretations using overrepresentation analysis of predicted
transcription factor binding sites with the primo algorithm.
biocViews: GeneExpression, Microarray, GO , Visualization
Author: Morten Hansen, Jorgen Olsen
Maintainer: Morten Hansen <mhansen@sund.ku.dk>
MD5sum: c4618a07df32b137795a371f61387061
source.ver: src/contrib/pcaGoPromoter_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/pcaGoPromoter_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/pcaGoPromoter_1.2.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/pcaGoPromoter/inst/doc/pcaGoPromoter.pdf
vignetteTitles: pcaGoPromoter
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/pcaGoPromoter/inst/doc/pcaGoPromoter.R
Package: pcaMethods
Version: 1.48.0
Depends: Biobase, methods, Rcpp (>= 0.8.7)
Imports: BiocGenerics, MASS
LinkingTo: Rcpp
Suggests: matrixStats, lattice
License: GPL (>= 3)
Archs: i386, x64
Title: A collection of PCA methods.
Description: Provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
Inverse Non-Linear PCA and the conventional SVD PCA. A cluster
based method for missing value estimation is included for
comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA
on incomplete data as well as for accurate missing value
estimation. A set of methods for printing and plotting the
results is also provided. All PCA methods make use of the same
data structure (pcaRes) to provide a common interface to the
PCA results. Initiated at the Max-Planck Institute for
Molecular Plant Physiology, Golm, Germany.
biocViews: Bioinformatics
Author: Wolfram Stacklies, Henning Redestig, Kevin Wright
Maintainer: Henning Redestig <henning.red@gmail.com>
SystemRequirements: Rcpp
MD5sum: 629c96fd661fa7e85f0b62db9c6928f3
source.ver: src/contrib/pcaMethods_1.48.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/pcaMethods_1.48.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/pcaMethods_1.48.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/pcaMethods/inst/doc/missingValues.pdf,
vignettes/pcaMethods/inst/doc/outliers.pdf,
vignettes/pcaMethods/inst/doc/pcaMethods.pdf
vignetteTitles: Missing value imputation, Data with outliers,
Introduction
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/pcaMethods/inst/doc/missingValues.R,
vignettes/pcaMethods/inst/doc/outliers.R,
vignettes/pcaMethods/inst/doc/pcaMethods.R
dependsOnMe: DeconRNASeq
Package: pcot2
Version: 1.26.0
Depends: R (>= 2.0.0), grDevices, Biobase, amap
Suggests: multtest, hu6800.db, KEGG.db, mvtnorm
License: GPL (>= 2)
Title: Principal Coordinates and Hotelling's T-Square method
Description: PCOT2 is a permutation-based method for investigating
changes in the activity of multi-gene networks. It utilizes
inter-gene correlation information to detect significant
alterations in gene network activities. Currently it can be
applied to two-sample comparisons.
biocViews: Microarray, DifferentialExpression
Author: Sarah Song, Mik Black
Maintainer: Sarah Song <qson003@stat.auckland.ac.nz>
MD5sum: d91498a68d39756a11f0bfe55b9779f9
source.ver: src/contrib/pcot2_1.26.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/pcot2_1.26.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/pcot2_1.26.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/pcot2/inst/doc/HowToUseGeneLocator.pdf,
vignettes/pcot2/inst/doc/pcot2.pdf
vignetteTitles: HowToUseGeneLocator.pdf, PCOT2 Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/pcot2/inst/doc/pcot2.R
Package: PCpheno
Version: 1.20.0
Depends: R (>= 2.10), Category, ScISI (>= 1.3.0), SLGI, ppiStats,
ppiData, annotate (>= 1.17.4)
Imports: AnnotationDbi, Biobase, Category, GO.db, graph, graphics,
GSEABase, KEGG.db, methods, ScISI, stats, stats4
Suggests: KEGG.db, GO.db, org.Sc.sgd.db
License: Artistic-2.0
Title: Phenotypes and cellular organizational units
Description: Tools to integrate, annotate, and link phenotypes to
cellular organizational units such as protein complexes and
pathways.
biocViews: GraphsAndNetworks, Proteomics, NetworkAnalysis
Author: Nolwenn Le Meur and Robert Gentleman
Maintainer: Nolwenn Le Meur <nlemeur@gmail.com>
MD5sum: ce5603dd07b259283d426e917513821b
source.ver: src/contrib/PCpheno_1.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/PCpheno_1.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/PCpheno_1.20.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/PCpheno/inst/doc/PCpheno.pdf
vignetteTitles: PCpheno Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/PCpheno/inst/doc/PCpheno.R
Package: pdInfoBuilder
Version: 1.22.0
Depends: R (>= 2.15.0), methods, Biobase (>= 2.17.7), RSQLite (>=
0.11.1), affxparser (>= 1.29.12), oligo (>= 1.21.5)
Imports: Biostrings (>= 2.25.12), IRanges (>= 1.15.44)
License: Artistic-2.0
Archs: i386, x64
Title: Platform Design Information Package Builder
Description: Builds platform design information packages. These consist
of a SQLite database containing feature-level data such as x, y
position on chip and featureSet ID. The database also
incorporates featureSet-level annotation data. The products of
this packages are used by the oligo pkg.
biocViews: Annotation, Infrastructure
Author: Seth Falcon, Benilton Carvalho with contributions by Vince
Carey, Matt Settles and Kristof de Beuf
Maintainer: Benilton Carvalho <Benilton.Carvalho@cancer.org.uk>
MD5sum: 4dd63999ba943c11078fd15f6718ba86
source.ver: src/contrib/pdInfoBuilder_1.22.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/pdInfoBuilder_1.22.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/pdInfoBuilder_1.22.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/pdInfoBuilder/inst/doc/BuildingPDInfoPkgs.pdf,
vignettes/pdInfoBuilder/inst/doc/howto-AffymetrixMapping.pdf
vignetteTitles: Building Annotation Packages with pdInfoBuilder for Use
with the oligo Package, PDInfo Package Building Affymetrix
Mapping Chips
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/pdInfoBuilder/inst/doc/BuildingPDInfoPkgs.R,
vignettes/pdInfoBuilder/inst/doc/howto-AffymetrixMapping.R
Package: pdmclass
Version: 1.30.0
Depends: Biobase (>= 1.4.22), R (>= 1.9.0), fibroEset, mda
License: Artistic-2.0
Title: Classification of Microarray Samples using Penalized
Discriminant Methods
Description: This package can be used to classify microarray data using
one of three penalized regression methods; partial least
squares, principal components regression, or ridge regression.
biocViews: Classification
Author: James W. MacDonald, Debashis Ghosh, based in part on pls code
of Mike Denham
Maintainer: James W. MacDonald <jmacdon@med.umich.edu>
MD5sum: e12714c49c8451292fcd9f869907436c
source.ver: src/contrib/pdmclass_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/pdmclass_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/pdmclass_1.30.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/pdmclass/inst/doc/pdmclass.pdf
vignetteTitles: pdmclass Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/pdmclass/inst/doc/pdmclass.R
suggestsMe: oneChannelGUI
Package: PGSEA
Version: 1.32.0
Depends: R (>= 2.10), GO.db, KEGG.db, AnnotationDbi, annaffy, methods,
Biobase (>= 2.5.5)
Suggests: GSEABase, GEOquery, org.Hs.eg.db, hgu95av2.db, limma
License: GPL-2
Title: Parametric Gene Set Enrichment Analysis
Description: Parametric Analysis of Gene Set Enrichment
biocViews: Microarray
Author: Kyle Furge <kyle.furge@vai.org> and Karl Dykema
<karl.dykema@vai.org>
Maintainer: Karl Dykema <karl.dykema@vai.org>
MD5sum: 27599aca3b0a2fe0e7651bf4e1d23ce9
source.ver: src/contrib/PGSEA_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/PGSEA_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/PGSEA_1.32.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/PGSEA/inst/doc/PGSEA2.pdf,
vignettes/PGSEA/inst/doc/PGSEA.pdf
vignetteTitles: HOWTO: PGSEA Example Workflow, HOWTO: PGSEA
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/PGSEA/inst/doc/PGSEA2.R,
vignettes/PGSEA/inst/doc/PGSEA.R
dependsOnMe: GeneExpressionSignature
Package: pgUtils
Version: 1.30.0
Depends: R (>= 1.8.0), methods, RPostgreSQL (>= 0.1)
Imports: methods, RPostgreSQL (>= 0.1)
License: LGPL (>= 2)
Title: Utility functions for PostgreSQL databases
Description: Functions for creating PostgreSQL database tables, with
auto incrementing primary keys, selection of foreign keys to
allow referential integrity and a logging mechanism.
biocViews: Infrastructure
Author: Johannes Rainer <johannes.rainer@i-med.ac.at>
Maintainer: Johannes Rainer <johannes.rainer@i-med.ac.at>
MD5sum: 0a043fc6d586a08df1a177ee68e095f4
source.ver: src/contrib/pgUtils_1.30.0.tar.gz
mac.binary.leopard.ver:
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vignettes: vignettes/pgUtils/inst/doc/pgUtils.pdf
vignetteTitles: pgUtils.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: maDB
Package: phenoDist
Version: 1.6.0
Depends: R (>= 2.9.0), imageHTS, e1071
Suggests: GOstats, MASS
License: LGPL-2.1
Title: Phenotypic distance measures
Description: PhenoDist is designed for measuring phenotypic distance in
image-based high-throughput screening, in order to identify
strong phenotypes and to group treatments into functional
clusters.
biocViews: CellBasedAssays, Bioinformatics
Author: Xian Zhang, Gregoire Pau, Wolfgang Huber, Michael Boutros
Maintainer: Xian Zhang <x.zhang@dkfz.de>
URL: http://www.dkfz.de/signaling,
http://www.embl.de/research/units/genome_biology/huber/
MD5sum: 59de5e43ff0ac89d88d2f6ba06053463
source.ver: src/contrib/phenoDist_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/phenoDist_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/phenoDist_1.6.0.zip
vignettes: vignettes/phenoDist/inst/doc/phenoDist.pdf
vignetteTitles: Introduction to phenoDist
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/phenoDist/inst/doc/phenoDist.R
Package: phenoTest
Version: 1.6.0
Depends: R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA
Imports: survival, limma, Hmisc, gplots, Category, AnnotationDbi,
hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv,
SNPchip, hgu133a.db, HTSanalyzeR
Suggests: GSEABase, KEGG.db, GO.db
Enhances: multicore, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Hs.eg.db, org.Dm.eg.db
License: GPL (>=2)
Title: Tools to test association between gene expression and phenotype
in a way that is efficient, structured, fast and scalable. We
also provide tools to do GSEA (Gene set enrichment analysis)
and copy number variation.
Description: Tools to test correlation between gene expression and
phenotype in a way that is efficient, structured, fast and
scalable. GSEA is also provided.
biocViews: Microarray, Bioinformatics, DifferentialExpression,
MultipleComparisons, Clustering, Classification
Author: Evarist Planet
Maintainer: Evarist Planet <evarist.planet@irbbarcelona.org>
MD5sum: 568ff3ba7855bb26b0f60d71b359afe3
source.ver: src/contrib/phenoTest_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/phenoTest_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/phenoTest_1.6.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/phenoTest/inst/doc/phenoTest.pdf
vignetteTitles: Manual for the phenoTest library
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/phenoTest/inst/doc/phenoTest.R
Package: phyloseq
Version: 1.2.1
Depends: R (>= 2.15.0), methods, ade4 (>= 1.4), ggplot2 (>= 0.9.2),
picante (>= 1.3)
Imports: ape (>= 3.0), foreach (>= 1.3), igraph0 (>= 0.5), multtest (>=
2.8), plyr (>= 1.7.1), reshape (>= 0.8.4), RJSONIO (>= 0.98),
scales (>= 0.2.2), vegan (>= 2.0)
Suggests: genefilter, testthat
Enhances: doParallel (>= 1.0)
License: AGPL-3
Title: Handling and analysis of high-throughput phylogenetic sequence
data.
Description: phyloseq provides a set of classes and tools to facilitate
the import, storage, analysis, and graphical display of
phylogenetic sequencing data.
biocViews: Clustering, Classification, MultipleComparisons,
QualityControl, GeneticVariability, HighThroughputSequencing
Author: Paul J. McMurdie <mcmurdie@stanford.edu>, Susan Holmes
<susan@stat.stanford.edu>
Maintainer: Paul J. McMurdie <mcmurdie@stanford.edu>
URL: http://joey711.github.com/phyloseq/
MD5sum: 89790d32a0631672fadeb6186c661c8b
source.ver: src/contrib/phyloseq_1.2.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/phyloseq_1.2.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/phyloseq_1.2.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/phyloseq/inst/doc/phyloseq_analysis.pdf,
vignettes/phyloseq/inst/doc/phyloseq_basics.pdf,
vignettes/phyloseq/inst/doc/phyloseq_classes_4.pdf
vignetteTitles: Analysis examples using phyloseq, Basic data
manipulation using phyloseq, phyloseq_classes_4.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/phyloseq/inst/doc/phyloseq_analysis.R,
vignettes/phyloseq/inst/doc/phyloseq_basics.R
Package: pickgene
Version: 1.30.0
Imports: graphics, grDevices, MASS, stats, utils
License: GPL (>= 2)
Title: Adaptive Gene Picking for Microarray Expression Data Analysis
Description: Functions to Analyze Microarray (Gene Expression) Data.
biocViews: Microarray, DifferentialExpression
Author: Brian S. Yandell <yandell@stat.wisc.edu>
Maintainer: Brian S. Yandell <yandell@stat.wisc.edu>
URL: http://www.stat.wisc.edu/~yandell/statgen
MD5sum: 001227a0de1f4c136b7a5c11bb3bf827
source.ver: src/contrib/pickgene_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/pickgene_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/pickgene_1.30.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/pickgene/inst/doc/pickgene.pdf
vignetteTitles: Adaptive Gene Picking for Microarray Expression Data
Analysis
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/pickgene/inst/doc/pickgene.R
Package: PICS
Version: 2.2.0
Depends: R (>= 2.14.0), BiocGenerics (>= 0.1.3)
Imports: methods, stats4, IRanges, GenomicRanges, graphics, grDevices,
stats
Suggests: ShortRead, rtracklayer, parallel
License: Artistic-2.0
Archs: i386, x64
Title: Probabilistic inference of ChIP-seq
Description: Probabilistic inference of ChIP-Seq using an empirical
Bayes mixture model approach.
biocViews: Clustering, Visualization, Sequencing, ChIPseq
Author: Xuekui Zhang <xzhang@stat.ubc.ca>, Raphael Gottardo
<rgottard@fhcrc.org>
Maintainer: Renan Sauteraud <rsautera@fhcrc.org>
MD5sum: 04c340fd738d52394e49f9d14b4b7171
source.ver: src/contrib/PICS_2.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/PICS_2.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/PICS_2.2.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PICS_2.2.0.tgz
vignettes: vignettes/PICS/inst/doc/PICS.pdf
vignetteTitles: The PICS users guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/PICS/inst/doc/PICS.R
importsMe: PING
Package: PING
Version: 2.2.0
Depends: R(>= 2.15.0), chipseq, IRanges, GenomicRanges
Imports: methods, PICS, graphics, grDevices, stats, Gviz, fda,
BSgenome, stats4, BiocGenerics, Rsamtools
Suggests: parallel, ShortRead, rtracklayer
License: Artistic-2.0
Archs: i386, x64
Title: Probabilistic inference for Nucleosome Positioning with
MNase-based or Sonicated Short-read Data
Description: Probabilistic inference of ChIP-Seq using an empirical
Bayes mixture model approach.
biocViews: Clustering, Statistics, Visualization, Sequencing
Author: Xuekui Zhang <xuezhang@jhsph.edu>, Raphael Gottardo
<raph@stat.ubc.ca>, Sangsoon Woo, <swoo@fhcrc.org>
Maintainer: Renan Sauteraud <rsautera@fhcrc.org>
MD5sum: fbcfc67b07fab4c6adb688d2ebe4ccb8
source.ver: src/contrib/PING_2.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/PING_2.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/PING_2.2.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PING_2.2.0.tgz
vignettes: vignettes/PING/inst/doc/PING.pdf,
vignettes/PING/inst/doc/PING-PE.pdf
vignetteTitles: The PING users guide, Using PING with paired-end
sequencing data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/PING/inst/doc/PING-PE.R,
vignettes/PING/inst/doc/PING.R
Package: pint
Version: 1.10.0
Depends: mvtnorm, methods, graphics, Matrix, dmt
License: FreeBSD
Title: Pairwise INTegration of functional genomics data
Description: Pairwise data integration for functional genomics,
including tools for DNA/RNA/miRNA dependency screens.
biocViews: aCGH, GeneExpression, Genetics, DifferentialExpression,
Microarray
Author: Olli-Pekka Huovilainen <ohuovila@gmail.com> and Leo Lahti
<leo.lahti@iki.fi>
Maintainer: Olli-Pekka Huovilainen <ohuovila@gmail.com>
MD5sum: 9ac44bcdaca68d40aeedd3e189bf9f39
source.ver: src/contrib/pint_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/pint_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/pint_1.10.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pint_1.10.0.tgz
vignettes: vignettes/pint/inst/doc/depsearch.pdf
vignetteTitles: pint
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/pint/inst/doc/depsearch.R
Package: pkgDepTools
Version: 1.24.0
Depends: methods, graph, RBGL
Imports: graph, RBGL
Suggests: Biobase, Rgraphviz, RCurl, BiocInstaller
License: GPL-2
Title: Package Dependency Tools
Description: This package provides tools for computing and analyzing
dependency relationships among R packages. It provides tools
for building a graph-based representation of the dependencies
among all packages in a list of CRAN-style package
repositories. There are also utilities for computing
installation order of a given package. If the RCurl package is
available, an estimate of the download size required to install
a given package and its dependencies can be obtained.
biocViews: Infrastructure, GraphsAndNetworks
Author: Seth Falcon
Maintainer: Seth Falcon <seth@userprimary.net>
MD5sum: 0f2feaac291f513ffd14f57961710a59
source.ver: src/contrib/pkgDepTools_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/pkgDepTools_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/pkgDepTools_1.24.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/pkgDepTools/inst/doc/pkgDepTools.pdf
vignetteTitles: How to Use pkgDepTools
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/pkgDepTools/inst/doc/pkgDepTools.R
Package: plateCore
Version: 1.16.0
Depends: R (>= 2.10), flowCore, flowViz, lattice, latticeExtra
Imports: Biobase, flowCore, graphics, grDevices, lattice, MASS,
methods, robustbase, stats, utils
Suggests: gplots
License: Artistic-2.0
Title: Statistical tools and data structures for plate-based flow
cytometry
Description: Provides basic S4 data structures and routines for
analyzing plate based flow cytometry data.
biocViews: FlowCytometry, Infrastructure, CellBasedAssays
Author: Errol Strain, Florian Hahne, and Perry Haaland
Maintainer: Errol Strain <estrain@gmail.com>
URL: http://www.bioconductor.org
MD5sum: d5f36acb4e3c655832868d1197a15203
source.ver: src/contrib/plateCore_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/plateCore_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/plateCore_1.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/plateCore/inst/doc/expDens.pdf,
vignettes/plateCore/inst/doc/plateCoreVig.pdf
vignetteTitles: expDens.pdf, An R Package for Analysis of High
Throughput Flow Cytometry Data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/plateCore/inst/doc/plateCoreVig.R
Package: plgem
Version: 1.30.0
Depends: R (>= 2.10), Biobase (>= 2.5.5), MASS
Imports: utils
License: GPL-2
Title: Detect differential expression in microarray and proteomics
datasets with the Power Law Global Error Model (PLGEM)
Description: The Power Law Global Error Model (PLGEM) has been shown to
faithfully model the variance-versus-mean dependence that
exists in a variety of genome-wide datasets, including
microarray and proteomics data. The use of PLGEM has been shown
to improve the detection of differentially expressed genes or
proteins in these datasets.
biocViews: Microarray, DifferentialExpression, Proteomics
Author: Mattia Pelizzola <mattia.pelizzola@gmail.com> and Norman
Pavelka <normanpavelka@gmail.com>
Maintainer: Norman Pavelka <normanpavelka@gmail.com>
URL: http://www.genopolis.it
MD5sum: 6a1d3842ac621d0b042a3413af6d7f71
source.ver: src/contrib/plgem_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/plgem_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/plgem_1.30.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/plgem/inst/doc/plgem.pdf
vignetteTitles: An introduction to PLGEM
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/plgem/inst/doc/plgem.R
Package: plier
Version: 1.28.0
Depends: R (>= 2.0), methods
Imports: affy, Biobase, methods
License: GPL (>= 2)
Archs: i386, x64
Title: Implements the Affymetrix PLIER algorithm
Description: The PLIER (Probe Logarithmic Error Intensity Estimate)
method produces an improved signal by accounting for
experimentally observed patterns in probe behavior and handling
error at the appropriately at low and high signal values.
biocViews: Software
Author: Affymetrix Inc., Crispin J Miller, PICR
Maintainer: Crispin Miller <cmiller@picr.man.ac.uk>
MD5sum: 7d8ca1dc5d401e03c07056399611e60e
source.ver: src/contrib/plier_1.28.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/plier_1.28.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/plier_1.28.0.zip
mac.binary.leopard.ver:
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hasREADME: TRUE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
suggestsMe: virtualArray
Package: PLPE
Version: 1.18.0
Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods
License: GPL (>= 2)
Title: Local Pooled Error Test for Differential Expression with Paired
High-throughput Data
Description: This package performs tests for paired high-throughput
data.
biocViews: Proteomics, Microarray, DifferentialExpression
Author: HyungJun Cho <hj4cho@korea.ac.kr> and Jae K. Lee
<jaeklee@virginia.edu>
Maintainer: Soo-heang Eo <hanansh@korea.ac.kr>
URL: http://www.korea.ac.kr/~stat2242/
MD5sum: 8a8958f32d4b95a3378813e9f3147625
source.ver: src/contrib/PLPE_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/PLPE_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/PLPE_1.18.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PLPE_1.18.0.tgz
vignettes: vignettes/PLPE/inst/doc/PLPE.pdf
vignetteTitles: PLPE Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/PLPE/inst/doc/PLPE.R
Package: plw
Version: 1.18.0
Depends: R (>= 2.10), affy (>= 1.23.4)
Imports: MASS, affy, graphics, splines, stats
Suggests: limma
License: GPL-2
Archs: i386, x64
Title: Probe level Locally moderated Weighted t-tests.
Description: Probe level Locally moderated Weighted median-t (PLW) and
Locally Moderated Weighted-t (LMW).
biocViews: Microarray, OneChannel, TwoChannel, Bioinformatics,
DifferentialExpression
Author: Magnus Astrand
Maintainer: Magnus Astrand <magnus.astrand@astrazeneca.com>
MD5sum: 1416b79d5832c16c8f4509070ba4aa75
source.ver: src/contrib/plw_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/plw_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/plw_1.18.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/plw_1.18.0.tgz
vignettes: vignettes/plw/inst/doc/HowToPLW.pdf
vignetteTitles: HowTo plw
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/plw/inst/doc/HowToPLW.R
Package: ppiStats
Version: 1.24.0
Depends: ScISI (>= 1.13.2), lattice, ppiData (>= 0.1.6)
Imports: Biobase, Category, graph, graphics, grDevices, lattice,
methods, RColorBrewer, stats
Suggests: yeastExpData, xtable
License: Artistic-2.0
Title: Protein-Protein Interaction Statistical Package
Description: Tools for the analysis of protein interaction data.
biocViews: Proteomics, GraphsAndNetworks, NetworkAnalysis
Author: T. Chiang and D. Scholtens with contributions from W. Huber and
L. Wang
Maintainer: Tony Chiang <tchiang@fhcrc.org>
MD5sum: db0fda03dd3031dbe28aea1c079368c0
source.ver: src/contrib/ppiStats_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ppiStats_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ppiStats_1.24.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ppiStats/inst/doc/ppiStats.pdf
vignetteTitles: ppiStats
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ppiStats/inst/doc/ppiStats.R
dependsOnMe: PCpheno
suggestsMe: BiocCaseStudies, RpsiXML
Package: prada
Version: 1.34.0
Depends: R (>= 2.10.0), Biobase, RColorBrewer, grid, methods, rrcov
Imports: Biobase, BiocGenerics, graphics, grDevices, grid, MASS,
methods, RColorBrewer, rrcov, stats4, utils
Suggests: cellHTS, tcltk
License: LGPL
Archs: i386, x64
Title: Data analysis for cell-based functional assays
Description: Tools for analysing and navigating data from
high-throughput phenotyping experiments based on cellular
assays and fluorescent detection (flow cytometry (FACS),
high-content screening microscopy).
biocViews: CellBasedAssays, Visualization
Author: Florian Hahne <florian.hahne@novartis.com>, Wolfgang Huber
<huber@ebi.ac.uk>, Markus Ruschhaupt, Joern Toedling
<toedling@ebi.ac.uk>
Maintainer: Florian Hahne <florian.hahne@novartis.com>
URL: http://www.dkfz.de/mga/whuber, http://www.dkfz.de/LIFEdb
MD5sum: 59767f81cdbf84dafc9163bbd2633544
source.ver: src/contrib/prada_1.34.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/prada_1.34.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/prada_1.34.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/prada/inst/doc/norm2.pdf,
vignettes/prada/inst/doc/prada2cellHTS.pdf
vignetteTitles: Removal of contaminants from FACS data, Combining prada
output and cellHTS
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/prada/inst/doc/norm2.R,
vignettes/prada/inst/doc/prada2cellHTS.R
htmlDocs: vignettes/prada/inst/doc/fcs3.html
dependsOnMe: cellHTS, domainsignatures, RNAither
importsMe: cellHTS2
Package: PREDA
Version: 1.4.0
Depends: R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats,
methods, annotate
Suggests: quantsmooth, qvalue, samr, limma, caTools, affy,
PREDAsampledata
Enhances: Rmpi, rsprng
License: GPL-2
Title: Position RElated Data Anlysis
Description: Package for the position related analysis of quantitative
functional genomics data.
biocViews: Software, CopyNumberVariants, GeneExpression, Genetics
Author: Francesco Ferrari <francesco.ferrari@unimore.it>
Maintainer: Francesco Ferrari <francesco.ferrari@unimore.it>
MD5sum: 00b67fbef31ff576597e3d1d63243c81
source.ver: src/contrib/PREDA_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/PREDA_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/PREDA_1.4.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PREDA_1.4.0.tgz
vignettes: vignettes/PREDA/inst/doc/PREDAclasses.pdf,
vignettes/PREDA/inst/doc/PREDAtutorial.pdf
vignetteTitles: PREDA S4-classes, PREDA tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/PREDA/inst/doc/PREDAclasses.R,
vignettes/PREDA/inst/doc/PREDAtutorial.R
Package: predictionet
Version: 1.4.0
Depends: igraph0, catnet
Imports: penalized, RBGL, MASS
Suggests: network, minet, knitr
License: Artistic-2.0
Title: Inference for predictive networks designed for (but not limited
to) genomic data
Description: This package contains a set of functions related to
network inference combining genomic data and prior information
extracted from biomedical literature and structured biological
databases. The main function is able to generate networks using
Bayesian or regression-based inference methods; while the
former is limited to < 100 of variables, the latter may infer
networks with hundreds of variables. Several statistics at the
edge and node levels have been implemented (edge stability,
predictive ability of each node, ...) in order to help the user
to focus on high quality subnetworks. Ultimately, this package
is used in the 'Predictive Networks' web application developed
by the Dana-Farber Cancer Institute in collaboration with
Entagen.
biocViews: GraphsAndNetworks, NetworkInference
Author: Benjamin Haibe-Kains, Catharina Olsen, Gianluca Bontempi, John
Quackenbush
Maintainer: Benjamin Haibe-Kains <bhaibeka@jimmy.harvard.edu>,
Catharina Olsen <colsen@ulb.ac.be>
URL: http://compbio.dfci.harvard.edu, http://www.ulb.ac.be/di/mlg
MD5sum: f5b0e11b149158b1f4418ef0c0af5205
source.ver: src/contrib/predictionet_1.4.0.tar.gz
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/predictionet_1.4.0.tgz
vignettes:
vignettes/predictionet/inst/doc/predictionet-boxplotr2pwcvfig2.pdf,
vignettes/predictionet/inst/doc/predictionet-boxplotstabpwcvfig2.pdf,
vignettes/predictionet/inst/doc/predictionet-cytoscape.pdf,
vignettes/predictionet/inst/doc/predictionet-edgecoldiffig.pdf,
vignettes/predictionet/inst/doc/predictionet-edgestabfig.pdf,
vignettes/predictionet/inst/doc/predictionet-genepredabmccfig.pdf,
vignettes/predictionet/inst/doc/predictionet-genepredabmcctestfig.pdf,
vignettes/predictionet/inst/doc/predictionet-genepredabr2fig.pdf,
vignettes/predictionet/inst/doc/predictionet-genepredabr2testfig.pdf,
vignettes/predictionet/inst/doc/predictionet.pdf,
vignettes/predictionet/inst/doc/predictionet-pn_webapp_ras.pdf,
vignettes/predictionet/inst/doc/predictionet-regnetcvpriorsweightfig2.pdf,
vignettes/predictionet/inst/doc/predictionet-regnetcvtopo1topo2fig2.pdf,
vignettes/predictionet/inst/doc/predictionet-regnetcvtopo1topo2predfig2.pdf,
vignettes/predictionet/inst/doc/predictionet-regnetcvtopo1topo2stabfig2.pdf,
vignettes/predictionet/inst/doc/predictionet-regrnet_design.pdf,
vignettes/predictionet/inst/doc/predictionet-regrnetopofig.pdf
vignetteTitles: predictionet-boxplotr2pwcvfig2.pdf,
predictionet-boxplotstabpwcvfig2.pdf,
predictionet-cytoscape.pdf, predictionet-edgecoldiffig.pdf,
predictionet-edgestabfig.pdf,
predictionet-genepredabmccfig.pdf,
predictionet-genepredabmcctestfig.pdf,
predictionet-genepredabr2fig.pdf,
predictionet-genepredabr2testfig.pdf, predictionet,
predictionet-pn_webapp_ras.pdf,
predictionet-regnetcvpriorsweightfig2.pdf,
predictionet-regnetcvtopo1topo2fig2.pdf,
predictionet-regnetcvtopo1topo2predfig2.pdf,
predictionet-regnetcvtopo1topo2stabfig2.pdf,
predictionet-regrnet_design.pdf, predictionet-regrnetopofig.pdf
hasREADME: TRUE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/predictionet/inst/doc/predictionet.R
Package: preprocessCore
Version: 1.20.0
Depends: methods
Imports: stats
License: LGPL (>= 2)
Archs: i386, x64
Title: A collection of pre-processing functions
Description: A library of core preprocessing routines
biocViews: Infrastructure
Author: Benjamin Milo Bolstad <bmb@bmbolstad.com>
Maintainer: Benjamin Milo Bolstad <bmb@bmbolstad.com>
MD5sum: b52c0a508ab4a3c148b925b4525f74a8
source.ver: src/contrib/preprocessCore_1.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/preprocessCore_1.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/preprocessCore_1.20.0.zip
mac.binary.leopard.ver:
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hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: affyPLM, cqn, crlmm, RefPlus, virtualArray
importsMe: affy, AffyTiling, charm, cn.farms, frma, frmaTools, lumi,
MBCB, minfi, MSnbase, oligo, waveTiling
suggestsMe: oneChannelGUI
Package: PROcess
Version: 1.34.0
Depends: Icens
Imports: graphics, grDevices, Icens, stats, utils
License: Artistic-2.0
Title: Ciphergen SELDI-TOF Processing
Description: A package for processing protein mass spectrometry data.
biocViews: MassSpectrometry, Proteomics
Author: Xiaochun Li
Maintainer: Xiaochun Li <xiaochun@jimmy.harvard.edu>
MD5sum: fb423b67ec7c5d7ae0d9a36fd505b288
source.ver: src/contrib/PROcess_1.34.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/PROcess_1.34.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/PROcess_1.34.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/PROcess_1.34.0.tgz
vignettes: vignettes/PROcess/inst/doc/howtoprocess.pdf
vignetteTitles: HOWTO PROcess
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/PROcess/inst/doc/howtoprocess.R
Package: procoil
Version: 1.8.0
Depends: R (>= 2.10.1), methods
Imports: methods, stats, graphics, utils
Suggests: Biostrings
License: GPL (>= 2)
Title: Prediction of Oligomerization of Coiled Coil Proteins
Description: The procoil package allows to predict whether a coiled
coil sequence (amino acid sequence plus heptad register) is
more likely to form a dimer or more likely to form a trimer.
The predict function not only computes the prediction itself,
but also a profile which allows to determine the strengths to
which the individual residues are indicative for either class.
Profiles can also be plotted and exported to files.
biocViews: Proteomics, Classification
Author: Ulrich Bodenhofer
Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
URL: http://www.bioinf.jku.at/software/procoil/
MD5sum: 72b2e6a3777e1612b0f43a2be3b6d035
source.ver: src/contrib/procoil_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/procoil_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/procoil_1.8.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/procoil/inst/doc/procoil.pdf
vignetteTitles: PrOCoil - A Web Service and an R Package for Predicting
the Oligomerization of Coiled-Coil Proteins
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/procoil/inst/doc/procoil.R
Package: PROMISE
Version: 1.10.0
Depends: R (>= 2.11.0), Biobase, GSEABase
Imports: Biobase, GSEABase, stats
License: GPL (>= 2)
Title: PRojection Onto the Most Interesting Statistical Evidence
Description: A general tool to identify genomic features with a
specific biologically interesting pattern of associations with
multiple endpoint variables as described in Pounds et. al.
(2009) Bioinformatics 25: 2013-2019
biocViews: Microarray, OneChannel, Bioinformatics, MultipleComparisons,
GeneExpression
Author: Stan Pounds <stanley.pounds@stjude.org>, Xueyuan Cao
<xueyuan.cao@stjude.org>
Maintainer: Stan Pounds <stanley.pounds@stjude.org>, Xueyuan Cao
<xueyuan.cao@stjude.org>
MD5sum: 464bae33ad8d6e0fc3af34ef453322ce
source.ver: src/contrib/PROMISE_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/PROMISE_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/PROMISE_1.10.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/PROMISE/inst/doc/PROMISE.pdf
vignetteTitles: An introduction to PROMISE
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/PROMISE/inst/doc/PROMISE.R
Package: puma
Version: 3.0.0
Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.23.4), graphics,
grDevices, methods, stats, utils, mclust
Imports: Biobase (>= 2.5.5), affy (>= 1.23.4)
Suggests: pumadata, affydata, snow, limma, annotate, ROCR
License: LGPL
Archs: i386, x64
Title: Propagating Uncertainty in Microarray Analysis
Description: Most analyses of Affymetrix GeneChip data are based on
point estimates of expression levels and ignore the uncertainty
of such estimates. By propagating uncertainty to downstream
analyses we can improve results from microarray analyses. For
the first time, the puma package makes a suite of uncertainty
propagation methods available to a general audience. puma also
offers improvements in terms of scope and speed of execution
over previously available uncertainty propagation methods.
Included are summarisation, differential expression detection,
clustering and PCA methods, together with useful plotting and
data manipulation functions.
biocViews: Microarray, OneChannel, Preprocessing, Bioinformatics,
DifferentialExpression, Clustering
Author: Richard D. Pearson, Xuejun Liu, Magnus Rattray, Marta Milo,
Neil D. Lawrence, Guido Sanguinetti, Li Zhang
Maintainer: Richard Pearson <richard.pearson@well.ox.ac.uk>
URL: http://umber.sbs.man.ac.uk/resources/puma
MD5sum: 1a671edcd1062cbab611831698064302
source.ver: src/contrib/puma_3.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/puma_3.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/puma_3.0.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/puma_3.0.0.tgz
vignettes: vignettes/puma/inst/doc/puma-014.pdf,
vignettes/puma/inst/doc/puma-015.pdf,
vignettes/puma/inst/doc/puma-016.pdf,
vignettes/puma/inst/doc/puma-022.pdf,
vignettes/puma/inst/doc/puma-023.pdf,
vignettes/puma/inst/doc/puma-024.pdf,
vignettes/puma/inst/doc/puma.pdf
vignetteTitles: puma-014.pdf, puma-015.pdf, puma-016.pdf, puma-022.pdf,
puma-023.pdf, puma-024.pdf, puma.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
importsMe: tigre
suggestsMe: tigre
Package: pvac
Version: 1.6.0
Depends: R (>= 2.8.0)
Imports: affy (>= 1.20.0), stats, Biobase
Suggests: pbapply, affydata, ALLMLL, genefilter
License: LGPL (>= 2.0)
Title: PCA-based gene filtering for Affymetrix arrays
Description: The package contains the function for filtering genes by
the proportion of variation accounted for by the first
principal component (PVAC).
biocViews: Bioinformatics, Microarray, OneChannel, QualityControl
Author: Jun Lu and Pierre R. Bushel
Maintainer: Jun Lu <jlu276@gmail.com>, Pierre R. Bushel
<bushel@niehs.nih.gov>
MD5sum: a8def8f89aed67c11078379b09357603
source.ver: src/contrib/pvac_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/pvac_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/pvac_1.6.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pvac_1.6.0.tgz
vignettes: vignettes/pvac/inst/doc/density.pdf,
vignettes/pvac/inst/doc/pvac.pdf
vignetteTitles: density.pdf, PCA-based gene filtering for Affymetrix
GeneChips
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/pvac/inst/doc/pvac.R
Package: PWMEnrich
Version: 1.2.0
Depends: methods, Biostrings, grid
Imports: seqLogo, gdata, evd
Suggests: BSgenome.Dmelanogaster.UCSC.dm3,
PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel
License: GPL-3
Title: PWM enrichment analysis
Description: Asses the enrichment of already known PWMs (e.g. from
JASPAR) in DNA sequences. Motif hits in a sequence or DNA
region are considered together and P-values derived for their
joint pattern. The package implements multiple algorithms,
including fixed-threshold (Z-score) and threshold-free
(Lognormal normalization and Clover) methods. The main goal is
to identify a set of transcription factors that most likely
bind to a single sequence, group of sequences, or show
significantly different binding affinity between two sets of
sequences.
biocViews: Bioinformatics, SequenceMatching
Author: Robert Stojnic
Maintainer: Robert Stojnic <robert.stojnic@gmail.com>
MD5sum: 7016dd8acac0ab5c153f9f06cc8d5155
source.ver: src/contrib/PWMEnrich_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/PWMEnrich_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/PWMEnrich_1.2.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/PWMEnrich_1.2.0.tgz
vignettes: vignettes/PWMEnrich/inst/doc/PWMEnrich.pdf
vignetteTitles: Overview of the 'PWMEnrich' package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/PWMEnrich/inst/doc/PWMEnrich.R
Package: qpcrNorm
Version: 1.16.0
Depends: methods, Biobase, limma, affy
License: LGPL (>= 2)
Title: Data-driven normalization strategies for high-throughput qPCR
data.
Description: The package contains functions to perform normalization of
high-throughput qPCR data. Basic functions for processing raw
Ct data plus functions to generate diagnostic plots are also
available.
biocViews: Preprocessing, GeneExpression
Author: Jessica Mar
Maintainer: Jessica Mar <jess@jimmy.harvard.edu>
MD5sum: c6aa1ef197643c05eae377031150d495
source.ver: src/contrib/qpcrNorm_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/qpcrNorm_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/qpcrNorm_1.16.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/qpcrNorm_1.16.0.tgz
vignettes: vignettes/qpcrNorm/inst/doc/qpcrNorm.pdf
vignetteTitles: qPCR Normalization Example
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/qpcrNorm/inst/doc/qpcrNorm.R
suggestsMe: EasyqpcR
Package: qpgraph
Version: 1.14.4
Depends: R (>= 2.10), methods
Imports: methods, annotate, Matrix, graph, Biobase, GGBase,
AnnotationDbi
Suggests: Matrix, mvtnorm, graph, genefilter, Category,
org.EcK12.eg.db, GOstats
Enhances: rlecuyer, snow, Rgraphviz
License: GPL (>= 2)
Archs: i386, x64
Title: Reverse engineering of molecular regulatory networks with
qp-graphs
Description: q-order partial correlation graphs, or qp-graphs for
short, are undirected Gaussian graphical Markov models built
from q-order partial correlations. They are useful for learning
undirected graphical Gaussian Markov models from data sets
where the number of random variables p exceeds the available
sample size n as, for instance, in the case of microarray data
where they can be employed to reverse engineer a molecular
regulatory network.
biocViews: Microarray, GeneExpression, Transcription, Pathways,
NetworkInference, GraphsAndNetworks, GeneRegulation
Author: R. Castelo and A. Roverato
Maintainer: Robert Castelo <robert.castelo@upf.edu>
URL: http://functionalgenomics.upf.edu/qpgraph
MD5sum: 25d37d01a74fa8bbbb1fc82fb2d9255d
source.ver: src/contrib/qpgraph_1.14.4.tar.gz
win.binary.ver: bin/windows/contrib/2.15/qpgraph_1.14.4.zip
win64.binary.ver: bin/windows64/contrib/2.15/qpgraph_1.14.4.zip
mac.binary.leopard.ver:
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vignettes: vignettes/qpgraph/inst/doc/BasicUsersGuide.pdf,
vignettes/qpgraph/inst/doc/qpTxRegNet.pdf
vignetteTitles: BasicUsersGuide.pdf, Reverse-engineer transcriptional
regulatory networks using qpgraph
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/qpgraph/inst/doc/qpTxRegNet.R
Package: qrqc
Version: 1.12.0
Depends: reshape, ggplot2, Biostrings, biovizBase, brew, xtable,
Rsamtools (>= 1.3.28), testthat
Imports: reshape, ggplot2, Biostrings, biovizBase, graphics, methods,
plyr, stats
LinkingTo: Rsamtools
License: GPL (>=2)
Archs: i386, x64
Title: Quick Read Quality Control
Description: Quickly scans reads and gathers statistics on base and
quality frequencies, read length, k-mers by position, and
frequent sequences. Produces graphical output of statistics for
use in quality control pipelines, and an optional HTML quality
report. S4 SequenceSummary objects allow specific tests and
functionality to be written around the data collected.
biocViews: Sequencing, QualityControl, DataImport, Preprocessing,
Visualization, HighThroughputSequencing
Author: Vince Buffalo
Maintainer: Vince Buffalo <vsbuffalo@ucdavis.edu>
URL: http://github.com/vsbuffalo/qrqc
MD5sum: 738349207336256b6e3b87b9c6f168d9
source.ver: src/contrib/qrqc_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/qrqc_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/qrqc_1.12.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/qrqc_1.12.0.tgz
vignettes: vignettes/qrqc/inst/doc/qrqc.pdf
vignetteTitles: Using the qrqc package to gather information about
sequence qualities
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/qrqc/inst/doc/qrqc.R
Package: QUALIFIER
Version: 1.2.0
Depends: R (>=
2.14.0),reshape,flowWorkspace,flowViz,flowCore,RColorBrewer
Imports:
MASS,hwriter,RSVGTipsDevice,lattice,stats4,flowCore,flowViz,methods,flowWorkspace,reshape
Enhances: ncdfFlow
License: Artistic-2.0
Title: Qualitiy Control of Gated Flow Cytometry Experiments
Description: Provides quality control and quality assessment tools for
gated flow cytometry data.
biocViews: Infrastructure, Flowcytometry, CellBasedAssays
Author: Mike Jiang,Greg Finak,Raphael Gottardo
Maintainer: Mike Jiang <wjiang2@fhcrc.org>
MD5sum: 7df1b07a9a838988eb6d3642165298f5
source.ver: src/contrib/QUALIFIER_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/QUALIFIER_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/QUALIFIER_1.2.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/QUALIFIER/inst/doc/QUALIFIER.pdf
vignetteTitles: Quality assessment for gated Flow Cytometry Data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/QUALIFIER/inst/doc/QUALIFIER.R
Package: quantsmooth
Version: 1.24.0
Depends: R(>= 2.10.0), quantreg, grid
License: GPL-2
Title: Quantile smoothing and genomic visualization of array data
Description: Implements quantile smoothing as introduced in: Quantile
smoothing of array CGH data; Eilers PH, de Menezes RX;
Bioinformatics. 2005 Apr 1;21(7):1146-53.
biocViews: Visualization, CopyNumberVariants
Author: Jan Oosting, Paul Eilers, Renee Menezes
Maintainer: Jan Oosting <j.oosting@lumc.nl>
MD5sum: e2d82df1c3adf2fb35415b0cc8480e31
source.ver: src/contrib/quantsmooth_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/quantsmooth_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/quantsmooth_1.24.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/quantsmooth/inst/doc/quantsmooth.pdf
vignetteTitles: quantsmooth
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/quantsmooth/inst/doc/quantsmooth.R
dependsOnMe: beadarraySNP
importsMe: GWASTools, SIM
suggestsMe: PREDA
Package: qvalue
Version: 1.32.0
Imports: graphics, grDevices, stats, tcltk
License: LGPL
Title: Q-value estimation for false discovery rate control
Description: This package takes a list of p-values resulting from the
simultaneous testing of many hypotheses and estimates their
q-values. The q-value of a test measures the proportion of
false positives incurred (called the false discovery rate) when
that particular test is called significant. Various plots are
automatically generated, allowing one to make sensible
significance cut-offs. Several mathematical results have
recently been shown on the conservative accuracy of the
estimated q-values from this software. The software can be
applied to problems in genomics, brain imaging, astrophysics,
and data mining.
biocViews: MultipleComparisons
Author: Alan Dabney <adabney@u.washington.edu> and John D. Storey
<jstorey@u.washington.edu>, with assistance from Gregory R.
Warnes <gregory_r_warnes@groton.pfizer.com>
Maintainer: John D. Storey <jstorey@u.washington.edu>
MD5sum: 26b6e5571d2b884f38160dc14897c9e6
source.ver: src/contrib/qvalue_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/qvalue_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/qvalue_1.32.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/qvalue/inst/doc/manual.pdf,
vignettes/qvalue/inst/doc/pHist.pdf,
vignettes/qvalue/inst/doc/qHist.pdf,
vignettes/qvalue/inst/doc/qPlots.pdf,
vignettes/qvalue/inst/doc/qvalue.pdf
vignetteTitles: manual.pdf, pHist.pdf, qHist.pdf, qPlots.pdf, qvalue
Tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/qvalue/inst/doc/qvalue.R
dependsOnMe: anota, CancerMutationAnalysis, DEGseq, netresponse, SSPA,
webbioc
importsMe: anota, DOSE, ReactomePA, synapter, trigger, webbioc
suggestsMe: LBE, maanova, PREDA
Package: r3Cseq
Version: 1.4.0
Depends: R (>= 2.14.0), IRanges, BSgenome,ShortRead, rtracklayer,
RColorBrewer, methods
Suggests: BSgenome.Mmusculus.UCSC.mm9
License: GPL-3
Title: Analysis of Chromosome Conformation Capture and Next-generation
Sequencing (3C-seq)
Description: This package is an implementation of data analysis for the
long-range interactions from 3C-seq assay.
biocViews: Preprocessing, Sequencing, HighThroughputSequencing,
Author: Supat Thongjuea, Bergen Center for Computational Science,
Norway <supat.thongjuea@bccs.uib.no>
Maintainer: Supat Thongjuea <supat.thongjuea@bccs.uib.no>
MD5sum: 816dd54acfe2aba2b3169ee99b4ed7a9
source.ver: src/contrib/r3Cseq_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/r3Cseq_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/r3Cseq_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/r3Cseq/inst/doc/r3Cseq.pdf
vignetteTitles: r3Cseq
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/r3Cseq/inst/doc/r3Cseq.R
Package: R453Plus1Toolbox
Version: 1.8.1
Depends: R (>= 2.12.0), BiocGenerics, Biobase, Biostrings,
BSgenome.Scerevisiae.UCSC.sacCer2,TeachingDemos
Imports: BiocGenerics (>= 0.1.3), Biobase (>= 2.15.1), biomaRt,
Biostrings, BSgenome, IRanges (>= 1.13.10), methods, R2HTML,
Rsamtools, rtracklayer, ShortRead, VariantAnnotation
Suggests: rtracklayer, ShortRead, Rsamtools,
BSgenome.Hsapiens.UCSC.hg19
License: LGPL-3
Archs: i386, x64
Title: A package for importing and analyzing data from Roche's Genome
Sequencer System.
Description: The R453Plus1 Toolbox comprises useful functions for the
analysis of data generated by Roche's 454 sequencing platform.
It adds functions for quality assurance as well as for
annotation and visualization of detected variants,
complementing the software tools shipped by Roche with their
product. Further, a pipeline for the detection of structural
variants is provided.
biocViews: HighThroughputSequencing, Infrastructure, DataImport,
DataRepresentation, Visualization, QualityControl,
ReportWriting
Author: Hans-Ulrich Klein, Christoph Bartenhagen, Christian Ruckert
Maintainer: Hans-Ulrich Klein <h.klein@uni-muenster.de>
MD5sum: 8ba8df3f10abba6ed2a82265da4dc5f0
source.ver: src/contrib/R453Plus1Toolbox_1.8.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/R453Plus1Toolbox_1.8.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/R453Plus1Toolbox_1.8.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/R453Plus1Toolbox/inst/doc/vignette.pdf
vignetteTitles: A package for importing and analyzing data from Roche's
Genome Sequencer System
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/R453Plus1Toolbox/inst/doc/vignette.R
Package: rama
Version: 1.32.0
Depends: R(>= 2.5.0)
License: GPL (>= 2)
Archs: i386, x64
Title: Robust Analysis of MicroArrays
Description: Robust estimation of cDNA microarray intensities with
replicates. The package uses a Bayesian hierarchical model for
the robust estimation. Outliers are modeled explicitly using a
t-distribution, and the model also addresses classical issues
such as design effects, normalization, transformation, and
nonconstant variance.
biocViews: Microarray, TwoChannel, QualityControl, Preprocessing
Author: Raphael Gottardo
Maintainer: Raphael Gottardo <raph@stat.ubc.ca>
MD5sum: 58f85db6c04a5716fd3f8ea6fb45b1c3
source.ver: src/contrib/rama_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/rama_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/rama_1.32.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rama_1.32.0.tgz
vignettes: vignettes/rama/inst/doc/rama.pdf
vignetteTitles: rama Tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/rama/inst/doc/rama.R
dependsOnMe: bridge
Package: RamiGO
Version: 1.4.0
Depends: gsubfn,methods
Imports: igraph,RCurl,png,RCytoscape,graph
License: Artistic-2.0
Title: AmiGO visualize R interface
Description: R interface sending requests to AmiGO visualize,
retrieving DAG GO trees, parsing GraphViz DOT format files and
exporting GML files for Cytoscape. Also uses RCytoscape to
interactively display AmiGO trees in Cytoscape.
biocViews: GO, NetworkVisualization, GraphsAndNetworks, Classification,
ConnectTools
Author: Markus Schroeder, Daniel Gusenleitner, John Quackenbush, Aedin
Culhane, Benjamin Haibe-Kains
Maintainer: Markus Schroeder <mschroed@jimmy.harvard.edu>
MD5sum: 76e8783ef58723c0b94494f063e874ce
source.ver: src/contrib/RamiGO_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RamiGO_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RamiGO_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/RamiGO/inst/doc/RamiGO.pdf
vignetteTitles: RamiGO: An Introduction (HowTo)
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RamiGO/inst/doc/RamiGO.R
Package: randPack
Version: 1.4.0
Depends: methods
Imports: Biobase
License: Artistic 2.0
Title: Randomization routines for Clinical Trials
Description: A suite of classes and functions for randomizing patients
in clinical trials.
biocViews: Statistics
Author: Vincent Carey <stvjc@channing.harvard.edu> and Robert Gentleman
Maintainer: Robert Gentleman <rgentlem@gmail.com>
MD5sum: e75f8691683e237ccf0f4da191dadc7d
source.ver: src/contrib/randPack_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/randPack_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/randPack_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/randPack/inst/doc/randPack.pdf
vignetteTitles: Clinical trial randomization infrastructure
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/randPack/inst/doc/randPack.R
Package: RankProd
Version: 2.30.0
Depends: R (>= 1.9.0)
Imports: graphics
License: file LICENSE
Title: Rank Product method for identifying differentially expressed
genes with application in meta-analysis
Description: Non-parametric method for identifying differentially
expressed (up- or down- regulated) genes based on the estimated
percentage of false predictions (pfp). The method can combine
data sets from different origins (meta-analysis) to increase
the power of the identification.
biocViews: DifferentialExpression
Author: Fangxin Hong <fxhong@jimmy.harvard.edu> and Ben Wittner
<Wittner.Ben@mgh.harvard.edu> with contribution from Rainer
Breitling <r.breitling@bio.gla.ac.uk>, Colin Smith
<colin@colinsmith.org>, and Florian Battke
<battke@informatik.uni-tuebingen.de>
Maintainer: Fangxin Hong <fxhong@jimmy.harvard.edu>
MD5sum: a471628af2591dd0fd0398fad4b9ea39
source.ver: src/contrib/RankProd_2.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RankProd_2.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RankProd_2.30.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/RankProd/inst/doc/RankProd.pdf
vignetteTitles: RankProd Tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/RankProd/inst/doc/RankProd.R
dependsOnMe: RNAither
importsMe: HTSanalyzeR
suggestsMe: oneChannelGUI
Package: RbcBook1
Version: 1.26.0
Depends: R (>= 2.10), Biobase, graph, rpart
License: Artistic-2.0
Title: Support for Springer monograph on Bioconductor
Description: tools for building book
biocViews: Software
Author: Vince Carey <stvjc@channing.harvard.edu> and Wolfgang Huber
<huber@ebi.ac.uk>
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
URL: http://www.biostat.harvard.edu/~carey
MD5sum: 2c91fd0bf80a236000600469531dc6b6
source.ver: src/contrib/RbcBook1_1.26.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RbcBook1_1.26.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RbcBook1_1.26.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/RbcBook1/inst/doc/RbcBook1.pdf
vignetteTitles: RbcBook1 Primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RbcBook1/inst/doc/RbcBook1.R
Package: RBGL
Version: 1.34.0
Depends: graph, methods
Imports: methods
Suggests: Rgraphviz, XML
License: Artistic-2.0
Archs: i386, x64
Title: An interface to the BOOST graph library
Description: A fairly extensive and comprehensive interface to the
graph algorithms contained in the BOOST library.
biocViews: GraphsAndNetworks, NetworkAnalysis
Author: Vince Carey <stvjc@channing.harvard.edu>, Li Long
<li.long@isb-sib.ch>, R. Gentleman
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
URL: http://www.bioconductor.org
MD5sum: bf928c19e200cc6cf68f0386271bedfd
source.ver: src/contrib/RBGL_1.34.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RBGL_1.34.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RBGL_1.34.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RBGL_1.34.0.tgz
vignettes: vignettes/RBGL/inst/doc/filedep.pdf,
vignettes/RBGL/inst/doc/RBGL.pdf
vignetteTitles: filedep.pdf, RBGL Overview
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RBGL/inst/doc/RBGL.R
dependsOnMe: apComplex, BioNet, CellNOptR, flowWorkspace, gene2pathway,
joda, pkgDepTools, RpsiXML
importsMe: biocViews, CAMERA, Category, DEGraph, GeneAnswers, GOstats,
NCIgraph, nem, OrganismDbi, pkgDepTools, predictionet, Streamer
suggestsMe: BiocCaseStudies, DEGraph, graph, KEGGgraph
Package: RBioinf
Version: 1.18.1
Depends: graph, methods
Suggests: Rgraphviz
License: Artistic-2.0
Archs: i386, x64
Title: RBioinf
Description: Functions and datasets and examples to accompany the
monograph R For Bioinformatics.
biocViews: GeneExpression, Microarray, Preprocessing, QualityControl,
Classification, Clustering, MultipleComparison, Annotation
Author: Robert Gentleman
Maintainer: Robert Gentleman <rgentlem@gmail.com>
MD5sum: 98463365110bddedeaa53e63e0a150a7
source.ver: src/contrib/RBioinf_1.18.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RBioinf_1.18.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/RBioinf_1.18.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/RBioinf/inst/doc/RBioinf.pdf
vignetteTitles: RBioinf Introduction
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RBioinf/inst/doc/RBioinf.R
Package: rbsurv
Version: 2.16.0
Depends: R (>= 2.5.0), Biobase (>= 2.5.5), survival
License: GPL (>= 2)
Title: Robust likelihood-based survival modeling with microarray data
Description: This package selects genes associated with survival.
biocViews: Microarray, Bioinformatics
Author: HyungJun Cho <hj4cho@korea.ac.kr>, Sukwoo Kim
<s4kim@korea.ac.kr>, Soo-heang Eo <hanansh@korea.ac.kr>, Jaewoo
Kang <kangj@korea.ac.kr>
Maintainer: Soo-heang Eo <hanansh@korea.ac.kr>
URL: http://www.korea.ac.kr/~stat2242/
MD5sum: acbf9168b9c18a98c83a02a4154aa70d
source.ver: src/contrib/rbsurv_2.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/rbsurv_2.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/rbsurv_2.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/rbsurv/inst/doc/rbsurv.pdf
vignetteTitles: Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/rbsurv/inst/doc/rbsurv.R
Package: Rcade
Version: 1.0.0
Depends: R (>= 2.14.0), methods, GenomicRanges, baySeq, Rsamtools
Imports: graphics, IRanges, rgl
Suggests: limma, biomaRt, RUnit, BiocGenerics
License: GPL-2
Title: R-based analysis of ChIP-seq And Differential Expression - a
tool for integrating a count-based ChIP-seq analysis with
differential expression summary data.
Description: Rcade (which stands for "R-based analysis of ChIP-seq And
Differential Expression") is a tool for integrating ChIP-seq
data with differential expression summary data, through a
Bayesian framework. A key application is in identifing the
genes targeted by a transcription factor of interest - that is,
we collect genes that are associated with a ChIP-seq peak, and
differential expression under some perturbation related to that
TF.
biocViews: DifferentialExpression, GeneExpression, Transcription,
ChIPseq, Sequencing, Genetics
Author: Jonathan Cairns
Maintainer: Jonathan Cairns <jonathan.cairns@cancer.org.uk>
MD5sum: 258e80edd638eda0ebe5649806cefcb7
source.ver: src/contrib/Rcade_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Rcade_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Rcade_1.0.0.zip
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vignettes: vignettes/Rcade/inst/doc/Rcade.pdf
vignetteTitles: Rcade Vignette
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Rcade/inst/doc/Rcade.R
Package: RCASPAR
Version: 1.4.0
License: GPL (>=3)
Title: A package for survival time prediction based on a piecewise
baseline hazard Cox regression model.
Description: The package is the R-version of the C-based software
\bold{CASPAR} (Kaderali,2006:
\url{http://bioinformatics.oxfordjournals.org/content/22/12/1495}).
It is meant to help predict survival times in the presence of
high-dimensional explanatory covariates. The model is a
piecewise baseline hazard Cox regression model with an Lq-norm
based prior that selects for the most important regression
coefficients, and in turn the most relevant covariates for
survival analysis. It was primarily tried on gene expression
and aCGH data, but can be used on any other type of
high-dimensional data and in disciplines other than biology and
medicine.
biocViews: aCGH, GeneExpression, Genetics, Proteomics, Visualization
Author: Douaa Mugahid
Maintainer: Douaa Mugahid <douaa.mugahid@gmail.com>, Lars Kaderali
<lars.kaderali@bioquant.uni-heidelberg.de>
MD5sum: ae0fff4c0925c89e96eced8860e3eeca
source.ver: src/contrib/RCASPAR_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RCASPAR_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RCASPAR_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/RCASPAR/inst/doc/RCASPAR.pdf
vignetteTitles: RCASPAR: Software for high-dimentional-data driven
survival time prediction
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RCASPAR/inst/doc/RCASPAR.R
Package: RchyOptimyx
Version: 1.2.0
Depends: R (>= 2.10)
Imports: Rgraphviz, sfsmisc, graphics, methods, graph, grDevices
Suggests: flowCore, flowType
License: Artistic-2.0
Archs: i386, x64
Title: Optimyzed Cellular Hierarchies for Flow Cytometry
Description: Constructs a hierarchy of cells using flow cytometry for
maximization of an external variable (e.g., a clinical outcome
or a cytokine response).
biocViews: FlowCytometry
Author: Adrin Jalali, Nima Aghaeepour
Maintainer: Adrin Jalali <adrin.jalali@gmail.com>, Nima Aghaeepour
<naghaeep@bccrc.ca>
MD5sum: e736ae547ae9c7d7523210bc490285e4
source.ver: src/contrib/RchyOptimyx_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RchyOptimyx_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RchyOptimyx_1.2.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/RchyOptimyx/inst/doc/RchyOptimyx.pdf
vignetteTitles: flowType package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RchyOptimyx/inst/doc/RchyOptimyx.R
Package: RCytoscape
Version: 1.8.2
Depends: R (>= 2.14.0), graph (>= 1.31.0), XMLRPC (>= 0.2.4)
Imports: methods, XMLRPC, BiocGenerics
Suggests: RUnit
License: GPL-2
Title: Display and manipulate graphs in Cytoscape
Description: Interactvive viewing and exploration of graphs, connecting
R to Cytoscape.
biocViews: NetworkVisualization, GraphsAndNetworks, ConnectTools
Author: Paul Shannon
Maintainer: Paul Shannon <pshannon@systemsbiology.org>
URL: http://rcytoscape.systemsbiology.net
MD5sum: 9b743a542a01363e09fa29680f0f49c4
source.ver: src/contrib/RCytoscape_1.8.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RCytoscape_1.8.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/RCytoscape_1.8.2.zip
mac.binary.leopard.ver:
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vignettes: vignettes/RCytoscape/inst/doc/RCytoscape.pdf
vignetteTitles: RCytoscape Overview
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RCytoscape/inst/doc/RCytoscape.R
importsMe: categoryCompare, NCIgraph
suggestsMe: GeneNetworkBuilder, graphite
Package: Rdisop
Version: 1.18.0
Depends: R (>= 2.0.0), RcppClassic, Rcpp
LinkingTo: RcppClassic, Rcpp
Suggests: RUnit
License: GPL-2
Archs: i386, x64
Title: Decomposition of Isotopic Patterns
Description: Identification of metabolites using high precision mass
spectrometry. MS Peaks are used to derive a ranked list of sum
formulae, alternatively for a given sum formula the theoretical
isotope distribution can be calculated to search in MS peak
lists.
biocViews: MassSpectrometry
Author: Anton Pervukhin <apervukh@minet.uni-jena.de>, Steffen Neumann
<sneumann@ipb-halle.de>
Maintainer: Steffen Neumann <sneumann@ipb-halle.de>
URL: http://msbi.ipb-halle.de/
SystemRequirements: None
MD5sum: d2ed19308aca11a278e02df80dd3a78c
source.ver: src/contrib/Rdisop_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Rdisop_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Rdisop_1.18.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Rdisop/inst/doc/Rdisop.pdf
vignetteTitles: Molecule Identification with Rdisop
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: TRUE
hasLICENSE: FALSE
Rfiles: vignettes/Rdisop/inst/doc/Rdisop.R
suggestsMe: MSnbase
Package: RDRToolbox
Version: 1.8.0
Depends: R (>= 2.9.0),rgl
Imports: graphics, grDevices, methods, stats, MASS, rgl
Suggests: golubEsets
License: GPL (>= 2)
Title: A package for nonlinear dimension reduction with Isomap and LLE.
Description: A package for nonlinear dimension reduction using the
Isomap and LLE algorithm. It also includes a routine for
computing the Davis-Bouldin-Index for cluster validation, a
plotting tool and a data generator for microarray gene
expression data and for the Swiss Roll dataset.
biocViews:
Dimension,DimensionReduction,FeatureExtraction,Visualization,ClusterValidation,Microarray
Author: Christoph Bartenhagen
Maintainer: Christoph Bartenhagen <christoph.bartenhagen@ukmuenster.de>
MD5sum: 36950f7eaba5fdacb97d34051ba61cdf
source.ver: src/contrib/RDRToolbox_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RDRToolbox_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RDRToolbox_1.8.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/RDRToolbox/inst/doc/plot3D.pdf,
vignettes/RDRToolbox/inst/doc/RDRToolbox-003.pdf,
vignettes/RDRToolbox/inst/doc/SwissRoll.pdf,
vignettes/RDRToolbox/inst/doc/vignette.pdf
vignetteTitles: plot3D.pdf, RDRToolbox-003.pdf, SwissRoll.pdf, A
package for nonlinear dimension reduction with Isomap and LLE.
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RDRToolbox/inst/doc/vignette.R
Package: ReactomePA
Version: 1.2.1
Depends: R (>= 2.10), DOSE
Imports: methods, AnnotationDbi, reactome.db, stats4, plyr, igraph,
qvalue, graphics
Suggests: clusterProfiler, GOSemSim, org.Hs.eg.db
License: GPL-2
Title: Reactome Pathway Analysis
Description: This package provides functions for pathway analysis based
on REACTOME pathway database. It will implement enrichment
analysis, gene set enrichment analysis and functional modules
detection.
biocViews: Bioinformatics, Pathways, Visualization
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
MD5sum: fd7c1115bff62196f563f9cd4f21d3ff
source.ver: src/contrib/ReactomePA_1.2.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ReactomePA_1.2.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/ReactomePA_1.2.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ReactomePA/inst/doc/cnetplot.pdf,
vignettes/ReactomePA/inst/doc/ReactomePA.pdf,
vignettes/ReactomePA/inst/doc/rPAclusterProfiler.pdf
vignetteTitles: cnetplot.pdf, An introduction to ReactomePA,
rPAclusterProfiler.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ReactomePA/inst/doc/ReactomePA.R
suggestsMe: clusterProfiler, DOSE
Package: ReadqPCR
Version: 1.4.0
Depends: R(>= 2.14.0), Biobase, methods, affy
Imports: Biobase
License: LGPL-3
Title: Read qPCR data
Description: The package provides functions to read raw RT-qPCR data of
different platforms.
biocViews: DataImport, MicrotitrePlateAssay, GeneExpression, qPCR
Author: James Perkins, Matthias Kohl
Maintainer: James Perkins <jperkins@biochem.ucl.ac.uk>
URL:
http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.html
MD5sum: 806887aa162c6e48bf0cb196a726a816
source.ver: src/contrib/ReadqPCR_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ReadqPCR_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ReadqPCR_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ReadqPCR/inst/doc/ReadqPCR.pdf
vignetteTitles: Functions to load RT-qPCR data into R
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ReadqPCR/inst/doc/ReadqPCR.R
dependsOnMe: NormqPCR
importsMe: NormqPCR
Package: reb
Version: 1.36.0
Depends: R (>= 2.0), Biobase, idiogram (>= 1.5.3)
License: GPL-2
Archs: i386, x64
Title: Regional Expression Biases
Description: A set of functions to dentify regional expression biases
biocViews: Microarray, CopyNumberVariants, Visualization
Author: Kyle A. Furge <kyle.furge@vai.org> and Karl Dykema
<karl.dykema@vai.org>
Maintainer: Karl J. Dykema <karl.dykema@vai.org>
MD5sum: 028bc3e685a14d3df0c9bc593dc94b27
source.ver: src/contrib/reb_1.36.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/reb_1.36.0.zip
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vignettes: vignettes/reb/inst/doc/reb.pdf
vignetteTitles: Smoothing of Microarray Data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/reb/inst/doc/reb.R
Package: RedeR
Version: 1.6.1
Depends: R (>= 2.15), methods, igraph, RCurl, XML
Imports: rJava, XMLRPC
Suggests: PANR, pvclust
License: GPL (>= 2)
Title: Interactive visualization and manipulation of nested networks.
Description: RedeR is an R-based package combined with a stand-alone
Java application for interactive visualization and manipulation
of modular structures, nested networks and multiple levels of
hierarchical associations. It implements a callback engine by
using a low-level R-to-Java interface to build and run common
plugins. In this sense, RedeR takes advantage of R to run
robust statistics, while the R-to-Java interface bridges the
gap between network analysis and visualization.
biocViews: GraphsAndNetworks, NetworkVisualization, Networks, Software,
Visualization
Author: Mauro Castro, Xin Wang, Florian Markowetz
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
URL: http://www.markowetzlab.org/software/networks.html
MD5sum: 1dca5af0d388dc71e645519bf8914f04
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vignettes: vignettes/RedeR/inst/doc/fig1.pdf,
vignettes/RedeR/inst/doc/fig2.pdf,
vignettes/RedeR/inst/doc/fig3.pdf,
vignettes/RedeR/inst/doc/fig4.pdf,
vignettes/RedeR/inst/doc/fig5a.pdf,
vignettes/RedeR/inst/doc/fig5b.pdf,
vignettes/RedeR/inst/doc/fig5c.pdf,
vignettes/RedeR/inst/doc/fig6.pdf,
vignettes/RedeR/inst/doc/RedeR.pdf
vignetteTitles: fig1.pdf, fig2.pdf, fig3.pdf, fig4.pdf, fig5a.pdf,
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hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RedeR/inst/doc/RedeR.R
suggestsMe: PANR
Package: REDseq
Version: 1.4.0
Depends: R (>= 2.15.0), BiocGenerics (>= 0.1.0),
BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome,
ChIPpeakAnno
Imports: BiocGenerics, AnnotationDbi, Biostrings, ChIPpeakAnno,
graphics, IRanges (>= 1.13.5), multtest, stats, utils
License: GPL (>=2)
Title: Analysis of high-throughput sequencing data processed by
restriction enzyme digestion
Description: The package includes functions to build restriction enzyme
cut site (RECS) map, distribute mapped sequences on the map
with five different approaches, find enriched/depleted RECSs
for a sample, and identify differentially enriched/depleted
RECSs between samples.
biocViews: Sequencing, SequenceMatching, Preprocessing
Author: Lihua Julie Zhu and Thomas Fazzio
Maintainer: Lihua Julie Zhu <julie.zhu@umassmed.edu>
MD5sum: 060fc8d5cf8b7ff853cca6051e0d48ba
source.ver: src/contrib/REDseq_1.4.0.tar.gz
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vignettes: vignettes/REDseq/inst/doc/REDseq.pdf
vignetteTitles: REDseq Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/REDseq/inst/doc/REDseq.R
Package: RefPlus
Version: 1.28.0
Depends: R (>= 2.8.0), Biobase (>= 2.1.0), affy (>= 1.20.0), affyPLM
(>= 1.18.0), preprocessCore (>= 1.4.0)
Suggests: affydata
License: GPL (>= 2)
Title: A function set for the Extrapolation Strategy (RMA+) and
Extrapolation Averaging (RMA++) methods.
Description: The package contains functions for pre-processing
Affymetrix data using the RMA+ and the RMA++ methods.
biocViews: Microarray, OneChannel, Preprocessing
Author: Kai-Ming Chang <kaiming@gmail.com>, Chris Harbron
<Chris.Harbron@astrazeneca.com>, Marie C South
<Marie.C.South@astrazeneca.com>
Maintainer: Kai-Ming Chang <kaiming@gmail.com>
MD5sum: 36f76da73edc1c7e626f44497a39ba0e
source.ver: src/contrib/RefPlus_1.28.0.tar.gz
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mac.binary.leopard.ver:
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vignettes:
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vignettes/RefPlus/inst/doc/Extensions_to_RMA_Algorithm.pdf,
vignettes/RefPlus/inst/doc/RefPlus.pdf
vignetteTitles: An_Exploration_of_Extensions_to_the_RMA_Algorithm.pdf,
Extensions_to_RMA_Algorithm.pdf, RefPlus Manual
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RefPlus/inst/doc/RefPlus.R
htmlDocs: vignettes/RefPlus/inst/doc/index.html
Package: Repitools
Version: 1.4.2
Depends: R (>= 2.13.0), methods, BiocGenerics (>= 0.1.0), GenomicRanges
(>= 1.7.8)
Imports: BiocGenerics, IRanges (>= 1.13.5), GenomicRanges, BSgenome,
gplots, grid, MASS, gsmoothr, edgeR (>= 2.99.2), DNAcopy,
Ringo, aroma.affymetrix
Suggests: GenomicRanges, IRanges, BSgenome, gplots, grid, MASS,
gsmoothr, edgeR, DNAcopy, Ringo, aroma.affymetrix, ShortRead,
BSgenome.Hsapiens.UCSC.hg18
License: LGPL (>= 2)
Title: Epigenomic tools
Description: Tools for the analysis of enrichment-based epigenomic
data. Features include summarization and visualization of
epigenomic data across promoters according to gene expression
context, finding regions of differential methylation/binding,
etc.
biocViews: DNAMethylation, GeneExpression, Methylseq
Author: Mark Robinson <mark.robinson@imls.uzh.ch>, Dario Strbenac
<d.strbenac@garvan.org.au>, Aaron Statham
<a.statham@garvan.org.au>
Maintainer: Mark Robinson <mark.robinson@imls.uzh.ch>
MD5sum: a7128fb877c1bfa482405f5edbfc9379
source.ver: src/contrib/Repitools_1.4.2.tar.gz
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mac.binary.leopard.ver:
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vignettes: vignettes/Repitools/inst/doc/qc-cpgPlot.pdf,
vignettes/Repitools/inst/doc/qc-enrPlot.pdf,
vignettes/Repitools/inst/doc/Repitools_vignette.pdf,
vignettes/Repitools/inst/doc/visualisations-binPlotsHeatmap.pdf,
vignettes/Repitools/inst/doc/visualisations-binPlotsLine.pdf,
vignettes/Repitools/inst/doc/visualisations-cluPlots3.pdf,
vignettes/Repitools/inst/doc/visualisations-profPlots.pdf
vignetteTitles: qc-cpgPlot.pdf, qc-enrPlot.pdf, Using Repitools for
Epigenomic Sequencing Data, visualisations-binPlotsHeatmap.pdf,
visualisations-binPlotsLine.pdf, visualisations-cluPlots3.pdf,
visualisations-profPlots.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Repitools/inst/doc/Repitools_vignette.R
Package: ReportingTools
Version: 1.0.0
Depends: methods
Imports:
Biobase,hwriter,Category,GOstats,limma,lattice,AnnotationDbi,edgeR,
annotate,PFAM.db, GSEABase, BiocGenerics(>= 0.1.6)
Suggests: RUnit
License: Artistic-2.0
Title: Tools for making reports in various formats
Description: The ReportingTools software package enables users to
easily display reports of analysis results generated from
sources such as microarray and sequencing data. The package
allows users to create HTML pages that may be viewed on a web
browser such as Safari, or in other formats readable by
programs such as Excel. Users can generate tables with
sortable and filterable columns, make and display plots, and
link table entries to other data sources such as NCBI or larger
plots within the HTML page. Using the package, users can also
produce a table of contents page to link various reports
together for a particular project that can be viewed in a web
browser.
biocViews: Bioinformatics, Software, Visualization, Microarray, RNAseq,
GO
Author: Jason A. Hackney, Melanie Huntley, Jessica L. Larson, Christina
Chaivorapol, and Josh Kaminker
Maintainer: Jason A. Hackney <hackney.jason@gene.com>
MD5sum: afe725f98aa14450496cca83d7e1219a
source.ver: src/contrib/ReportingTools_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ReportingTools_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ReportingTools_1.0.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ReportingTools/inst/doc/basicReportingTools.pdf,
vignettes/ReportingTools/inst/doc/microarrayAnalysis.pdf,
vignettes/ReportingTools/inst/doc/rnaseqAnalysis.pdf
vignetteTitles: ReportingTools basics, Reporting on microarray
differential expression, Reporting on RNA-seq differential
expression
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ReportingTools/inst/doc/basicReportingTools.R,
vignettes/ReportingTools/inst/doc/microarrayAnalysis.R,
vignettes/ReportingTools/inst/doc/rnaseqAnalysis.R
Package: ReQON
Version: 1.4.0
Depends: R (>= 2.15.0), Rsamtools, seqbias
Imports: rJava, graphics, stats, utils, grDevices
License: GPL-2
Title: Recalibrating Quality Of Nucleotides
Description: Algorithm for recalibrating the base quality scores for
aligned sequencing data in BAM format.
biocViews: Sequencing, HighThroughputSequencing, Preprocessing,
QualityControl
Author: Christopher Cabanski, Keary Cavin, Chris Bizon
Maintainer: Christopher Cabanski <cabanski@dom.wustl.edu>
SystemRequirements: Java version >= 1.6
MD5sum: e28f212d91336337db877a0ad6dd83c9
source.ver: src/contrib/ReQON_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ReQON_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ReQON_1.4.0.zip
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vignettes: vignettes/ReQON/inst/doc/ReQON.pdf
vignetteTitles: ReQON Tutorial
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ReQON/inst/doc/ReQON.R
Package: Resourcerer
Version: 1.32.0
Depends: R (>= 1.9.0), Biobase, AnnotationDbi (>= 1.4.0)
Suggests: human.db0, mouse.db0, rat.db0
License: LGPL
Title: Reads annotation data from TIGR Resourcerer or convert the
annotation data into Bioconductor data pacakge.
Description: This package allows user either to read an annotation data
file from TIGR Resourcerer as a matrix or convert the file into
a Bioconductor annotation data package using the AnnBuilder
package.
biocViews: Annotation, Microarray
Author: Jianhua Zhang
Maintainer: Jianhua Zhang <jzhang@jimmy.harvard.edu>
MD5sum: 1bfc04bd71a456989d619d9d27520aca
source.ver: src/contrib/Resourcerer_1.32.0.tar.gz
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win64.binary.ver: bin/windows64/contrib/2.15/Resourcerer_1.32.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Resourcerer/inst/doc/Resourcerer.pdf
vignetteTitles: Resourcerer Resourcerer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Resourcerer/inst/doc/Resourcerer.R
Package: rGADEM
Version: 2.6.0
Depends: R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo
Imports: Biostrings, IRanges, methods, graphics, seqLogo
Suggests: BSgenome.Hsapiens.UCSC.hg18
License: Artistic-2.0
Archs: i386, x64
Title: de novo motif discovery
Description: rGADEM is an efficient de novo motif discovery tool for
large-scale genomic sequence data. It is an open-source R
package, which is based on the GADEM software.
biocViews: Microarray, ChIPchip, Sequencing, ChIPseq, GenomicSequence,
MotifDiscovery
Author: Arnaud Droit, Raphael Gottardo, Gordon Robertson and Leiping Li
Maintainer: Arnaud Droit <arnaud.droit@crchuq.ulaval.ca>
MD5sum: 6fc80bc424fe9a61f54be1791d97735d
source.ver: src/contrib/rGADEM_2.6.0.tar.gz
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mac.binary.leopard.ver:
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vignettes: vignettes/rGADEM/inst/doc/rGADEM.pdf
vignetteTitles: The rGADEM users guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/rGADEM/inst/doc/rGADEM.R
importsMe: MotIV
Package: RGalaxy
Version: 1.0.0
Depends: XML, methods, tools, optparse, digest
Imports: BiocGenerics, Biobase, roxygen2
Suggests: RUnit, hgu95av2.db
License: Artistic-2.0
Title: Make an R function available in the Galaxy web platform
Description: Given an R function and its manual page, make the
documented function available in Galaxy.
biocViews: Infrastructure
Author: The Bioconductor Dev Team
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: 529123a7d22c550db249c00fde7dd80a
source.ver: src/contrib/RGalaxy_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RGalaxy_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RGalaxy_1.0.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/RGalaxy/inst/doc/RGalaxy-vignette.pdf
vignetteTitles: Adding R functions to Galaxy
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RGalaxy/inst/doc/Rgalaxy-vignette.R,
vignettes/RGalaxy/inst/doc/RGalaxy-vignette.R
Package: Rgraphviz
Version: 2.2.1
Depends: R (>= 2.6.0), methods, utils, graph, grid
Imports: stats4, graph, graphics, grDevices, grid, methods, utils
Suggests: RUnit, BiocGenerics, XML
License: file LICENSE
Archs: i386, x64
Title: Provides plotting capabilities for R graph objects
Description: Interfaces R with the AT and T graphviz library for
plotting R graph objects from the graph package. Users on all
platforms must install graphviz; see the README file, available
in the source distribution of this file, for details.
biocViews: GraphsAndNetworks, NetworkVisualization
Author: Jeff Gentry, Li Long, Robert Gentleman, Seth Falcon, Florian
Hahne, Deepayan Sarkar, Kasper Daniel Hansen
Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>
SystemRequirements: Graphviz (>= 2.16)
MD5sum: dfb5ee6dd2cc11f08ef720fbf237e499
source.ver: src/contrib/Rgraphviz_2.2.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Rgraphviz_2.2.1.zip
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mac.binary.leopard.ver:
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vignettes: vignettes/Rgraphviz/inst/doc/newRgraphvizInterface.pdf,
vignettes/Rgraphviz/inst/doc/Rgraphviz.pdf
vignetteTitles: A New Interface to Plot Graphs Using Rgraphviz, How To
Plot A Graph Using Rgraphviz
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/Rgraphviz/inst/doc/newRgraphvizInterface.R,
vignettes/Rgraphviz/inst/doc/Rgraphviz.R
dependsOnMe: biocGraph, BioMVCClass, flowMerge, GOFunction, hyperdraw,
nem, netresponse, pathRender, TDARACNE
importsMe: apComplex, biocGraph, DEGraph, GeneAnswers, GOFunction, nem,
RchyOptimyx
suggestsMe: altcdfenvs, annotate, BiocCaseStudies, Category, CNORfuzzy,
ddgraph, DEGraph, flowCore, flowMerge, flowWorkspace,
GeneNetworkBuilder, geneplotter, GlobalAncova, globaltest,
GOstats, GSEABase, KEGGgraph, MLP, NCIgraph, oneChannelGUI,
pcaGoPromoter, pkgDepTools, RBGL, RBioinf, Rtreemix, safe,
SPIA, SRAdb, Streamer, topGO
Package: rhdf5
Version: 2.2.0
Depends: methods
Imports: zlibbioc
License: Artistic-2.0
Archs: i386, x64
Title: HDF5 interface to R
Description: This R/Bioconductor package provides an interface between
HDF5 and R. HDF5's main features are the ability to store and
access very large and/or complex datasets and a wide variety of
metadata on mass storage (disk) through a completely portable
file format. The rhdf5 package is thus suited for the exchange
of large and/or complex datasets between R and other software
package, and for letting R applications work on datasets that
are larger than the available RAM.
biocViews: Infrastructure
Author: Bernd Fischer, Gregoire Pau
Maintainer: Bernd Fischer <bernd.fischer@embl.de>
SystemRequirements: GNU make
MD5sum: 15d4c2959a983106b903cd53d9c1b771
source.ver: src/contrib/rhdf5_2.2.0.tar.gz
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vignettes: vignettes/rhdf5/inst/doc/chunksize.pdf,
vignettes/rhdf5/inst/doc/rhdf5.pdf
vignetteTitles: chunksize.pdf, rhdf5
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/rhdf5/inst/doc/rhdf5.R,
vignettes/rhdf5/inst/doc/Rhdf5.R
Package: rHVDM
Version: 1.24.0
Depends: R (>= 2.10), R2HTML (>= 1.5), affy (>= 1.23.4), minpack.lm (>=
1.0-5), Biobase (>= 2.5.5)
License: GPL-2
Title: Hidden Variable Dynamic Modeling
Description: A R implementation of HVDM (Genome Biol 2006, V7(3) R25)
biocViews: Microarray, GraphsAndNetworks, Transcription,
Classification, NetworkInference
Author: Martino Barenco
Maintainer: Martino Barenco<m.barenco@ucl.ac.uk>
MD5sum: 63fe98ac6a0f35e56ba20930fd8186a4
source.ver: src/contrib/rHVDM_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/rHVDM_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/rHVDM_1.24.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/rHVDM/inst/doc/rHVDM.pdf
vignetteTitles: rHVDM primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/rHVDM/inst/doc/rHVDM.R
Package: Ringo
Version: 1.22.0
Depends: methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix,
grid
Imports: BiocGenerics (>= 0.1.11), genefilter, limma, vsn, stats4
Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0)
License: Artistic-2.0
Archs: i386, x64
Title: R Investigation of ChIP-chip Oligoarrays
Description: The package Ringo facilitates the primary analysis of
ChIP-chip data. The main functionalities of the package are
data read-in, quality assessment, data visualisation and
identification of genomic regions showing enrichment in
ChIP-chip. The package has functions to deal with two-color
oligonucleotide microarrays from NimbleGen used in ChIP-chip
projects, but also contains more general functions for
ChIP-chip data analysis, given that the data is supplied as
RGList (raw) or ExpressionSet (pre- processed). The package
employs functions from various other packages of the
Bioconductor project and provides additional ChIP-chip-specific
and NimbleGen-specific functionalities.
biocViews:
Microarray,TwoChannel,DataImport,QualityControl,Preprocessing
Author: Joern Toedling, Oleg Sklyar, Tammo Krueger, Matt Ritchie,
Wolfgang Huber
Maintainer: J. Toedling <j.toedling@imb-mainz.de>
MD5sum: cc4104c9584023f5de594dc988692fdf
source.ver: src/contrib/Ringo_1.22.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Ringo_1.22.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Ringo_1.22.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Ringo/inst/doc/Ringo.pdf
vignetteTitles: R Investigation of NimbleGen Oligoarrays
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Ringo/inst/doc/Ringo.R
dependsOnMe: Starr
importsMe: Repitools
suggestsMe: Repitools
Package: Risa
Version: 1.0.0
Depends: R (>= 2.0.9), Biobase (>= 2.4.0), methods, Rcpp (>= 0.9.13)
Imports: xcms
Suggests: faahKO (>= 1.2.11)
License: LGPL
Title: Converting experimental metadata from ISA-tab into Bioconductor
data structures
Description: The Investigation / Study / Assay (ISA) tab-delimited
format is a general purpose framework with which to collect and
communicate complex metadata (i.e. sample characteristics,
technologies used, type of measurements made) from experiments
employing a combination of technologies, spanning from
traditional approaches to high-throughput techniques. Risa
allows to access metadata/data in ISA-Tab format and build
Bioconductor data structures. Currently, data generated from
microarray, flow cytometry and metabolomics-based (i.e. mass
spectrometry) assays are supported. The package is extendable
and efforts are undergoing to support metadata associated to
proteomics assays.
biocViews: Annotation, DataImport, MassSpectrometry
Author: Alejandra Gonzalez-Beltran, Audrey Kauffmann, Steffen Neumann,
Gabriella Rustici, ISA Team
Maintainer: Alejandra Gonzalez-Beltran, ISA Team
<isatools@googlegroups.com>
URL: <http://isatab.sourceforge.net/>
MD5sum: b223e3dec07f27787af4fcf50e964fc8
source.ver: src/contrib/Risa_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Risa_1.0.0.zip
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vignettes: vignettes/Risa/inst/doc/Risa.pdf
vignetteTitles: Risa: converts experimental metadata from ISA-tab into
Bioconductor data structures
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Risa/inst/doc/Risa.R
Package: RLMM
Version: 1.20.0
Depends: R (>= 2.1.0)
Imports: graphics, grDevices, MASS, stats, utils
License: LGPL (>= 2)
Title: A Genotype Calling Algorithm for Affymetrix SNP Arrays
Description: A classification algorithm, based on a multi-chip,
multi-SNP approach for Affymetrix SNP arrays. Using a large
training sample where the genotype labels are known, this
aglorithm will obtain more accurate classification results on
new data. RLMM is based on a robust, linear model and uses the
Mahalanobis distance for classification. The chip-to-chip
non-biological variation is removed through normalization. This
model-based algorithm captures the similarities across genotype
groups and probes, as well as thousands other SNPs for accurate
classification. NOTE: 100K-Xba only at for now.
biocViews: Microarray, OneChannel, SNP, GeneticVariability
Author: Nusrat Rabbee <nrabbee@post.harvard.edu>, Gary Wong
<wongg62@berkeley.edu>
Maintainer: Nusrat Rabbee <nrabbee@post.harvard.edu>
URL: http://www.stat.berkeley.edu/users/nrabbee/RLMM
SystemRequirements: Internal files Xba.CQV, Xba.regions (or other
regions file)
MD5sum: 9aa19e7b252701142b9915c7c03394d7
source.ver: src/contrib/RLMM_1.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RLMM_1.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RLMM_1.20.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RLMM_1.20.0.tgz
vignettes: vignettes/RLMM/inst/doc/RLMM.pdf
vignetteTitles: RLMM Doc
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RLMM/inst/doc/RLMM.R
Package: Rmagpie
Version: 1.14.0
Depends: R (>= 2.6.1), Biobase (>= 2.5.5)
Imports: Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab,
methods, pamr, stats, utils
Suggests: xtable
License: GPL (>= 3)
Title: MicroArray Gene-expression-based Program In Error rate
estimation
Description: Microarray Classification is designed for both biologists
and statisticians. It offers the ability to train a classifier
on a labelled microarray dataset and to then use that
classifier to predict the class of new observations. A range of
modern classifiers are available, including support vector
machines (SVMs), nearest shrunken centroids (NSCs)... Advanced
methods are provided to estimate the predictive error rate and
to report the subset of genes which appear essential in
discriminating between classes.
biocViews: Microarray, Classification
Author: Camille Maumet <Rmagpie@gmail.com>, with contributions from C.
Ambroise J. Zhu
Maintainer: Camille Maumet <Rmagpie@gmail.com>
URL: http://www.bioconductor.org/
MD5sum: 0adfc1374e560c9407bee605b0f6aa19
source.ver: src/contrib/Rmagpie_1.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Rmagpie_1.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Rmagpie_1.14.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Rmagpie/inst/doc/Magpie_examples.pdf
vignetteTitles: Rmagpie Examples
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Rmagpie/inst/doc/Magpie_examples.R
Package: RMAPPER
Version: 1.8.0
Depends: methods
Suggests: RCurl
License: Artistic 2.0
Title: R interface to the MAPPER database of transcription factor
binding sites
Description: The RMAPPER package allows you to retrieve a set of
predicted transcription factor binding sites from the MAPPER
database (http://genome.ufl.edu/mapper/) through a simple HTTP
request.
biocViews: Annotation, Genetics
Author: VJ Carey <stvjc@channing.harvard.edu>
Maintainer: Heike Sichtig <hsichtig@ufl.edu>, Alberto Riva
<ariva@ufl.edu>
MD5sum: 70eecd397096c1dc9f03620a9fe2cbb4
source.ver: src/contrib/RMAPPER_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RMAPPER_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RMAPPER_1.8.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/RMAPPER/inst/doc/readMAPPER.pdf
vignetteTitles: Interface to MAPPER TFBS database
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RMAPPER/inst/doc/readMAPPER.R
Package: RMassBank
Version: 1.0.0
Depends: rcdk,yaml,mzR,methods
Imports: XML,RCurl
Suggests: gplots,RMassBankData,xcms
License: Artistic-2.0
Title: Workflow to process tandem MS files and build MassBank records
Description: Workflow to process tandem MS files and build MassBank
records. Functions include automated extraction of tandem MS
spectra, formula assignment to tandem MS fragments,
recalibration of tandem MS spectra with assigned fragments,
spectrum cleanup, automated retrieval of compound information
from Internet databases, and export to MassBank records.
biocViews: Bioinformatics, MassSpectrometry, Metabolomics, Software
Author: Michael Stravs, Emma Schymanski
Maintainer: Michael Stravs, Emma Schymanski <massbank@eawag.ch>
SystemRequirements: OpenBabel
MD5sum: 9bb56bcb3d3595e8249eeb70493a1224
source.ver: src/contrib/RMassBank_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RMassBank_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RMassBank_1.0.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/RMassBank_1.0.0.tgz
vignettes: vignettes/RMassBank/inst/doc/RMassBank.pdf
vignetteTitles: RMassBank walkthrough
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RMassBank/inst/doc/RMassBank.R
Package: rMAT
Version: 3.8.0
Depends: R(>= 2.9.0), BiocGenerics (>= 0.1.3), IRanges (>= 1.13.10),
Biobase (>= 2.15.1), affxparser
Imports: stats, methods, BiocGenerics, IRanges, Biobase, affxparser,
stats4
Suggests: GenomeGraphs, rtracklayer
License: Artistic-2.0
Title: R implementation from MAT program to normalize and analyze
tiling arrays and ChIP-chip data.
Description: This package is an R version of the package MAT and
contains functions to parse and merge Affymetrix BPMAP and CEL
tiling array files (using C++ based Fusion SDK and Bioconductor
package affxparser), normalize tiling arrays using sequence
specific models, detect enriched regions from ChIP-chip
experiments. Note: users should have GSL and GenomeGraphs
installed. Windows users: 'consult the README file available in
the inst directory of the source distribution for necessary
configuration instructions'. Snow Leopard users can take
advantage of increase speed with Grand Central Dispatch!
biocViews: Microarray, Preprocessing
Author: Charles Cheung and Arnaud Droit and Raphael Gottardo
Maintainer: Arnaud Droit <arnaud.droit@crchuq.ulaval.ca> and Raphael
Gottardo <rgottard@fhcrc.org>
URL: http://www.rglab.org
MD5sum: 1a0da79520faa271741f37112c2e9909
source.ver: src/contrib/rMAT_3.8.0.tar.gz
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rMAT_3.8.0.tgz
vignettes: vignettes/rMAT/inst/doc/rMAT.pdf
vignetteTitles: The rMAT users guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/rMAT/inst/doc/rMAT.R
Package: RmiR
Version: 1.14.0
Depends: R (>= 2.7.0), RmiR.Hs.miRNA, RSVGTipsDevice
Imports: DBI, methods, stats
Suggests: hgug4112a.db,org.Hs.eg.db
License: Artistic-2.0
Title: Package to work with miRNAs and miRNA targets with R
Description: Useful functions to merge microRNA and respective targets
using differents databases
biocViews: Software,GeneExpression,Microarray,TimeCourse,Visualization
Author: Francesco Favero
Maintainer: Francesco Favero <favero.francesco@gmail.com>
MD5sum: 0f711b8b2d583283cfe1f052a62436c4
source.ver: src/contrib/RmiR_1.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RmiR_1.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RmiR_1.14.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RmiR_1.14.0.tgz
vignettes: vignettes/RmiR/inst/doc/RmiR.pdf
vignetteTitles: RmiR Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RmiR/inst/doc/RmiR.R
suggestsMe: oneChannelGUI
Package: RNAinteract
Version: 1.6.0
Depends: R (>= 2.12.0), abind, locfit, Biobase
Imports: RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid,
hwriter, lattice, latticeExtra, limma, methods, splots (>=
1.13.12)
License: Artistic-2.0
Title: Estimate Pairwise Interactions from multidimensional features
Description: RNAinteract estimates genetic interactions from
multi-dimensional read-outs like features extracted from
images. The screen is assumed to be performed in multi-well
plates or similar designs. Starting from a list of features
(e.g. cell number, area, fluorescence intensity) per well,
genetic interactions are estimated. The packages provides
functions for reporting interacting gene pairs, plotting
heatmaps and double RNAi plots. An HTML report can be written
for quality control and analysis.
biocViews: CellBasedAssays, QualityControl, Preprocessing,
Visualization
Author: Bernd Fischer <bernd.fischer@embl.de>
Maintainer: Bernd Fischer <bernd.fischer@embl.de>
MD5sum: 55736e53d9dde50f17377fa4ffd4f36e
source.ver: src/contrib/RNAinteract_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RNAinteract_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RNAinteract_1.6.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/RNAinteract/inst/doc/RNAinteract.pdf
vignetteTitles: RNAinteract
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RNAinteract/inst/doc/RNAinteract.R
Package: RNAither
Version: 2.6.0
Depends: R (>= 2.10), topGO, RankProd, prada
Imports: geneplotter, limma, biomaRt, car, splots, methods
License: Artistic-2.0
Title: Statistical analysis of high-throughput RNAi screens
Description: RNAither analyzes cell-based RNAi screens, and includes
quality assessment, customizable normalization and statistical
tests, leading to lists of significant genes and biological
processes.
biocViews: CellBasedAssays, QualityControl, Preprocessing,
Visualization, Bioinformatics, Annotation, GO
Author: Nora Rieber and Lars Kaderali, University of Heidelberg,
Viroquant Research Group Modeling, Im Neuenheimer Feld 267,
69120 Heidelberg, Germany
Maintainer: Nora Rieber <RNAither@gmx.de>
MD5sum: 7514f18533ffcc10b93097b009a49f84
source.ver: src/contrib/RNAither_2.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RNAither_2.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RNAither_2.6.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/RNAither/inst/doc/vignetteRNAither.pdf
vignetteTitles: RNAither,, an automated pipeline for the statistical
analysis of high-throughput RNAi screens
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RNAither/inst/doc/vignetteRNAither.R
Package: rnaSeqMap
Version: 2.12.0
Depends: R (>= 2.11.0), methods, xmapcore, Biobase, Rsamtools
Imports: GenomicRanges, IRanges, edgeR, DESeq, DBI, RMySQL (>= 0.6-0)
License: GPL-2
Title: rnaSeq secondary analyses
Description: The rnaSeqMap library provides classes and functions to
analyze the RNA-sequencing data using the coverage profiles in
multiple samples at a time
biocViews: Annotation, Bioinformatics, ReportWriting, Transcription,
GeneExpression, DifferentialExpression,
HighThroughputSequencing, RNAseq, SAGE, Visualization
Author: Anna Lesniewska <alesniewska@cs.put.poznan.pl>; Michal
Okoniewski <michal@fgcz.ethz.ch>
Maintainer: Michal Okoniewski <michal@fgcz.ethz.ch>
MD5sum: c6459a1e233debcc2f1622e650317c8d
source.ver: src/contrib/rnaSeqMap_2.12.0.tar.gz
mac.binary.leopard.ver:
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vignettes: vignettes/rnaSeqMap/inst/doc/rnaSeqMap.pdf
vignetteTitles: rnaSeqMap primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/rnaSeqMap/inst/doc/rnaSeqMap.R
Package: ROC
Version: 1.34.0
Depends: R (>= 1.9.0), utils, methods
Suggests: Biobase
License: Artistic-2.0
Archs: i386, x64
Title: utilities for ROC, with uarray focus
Description: utilities for ROC, with uarray focus
biocViews: Bioinformatics, DifferentialExpression
Author: Vince Carey <stvjc@channing.harvard.edu>, Henning Redestig for
C++ language enhancements
Maintainer: Vince Carey <stvjc@channing.harvard.edu>
URL: http://www.bioconductor.org
MD5sum: f316540fd92c5700b726630235b8359e
source.ver: src/contrib/ROC_1.34.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ROC_1.34.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ROC_1.34.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ROC_1.34.0.tgz
vignettes: vignettes/ROC/inst/doc/ROCnotes.pdf
vignetteTitles: ROC notes
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ROC/inst/doc/ROCnotes.R
importsMe: clst
suggestsMe: genefilter, MCRestimate
Package: Rolexa
Version: 1.14.0
Depends: R (>= 2.9.0), graphics, grDevices, methods, ShortRead
Imports: mclust, Biostrings, graphics, grDevices, IRanges, methods,
ShortRead, stats
Enhances: fork
License: GPL-2
Title: Statistical analysis of Solexa sequencing data
Description: Provides probabilistic base calling, quality checks and
diagnostic plots for Solexa sequencing data
biocViews: Sequencing, DataImport, Preprocessing, QualityControl
Author: Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent
Farinelli, Ioannis Xenarios, Felix Naef
Maintainer: Jacques Rougemont <jacques.rougemont@epfl.ch>
MD5sum: a504b2f6a8d7e32644fafe84e6480109
source.ver: src/contrib/Rolexa_1.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Rolexa_1.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Rolexa_1.14.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Rolexa/inst/doc/Rolexa-vignette.pdf
vignetteTitles: Rolexa
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Rolexa/inst/doc/Rolexa-vignette.R
Package: rols
Version: 1.0.2
Depends: methods
Imports: XMLSchema (>= 0.6.0), SSOAP (>= 0.8.0), Biobase
Suggests: xtable, GO.db, knitr
License: GPL-2
Title: An R interface to the Ontology Lookup Service
Description: This package allows to query EBI's Ontology Lookup Service
(OLS) using Simple Object Access Protocol (SOAP).
biocViews: Software, Annotation, MassSpectrometry, GO
Author: Laurent Gatto <lg390@cam.ac.uk>
Maintainer: Laurent Gatto <lg390@cam.ac.uk>
URL: http://lgatto.github.com/rols/
MD5sum: 8a7605c81698fd9d90bb0ff6166e52a3
source.ver: src/contrib/rols_1.0.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/rols_1.0.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/rols_1.0.2.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rols_1.0.2.tgz
vignettes: vignettes/rols/inst/doc/rols.pdf
vignetteTitles: rols
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/rols/inst/doc/rols.R
suggestsMe: MSnbase
Package: RPA
Version: 1.14.0
Depends: R (>= 2.15.1), affy, affydata, methods, parallel
License: FreeBSD
Title: RPA: Robust Probabilistic Averaging for probe-level analysis
Description: Probabilistic analysis of probe reliability and
differential gene expression on short oligonucleotide arrays.
Lahti et al. "Probabilistic Analysis of Probe Reliability in
Differential Gene Expression Studies with Short Oligonucleotide
Arrays", TCBB/IEEE, 2011.
http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.38
biocViews: GeneExpression, Microarray, Preprocessing, QualityControl
Author: Leo Lahti <leo.lahti@iki.fi>
Maintainer: Leo Lahti <leo.lahti@iki.fi>
MD5sum: db84efe6be234d3f78aec30c66f04c3e
source.ver: src/contrib/RPA_1.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RPA_1.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RPA_1.14.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RPA_1.14.0.tgz
vignettes: vignettes/RPA/inst/doc/RPA.pdf
vignetteTitles: RPA
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/RPA/inst/doc/RPA.R
Package: RpsiXML
Version: 1.18.1
Depends: methods, annotate (>= 1.21.0), graph (>= 1.21.0), Biobase,
RBGL (>= 1.17.0), XML (>= 2.4.0), hypergraph (>= 1.15.2),
AnnotationDbi
Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Rn.eg.db,
org.Sc.sgd.db,hom.Hs.inp.db, hom.Mm.inp.db, hom.Dm.inp.db,
hom.Rn.inp.db, hom.Sc.inp.db,Rgraphviz, ppiStats, ScISI
License: LGPL-3
Title: R interface to PSI-MI 2.5 files
Description: Queries, data structure and interface to visualization of
interaction datasets. This package inplements the PSI-MI 2.5
standard and supports up to now 8 databases. Further databases
supporting PSI-MI 2.5 standard will be added continuously.
biocViews: Infrastructure, Proteomics
Author: Jitao David Zhang, Stefan Wiemann, Marc Carlson, with
contributions from Tony Chiang
Maintainer: Jitao David Zhang <jitao_david.zhang@roche.com>
URL: http://www.bioconductor.org
MD5sum: e4ce7791ddca07a77645f0b61f75937c
source.ver: src/contrib/RpsiXML_1.18.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RpsiXML_1.18.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/RpsiXML_1.18.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/RpsiXML/inst/doc/RpsiXMLApp.pdf,
vignettes/RpsiXML/inst/doc/RpsiXML.pdf
vignetteTitles: Application Examples of RpsiXML package, Reading PSI-25
XML files
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RpsiXML/inst/doc/RpsiXMLApp.R,
vignettes/RpsiXML/inst/doc/RpsiXML.R
dependsOnMe: ScISI
importsMe: ScISI
Package: rqubic
Version: 1.4.0
Depends: methods, Biobase, biclust
Imports: Biobase, biclust
Suggests: RColorBrewer
License: GPL-2
Archs: i386, x64
Title: Qualitative biclustering algorithm for expression data analysis
in R
Description: This package implements the QUBIC algorithm introduced by
Li et al. for the qualitative biclustering with gene expression
data.
biocViews: Microarray, Clustering
Author: Jitao David Zhang, with inputs from Laura Badi and Martin
Ebeling
Maintainer: Jitao David Zhang <jitao_david.zhang@roche.com>
MD5sum: a84679abd859e7d7888499e08a998a37
source.ver: src/contrib/rqubic_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/rqubic_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/rqubic_1.4.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/rqubic_1.4.0.tgz
vignettes: vignettes/rqubic/inst/doc/rqubic.pdf
vignetteTitles: Qualitative Biclustering with Bioconductor Package
rqubic
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/rqubic/inst/doc/rqubic.R
Package: Rsamtools
Version: 1.10.2
Depends: methods, IRanges (>= 1.15.35), GenomicRanges (>= 1.9.48),
Biostrings (>= 2.25.6)
Imports: methods, utils, IRanges, GenomicRanges, Biostrings, zlibbioc,
bitops, BiocGenerics (>= 0.1.3)
LinkingTo: Biostrings, IRanges
Suggests: ShortRead (>= 1.13.19), GenomicFeatures,
TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, RUnit
License: Artistic-2.0 + file LICENSE
Archs: i386, x64
Title: Binary alignment (BAM), variant call (BCF), or tabix file import
Description: This package provides an interface to the 'samtools',
'bcftools', and 'tabix' utilities (see 'LICENCE') for
manipulating SAM (Sequence Alignment / Map), binary variant
call (BCF) and compressed indexed tab-delimited (tabix) files.
biocViews: DataImport, Sequencing, HighThroughputSequencing
Author: Martin Morgan, Herv\'e Pag\`es
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
URL: http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
MD5sum: 473d7bac553f2b544ebb4268f3716ce4
source.ver: src/contrib/Rsamtools_1.10.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Rsamtools_1.10.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/Rsamtools_1.10.2.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Rsamtools/inst/doc/Rsamtools-Overview.pdf,
vignettes/Rsamtools/inst/doc/Rsamtools-UsingCLibraries.pdf
vignetteTitles: An introduction to Rsamtools, Using samtools C
libraries
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/Rsamtools/inst/doc/Rsamtools-Overview.R,
vignettes/Rsamtools/inst/doc/Rsamtools-UsingCLibraries.R
dependsOnMe: ArrayExpressHTS, BitSeq, deepSNV, easyRNASeq, EDASeq,
exomeCopy, GGtools, girafe, oneChannelGUI, qrqc, Rcade, ReQON,
rnaSeqMap, ShortRead, TEQC, VariantAnnotation
importsMe: annmap, ArrayExpressHTS, biovizBase, deepSNV, FunciSNP,
ggbio, gmapR, HTSeqGenie, PING, R453Plus1Toolbox, rtracklayer,
ShortRead, VariantAnnotation, VariantTools
suggestsMe: GenomicFeatures, GenomicRanges, R453Plus1Toolbox, seqbias,
Streamer
Package: rsbml
Version: 2.16.0
Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils
Imports: BiocGenerics, graph, utils
License: Artistic-2.0
Archs: i386, x64
Title: R support for SBML, using libsbml
Description: Links R to libsbml for SBML parsing, validating output,
provides an S4 SBML DOM, converts SBML to R graph objects.
Optionally links to the SBML ODE Solver Library (SOSLib) for
simulating models.
biocViews: GraphsAndNetworks, Pathways, NetworkAnalysis
Author: Michael Lawrence <michafla@gene.com>
Maintainer: Michael Lawrence <michafla@gene.com>
URL: http://www.sbml.org
SystemRequirements: libsbml (>=3.0.3)
MD5sum: fafa67254298ad650f3115dd4d7d4891
source.ver: src/contrib/rsbml_2.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/rsbml_2.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/rsbml_2.16.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/rsbml/inst/doc/quick-start.pdf
vignetteTitles: Quick start for rsbml
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/rsbml/inst/doc/quick-start.R
Package: rSFFreader
Version: 0.6.0
Depends: R (>= 2.13.0), Biostrings (>= 2.25.12), IRanges(>= 1.15.42),
GenomicRanges, ShortRead(>= 1.15.9), xtable, methods
Imports: methods, Biostrings, IRanges, ShortRead, GenomicRanges,
Biobase
LinkingTo: Biostrings, IRanges
License: Artistic-2.0
Title: rSFFreader reads in sff files generated by Roche 454 and Life
Sciences Ion Torrent sequencers
Description: rSFFreader reads sequence, qualities and clip point values
from sff files generated by Roche 454 and Life Sciences Ion
Torrent sequencers. The plan is to also write out sff files and
to read in flowgrams with some utils
biocViews: DataImport, Sequencing, HighThroughputSequencing
Author: Matt Settles <msettles@uidaho.edu>, Sam Hunter, Brice Sarver,
Ilia Zhbannikov, Kyu-Chul Cho
Maintainer: Matt Settles <msettles@uidaho.edu>
MD5sum: 65958e415aba3c4b13a45e40819e8e8d
source.ver: src/contrib/rSFFreader_0.6.0.tar.gz
mac.binary.leopard.ver:
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vignettes: vignettes/rSFFreader/inst/doc/rSFFreader.pdf
vignetteTitles: An introduction to rSFFreader
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/rSFFreader/inst/doc/rSFFreader.R
Package: Rsubread
Version: 1.8.2
License: GPL-3
Title: Rsubread: a super fast, sensitive and accurate read aligner for
mapping next-generation sequencing reads
Description: This package performs read mapping, exon junction
detection and other tasks for next-generation sequencing data.
The read mapping function implements a novel mapping paradigm
based on seed-and-vote. It can be used to map both short reads
and long reads (>200bp) and reads of variable lengths. It also
provides functions to summarize read counts to genes or exons
and gives detection p values for each gene in the RNA-seq data.
biocViews: Sequencing, HighThroughputSequencing
Author: Wei Shi, Yang Liao, Jenny Zhiyin Dai and Timothy Triche, Jr.
Maintainer: Wei Shi <shi@wehi.edu.au>
URL: http://bioconductor.org/packages/release/bioc/html/Rsubread.html
MD5sum: 417a9b4a0d014f42612375e473b80d8f
source.ver: src/contrib/Rsubread_1.8.2.tar.gz
vignettes: vignettes/Rsubread/inst/doc/Rsubread.pdf
vignetteTitles: Rsubread Vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Rsubread/inst/doc/Rsubread.R
Package: RTCA
Version: 1.10.0
Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools
Suggests: xtable
License: LGPL-3
Title: Open-source toolkit to analyse data from xCELLigence System
(RTCA)
Description: Import, analyze and visualize data from Roche(R)
xCELLigence RTCA systems. The package imports real-time cell
electrical impedance data into R. As an alternative to
commercial software shipped along the system, the Bioconductor
package RTCA provides several unique transformation
(normalization) strategies and various visualization tools.
biocViews: CellBasedAssays, Infrastructure, Visualization, TimeCourse
Author: Jitao David Zhang
Maintainer: Jitao David Zhang <davidvonpku@gmail.com>
URL: http://code.google.com/p/xcelligence/,
http://www.xcelligence.roche.com/,
http://www.nextbiomotif.com/Home/scientific-programming
MD5sum: aa0ecb2d5e4750f7981afc58853317e9
source.ver: src/contrib/RTCA_1.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RTCA_1.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/RTCA_1.10.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RTCA_1.10.0.tgz
vignettes: vignettes/RTCA/inst/doc/aboutRTCA.pdf,
vignettes/RTCA/inst/doc/RTCAtransformation.pdf
vignetteTitles: Introduction to Data Analysis of the Roche xCELLigence
System with RTCA Package, RTCAtransformation: Discussion of
transformation methods of RTCA data
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/RTCA/inst/doc/aboutRTCA.R,
vignettes/RTCA/inst/doc/RTCAtransformation.R
Package: RTopper
Version: 1.4.1
Depends: R (>= 2.11.0), Biobase
Imports: limma, multtest
Suggests: limma, org.Hs.eg.db, KEGG.db, GO.db
License: GPL (>= 3)
Title: This package is designed to perform Gene Set Analysis across
multiple genomic platforms
Description: the RTopper package is designed to perform and integrate
gene set enrichment results across multiple genomic platforms.
biocViews: Microarray
Author: Luigi Marchionni <marchion@jhu.edu>, Svitlana Tyekucheva
<svitlana@jimmy.harvard.edu>
Maintainer: Luigi Marchionni <marchion@jhu.edu>
MD5sum: 005d41fdbc5a225f0df232e4f972d669
source.ver: src/contrib/RTopper_1.4.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/RTopper_1.4.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/RTopper_1.4.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/RTopper/inst/doc/RTopper.pdf
vignetteTitles: RTopper user's manual
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/RTopper/inst/doc/RTopper.R
Package: rtracklayer
Version: 1.18.2
Depends: R (>= 2.10), methods, GenomicRanges (>= 1.9.6)
Imports: XML (>= 1.98-0), BiocGenerics (>= 0.1.0), IRanges (>=
1.15.37), GenomicRanges, Biostrings (>= 2.25.6), BSgenome (>=
1.23.1), zlibbioc, RCurl (>= 1.4-2), Rsamtools (>= 1.7.3)
LinkingTo: IRanges
Suggests: humanStemCell, microRNA (>= 1.1.1), genefilter, limma,
org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, hgu133plus2.db
License: Artistic-2.0
Archs: i386, x64
Title: R interface to genome browsers and their annotation tracks
Description: Extensible framework for interacting with multiple genome
browsers (currently UCSC built-in) and manipulating annotation
tracks in various formats (currently GFF, BED, bedGraph, BED15,
WIG, BigWig and 2bit built-in). The user may export/import
tracks to/from the supported browsers, as well as query and
modify the browser state, such as the current viewport.
biocViews: Annotation,Visualization,DataImport
Author: Michael Lawrence, Vince Carey, Robert Gentleman
Maintainer: Michael Lawrence <michafla@gene.com>
MD5sum: fc691eb429941ca2cd4fa41e2260ba03
source.ver: src/contrib/rtracklayer_1.18.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/rtracklayer_1.18.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/rtracklayer_1.18.2.zip
mac.binary.leopard.ver:
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vignettes: vignettes/rtracklayer/inst/doc/rtracklayer.pdf
vignetteTitles: rtracklayer
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/rtracklayer/inst/doc/rtracklayer.R
dependsOnMe: cummeRbund, r3Cseq
importsMe: ChromHeatMap, GenomicFeatures, ggbio, gmapR, Gviz,
HTSeqGenie, methyAnalysis, MotifDb, R453Plus1Toolbox
suggestsMe: biovizBase, GenomicFeatures, GenomicRanges, gwascat, MotIV,
NarrowPeaks, oneChannelGUI, PICS, PING, R453Plus1Toolbox,
Ringo, rMAT, TSSi
Package: Rtreemix
Version: 1.20.0
Depends: R (>= 2.5.0), methods, graph, Biobase
Imports: methods, graph, Biobase, Hmisc
Suggests: Rgraphviz
License: LGPL
Archs: i386, x64
Title: Rtreemix: Mutagenetic trees mixture models.
Description: Rtreemix is a package that offers an environment for
estimating the mutagenetic trees mixture models from
cross-sectional data and using them for various predictions. It
includes functions for fitting the trees mixture models,
likelihood computations, model comparisons, waiting time
estimations, stability analysis, etc.
biocViews: Bioinformatics
Author: Jasmina Bogojeska
Maintainer: Jasmina Bogojeska <jasmina@mpi-inf.mpg.de>
MD5sum: 817a35abca0dc903170136429b8d31f2
source.ver: src/contrib/Rtreemix_1.20.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Rtreemix_1.20.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Rtreemix_1.20.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Rtreemix/inst/doc/ClassDiagram.pdf,
vignettes/Rtreemix/inst/doc/ExtendedVignette.pdf,
vignettes/Rtreemix/inst/doc/Rtreemix.pdf,
vignettes/Rtreemix/inst/doc/topologies.pdf
vignetteTitles: ClassDiagram.pdf, ExtendedVignette.pdf, Rtreemix,
topologies.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Rtreemix/inst/doc/Rtreemix.R
Package: RWebServices
Version: 1.22.0
Depends: SJava (>= 0.69-4), TypeInfo, methods, tools (>= 2.10.0), R (>=
2.5.0)
Imports: RCurl
License: file LICENSE
Title: Expose R functions as web services through Java/Axis/Apache
Description: This package provides mechanisms for automatic function
prototyping and exposure of R functionality in a web services
environment.
biocViews: Infrastructure
Author: Nianhua Li, MT Morgan
Maintainer: Martin Morgan <mtmorgan@fhcrc.org>
MD5sum: 01570cf0ef739a43832840f2a5fb8fba
source.ver: src/contrib/RWebServices_1.22.0.tar.gz
vignettes: vignettes/RWebServices/inst/doc/EnablingPackages.pdf,
vignettes/RWebServices/inst/doc/InstallingAndTesting.pdf,
vignettes/RWebServices/inst/doc/LessonsLearned.pdf,
vignettes/RWebServices/inst/doc/RelatedWork.pdf,
vignettes/RWebServices/inst/doc/RToJava.pdf
vignetteTitles: Enabling packages as web services, Installing and
testing RWebServices and enabled packages, Lessons learned
exposing web services, RelatedWork, From R to Java
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/RWebServices/inst/doc/EnablingPackages.R,
vignettes/RWebServices/inst/doc/InstallingAndTesting.R,
vignettes/RWebServices/inst/doc/LessonsLearned.R,
vignettes/RWebServices/inst/doc/RelatedWork.R,
vignettes/RWebServices/inst/doc/RToJava.R
Package: safe
Version: 2.18.0
Depends: R (>= 2.4.0), Biobase, annotate, methods
Imports: SparseM, GO.db, annotate, AnnotationDbi, survival, Biobase
Suggests: GO.db, GOstats, Rgraphviz, multtest, hu6800.db, survival
License: GPL (>= 2)
Title: Significance Analysis of Function and Expression
Description: SAFE is a resampling-based method for testing functional
categories in gene expression experiments. SAFE can be applied
to 2-sample and multi-class comparisons, or simple linear
regressions. Other experimental designs can also be
accommodated through user-defined functions.
biocViews: GeneExpression, FunctionalAnnotation
Author: William T. Barry
Maintainer: William T. Barry <bill.barry@duke.edu>
URL: http://www.duke.edu/~dinbarry/SAFE/
MD5sum: 13dde4e6d832afafe9dc53b7edebad2e
source.ver: src/contrib/safe_2.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/safe_2.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/safe_2.18.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/safe_2.18.0.tgz
vignettes: vignettes/safe/inst/doc/SAFEmanual2.pdf
vignetteTitles: SAFE manual
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/safe/inst/doc/SAFEmanual2.R
Package: sagenhaft
Version: 1.28.0
Depends: R (>= 2.10), SparseM (>= 0.73), methods
Imports: graphics, methods, SparseM, stats, utils
License: GPL (>= 2)
Title: Collection of functions for reading and comparing SAGE libraries
Description: This package implements several functions useful for
analysis of gene expression data by sequencing tags as done in
SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction
of a SAGE library from sequence files, sequence error
correction, library comparison. Sequencing error correction is
implementing using an Expectation Maximization Algorithm based
on a Mixture Model of tag counts.
biocViews: SAGE
Author: Tim Beissbarth <beissbarth@wehi.edu.au>, with contributions
from Gordon Smyth <smyth@wehi.edu.au> and Lavinia Hyde
<hyde@wehi.edu.au>.
Maintainer: Tim Beissbarth <beissbarth@wehi.edu.au>
URL: http://tagcalling.mbgproject.org
MD5sum: 3656eb367968201f9690310ec5f019bb
source.ver: src/contrib/sagenhaft_1.28.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/sagenhaft_1.28.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/sagenhaft_1.28.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/sagenhaft/inst/doc/SAGEnhaft.pdf
vignetteTitles: SAGEnhaft
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/sagenhaft/inst/doc/SAGEnhaft.R
Package: SAGx
Version: 1.32.0
Depends: R (>= 2.5.0), stats, multtest, methods
Imports: Biobase, stats4
Suggests: KEGG.db, hu6800.db, MASS
License: GPL-3
Archs: i386, x64
Title: Statistical Analysis of the GeneChip
Description: A package for retrieval, preparation and analysis of data
from the Affymetrix GeneChip. In particular the issue of
identifying differentially expressed genes is addressed.
biocViews: Microarray, OneChannel, Preprocessing, DataImport,
Bioinformatics, DifferentialExpression, Clustering,
MultipleComparisons
Author: Per Broberg
Maintainer: Per Broberg, <pi.broberg@gmail.com>
URL: http://home.swipnet.se/pibroberg/expression_hemsida1.html
MD5sum: 70cac79f7e14bd2f09169b7c3fb49d59
source.ver: src/contrib/SAGx_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/SAGx_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/SAGx_1.32.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SAGx_1.32.0.tgz
vignettes: vignettes/SAGx/inst/doc/samroc-ex.pdf
vignetteTitles: samroc - example
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SAGx/inst/doc/samroc-ex.R
Package: SamSPECTRAL
Version: 1.12.0
Depends: R (>= 2.10)
Imports: methods
License: GPL version 2 or newer
Archs: i386, x64
Title: Identifies cell population in flow cytometry data.
Description: Given a matrix of coordinates as input, SamSPECTRAL first
builds the communities to sample the data points. Then, it
builds a graph and after weighting the edges by conductance
computation, the graph is passed to a classic spectral
clustering algorithm to find the spectral clusters. The last
stage of SamSPECTRAL is to combine the spectral clusters. The
resulting "connected components" estimate biological cell
populations in the data sample. For instructions on manual
installation, refer to the PDF file provided in the following
documentation.
biocViews: Bioinformatics, FlowCytometry, CellBiology, Clustering,
Cancer, FlowCytData, StemCells, HIV
Author: Habil Zare and Parisa Shooshtari
Maintainer: Habil Zare <habil_zare@yahoo.com>
MD5sum: 24e444be16fca3a9ebfd4bf8ef5d0f1c
source.ver: src/contrib/SamSPECTRAL_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/SamSPECTRAL_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/SamSPECTRAL_1.12.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/SamSPECTRAL/inst/doc/Clustering_by_SamSPECTRAL.pdf
vignetteTitles: A modified spectral clustering method for clustering
Flow Cytometry Data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SamSPECTRAL/inst/doc/Clustering_by_SamSPECTRAL.R
Package: SBMLR
Version: 1.54.0
Depends: XML, deSolve
License: GPL-2
Title: SBML-R Interface and Analysis Tools
Description: This package contains a systems biology markup language
(SBML) interface and biochemical system analysis tools with
illustrative examples.
biocViews: GraphsAndNetworks, Pathways, NetworkAnalysis
Author: Tomas Radivoyevitch
Maintainer: Tomas Radivoyevitch <txr24@case.edu>
URL: http://epbi-radivot.cwru.edu/SBMLR/SBMLR.html
MD5sum: 42c08b85e20ad21e189514a265388d33
source.ver: src/contrib/SBMLR_1.54.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/SBMLR_1.54.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/SBMLR_1.54.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/SBMLR/inst/doc/BMC.BioInformatics04.pdf,
vignettes/SBMLR/inst/doc/manual.pdf,
vignettes/SBMLR/inst/doc/quick-start.pdf
vignetteTitles: BMC.BioInformatics04.pdf, manual.pdf, Quick intro to
SBMLR
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SBMLR/inst/doc/quick-start.R
Package: SCAN.UPC
Version: 1.0.0
Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings
Imports: utils, methods
Suggests: pd.hg.u95a
License: MIT
Title: Single-channel array normalization (SCAN)
Description: SCAN is a microarray normalization method to facilitate
personalized-medicine workflows. Rather than processing
microarray samples as groups, which can introduce biases and
present logistical challenges, SCAN normalizes each sample
individually by modeling and removing probe- and array-specific
background noise using only data from within each array. (The
Universal Probability of expression Codes (UPC) method is an
extension of SCAN and will be added to this package soon.)
biocViews: Software, Microarray, Preprocessing
Author: Stephen R. Piccolo and W. Evan Johnson
Maintainer: Stephen R. Piccolo <stephen.piccolo@hsc.utah.edu>
URL: http://bioconductor.org, http://jlab.bu.edu/software/scan-upc
MD5sum: 7671f8c57aafbcf949f707fa4f5aaa90
source.ver: src/contrib/SCAN.UPC_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/SCAN.UPC_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/SCAN.UPC_1.0.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/SCAN.UPC/inst/doc/SCAN.vignette.pdf
vignetteTitles: SCAN - Primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/SCAN.UPC/inst/doc/SCAN.vignette.R
Package: ScISI
Version: 1.30.0
Depends: R (>= 2.10), GO.db, RpsiXML, annotate, apComplex
Imports: AnnotationDbi, GO.db, RpsiXML, annotate, methods,
org.Sc.sgd.db, utils
Suggests: ppiData, xtable
License: LGPL
Title: In Silico Interactome
Description: Package to create In Silico Interactomes
biocViews: GraphsAndNetworks, Proteomics, NetworkInference
Author: Tony Chiang <tchiang@fhcrc.org>
Maintainer: Tony Chiang <tchiang@fhcrc.org>
MD5sum: 18bcc4116ef26a48aa3a642441e02b82
source.ver: src/contrib/ScISI_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ScISI_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ScISI_1.30.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ScISI/inst/doc/vignette.pdf
vignetteTitles: ScISI Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ScISI/inst/doc/vignette.R
dependsOnMe: PCpheno, ppiStats, SLGI
importsMe: PCpheno, SLGI
suggestsMe: RpsiXML
Package: segmentSeq
Version: 1.10.1
Depends: R (>= 2.3.0), methods, baySeq (>= 1.11.1), ShortRead,
GenomicRanges, IRanges
Imports: baySeq, graphics, grDevices, IRanges, methods, utils,
GenomicRanges
Suggests: snow
License: GPL-3
Title: Methods for identifying small RNA loci from high-throughput
sequencing data
Description: High-throughput sequencing technologies allow the
production of large volumes of short sequences, which can be
aligned to the genome to create a set of matches to the genome.
By looking for regions of the genome which to which there are
high densities of matches, we can infer a segmentation of the
genome into regions of biological significance. The methods in
this package allow the simultaneous segmentation of data from
multiple samples, taking into account replicate data, in order
to create a consensus segmentation. This has obvious
applications in a number of classes of sequencing experiments,
particularly in the discovery of small RNA loci and novel mRNA
transcriptome discovery.
biocViews: Bioinformatics, HighThroughputSequencing,
MultipleComparisons
Author: Thomas J. Hardcastle
Maintainer: Thomas J. Hardcastle <tjh48@cam.ac.uk>
MD5sum: 3e47e7afbdd8f9b63233c67cc9aa479d
source.ver: src/contrib/segmentSeq_1.10.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/segmentSeq_1.10.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/segmentSeq_1.10.1.zip
mac.binary.leopard.ver:
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vignettes: vignettes/segmentSeq/inst/doc/segmentSeq.pdf
vignetteTitles: segmentSeq
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/segmentSeq/inst/doc/segmentSeq.R
Package: seqbias
Version: 1.6.0
Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0), Biostrings (>=
2.15.0), methods
Imports: zlibbioc
LinkingTo: Rsamtools
Suggests: Rsamtools, ggplot2
License: LGPL-3
Archs: i386, x64
Title: Estimation of per-position bias in high-throughput sequencing
data
Description: This package implements a model of per-position sequencing
bias in high-throughput sequencing data using a simple Bayesian
network, the structure and parameters of which are trained on a
set of aligned reads and a reference genome sequence.
biocViews: Sequencing, HighThroughputSequencing
Author: Daniel Jones <dcjones@cs.washington.edu>
Maintainer: Daniel Jones <dcjones@cs.washington.edu>
MD5sum: 769295cc544d5545bc8b1518011bbff4
source.ver: src/contrib/seqbias_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/seqbias_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/seqbias_1.6.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/seqbias/inst/doc/overview.pdf
vignetteTitles: Assessing and Adjusting for Technical Bias in High
Throughput Sequencing Data
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/seqbias/inst/doc/overview.R
dependsOnMe: ReQON
Package: seqLogo
Version: 1.24.0
Depends: methods, grid
License: LGPL (>= 2)
Title: Sequence logos for DNA sequence alignments
Description: seqLogo takes the position weight matrix of a DNA sequence
motif and plots the corresponding sequence logo as introduced
by Schneider and Stephens (1990).
biocViews: SequenceMatching
Author: Oliver Bembom
Maintainer: Oliver Bembom <oliver.bembom@gmail.com>
MD5sum: 26d8427faeb909346d2fa4f32f6d3ebf
source.ver: src/contrib/seqLogo_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/seqLogo_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/seqLogo_1.24.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/seqLogo/inst/doc/seqLogo.pdf
vignetteTitles: Sequence logos for DNA sequence alignments
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/seqLogo/inst/doc/seqLogo.R
dependsOnMe: rGADEM
importsMe: motifRG, PWMEnrich, rGADEM
suggestsMe: BCRANK, MotifDb
Package: ShortRead
Version: 1.16.4
Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.4),
GenomicRanges (>= 1.7.43), Biostrings (>= 2.25.6), lattice,
Rsamtools (>= 1.7.42), latticeExtra
Imports: BiocGenerics, IRanges, GenomicRanges, Biostrings, Biobase,
hwriter, Rsamtools, zlibbioc, lattice
LinkingTo: IRanges, Biostrings
Suggests: biomaRt, RUnit, GenomicFeatures, yeastNagalakshmi
Enhances: Rmpi, parallel
License: Artistic-2.0
Archs: i386, x64
Title: Classes and methods for high-throughput short-read sequencing
data.
Description: Base classes, functions, and methods for representation of
high-throughput, short-read sequencing data.
biocViews: DataImport, Sequencing, HighThroughputSequencing,
QualityControl
Author: Martin Morgan, Michael Lawrence, Simon Anders
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
MD5sum: d93c39673d98d300592e07265ce3d862
source.ver: src/contrib/ShortRead_1.16.4.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ShortRead_1.16.4.zip
win64.binary.ver: bin/windows64/contrib/2.15/ShortRead_1.16.4.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ShortRead/inst/doc/Overview.pdf,
vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf
vignetteTitles: An introduction to ShortRead,
ShortRead_and_HilbertVis.pdf
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ShortRead/inst/doc/Overview.R
dependsOnMe: chipseq, ChIPseqR, easyRNASeq, EDASeq, girafe, HTSeqGenie,
nucleR, OTUbase, Rolexa, segmentSeq
importsMe: ArrayExpressHTS, chipseq, ChIPseqR, ChIPsim, HiTC, nucleR,
OTUbase, R453Plus1Toolbox, Rolexa, rSFFreader
suggestsMe: CSAR, DBChIP, Genominator, PICS, PING, R453Plus1Toolbox,
Repitools, Rsamtools
Package: sigaR
Version: 1.2.1
Depends: Biobase, CGHbase, methods, mvtnorm, penalized
Imports: corpcor (>= 1.6.2), graphics, igraph, marray, MASS, mvtnorm,
quadprog, penalized (>= 0.9-39), snowfall, stats
License: GPL (>= 2)
Title: statistics for integrative genomics analyses in R
Description: Facilites the joint analysis of high-throughput data from
multiple molecular levels. Contains functions for manipulation
of objects, various analysis types, and some visualization.
biocViews: Microarray, Bioinformatics, DifferentialExpression, aCGH,
GeneExpression, Pathways
Author: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
URL: http://www.few.vu.nl/~wvanwie
MD5sum: 92c073b8d0b2f647c1317633e91566e0
source.ver: src/contrib/sigaR_1.2.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/sigaR_1.2.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/sigaR_1.2.1.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/sigaR_1.2.1.tgz
vignettes: vignettes/sigaR/inst/doc/sigaR.pdf,
vignettes/sigaR/inst/doc/statisticalUnit.pdf
vignetteTitles: sigaR, statisticalUnit.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/sigaR/inst/doc/sigaR.R
Package: siggenes
Version: 1.32.0
Depends: methods, Biobase, multtest, splines, graphics
Imports: stats4
Suggests: affy, annotate, genefilter, KernSmooth, scrime (>= 1.2.5)
License: LGPL (>= 2)
Title: Multiple testing using SAM and Efron's empirical Bayes
approaches
Description: Identification of differentially expressed genes and
estimation of the False Discovery Rate (FDR) using both the
Significance Analysis of Microarrays (SAM) and the Empirical
Bayes Analyses of Microarrays (EBAM).
biocViews: MultipleComparisons, Microarray, GeneExpression, SNP,
ExonArray, DifferentialExpression
Author: Holger Schwender
Maintainer: Holger Schwender <holger.schw@gmx.de>
MD5sum: 772d7f8ca1f47a921ef099111359e5f5
source.ver: src/contrib/siggenes_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/siggenes_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/siggenes_1.32.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/siggenes/inst/doc/siggenes.pdf,
vignettes/siggenes/inst/doc/siggenesRnews.pdf
vignetteTitles: siggenes Manual, siggenesRnews.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/siggenes/inst/doc/siggenes.R
htmlDocs: vignettes/siggenes/inst/doc/identify.sam.html,
vignettes/siggenes/inst/doc/plot.ebam.html,
vignettes/siggenes/inst/doc/plot.finda0.html,
vignettes/siggenes/inst/doc/plot.sam.html,
vignettes/siggenes/inst/doc/print.ebam.html,
vignettes/siggenes/inst/doc/print.finda0.html,
vignettes/siggenes/inst/doc/print.sam.html,
vignettes/siggenes/inst/doc/summary.ebam.html,
vignettes/siggenes/inst/doc/summary.sam.html
dependsOnMe: KCsmart, oneChannelGUI
importsMe: charm, GeneSelector, minfi
suggestsMe: GeneSelector, logicFS, XDE
Package: sigPathway
Version: 1.26.0
Depends: R (>= 2.10)
Suggests: hgu133a.db (>= 1.10.0), XML (>= 1.6-3), AnnotationDbi (>=
1.3.12)
License: GPL-2
Archs: i386, x64
Title: Pathway Analysis
Description: Conducts pathway analysis by calculating the NT_k and NE_k
statistics as described in Tian et al. (2005)
biocViews: Bioinformatics, DifferentialExpression, MultipleComparisons
Author: Weil Lai (optimized R and C code), Lu Tian and Peter Park
(algorithm development and initial R code)
Maintainer: Weil Lai <wlai@alum.mit.edu>
URL: http://www.pnas.org/cgi/doi/10.1073/pnas.0506577102,
http://www.chip.org/~ppark/Supplements/PNAS05.html
MD5sum: 5ddb41201f942faf8041912e5d4ef6ae
source.ver: src/contrib/sigPathway_1.26.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/sigPathway_1.26.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/sigPathway_1.26.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/sigPathway/inst/doc/sigPathway-vignette.pdf
vignetteTitles: sigPathway
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/sigPathway/inst/doc/sigPathway-vignette.R
Package: SIM
Version: 1.28.2
Depends: R (>= 2.4), quantreg
Imports: graphics, stats, globaltest, quantsmooth
Suggests: biomaRt, RColorBrewer
License: GPL (>= 2)
Archs: i386, x64
Title: Integrated Analysis on two human genomic datasets
Description: Finds associations between two human genomic datasets.
biocViews: Microarray, Bioinformatics, Visualization
Author: Renee X. de Menezes and Judith M. Boer
Maintainer: Renee X. de Menezes <r.xavierdemenezes@vumc.nl>
MD5sum: c8cc9d5e8ee70af1805bf0be41379bb1
source.ver: src/contrib/SIM_1.28.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/SIM_1.28.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/SIM_1.28.2.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SIM_1.28.2.tgz
vignettes: vignettes/SIM/inst/doc/SIM.pdf
vignetteTitles: SIM vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SIM/inst/doc/SIM.R
Package: simpleaffy
Version: 2.34.0
Depends: R (>= 2.0.0), methods, utils, grDevices, graphics, stats,
BiocGenerics (>= 0.1.12), Biobase, affy (>= 1.33.6),
genefilter, gcrma
Imports: methods, utils, grDevices, graphics, stats, BiocGenerics,
Biobase, affy, genefilter, gcrma
License: GPL (>= 2)
Archs: i386, x64
Title: Very simple high level analysis of Affymetrix data
Description: Provides high level functions for reading Affy .CEL files,
phenotypic data, and then computing simple things with it, such
as t-tests, fold changes and the like. Makes heavy use of the
affy library. Also has some basic scatter plot functions and
mechanisms for generating high resolution journal figures...
biocViews: Microarray, OneChannel, QualityControl, Preprocessing,
Transcription, DataImport, Bioinformatics,
DifferentialExpression, Annotation, ReportWriting,
Visualization
Author: Crispin J Miller
Maintainer: Crispin Miller <cmiller@picr.man.ac.uk>
URL: http://www.bioconductor.org,
http://bioinformatics.picr.man.ac.uk/simpleaffy/
MD5sum: 63e0aa6b2b1737ee748cd55f646a8e80
source.ver: src/contrib/simpleaffy_2.34.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/simpleaffy_2.34.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/simpleaffy_2.34.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/simpleaffy/inst/doc/QCandSimpleaffy.pdf,
vignettes/simpleaffy/inst/doc/simpleAffy.pdf
vignetteTitles: QCandSimpleaffy.pdf, simpleaffy primer
hasREADME: TRUE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/simpleaffy/inst/doc/simpleAffy.R
dependsOnMe: yaqcaffy
importsMe: affyQCReport, arrayMvout, arrayQualityMetrics
suggestsMe: AffyExpress, ArrayTools
Package: sizepower
Version: 1.28.0
Depends: stats
License: LGPL
Title: Sample Size and Power Calculation in Micorarray Studies
Description: This package has been prepared to assist users in
computing either a sample size or power value for a microarray
experimental study. The user is referred to the cited
references for technical background on the methodology
underpinning these calculations. This package provides support
for five types of sample size and power calculations. These
five types can be adapted in various ways to encompass many of
the standard designs encountered in practice.
biocViews: Microarray, Bioinformatics
Author: Weiliang Qiu <weiliang.qiu@gmail.com> and Mei-Ling Ting Lee
<meilinglee@sph.osu.edu> and George Alex Whitmore
<george.whitmore@mcgill.ca>
Maintainer: Weiliang Qiu <weiliang.qiu@gmail.com>
MD5sum: 6183136e05416d96c922f8a277578702
source.ver: src/contrib/sizepower_1.28.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/sizepower_1.28.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/sizepower_1.28.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/sizepower/inst/doc/sizepower.pdf
vignetteTitles: package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/sizepower/inst/doc/sizepower.R
suggestsMe: oneChannelGUI
Package: SJava
Version: 0.84.0
Depends: R (>= 2.10.0), methods
Imports: methods
License: GPL (>= 2)
Title: The Omegahat interface for R and Java.
Description: An interface from R to Java to create and call Java
objects and methods.
biocViews: Infrastructure
Author: Duncan Temple Lang, John Chambers
Maintainer: Martin Morgan <mtmorgan@fhcrc.org>
MD5sum: 0366ad5aad8934bb0b19a23a5fdb08fe
source.ver: src/contrib/SJava_0.84.0.tar.gz
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
dependsOnMe: RWebServices
Package: SLGI
Version: 1.18.0
Depends: R (>= 2.10), ScISI, lattice
Imports: AnnotationDbi, Biobase, GO.db, ScISI, graphics, lattice,
methods, stats, BiocGenerics
Suggests: GO.db, org.Sc.sgd.db
License: Artistic-2.0
Title: Synthetic Lethal Genetic Interaction
Description: A variety of data files and functions for the analysis of
genetic interactions
biocViews: GraphsAndNetworks, Proteomics, Genetics, NetworkAnalysis
Author: Nolwenn LeMeur, Zhen Jiang, Ting-Yuan Liu, Jess Mar and Robert
Gentleman
Maintainer: Nolwenn Le Meur <nlemeur@gmail.com>
MD5sum: 009af5b9c44567313c8d5bbd2e833ebe
source.ver: src/contrib/SLGI_1.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/SLGI_1.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/SLGI_1.18.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SLGI_1.18.0.tgz
vignettes: vignettes/SLGI/inst/doc/SLGI.pdf
vignetteTitles: SLGI Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SLGI/inst/doc/SLGI.R
dependsOnMe: PCpheno
Package: SLqPCR
Version: 1.24.0
Depends: R(>= 2.4.0)
Imports: stats
Suggests: RColorBrewer
License: GPL (>= 2)
Title: Functions for analysis of real-time quantitative PCR data at
SIRS-Lab GmbH
Description: Functions for analysis of real-time quantitative PCR data
at SIRS-Lab GmbH
biocViews: Bioinformatics, MicrotitrePlateAssay, qPCR
Author: Matthias Kohl
Maintainer: Matthias Kohl <kohl@sirs-lab.com>
MD5sum: b016ecb2c15d8bb854625eff90d3e46b
source.ver: src/contrib/SLqPCR_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/SLqPCR_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/SLqPCR_1.24.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/SLqPCR/inst/doc/SLqPCR.pdf
vignetteTitles: SLqPCR
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SLqPCR/inst/doc/SLqPCR.R
suggestsMe: EasyqpcR
Package: SMAP
Version: 1.22.0
Depends: R (>= 2.10), methods
License: GPL-2
Archs: i386, x64
Title: A Segmental Maximum A Posteriori Approach to Array-CGH Copy
Number Profiling
Description: Functions and classes for DNA copy number profiling of
array-CGH data
biocViews: Microarray, TwoChannel, CopyNumberVariants
Author: Robin Andersson <robin.andersson@lcb.uu.se>
Maintainer: Robin Andersson <robin.andersson@lcb.uu.se>
MD5sum: a19af9b7b46891c3c758c9c0b0b13112
source.ver: src/contrib/SMAP_1.22.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/SMAP_1.22.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/SMAP_1.22.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SMAP_1.22.0.tgz
vignettes: vignettes/SMAP/inst/doc/SMAP.pdf
vignetteTitles: SMAP
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SMAP/inst/doc/SMAP.R
Package: snapCGH
Version: 1.28.0
Depends: limma, DNAcopy, methods
Imports: aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma,
methods, stats, tilingArray, utils
License: GPL
Archs: i386, x64
Title: Segmentation, normalisation and processing of aCGH data.
Description: Methods for segmenting, normalising and processing aCGH
data; including plotting functions for visualising raw and
segmented data for individual and multiple arrays.
biocViews: Microarray, CopyNumberVariants, TwoChannel, Preprocessing
Author: Mike L. Smith, John C. Marioni, Steven McKinney, Thomas
Hardcastle, Natalie P. Thorne
Maintainer: John Marioni <marioni@uchicago.edu>
MD5sum: db4c2a1b1bd2721750137d86b25f204a
source.ver: src/contrib/snapCGH_1.28.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/snapCGH_1.28.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/snapCGH_1.28.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/snapCGH/inst/doc/snapCGHguide.pdf
vignetteTitles: Segmentation Overview
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/snapCGH/inst/doc/snapCGHguide.R
dependsOnMe: ADaCGH2
suggestsMe: beadarraySNP
Package: snm
Version: 1.6.0
Depends: R(>= 2.12.0), lme4, splines, corpcor
License: LGPL
Title: Supervised Normalization of Microarrays
Description: SNM is a modeling strategy especially designed for
normalizing high-throughput genomic data. The underlying
premise of our approach is that your data is a function of what
we refer to as study-specific variables. These variables are
either biological variables that represent the target of the
statistical analysis, or adjustment variables that represent
factors arising from the experimental or biological setting the
data is drawn from. The SNM approach aims to simultaneously
model all study-specific variables in order to more accurately
characterize the biological or clinical variables of interest.
biocViews: Microarray, OneChannel, TwoChannel, MultiChannel,
DifferentialExpression, ExonArray, GeneExpression,
Transcription, MultipleComparisons, Preprocessing,
QualityControl
Author: Brig Mecham <brig.mecham@sagebase.org> and John D. Storey
<jstorey@princeton.edu>
Maintainer: Brig Mecham <brig.mecham@sagebase.org>
MD5sum: 277cab311d5e0d86f0c8ec034327954e
source.ver: src/contrib/snm_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/snm_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/snm_1.6.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/snm_1.6.0.tgz
vignettes: vignettes/snm/inst/doc/snm.pdf
vignetteTitles: snm Tutorial
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/snm/inst/doc/snm.R
Package: SNPchip
Version: 2.4.0
Depends: R (>= 2.14.0)
Imports: graphics, lattice, grid, foreach, utils, methods, oligoClasses
(>= 1.19.30), Biobase, GenomicRanges
Suggests: crlmm, IRanges, RUnit
Enhances: doSNOW, VanillaICE, RColorBrewer
License: LGPL (>= 2)
Title: Visualizations for copy number alterations
Description: This package defines methods for visualizing
high-throughput genomic data
biocViews: CopyNumberVariants, SNP, GeneticVariability, Visualization
Author: Robert Scharpf <rscharpf@jhsph.edu> and Ingo Ruczinski
Maintainer: Robert Scharpf <rscharpf@jhsph.edu>
URL: http://www.biostat.jhsph.edu/~iruczins/software/snpchip.html
MD5sum: 0df8101997bcd6910feaec30a3eb539b
source.ver: src/contrib/SNPchip_2.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/SNPchip_2.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/SNPchip_2.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/SNPchip/inst/doc/PlottingIdiograms.pdf
vignetteTitles: Plotting Idiograms
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SNPchip/inst/doc/PlottingIdiograms.R
dependsOnMe: mBPCR
importsMe: crlmm, MinimumDistance, phenoTest
suggestsMe: Category, oligoClasses, VanillaICE
Package: snpStats
Version: 1.8.2
Depends: R(>= 2.10.0), survival, methods, Matrix
Imports: graphics, grDevices, methods, stats, survival, utils, Matrix,
BiocGenerics
Suggests: hexbin
License: GPL-3
Archs: i386, x64
Title: SnpMatrix and XSnpMatrix classes and methods
Description: Classes and statistical methods for large SNP association
studies, extending the snpMatrix package (now removed)
biocViews: Microarray, SNP, GeneticVariability
Author: David Clayton <dc208@cam.ac.uk>
Maintainer: David Clayton <dc208@cam.ac.uk>
MD5sum: 1b909fd6f7152b9e91d299b7413afd74
source.ver: src/contrib/snpStats_1.8.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/snpStats_1.8.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/snpStats_1.8.2.zip
mac.binary.leopard.ver:
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vignettes: vignettes/snpStats/inst/doc/data-input-vignette.pdf,
vignettes/snpStats/inst/doc/differences.pdf,
vignettes/snpStats/inst/doc/imputation-vignette.pdf,
vignettes/snpStats/inst/doc/ld-vignette.pdf,
vignettes/snpStats/inst/doc/pca-vignette.pdf,
vignettes/snpStats/inst/doc/snpStats-vignette.pdf,
vignettes/snpStats/inst/doc/tdt-vignette.pdf
vignetteTitles: Data input, snpMatrix-differences, Imputation and
meta-analysis, LD statistics, Principal components analysis,
snpStats introduction, TDT tests
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/snpStats/inst/doc/data-input-vignette.R,
vignettes/snpStats/inst/doc/differences.R,
vignettes/snpStats/inst/doc/imputation-vignette.R,
vignettes/snpStats/inst/doc/ld-vignette.R,
vignettes/snpStats/inst/doc/pca-vignette.R,
vignettes/snpStats/inst/doc/snpStats-vignette.R,
vignettes/snpStats/inst/doc/tdt-vignette.R
htmlDocs: vignettes/snpStats/inst/doc/index.html
dependsOnMe: GGBase, gwascat
importsMe: FunciSNP, GGtools
suggestsMe: crlmm, GWASTools, VariantAnnotation
Package: spade
Version: 1.6.0
Depends: R (>= 2.11), igraph0
Imports: Biobase, flowCore
Suggests: flowViz
License: GPL-2
Archs: i386, x64
Title: SPADE -- An analysis and visualization tool for Flow Cytometry
Description: SPADE, or Spanning tree Progression of Density normalized
Events, is an analysis and visualization tool for high
dimensional flow cytometry data that organizes cells into
hierarchies of related phenotypes.
biocViews: FlowCytometry, GraphsAndNetworks, GUI, Visualization,
Clustering
Author: M. Linderman, P. Qiu, E. Simonds, Z. Bjornson
Maintainer: Michael Linderman <michael.d.linderman@gmail.com>
URL: http://cytospade.org
MD5sum: 4590a0d20855e5a63efe93b27e9cc056
source.ver: src/contrib/spade_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/spade_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/spade_1.6.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/spade_1.6.0.tgz
vignettes: vignettes/spade/inst/doc/SPADE.pdf
vignetteTitles: spade package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/spade/inst/doc/SPADE.R
Package: SpeCond
Version: 1.12.0
Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13),
fields, hwriter (>= 1.1), RColorBrewer, methods
License: LGPL (>=2)
Title: Condition specific detection from expression data
Description: This package performs a gene expression data analysis to
detect condition-specific genes. Such genes are significantly
up- or down-regulated in a small number of conditions. It does
so by fitting a mixture of normal distributions to the
expression values. Conditions can be environmental conditions,
different tissues, organs or any other sources that you wish to
compare in terms of gene expression.
biocViews: Microarray, DifferentialExpression, Bioinformatics,
MultipleComparisons, Clustering, ReportWriting
Author: Florence Cavalli
Maintainer: Florence Cavalli <florence@ebi.ac.uk>
MD5sum: af49b00b65ae0d92b268af5b6da65625
source.ver: src/contrib/SpeCond_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/SpeCond_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/SpeCond_1.12.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/SpeCond/inst/doc/SpeCond.pdf
vignetteTitles: SpeCond
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SpeCond/inst/doc/SpeCond.R
Package: SPIA
Version: 2.8.0
Depends: R (>= 2.10), graphics
Imports: graphics
Suggests: graph, Rgraphviz, KEGGgraph, hgu133plus2.db
License: GPL (>= 2)
Title: Signaling Pathway Impact Analysis (SPIA) using combined evidence
of pathway over-representation and unusual signaling
perturbations
Description: This package implements the Signaling Pathway Impact
Analysis (SPIA) which uses the information form a list of
differentially expressed genes and their log fold changes
together with signaling pathways topology, in order to identify
the pathways most relevant to the condition under the study.
biocViews: Microarray, GraphsAndNetworks, NetworkEnrichment, Pathways
Author: Adi Laurentiu Tarca <atarca@med.wayne.edu>, Purvesh Kathri
<purvesh@cs.wayne.edu> and Sorin Draghici <sorin@wayne.edu>
Maintainer: Adi Laurentiu Tarca <atarca@med.wayne.edu>
URL: http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1
MD5sum: 7ad7fa734ff24aa6de6d4bca112a4cfd
source.ver: src/contrib/SPIA_2.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/SPIA_2.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/SPIA_2.8.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SPIA_2.8.0.tgz
vignettes: vignettes/SPIA/inst/doc/SPIA.pdf
vignetteTitles: SPIA
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SPIA/inst/doc/SPIA.R
suggestsMe: graphite, KEGGgraph
Package: spikeLI
Version: 2.18.0
Imports: graphics, grDevices, stats, utils
License: GPL-2
Title: Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
Description: SpikeLI is a package that performs the analysis of the
Affymetrix spike-in data using the Langmuir Isotherm. The aim
of this package is to show the advantages of a
physical-chemistry based analysis of the Affymetrix microarray
data compared to the traditional methods. The spike-in (or
Latin square) data for the HGU95 and HGU133 chipsets have been
downloaded from the Affymetrix web site. The model used in the
spikeLI package is described in details in E. Carlon and T.
Heim, Physica A 362, 433 (2006).
biocViews: Microarray, QualityControl
Author: Delphine Baillon, Paul Leclercq <paulleclercq@hotmail.com>,
Sarah Ternisien, Thomas Heim, Enrico Carlon
<enrico.carlon@fys.kuleuven.be>
Maintainer: Enrico Carlon <enrico.carlon@fys.kuleuven.be>
MD5sum: be40bcbb40fc4b22cc2bb472ec8927cf
source.ver: src/contrib/spikeLI_2.18.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/spikeLI_2.18.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/spikeLI_2.18.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/spikeLI_2.18.0.tgz
vignettes: vignettes/spikeLI/inst/doc/collapse_A14.pdf,
vignettes/spikeLI/inst/doc/Ivsc.pdf,
vignettes/spikeLI/inst/doc/IvsDG_TagE.pdf,
vignettes/spikeLI/inst/doc/langmuir2.pdf,
vignettes/spikeLI/inst/doc/spikeLI.pdf
vignetteTitles: collapse_A14.pdf, Ivsc.pdf, IvsDG_TagE.pdf,
langmuir2.pdf, spikeLI
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/spikeLI/inst/doc/spikeLI.R
Package: spkTools
Version: 1.14.0
Depends: R (>= 2.7.0), Biobase (>= 2.5.5)
Imports: Biobase (>= 2.5.5), graphics, grDevices, gtools, methods,
RColorBrewer, stats, utils
Suggests: xtable
License: GPL (>= 2)
Title: Methods for Spike-in Arrays
Description: The package contains functions that can be used to compare
expression measures on different array platforms.
biocViews: Software, AssayTechnologies, Microarray
Author: Matthew N McCall <mmccall@jhsph.edu>, Rafael A Irizarry
<rafa@jhu.edu>
Maintainer: Matthew N McCall <mmccall@jhsph.edu>
URL: http://bioconductor.org
MD5sum: 17425728178716e0bb23cbe61fb895da
source.ver: src/contrib/spkTools_1.14.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/spkTools_1.14.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/spkTools_1.14.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/spkTools_1.14.0.tgz
vignettes: vignettes/spkTools/inst/doc/spkDoc.pdf
vignetteTitles: spkTools: Spike-in Data Analysis and Visualization
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/spkTools/inst/doc/spkDoc.R
Package: splicegear
Version: 1.30.0
Depends: R (>= 2.6.0), methods, Biobase(>= 2.5.5)
Imports: annotate, Biobase, graphics, grDevices, grid, methods, utils,
XML
License: LGPL
Title: splicegear
Description: A set of tools to work with alternative splicing
biocViews: Infrastructure, Transcription
Author: Laurent Gautier <laurent@cbs.dtu.dk>
Maintainer: Laurent Gautier <laurent@cbs.dtu.dk>
MD5sum: 7813c754b2d7d47f296b066024dadc07
source.ver: src/contrib/splicegear_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/splicegear_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/splicegear_1.30.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/splicegear/inst/doc/splicegear.pdf
vignetteTitles: splicegear Introduction
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/splicegear/inst/doc/splicegear.R
Package: splots
Version: 1.24.0
Imports: grid, RColorBrewer
License: LGPL
Title: Visualization of high-throughput assays in microtitre plate or
slide format
Description: The splots package provides the plotScreen function for
visualising data in microtitre plate or slide format.
biocViews: Visualization, HighThroughputSequencing,
MicrotitrePlateAssay
Author: Wolfgang Huber, Oleg Sklyar
Maintainer: Wolfgang Huber <whuber@embl.de>
MD5sum: f2dcac542e11df5aad97284c75a907e6
source.ver: src/contrib/splots_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/splots_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/splots_1.24.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/splots/inst/doc/splotsHOWTO.pdf
vignetteTitles: Visualization of data from assays in microtitre plate
or slide format
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/splots/inst/doc/splotsHOWTO.R
dependsOnMe: cellHTS2
importsMe: RNAinteract, RNAither
Package: spotSegmentation
Version: 1.32.0
Depends: R (>= 2.10), mclust
License: GPL (>= 2)
Title: Microarray Spot Segmentation and Gridding for Blocks of
Microarray Spots
Description: Spot segmentation via model-based clustering and gridding
for blocks within microarray slides, as described in Li et al,
Robust Model-Based Segmentation of Microarray Images, Technical
Report no. 473, Department of Statistics, University of
Washington.
biocViews: Microarray, TwoChannel, QualityControl, Preprocessing
Author: Qunhua Li, Chris Fraley, Adrian Raftery Department of
Statistics, University of Washington
Maintainer: Chris Fraley <fraley@stat.washington.edu>
URL: http://www.stat.washington.edu/fraley
MD5sum: 74084cce372d13c76954fe138afc8a82
source.ver: src/contrib/spotSegmentation_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/spotSegmentation_1.32.0.zip
win64.binary.ver:
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mac.binary.leopard.ver:
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vignettes: vignettes/spotSegmentation/inst/doc/spotsegdoc.pdf
vignetteTitles: spotsegdoc.pdf
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: SQUADD
Version: 1.8.0
Depends: R (>= 2.11.0)
Imports: graphics, grDevices, methods, RColorBrewer, stats, utils
License: GPL (>=2)
Title: Add-on of the SQUAD Software
Description: This package SQUADD is a SQUAD add-on. It permits to
generate SQUAD simulation matrix, prediction Heat-Map and
Correlation Circle from PCA analysis.
biocViews: GraphsAndNetworks, NetworkAnalysis, Visualization
Author: Martial Sankar, supervised by Christian Hardtke and Ioannis
Xenarios
Maintainer: Martial Sankar <martial.sankar@unil.ch>
URL: http://www.unil.ch/dbmv/page21142_en.html
MD5sum: 009e89b8344454621b948fb1855bf73b
source.ver: src/contrib/SQUADD_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/SQUADD_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/SQUADD_1.8.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/SQUADD/inst/doc/SQUADD_ERK.pdf,
vignettes/SQUADD/inst/doc/SQUADD.pdf
vignetteTitles: SQUADD package, SQUADD package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SQUADD/inst/doc/SQUADD_ERK.R,
vignettes/SQUADD/inst/doc/SQUADD.R
Package: SRAdb
Version: 1.12.1
Depends: RSQLite (>= 0.8-4) , graph, RCurl
Imports: GEOquery
Suggests: Rgraphviz
License: Artistic-2.0
Title: A compilation of metadata from NCBI SRA and tools
Description: The Sequence Read Archive (SRA) is the largest public
repository of sequencing data from the next generation of
sequencing platforms including Roche 454 GS System, Illumina
Genome Analyzer, Applied Biosystems SOLiD System, Helicos
Heliscope, and others. However, finding data of interest can be
challenging using current tools. SRAdb is an attempt to make
access to the metadata associated with submission, study,
sample, experiment and run much more feasible. This is
accomplished by parsing all the NCBI SRA metadata into a SQLite
database that can be stored and queried locally. Fulltext
search in the package make querying metadata very flexible and
powerful. sra or sra-lite files can be downloaded for doing
alignment locally. The SQLite database is updated regularly as
new data is added to SRA and can be downloaded at will for the
most up-to-date metadata.
biocViews: Infrastructure, HighThroughputSequencing, DataImport
Author: Jack Zhu and Sean Davis
Maintainer: Jack Zhu <zhujack@mail.nih.gov>
URL: http://watson.nci.nih.gov/
MD5sum: 076795002b530b63997d26d166d5bbc5
source.ver: src/contrib/SRAdb_1.12.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/SRAdb_1.12.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/SRAdb_1.12.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/SRAdb_1.12.1.tgz
vignettes: vignettes/SRAdb/inst/doc/SRAdb.pdf
vignetteTitles: Using SRAdb to Query the Sequence Read Archive
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SRAdb/inst/doc/SRAdb.R
Package: sscore
Version: 1.30.0
Depends: R (>= 1.8.0), affy, affyio
Suggests: affydata
License: GPL (>= 2)
Title: S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
Description: This package contains an implementation of the S-Score
algorithm as described by Zhang et al (2002).
biocViews: Bioinformatics, DifferentialExpression
Author: Richard Kennedy <rkennedy@ms.soph.uab.edu>, based on C++ code
from Li Zhang <zhangli@odin.mdacc.tmc.edu> and Borland Delphi
code from Robnet Kerns <rtkerns@vcu.edu>.
Maintainer: Richard Kennedy <rkennedy@ms.soph.uab.edu>
URL: http://home.att.net/~richard-kennedy/professional.html
MD5sum: a6fa5f616d030173a3aa06957960d506
source.ver: src/contrib/sscore_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/sscore_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/sscore_1.30.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/sscore/inst/doc/sscore.pdf
vignetteTitles: SScore primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/sscore/inst/doc/sscore.R
Package: ssize
Version: 1.32.0
Depends: gdata, xtable
License: LGPL
Title: Estimate Microarray Sample Size
Description: Functions for computing and displaying sample size
information for gene expression arrays.
biocViews: Bioinformatics, Microarray, DifferentialExpression
Author: Gregory R. Warnes, Peng Liu, and Fasheng Li
Maintainer: Gregory R. Warnes <greg@random-technologies-llc.com>
MD5sum: be2534d4ac3e0a31cd0376ba0399872e
source.ver: src/contrib/ssize_1.32.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ssize_1.32.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ssize_1.32.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/ssize/inst/doc/ssize.pdf
vignetteTitles: package
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ssize/inst/doc/ssize.R
suggestsMe: oneChannelGUI
Package: SSPA
Version: 1.14.2
Depends: R (>= 2.8), methods, qvalue
Imports: graphics, limma, methods, stats
Suggests: multtest, quadprog, splines
License: GPL (>= 2)
Archs: i386, x64
Title: Sample Size and Power Analysis for Microarray Data
Description: Sample size and power analysis for microarray data, where
two groups are analysed.
biocViews: Microarray
Author: Maarten van Iterson
Maintainer: Maarten van Iterson <M.van_iterson.HG@lumc.nl>
URL: http://www.humgen.nl/MicroarrayAnalysisGroup.html
MD5sum: 789e53356ff034472ed0d85f877cdecb
source.ver: src/contrib/SSPA_1.14.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/SSPA_1.14.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/SSPA_1.14.2.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SSPA_1.14.2.tgz
vignettes: vignettes/SSPA/inst/doc/figChunk17.pdf,
vignettes/SSPA/inst/doc/SSPA.pdf
vignetteTitles: figChunk17.pdf, SSPA vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/SSPA/inst/doc/SSPA.R
Package: staRank
Version: 1.0.0
Depends: methods, cellHTS2, R (>= 2.10)
License: GPL
Title: Stability Ranking
Description: Detecting all relevant variables from a data set is
challenging, especially when only few samples are available and
data is noisy. Stability ranking provides improved variable
rankings of increased robustness using resampling or
subsampling.
biocViews: Bioinformatics, MultipleComparisons, CellBiology,
CellBasedAssays, MicrotitrePlateAssay
Author: Juliane Siebourg, Niko Beerenwinkel
Maintainer: Juliane Siebourg <juliane.siebourg@bsse.ethz.ch>
MD5sum: b5dd0738c9cca0c69faec77a742cd1e9
source.ver: src/contrib/staRank_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/staRank_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/staRank_1.0.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/staRank/inst/doc/staRank.pdf
vignetteTitles: Using staRank
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/staRank/inst/doc/staRank.R
Package: Starr
Version: 1.14.1
Depends: Ringo, affy, affxparser
Imports: pspline, MASS, zlibbioc
License: Artistic-2.0
Archs: i386, x64
Title: Simple tiling array analysis of Affymetrix ChIP-chip data
Description: Starr facilitates the analysis of ChIP-chip data, in
particular that of Affymetrix tiling arrays. The package
provides functions for data import, quality assessment, data
visualization and exploration. Furthermore, it includes
high-level analysis features like association of ChIP signals
with annotated features, correlation analysis of ChIP signals
and other genomic data (e.g. gene expression), peak-finding
with the CMARRT algorithm and comparative display of multiple
clusters of ChIP-profiles. It uses the basic Bioconductor
classes ExpressionSet and probeAnno for maximum compatibility
with other software on Bioconductor. All functions from Starr
can be used to investigate preprocessed data from the Ringo
package, and vice versa. An important novel tool is the the
automated generation of correct, up-to-date microarray probe
annotation (bpmap) files, which relies on an efficient mapping
of short sequences (e.g. the probe sequences on a microarray)
to an arbitrary genome.
biocViews:
Microarray,OneChannel,DataImport,QualityControl,Preprocessing,ChIPchip
Author: Benedikt Zacher, Johannes Soeding, Pei Fen Kuan, Matthias
Siebert, Achim Tresch
Maintainer: Benedikt Zacher <zacher@lmb.uni-muenchen.de>
MD5sum: 9d9a366de1b960f52aa6cefafb520879
source.ver: src/contrib/Starr_1.14.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Starr_1.14.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/Starr_1.14.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/Starr_1.14.1.tgz
vignettes: vignettes/Starr/inst/doc/Starr.pdf
vignetteTitles: Simple tiling array analysis
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Starr/inst/doc/Starr.R
Package: stepNorm
Version: 1.30.0
Depends: R (>= 1.8.0), marray, methods
Imports: marray, MASS, methods, stats
License: LGPL
Title: Stepwise normalization functions for cDNA microarrays
Description: Stepwise normalization functions for cDNA microarray data.
biocViews: Microarray, TwoChannel, Preprocessing
Author: Yuanyuan Xiao <yxiao@itsa.ucsf.edu>, Yee Hwa (Jean) Yang
<jean@biostat.ucsf.edu>
Maintainer: Yuanyuan Xiao <yxiao@itsa.ucsf.edu>
URL: http://www.biostat.ucsf.edu/jean/
MD5sum: ce38bffafdba0905cdfa187499971b32
source.ver: src/contrib/stepNorm_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/stepNorm_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/stepNorm_1.30.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/stepNorm_1.30.0.tgz
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Package: stepwiseCM
Version: 1.4.0
Depends: R (>= 2.14), randomForest, MAclinical, tspair, pamr, snowfall,
glmpath, penalized, e1071
License: GPL (http://www.gnu.org/copyleft/gpl.html)
Title: Stepwise Classification of Cancer Samples using Clinical and
Molecular Data
Description: Stepwise classification of cancer samples using both
clinical and molecular data
Author: Askar Obulkasim
Maintainer: Askar Obulkasim <askar.wubulikasimu@vumc.nl>
MD5sum: 7f0a816b36a1c51021faf92011dc68c5
source.ver: src/contrib/stepwiseCM_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/stepwiseCM_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/stepwiseCM_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/stepwiseCM/inst/doc/stepwiseCM.pdf
vignetteTitles: stepwiseCM
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/stepwiseCM/inst/doc/stepwiseCM.R
Package: Streamer
Version: 1.4.0
Imports: methods, graph, RBGL, parallel, BiocGenerics
Suggests: RUnit, Rsamtools (>= 1.5.53), Rgraphviz
License: Artistic-2.0
Archs: i386, x64
Title: Enabling stream processing of large files
Description: Large data files can be difficult to work with in R, where
data generally resides in memory. This package encourages a
style of programming where data is 'streamed' from disk into R
via a `producer' and through a series of `consumers' that,
typically reduce the original data to a manageable size. The
package provides useful Producer and Consumer stream components
for operations such as data input, sampling, indexing, and
transformation; see package?Streamer for details.
biocViews: Infrastructure, DataImport
Author: Martin Morgan, Nishant Gopalakrishnan
Maintainer: Martin Morgan <mtmorgan@fhcrc.org>
MD5sum: fe83281f8f6d3cbec30bdfdf7d41dc31
source.ver: src/contrib/Streamer_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Streamer_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Streamer_1.4.0.zip
mac.binary.leopard.ver:
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vignettes: vignettes/Streamer/inst/doc/Streamer.pdf
vignetteTitles: Streamer: A simple example
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Streamer/inst/doc/Streamer.R
Package: survcomp
Version: 1.8.1
Depends: R (>= 2.10), survival, prodlim
Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta
Suggests: Hmisc, CPE, clinfun, survJamda, Biobase, xtable
License: Artistic-2.0
Archs: i386, x64
Title: Performance Assessment and Comparison for Survival Analysis
Description: R package providing functions to assess and to compare the
performance of risk prediction (survival) models.
biocViews: GeneExpression, DifferentialExpression, Visualization
Author: Benjamin Haibe-Kains, Markus Schroeder, Catharina Olsen,
Christos Sotiriou, Gianluca Bontempi, John Quackenbush
Maintainer: Benjamin Haibe-Kains <bhaibeka@jimmy.harvard.edu>, Markus
Schroeder <mschroed@jimmy.harvard.edu>, Catharina Olsen
<colsen@ulb.ac.be>
URL: http://compbio.dfci.harvard.edu
MD5sum: 6d3a8115723d946788e31eb19087453e
source.ver: src/contrib/survcomp_1.8.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/survcomp_1.8.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/survcomp_1.8.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/survcomp_1.8.1.tgz
vignettes: vignettes/survcomp/inst/doc/survcomp.pdf
vignetteTitles: SurvComp: a package for performance assessment and
comparison for survival analysis
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/survcomp/inst/doc/survcomp.R
dependsOnMe: genefu
Package: sva
Version: 3.4.0
Depends: R (>= 2.8), corpcor, mgcv
Imports: graphics, stats
Suggests: limma,pamr,bladderbatch
License: Artistic-2.0
Archs: i386, x64
Title: Surrogate Variable Analysis
Description: The sva package contains functions for removing batch
effects and other unwanted variation in high-throughput
experiment. Specifically, the sva package contains functions
for the identifying and building surrogate variables for
high-dimensional data sets. Surrogate variables are covariates
constructed directly from high-dimensional data (like gene
expression/RNA sequencing/methylation/brain imaging data) that
can be used in subsequent analyses to adjust for unknown,
unmodeled, or latent sources of noise. The sva package can be
used to remove artifacts in two ways: (1) identifying and
estimating surrogate variables for unknown sources of variation
in high-throughput experiments (Leek and Storey 2007 PLoS
Genetics,2008 PNAS) and (2) directly removing known batch
effects using ComBat (Johnson et al. 2007 Biostatistics).
Removing batch effects and using surrogate variables in
differential expression analysis have been shown to reduce
dependence, stabilize error rate estimates, and improve
reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008
PNAS or Leek et al. 2011 Nat. Reviews Genetics). Surrogate
variable analysis and ComBat were developed in the context of
microarray experiments, but may be used as a general tool for
high throughput data sets where dependence may be involved.
biocViews: Microarray,Statistics,Preprocessing,MultipleComparisons
Author: Jeffrey T. Leek <jleek@jhsph.edu>, W. Evan Johnson
<wej@bu.edu>, Hilary S. Parker <hiparker@jhsph.edu>, Andrew E.
Jaffe <ajaffe@jhsph.edu>, John D. Storey
<jstorey@princeton.edu>,
Maintainer: Jeffrey T. Leek <jleek@jhsph.edu>
MD5sum: 249351a29adcd17008828218188189cc
source.ver: src/contrib/sva_3.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/sva_3.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/sva_3.4.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/sva_3.4.0.tgz
vignettes: vignettes/sva/inst/doc/sva.pdf
vignetteTitles: bladderbatchTutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/sva/inst/doc/sva.R
importsMe: trigger
Package: synapter
Version: 1.0.1
Depends: R (>= 2.15), methods, MSnbase
Imports: hwriter, tcltk, tcltk2, RColorBrewer, lattice, qvalue,
multtest, utils, Biobase
Suggests: synapterdata, knitr, xtable
License: GPL-2
Title: Label-free data analysis pipeline for optimal identification and
quantitation
Description: The synapter package provides functionality to reanalyse
label-free proteomics data acquired on a Synapt G2 mass
spectrometer. One or several runs, possibly processed with
additional ion mobility separation to increase identification
accuracy can be combined to other quantitation files to
maximise identification and quantitation accuracy.
biocViews: Bioinformatics, MassSpectrometry, Proteomics, GUI
Author: Laurent Gatto, Pavel V. Shliaha and Nick J. Bond
Maintainer: Laurent Gatto <lg390@cam.ac.uk>
URL: http://lgatto.github.com/synapter/
MD5sum: 0befe93da2bcfc7e17323b9f5bfe4581
source.ver: src/contrib/synapter_1.0.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/synapter_1.0.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/synapter_1.0.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/synapter_1.0.1.tgz
vignettes: vignettes/synapter/inst/doc/synapter.pdf
vignetteTitles: synapter
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/synapter/inst/doc/synapter.R
Package: TargetSearch
Version: 1.14.1
Depends: R (>= 2.7.0), mzR, methods
Imports: graphics, grDevices, methods, stats, tcltk, utils
Suggests: TargetSearchData
License: GPL (>= 2)
Archs: i386, x64
Title: A package for the analysis of GC-MS metabolite profiling data.
Description: This packages provides a targeted pre-processing method
for GC-MS data.
biocViews: MassSpectrometry,Preprocessing
Author: Alvaro Cuadros-Inostroza <inostroza@mpimp-golm.mpg.de>, Jan
Lisec <lisec@mpimp-golm.mpg.de>, Henning Redestig
<henning.red@googlemail.com>, Matt Hannah
<matthew.hannah@bayercropscience.com>
Maintainer: Alvaro Cuadros-Inostroza <inostroza@mpimp-golm.mpg.de>
MD5sum: a3b57ae617d448aefb6445242c213e7d
source.ver: src/contrib/TargetSearch_1.14.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/TargetSearch_1.14.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/TargetSearch_1.14.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/TargetSearch_1.14.1.tgz
vignettes: vignettes/TargetSearch/inst/doc/RICorrection.pdf,
vignettes/TargetSearch/inst/doc/TargetSearch.pdf
vignetteTitles: RI correction, The TargetSearch Package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TargetSearch/inst/doc/RICorrection.R,
vignettes/TargetSearch/inst/doc/TargetSearch.R
Package: TDARACNE
Version: 1.8.0
Depends: GenKern, Rgraphviz, Biobase
License: GPL-2
Title: Network reverse engineering from time course data.
Description: To infer gene networks from time-series measurements is a
current challenge into bioinformatics research area. In order
to detect dependencies between genes at different time delays,
we propose an approach to infer gene regulatory networks from
time-series measurements starting from a well known algorithm
based on information theory. The proposed algorithm is expected
to be useful in reconstruction of small biological directed
networks from time course data.
biocViews: Microarray, TimeCourse
Author: Zoppoli P.,Morganella S., Ceccarelli M.
Maintainer: Zoppoli Pietro <zoppoli.pietro@gmail.com>
MD5sum: a8fa6de3889e57e1ee90a38c36dff0fc
source.ver: src/contrib/TDARACNE_1.8.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/TDARACNE_1.8.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/TDARACNE_1.8.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/TDARACNE_1.8.0.tgz
vignettes: vignettes/TDARACNE/inst/doc/TDARACNE.pdf
vignetteTitles: TDARACNE
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TDARACNE/inst/doc/TDARACNE.R
Package: TEQC
Version: 2.6.0
Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5),
Rsamtools, hwriter
Imports: Biobase (>= 2.15.1)
License: GPL (>= 2)
Title: Quality control for target capture experiments
Description: Target capture experiments combine hybridization-based (in
solution or on microarrays) capture and enrichment of genomic
regions of interest (e.g. the exome) with high throughput
sequencing of the captured DNA fragments. This package provides
functionalities for assessing and visualizing the quality of
the target enrichment process, like specificity and sensitivity
of the capture, per-target read coverage and so on.
biocViews: QualityControl, Microarray, HighThroughputSequencing,
Bioinformatics, Genetics
Author: M. Hummel, S. Bonnin, E. Lowy, G. Roma
Maintainer: Manuela Hummel <manuela.hummel@crg.es>
MD5sum: a539311e2924979de6ac5364ef256471
source.ver: src/contrib/TEQC_2.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/TEQC_2.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/TEQC_2.6.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TEQC_2.6.0.tgz
vignettes: vignettes/TEQC/inst/doc/TEQC.pdf
vignetteTitles: TEQC
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TEQC/inst/doc/TEQC.R
Package: ternarynet
Version: 1.2.0
Depends: R (>= 2.10.0), methods
Imports: utils, igraph
License: GPL (>= 2)
Archs: i386, x64
Title: Ternary Network Estimation
Description: A computational Bayesian approach to ternary gene
regulatory network estimation from gene perturbation
experiments.
biocViews: Software, CellBiology, GraphsAndNetworks, Bioinformatics
Author: Matthew N. McCall <mccallm@gmail.com>, Anthony Almudevar
<Anthony_Almudevar@urmc.rochester.edu>
Maintainer: Matthew N. McCall <mccallm@gmail.com>
MD5sum: 0c80e63acc33091ff275b69c58fdb988
source.ver: src/contrib/ternarynet_1.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/ternarynet_1.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/ternarynet_1.2.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/ternarynet_1.2.0.tgz
vignettes: vignettes/ternarynet/inst/doc/ternarynet.pdf
vignetteTitles: ternarynet: A Computational Bayesian Approach to
Ternary Network Estimation
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/ternarynet/inst/doc/ternarynet.R
Package: tigre
Version: 1.12.0
Depends: R (>= 2.11.0), BiocGenerics, Biobase
Imports: methods, BiocGenerics, Biobase, AnnotationDbi, gplots,
graphics, puma, stats, utils, annotate, DBI, RSQLite
Suggests: puma, drosgenome1.db, annotate, lumi
License: AGPL-3
Archs: i386, x64
Title: Transcription factor Inference through Gaussian process
Reconstruction of Expression
Description: The tigre package implements our methodology of Gaussian
process differential equation models for analysis of gene
expression time series from single input motif networks. The
package can be used for inferring unobserved transcription
factor (TF) protein concentrations from expression measurements
of known target genes, or for ranking candidate targets of a
TF.
biocViews: Microarray, Bioinformatics, TimeCourse, GeneExpression,
Transcription
Author: Antti Honkela, Pei Gao, Jonatan Ropponen, Miika-Petteri
Matikainen, Magnus Rattray, Neil D. Lawrence
Maintainer: Antti Honkela <antti.honkela@hiit.fi>
URL: http://www.bioinf.manchester.ac.uk/resources/tiger/
MD5sum: 55e4daacdecd439123d96fdef95b47ec
source.ver: src/contrib/tigre_1.12.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/tigre_1.12.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/tigre_1.12.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/tigre_1.12.0.tgz
vignettes: vignettes/tigre/inst/doc/tigre.pdf,
vignettes/tigre/inst/doc/tigre_quick.pdf
vignetteTitles: tigre User Guide, tigre Quick Guide
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/tigre/inst/doc/tigre_quick.R,
vignettes/tigre/inst/doc/tigre.R
Package: tilingArray
Version: 1.36.0
Depends: R (>= 2.11.0), Biobase, methods, pixmap
Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4
License: Artistic-2.0
Archs: i386, x64
Title: Transcript mapping with high-density oligonucleotide tiling
arrays
Description: The package provides functionality that can be useful for
the analysis of high-density tiling microarray data (such as
from Affymetrix genechips) for measuring transcript abundance
and architecture. The main functionalities of the package are:
1. the class 'segmentation' for representing partitionings of a
linear series of data; 2. the function 'segment' for fitting
piecewise constant models using a dynamic programming algorithm
that is both fast and exact; 3. the function 'confint' for
calculating confidence intervals using the strucchange package;
4. the function 'plotAlongChrom' for generating pretty plots;
5. the function 'normalizeByReference' for probe-sequence
dependent response adjustment from a (set of) reference
hybridizations.
biocViews: Microarray, OneChannel, Preprocessing, Visualization
Author: Wolfgang Huber, Zhenyu Xu, Joern Toedling with contributions
from Matt Ritchie
Maintainer: Zhenyu Xu <zhenyu@ebi.ac.uk>
MD5sum: 7563316cd9646c75426043a043a47917
source.ver: src/contrib/tilingArray_1.36.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/tilingArray_1.36.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/tilingArray_1.36.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/tilingArray_1.36.0.tgz
vignettes: vignettes/tilingArray/inst/doc/assessNorm.pdf,
vignettes/tilingArray/inst/doc/costMatrix.pdf,
vignettes/tilingArray/inst/doc/findsegments.pdf,
vignettes/tilingArray/inst/doc/plotAlongChrom.pdf,
vignettes/tilingArray/inst/doc/segmentation.pdf
vignetteTitles: Normalisation with the normalizeByReference function in
the tilingArray package, Supplement. Calculation of the cost
matrix, Introduction to using the segment function to fit a
piecewise constant curve, Introduction to the plotAlongChrom
function, Segmentation demo
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/tilingArray/inst/doc/assessNorm.R,
vignettes/tilingArray/inst/doc/costMatrix.R,
vignettes/tilingArray/inst/doc/findsegments.R,
vignettes/tilingArray/inst/doc/plotAlongChrom.R,
vignettes/tilingArray/inst/doc/segmentation.R
dependsOnMe: ADaCGH2
importsMe: snapCGH
Package: timecourse
Version: 1.30.0
Depends: R (>= 2.1.1), MASS, methods
Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods,
stats
License: LGPL
Title: Statistical Analysis for Developmental Microarray Time Course
Data
Description: Functions for data analysis and graphical displays for
developmental microarray time course data.
biocViews: Microarray, TimeCourse, DifferentialExpression
Author: Yu Chuan Tai
Maintainer: Yu Chuan Tai <yuchuan@stat.berkeley.edu>
URL: http://www.bioconductor.org
MD5sum: 57883de8b544487bbb7cba6f5bd08ee7
source.ver: src/contrib/timecourse_1.30.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/timecourse_1.30.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/timecourse_1.30.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/timecourse_1.30.0.tgz
vignettes: vignettes/timecourse/inst/doc/timecourse.pdf
vignetteTitles: timecourse manual
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/timecourse/inst/doc/timecourse.R
Package: tkWidgets
Version: 1.36.0
Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>=
1.3.0), tools
Suggests: Biobase, hgu95av2
License: Artistic-2.0
Title: R based tk widgets
Description: Widgets to provide user interfaces. tcltk should have been
installed for the widgets to run.
biocViews: Infrastructure
Author: J. Zhang <jzhang@jimmy.harvard.edu>
Maintainer: J. Zhang <jzhang@jimmy.harvard.edu>
MD5sum: 17fce848671339e6b39416a04e9f1d85
source.ver: src/contrib/tkWidgets_1.36.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/tkWidgets_1.36.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/tkWidgets_1.36.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/tkWidgets_1.36.0.tgz
vignettes: vignettes/tkWidgets/inst/doc/importWizard.pdf,
vignettes/tkWidgets/inst/doc/tkWidgets.pdf
vignetteTitles: tkWidgets importWizard, tkWidgets contents
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/tkWidgets/inst/doc/importWizard.R,
vignettes/tkWidgets/inst/doc/tkWidgets.R
dependsOnMe: cosmoGUI, oneChannelGUI
importsMe: Mfuzz, OLINgui
suggestsMe: affy, affyQCReport, annotate, Biobase, genefilter, marray
Package: topGO
Version: 2.10.0
Depends: R (>= 2.10.0), methods, graph (>= 1.14.0), Biobase (>= 2.0.0),
GO.db (>= 2.3.0), AnnotationDbi (>= 1.7.19), SparseM (>= 0.73)
Imports: methods, graph, Biobase, SparseM, AnnotationDbi, lattice
Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest,
Rgraphviz, globaltest
License: LGPL
Title: topGO: Enrichment analysis for Gene Ontology
Description: topGO package provides tools for testing GO terms while
accounting for the topology of the GO graph. Different test
statistics and different methods for eliminating local
similarities and dependencies between GO terms can be
implemented and applied.
biocViews: Microarray,Bioinformatics,Visualization
Author: Adrian Alexa, Jorg Rahnenfuhrer
Maintainer: Adrian Alexa <alexa@mpi-inf.mpg.de>
MD5sum: 31a11437737b6ff16f0d376010e72f4b
source.ver: src/contrib/topGO_2.10.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/topGO_2.10.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/topGO_2.10.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/topGO_2.10.0.tgz
vignettes: vignettes/topGO/inst/doc/topGO_classes_v3.pdf,
vignettes/topGO/inst/doc/topGO.pdf
vignetteTitles: topGO_classes_v3.pdf, topGO
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/topGO/inst/doc/topGO.R
dependsOnMe: RNAither
suggestsMe: Ringo
Package: TransView
Version: 1.0.7
Depends: methods,GenomicRanges
Imports: Rsamtools,zlibbioc,gplots,IRanges
LinkingTo: Rsamtools
Suggests: RUnit,pasillaBamSubset
License: GPL-3
Archs: i386, x64
Title: Read density map construction and accession. Visualization of
ChIPSeq and RNASeq data sets.
Description: This package provides efficient tools to generate, access
and display read densities of sequencing based data sets such
as from RNA-Seq and ChIP-Seq.
biocViews: Bioinformatics,DNAMethylation,GeneExpression,Transcription,
Microarray,Sequencing,HighThroughputSequencing,ChIPseq,RNAseq,
Methylseq,DataImport,Visualization,Clustering,MultipleComparisons
Author: Julius Muller
Maintainer: Julius Muller <ju-mu@alumni.ethz.ch>
URL: http://bioconductor.org/packages/release/bioc/html/TransView.html
MD5sum: 4ebe4001910e39d83fdaded5aac8d50e
source.ver: src/contrib/TransView_1.0.7.tar.gz
win.binary.ver: bin/windows/contrib/2.15/TransView_1.0.7.zip
win64.binary.ver: bin/windows64/contrib/2.15/TransView_1.0.7.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/TransView_1.0.7.tgz
vignettes: vignettes/TransView/inst/doc/TransView.pdf
vignetteTitles: An introduction to TransView
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TransView/inst/doc/TransView.R
Package: triform
Version: 1.0.0
Depends: R (>= 2.11.0), IRanges, yaml
Imports: IRanges, yaml, BiocGenerics
Suggests: RUnit
License: GPL-2
Title: Triform finds enriched regions (peaks) in transcription factor
ChIP-sequencing data
Description: The Triform algorithm uses model-free statistics to
identify peak-like distributions of TF ChIP sequencing reads,
taking advantage of an improved peak definition in combination
with known profile characteristics.
biocViews: Sequencing, ChIPseq
Author: Karl Kornacker Developer [aut], Tony HÃ¥ndstad Developer [aut,
cre]
Maintainer: Tony HÃ¥ndstad Developer <tony.handstad@gmail.com>
MD5sum: f67ef3d26b2b70f1cb3aee14562eab35
source.ver: src/contrib/triform_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/triform_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/triform_1.0.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/triform_1.0.0.tgz
vignettes: vignettes/triform/inst/doc/triform.pdf
vignetteTitles: Triform users guide
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/triform/inst/doc/triform.R
Package: trigger
Version: 1.4.0
Depends: R (>= 2.14.0), corpcor, qtl
Imports: qvalue, methods, graphics, sva
License: GPL-3
Archs: i386, x64
Title: Transcriptional Regulatory Inference from Genetics of Gene
ExpRession
Description: This R package provides tools for the statistical analysis
of integrative genomic data that involve some combination of:
genotypes, high-dimensional intermediate traits (e.g., gene
expression, protein abundance), and higher-order traits
(phenotypes). The package includes functions to: (1) construct
global linkage maps between genetic markers and gene
expression; (2) analyze multiple-locus linkage (epistasis) for
gene expression; (3) quantify the proportion of genome-wide
variation explained by each locus and identify eQTL hotspots;
(4) estimate pair-wise causal gene regulatory probabilities and
construct gene regulatory networks; and (5) identify causal
genes for a quantitative trait of interest.
biocViews: GeneExpression, SNP, GeneticVariability, Microarray,
Genetics
Author: Lin S. Chen <lchen@health.bsd.uchicago.edu>, Dipen P.
Sangurdekar <dps@genomics.princeton.edu> and John D. Storey
<jstorey@princeton.edu>
Maintainer: John D. Storey <jstorey@princeton.edu>
MD5sum: 466aff98f2146bbe14e5ddfccbd2b03a
source.ver: src/contrib/trigger_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/trigger_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/trigger_1.4.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/trigger_1.4.0.tgz
vignettes: vignettes/trigger/inst/doc/net50.pdf,
vignettes/trigger/inst/doc/trigger.pdf
vignetteTitles: net50.pdf, Trigger Tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/trigger/inst/doc/trigger.R
Package: tspair
Version: 1.16.0
Depends: R (>= 2.10), Biobase (>= 2.4.0)
License: GPL-2
Archs: i386, x64
Title: Top Scoring Pairs for Microarray Classification
Description: These functions calculate the pair of genes that show the
maximum difference in ranking between two user specified
groups. This "top scoring pair" maximizes the average of
sensitivity and specificity over all rank based classifiers
using a pair of genes in the data set. The advantage of
classifying samples based on only the relative rank of a pair
of genes is (a) the classifiers are much simpler and often more
interpretable than more complicated classification schemes and
(b) if arrays can be classified using only a pair of genes, PCR
based tests could be used for classification of samples. See
the references for the tspcalc() function for references
regarding TSP classifiers.
biocViews: Microarray, Bioinformatics
Author: Jeffrey T. Leek <jtleek@jhu.edu>
Maintainer: Jeffrey T. Leek <jtleek@jhu.edu>
MD5sum: 4f84adf894961f3be7d453bb605113c4
source.ver: src/contrib/tspair_1.16.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/tspair_1.16.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/tspair_1.16.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/tspair_1.16.0.tgz
vignettes: vignettes/tspair/inst/doc/tsp1.pdf,
vignettes/tspair/inst/doc/tsp.pdf
vignetteTitles: tsp1.pdf, tspTutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/tspair/inst/doc/tsp.R
dependsOnMe: stepwiseCM
Package: TSSi
Version: 1.4.0
Depends: R (>= 2.13.2), BiocGenerics (>= 0.3.2)
Imports: BiocGenerics, methods, Hmisc, minqa, stats, Biobase (>=
0.3.2), plyr, IRanges
Suggests: rtracklayer
Enhances: multicore
License: GPL-3
Archs: i386, x64
Title: Transcription Start Site Identification
Description: Identify and normalize transcription start sites in
high-throughput sequencing data.
biocViews: Sequencing, HighThroughputSequencing, RNAseq, Genetics,
Preprocessing
Author: Clemens Kreutz, Julian Gehring
Maintainer: Julian Gehring <julian.gehring@embl.de>
URL: http://julian-gehring.github.com/TSSi/
MD5sum: 7420a6e03f30fb5964a42cf3164d5021
source.ver: src/contrib/TSSi_1.4.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/TSSi_1.4.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/TSSi_1.4.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TSSi_1.4.0.tgz
vignettes: vignettes/TSSi/inst/doc/TSSi.pdf
vignetteTitles: Introduction to the TSSi package: Identification of
Transcription Start Sites
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/TSSi/inst/doc/TSSi.R
Package: TurboNorm
Version: 1.6.2
Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray
Imports: stats, grDevices, affy, lattice
Suggests: affydata, affy, lattice
License: LGPL
Title: A fast scatterplot smoother suitable for microarray
normalization
Description: A fast scatterplot smoother based on B-splines with
second-order difference penalty. Functions for microarray
normalization of single-colour data i.e. Affymetrix/Illumina
and two-colour data supplied as marray MarrayRaw-objects or
limma RGList-objects are available.
biocViews: Microarray, OneChannel, TwoChannel, Preprocessing,
DNAMethylation, CpGIsland
Author: Maarten van Iterson and Chantal van Leeuwen
Maintainer: Maarten van Iterson <mviterson@gmail.com>
URL: http://www.humgen.nl/MicroarrayAnalysisGroup.html
MD5sum: 6db4b7faab10013d4d721397a705a382
source.ver: src/contrib/TurboNorm_1.6.2.tar.gz
win.binary.ver: bin/windows/contrib/2.15/TurboNorm_1.6.2.zip
win64.binary.ver: bin/windows64/contrib/2.15/TurboNorm_1.6.2.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/TurboNorm_1.6.2.tgz
vignettes: vignettes/TurboNorm/inst/doc/turbonorm.pdf
vignetteTitles: TurboNorm Overview
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TurboNorm/inst/doc/turbonorm.R
Package: tweeDEseq
Version: 1.4.1
Depends: R (>= 2.12.0)
Imports: MASS, limma, edgeR, parallel, cqn
Suggests: tweeDEseqCountData, xtable
License: GPL (>= 2)
Archs: i386, x64
Title: RNA-seq data analysis using the Poisson-Tweedie family of
distributions
Description: Differential expression analysis of RNA-seq using the
Poisson-Tweedie family of distributions.
biocViews: Statistics, DifferentialExpression,
HighThroughputSequencing, RNAseq
Author: Juan R Gonzalez <jrgonzalez@creal.cat> and Mikel Esnaola
<mesnaola@creal.cat> (with contributions from Robert Castelo
<robert.castelo@upf.edu>)
Maintainer: Juan R Gonzalez <jrgonzalez@creal.cat>
URL: http://www.creal.cat/jrgonzalez/software.htm
MD5sum: 3cda9b54f8936cbe473039a4be80c5f4
source.ver: src/contrib/tweeDEseq_1.4.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/tweeDEseq_1.4.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/tweeDEseq_1.4.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/tweeDEseq_1.4.1.tgz
vignettes: vignettes/tweeDEseq/inst/doc/tweeDEseq.pdf
vignetteTitles: tweeDEseq: analysis of RNA-seq data using the
Poisson-Tweedie family of distributions
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/tweeDEseq/inst/doc/tweeDEseq.R
Package: twilight
Version: 1.34.0
Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>=
1.12.0)
Imports: Biobase, graphics, grDevices, stats
Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2)
License: GPL (>= 2)
Archs: i386, x64
Title: Estimation of local false discovery rate
Description: In a typical microarray setting with gene expression data
observed under two conditions, the local false discovery rate
describes the probability that a gene is not differentially
expressed between the two conditions given its corrresponding
observed score or p-value level. The resulting curve of
p-values versus local false discovery rate offers an insight
into the twilight zone between clear differential and clear
non-differential gene expression. Package 'twilight' contains
two main functions: Function twilight.pval performs a
two-condition test on differences in means for a given input
matrix or expression set and computes permutation based
p-values. Function twilight performs a stochastic downhill
search to estimate local false discovery rates and effect size
distributions. The package further provides means to filter for
permutations that describe the null distribution correctly.
Using filtered permutations, the influence of hidden
confounders could be diminished.
biocViews: Microarray, Bioinformatics, DifferentialExpression,
MultipleComparisons
Author: Stefanie Scheid <stefanie.scheid@gmx.de>
Maintainer: Stefanie Scheid <stefanie.scheid@gmx.de>
URL: http://compdiag.molgen.mpg.de/software/twilight.shtml
MD5sum: fa6c201d51c8f60b90a0c842911c56c8
source.ver: src/contrib/twilight_1.34.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/twilight_1.34.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/twilight_1.34.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/twilight_1.34.0.tgz
vignettes: vignettes/twilight/inst/doc/bcb_logo.pdf,
vignettes/twilight/inst/doc/tr_2004_01.pdf
vignetteTitles: bcb_logo.pdf, Estimation of Local False Discovery Rates
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/twilight/inst/doc/tr_2004_01.R
dependsOnMe: OrderedList
importsMe: OrderedList
Package: TypeInfo
Version: 1.24.0
Depends: methods
Suggests: Biobase
License: BSD
Title: Optional Type Specification Prototype
Description: A prototype for a mechanism for specifying the types of
parameters and the return value for an R function. This is
meta-information that can be used to generate stubs for servers
and various interfaces to these functions. Additionally, the
arguments in a call to a typed function can be validated using
the type specifications. We allow types to be specified as
either i) by class name using either inheritance - is(x,
className), or strict instance of - class(x) %in% className, or
ii) a dynamic test given as an R expression which is evaluated
at run-time. More precise information and interesting tests can
be done via ii), but it is harder to use this information as
meta-data as it requires more effort to interpret it and it is
of course run-time information. It is typically more
meaningful.
biocViews: Infrastructure
Author: Duncan Temple Lang Robert Gentleman (<rgentlem@fhcrc.org>)
Maintainer: Duncan Temple Lang <duncan@wald.ucdavis.edu>
MD5sum: 8046a8b1b5406d8217d7edd8ab1e8fdc
source.ver: src/contrib/TypeInfo_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/TypeInfo_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/TypeInfo_1.24.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/TypeInfo_1.24.0.tgz
vignettes: vignettes/TypeInfo/inst/doc/TypeInfoNews.pdf
vignetteTitles: TypeInfo R News
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/TypeInfo/inst/doc/TypeInfoNews.R
htmlDocs: vignettes/TypeInfo/inst/doc/outline.html
dependsOnMe: RWebServices
Package: VanillaICE
Version: 1.20.3
Depends: R (>= 2.14.0)
Imports: stats, utils, methods, Biobase, oligoClasses (>=
1.19.36),lattice, IRanges (>= 1.13.22), grid, msm, crlmm,
foreach, GenomicRanges, matrixStats
Suggests: genomewidesnp6Crlmm, hapmapsnp6, RColorBrewer, genefilter,
RSQLite, foreach, RUnit, pd.mapping50k.hind240, SNPchip (>=
2.2.0)
Enhances: DNAcopy, crlmm
License: LGPL-2
Archs: i386, x64
Title: A Hidden Markov Model for high throughput genotyping arrays
Description: Hidden Markov Models for characterizing chromosomal
alterations in high throughput SNP arrays
biocViews: Bioinformatics, CopyNumberVariants, SNP, GeneticVariability,
Visualization
Author: Robert Scharpf <rscharpf@jhsph.edu>, Kevin Scharpf, and Ingo
Ruczinski <ingo@jhsph.edu>
Maintainer: Robert Scharpf <rscharpf@jhsph.edu>
MD5sum: 5b29803bc26952d3a9b2c99b328c1d53
source.ver: src/contrib/VanillaICE_1.20.3.tar.gz
win.binary.ver: bin/windows/contrib/2.15/VanillaICE_1.20.3.zip
win64.binary.ver: bin/windows64/contrib/2.15/VanillaICE_1.20.3.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/VanillaICE_1.20.3.tgz
vignettes: vignettes/VanillaICE/inst/doc/crlmmDownstream.pdf,
vignettes/VanillaICE/inst/doc/VanillaICE.pdf
vignetteTitles: crlmmDownstream, VanillaICE Vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/VanillaICE/inst/doc/crlmmDownstream.R,
vignettes/VanillaICE/inst/doc/VanillaICE.R
importsMe: MinimumDistance
suggestsMe: oligoClasses
Package: VariantAnnotation
Version: 1.4.12
Depends: R (>= 2.8.0), methods, GenomicRanges (>= 1.9.56), Rsamtools
(>= 1.9.4), IRanges (>= 1.15.48)
Imports: methods, BiocGenerics (>= 0.1.0), IRanges, Biobase (>=
2.15.1), Rsamtools (>= 1.9.4), AnnotationDbi (>= 1.17.11),
Biostrings (>= 2.25.2), zlibbioc, BSgenome, GenomicFeatures (>=
1.9.35), DBI
LinkingTo: IRanges, Biostrings, Rsamtools
Suggests: RUnit, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP.20110815, SIFT.Hsapiens.dbSNP132,
PolyPhen.Hsapiens.dbSNP131, snpStats
License: Artistic-2.0
Archs: i386, x64
Title: Annotation of Genetic Variants
Description: Annotate variants with respect to location and amino acid
coding
biocViews: DataImport, Sequencing, HighThroughputSequencing, SNP,
Annotation, Genetics, Homo_sapiens
Author: Valerie Obenchain, Martin Morgan, Michael Lawrence
Maintainer: Valerie Obenchain <vobencha@fhcrc.org>
MD5sum: b8054ca9398a2671a28052ad329f04dc
source.ver: src/contrib/VariantAnnotation_1.4.12.tar.gz
win.binary.ver: bin/windows/contrib/2.15/VariantAnnotation_1.4.12.zip
win64.binary.ver:
bin/windows64/contrib/2.15/VariantAnnotation_1.4.12.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/VariantAnnotation_1.4.12.tgz
vignettes: vignettes/VariantAnnotation/inst/doc/VariantAnnotation.pdf
vignetteTitles: Introduction to VariantAnnotation
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/VariantAnnotation/inst/doc/VariantAnnotation.R
dependsOnMe: VariantTools
importsMe: FunciSNP, ggbio, GGtools, gmapR, R453Plus1Toolbox,
VariantTools
suggestsMe: GenomicRanges, gmapR, GWASTools
Package: VariantTools
Version: 1.0.1
Depends: IRanges (>= 1.15.44), GenomicRanges (>= 1.9.52),
VariantAnnotation (>= 1.3.20), methods
Imports: IRanges, Rsamtools (>= 1.9.31), GenomicRanges, BiocGenerics,
Biostrings, parallel, gmapR (>= 0.99.28), GenomicFeatures,
VariantAnnotation, methods
Suggests: RUnit, LungCancerLines (>= 0.0.6)
License: Artistic-2.0
Title: Tools for Working with Genetic Variants
Description: Tools for Tools for detecting, filtering, calling,
comparing and plotting variants.
biocViews: Genetics, GeneticVariability, HighThroughputSequencing
Author: Michael Lawrence, Jeremiah Degenhardt, Robert Gentleman
Maintainer: Michael Lawrence <michafla@gene.com>
MD5sum: 1b9e5f0c9fac87d43ad315a833c742ea
source.ver: src/contrib/VariantTools_1.0.1.tar.gz
vignettes: vignettes/VariantTools/inst/doc/SNVsOmuC.pdf,
vignettes/VariantTools/inst/doc/VariantTools.pdf
vignetteTitles: SNVsOmuC.pdf, Introduction to VariantTools
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/VariantTools/inst/doc/VariantTools.R
Package: vbmp
Version: 1.26.0
Depends: R (>= 2.10)
Suggests: Biobase (>= 2.5.5), statmod
License: GPL (>= 2)
Title: Variational Bayesian Multinomial Probit Regression
Description: Variational Bayesian Multinomial Probit Regression with
Gaussian Process Priors. It estimates class membership
posterior probability employing variational and sparse
approximation to the full posterior. This software also
incorporates feature weighting by means of Automatic Relevance
Determination.
biocViews: Bioinformatics,Classification
Author: Nicola Lama <nicola.lama@unina2.it>, Mark Girolami
<girolami@dcs.gla.ac.uk>
Maintainer: Nicola Lama <nicola.lama@unina2.it>
URL:
http://bioinformatics.oxfordjournals.org/cgi/content/short/btm535v1
MD5sum: 66df78e52188b52adf10129032b510ce
source.ver: src/contrib/vbmp_1.26.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/vbmp_1.26.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/vbmp_1.26.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/vbmp_1.26.0.tgz
vignettes: vignettes/vbmp/inst/doc/vbmp.pdf
vignetteTitles: vbmp Tutorial
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/vbmp/inst/doc/vbmp.R
Package: Vega
Version: 1.6.0
Depends: R (>= 2.10)
License: GPL-2
Archs: i386, x64
Title: An R package for copy number data segmentation
Description: Vega (Variational Estimator for Genomic Aberrations) is an
algorithm that adapts a very popular variational model (Mumford
and Shah) used in image segmentation so that chromosomal
aberrant regions can be efficiently detected.
biocViews: aCGH, CopyNumberVariants
Author: Sandro Morganella
Maintainer: Sandro Morganella <morganellaalx@gmail.com>
MD5sum: 7d76d43137b98eb9353227e2a4e24110
source.ver: src/contrib/Vega_1.6.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/Vega_1.6.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/Vega_1.6.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Vega_1.6.0.tgz
vignettes: vignettes/Vega/inst/doc/Vega.pdf
vignetteTitles: Vega
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/Vega/inst/doc/Vega.R
Package: VegaMC
Version: 2.2.0
Depends: R (>= 2.10.0), biomaRt, Biobase, genoset
Imports: methods
License: GPL-2
Archs: i386, x64
Title: VegaMC: A Package Implementing a Variational Piecewise Smooth
Model for Identification of Driver Chromosomal Imbalances in
Cancer
Description: This package enables the detection of driver chromosomal
imbalances including loss of heterozygosity (LOH) from array
comparative genomic hybridization (aCGH) data. VegaMC performs
a joint segmentation of a dataset and uses a statistical
framework to distinguish between driver and passenger mutation.
VegaMC has been implemented so that it can be immediately
integrated with the output produced by PennCNV tool. In
addition, VegaMC produces in output two web pages that allows a
rapid navigation between both the detected regions and the
altered genes. In the web page that summarizes the altered
genes, the link to the respective Ensembl gene web page is
reported.
biocViews: Bioinformatics, aCGH, CopyNumberVariants
Author: S. Morganella and M. Ceccarelli
Maintainer: Sandro Morganella <morganella@unisannio.it>
MD5sum: 8609d4bc81efde0a6a418e28e508fb60
source.ver: src/contrib/VegaMC_2.2.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/VegaMC_2.2.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/VegaMC_2.2.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/VegaMC_2.2.0.tgz
vignettes: vignettes/VegaMC/inst/doc/VegaMC.pdf
vignetteTitles: VegaMC
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/VegaMC/inst/doc/VegaMC.R
Package: virtualArray
Version: 1.2.1
Depends: R (>= 2.3.0), methods, plyr, preprocessCore
Imports: affy, affyPLM, AnnotationDbi, Biobase, gcrma, GEOquery,
graphics, methods, reshape2, stats, utils
Suggests: affydata, plier, limma, lumi, org.Hs.eg.db
Enhances: parallel
License: GPL-3
Title: Build virtual array from different microarray platforms
Description: This package permits the user to combine raw data of
different microarray platforms into one virtual array. It
consists of several functions that act subsequently in a
semi-automatic way. Doing as much of the data combination and
letting the user concentrate on analysing the resulting virtual
array.
biocViews: Microarray, OneChannel, DataImport, Preprocessing,
Bioinformatics, MultipleComparisons
Author: Andreas Heider
Maintainer: Andreas Heider <aheider@trm.uni-leipzig.de>
MD5sum: 80d81ba648d88ca00c03d765c2273b96
source.ver: src/contrib/virtualArray_1.2.1.tar.gz
win.binary.ver: bin/windows/contrib/2.15/virtualArray_1.2.1.zip
win64.binary.ver: bin/windows64/contrib/2.15/virtualArray_1.2.1.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/virtualArray_1.2.1.tgz
vignettes: vignettes/virtualArray/inst/doc/virtualArray-016.pdf,
vignettes/virtualArray/inst/doc/virtualArray-022.pdf,
vignettes/virtualArray/inst/doc/virtualArray-023.pdf,
vignettes/virtualArray/inst/doc/virtualArray.pdf
vignetteTitles: virtualArray-016.pdf, virtualArray-022.pdf,
virtualArray-023.pdf, virtualArray Vignette
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/virtualArray/inst/doc/virtualArray.R
Package: vsn
Version: 3.26.0
Depends: R (>= 2.10), Biobase (>= 2.5.5)
Imports: methods, affy (>= 1.23.4), limma, lattice
Suggests: affydata, hgu95av2cdf
License: Artistic-2.0
Archs: i386, x64
Title: Variance stabilization and calibration for microarray data
Description: The package implements a method for normalising microarray
intensities, both between colours within array, and between
arrays. The method uses a robust variant of the
maximum-likelihood estimator for the stochastic model of
microarray data described in the references (see vignette). The
model incorporates data calibration (a.k.a. normalization), a
model for the dependence of the variance on the mean intensity,
and a variance stabilizing data transformation. Differences
between transformed intensities are analogous to "normalized
log-ratios". However, in contrast to the latter, their variance
is independent of the mean, and they are usually more sensitive
and specific in detecting differential transcription.
biocViews: Microarray, OneChannel, TwoChannel, Preprocessing
Author: Wolfgang Huber, with contributions from Anja von Heydebreck.
Many comments and suggestions by users are acknowledged, among
them Dennis Kostka, David Kreil, Hans-Ulrich Klein, Robert
Gentleman, Deepayan Sarkar and Gordon Smyth.
Maintainer: Wolfgang Huber <huber@ebi.ac.uk>
URL: http://www.r-project.org, http://www.ebi.ac.uk/huber
MD5sum: dc3543c14aa178d9f7a3fa4ee45fb43c
source.ver: src/contrib/vsn_3.26.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/vsn_3.26.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/vsn_3.26.0.zip
mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/vsn_3.26.0.tgz
vignettes: vignettes/vsn/inst/doc/convergence2.pdf,
vignettes/vsn/inst/doc/likelihoodcomputations.pdf,
vignettes/vsn/inst/doc/vsn.pdf
vignetteTitles: Verifying and assessing the performance with simulated
data, Likelihood Calculations for vsn, Introduction to vsn
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/vsn/inst/doc/convergence2.R,
vignettes/vsn/inst/doc/likelihoodcomputations.R,
vignettes/vsn/inst/doc/vsn.R
dependsOnMe: affyPara, cellHTS2, LVSmiRNA, MmPalateMiRNA, webbioc
importsMe: arrayQualityMetrics, imageHTS, MSnbase, Ringo, tilingArray
suggestsMe: adSplit, Agi4x44PreProcess, beadarray, BiocCaseStudies,
cellHTS, DESeq, GlobalAncova, globaltest, limma, lumi, twilight
Package: waveTiling
Version: 1.0.0
Depends: oligo, oligoClasses, Biobase, Biostrings, GenomeGraphs
Imports: methods, affy, preprocessCore, GenomicRanges, waveslim,
IRanges
Suggests: BSgenome, BSgenome.Athaliana.TAIR.TAIR9, waveTilingData,
pd.atdschip.tiling, TxDb.Athaliana.BioMart.plantsmart12
License: GPL (>=2)
Archs: i386, x64
Title: Wavelet-Based Models for Tiling Array Transcriptome Analysis
Description: This package is designed to conduct transcriptome analysis
for tiling arrays based on fast wavelet-based functional
models.
biocViews: MicroArray, DifferentialExpression, TimeCourse,
GeneExpression
Author: Kristof De Beuf <kristof.debeuf@UGent.be>, Peter Pipelers
<peter.pipelers@ugent.be> and Lieven Clement
<lieven.clement@gmail.com>
Maintainer: Kristof De Beuf <kristof.debeuf@UGent.be>
URL: https://r-forge.r-project.org/projects/wavetiling/
MD5sum: f39850a950cf0e1c14cd1f98e656fc05
source.ver: src/contrib/waveTiling_1.0.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/waveTiling_1.0.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/waveTiling_1.0.0.zip
mac.binary.leopard.ver:
bin/macosx/leopard/contrib/2.15/waveTiling_1.0.0.tgz
vignettes: vignettes/waveTiling/inst/doc/waveTiling-vignette.pdf
vignetteTitles: The waveTiling package
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/waveTiling/inst/doc/waveTiling-vignette.R
Package: weaver
Version: 1.24.0
Depends: R (>= 2.5.0), digest, tools, utils, codetools
Suggests: codetools
License: GPL-2
Title: Tools and extensions for processing Sweave documents
Description: This package provides enhancements on the Sweave()
function in the base package. In particular a facility for
caching code chunk results is included.
biocViews: Infrastructure
Author: Seth Falcon
Maintainer: Seth Falcon <seth@userprimary.net>
MD5sum: 3c4910eed517a0da223a0693deb78089
source.ver: src/contrib/weaver_1.24.0.tar.gz
win.binary.ver: bin/windows/contrib/2.15/weaver_1.24.0.zip
win64.binary.ver: bin/windows64/contrib/2.15/weaver_1.24.0.zip
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vignetteTitles: Using weaver to process Sweave documents
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Package: webbioc
Version: 1.30.0
Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma,
qvalue
Imports: multtest, qvalue, stats, utils, BiocInstaller
License: GPL (>= 2)
Title: Bioconductor Web Interface
Description: An integrated web interface for doing microarray analysis
using several of the Bioconductor packages. It is intended to
be deployed as a centralized bioinformatics resource for use by
many users. (Currently only Affymetrix oligonucleotide analysis
is supported.)
biocViews: Infrastructure, Microarray, OneChannel,
DifferentialExpression
Author: Colin A. Smith <webbioc@colinsmith.org>
Maintainer: Colin A. Smith <webbioc@colinsmith.org>
URL: http://www.bioconductor.org/
SystemRequirements: Unix, Perl (>= 5.6.0), Netpbm
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vignettes: vignettes/webbioc/inst/doc/demoscript.pdf,
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vignetteTitles: webbioc Demo Script, webbioc Overview
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Package: widgetTools
Version: 1.36.0
Depends: R (>= 2.4.0), methods, utils, tcltk
Suggests: Biobase
License: LGPL
Title: Creates an interactive tcltk widget
Description: This packages contains tools to support the construction
of tcltk widgets
biocViews: Infrastructure
Author: Jianhua Zhang
Maintainer: Jianhua Zhang <jzhang@jimmy.harvard.edu>
MD5sum: b9c03198f14965718e34823e6b24eb8c
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vignettes: vignettes/widgetTools/inst/doc/widget.pdf,
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vignetteTitles: widget.pdf, widgetTools Introduction
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Rfiles: vignettes/widgetTools/inst/doc/widgetTools.R
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importsMe: OLINgui
suggestsMe: affy
Package: xcms
Version: 1.34.0
Depends: R (>= 1.9.0), methods, mzR (>= 1.1.6)
Suggests: faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet (>=
1.5.2), RANN, snow, RUnit
Enhances: Rgraphviz, XML, KEGGSOAP
License: GPL (>= 2)
Archs: i386, x64
Title: LC/MS and GC/MS Data Analysis
Description: Framework for processing and visualization of
chromatographically separated and single-spectra mass spectral
data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML
files. Preprocesses data for high-throughput, untargeted
analyte profiling.
biocViews: MassSpectrometry, Metabolomics
Author: Colin A. Smith <csmith@scripps.edu>, Ralf Tautenhahn
<rtautenh@scripps.edu>, Steffen Neumann
<sneumann@ipb-halle.de>, Paul Benton
<hpaul.benton08@imperial.ac.uk>
Maintainer: Ralf Tautenhahn <rtautenh@scripps.edu>
URL: http://metlin.scripps.edu/download/
MD5sum: 44a5e9bd37787729d310b47e8d5a661a
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vignettes: vignettes/xcms/inst/doc/FlowChart.pdf,
vignettes/xcms/inst/doc/xcmsDirect.pdf,
vignettes/xcms/inst/doc/xcmsInstall.pdf,
vignettes/xcms/inst/doc/xcmsMSn.pdf,
vignettes/xcms/inst/doc/xcmsPreprocess.pdf
vignetteTitles: FlowChart.pdf, Grouping FTICR-MS data with xcms,
Installation Instructions for xcms, Processing Tandem-MS and
MS$^n$ data with xcms, LC/MS Preprocessing and Analysis with
xcms
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/xcms/inst/doc/xcmsDirect.R,
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vignettes/xcms/inst/doc/xcmsPreprocess.R
dependsOnMe: CAMERA, flagme
importsMe: CAMERA, Risa
suggestsMe: MassSpecWavelet
Package: XDE
Version: 2.4.1
Depends: R (>= 2.10.0), Biobase (>= 2.5.5), methods, graphics
Imports: Biobase, BiocGenerics, genefilter, graphics, grDevices,
gtools, MergeMaid, methods, stats, utils, mvtnorm
Suggests: siggenes, genefilter, MASS, RColorBrewer, GeneMeta, RUnit
Enhances: coda
License: LGPL-2
Archs: i386, x64
Title: XDE: a Bayesian hierarchical model for cross-study analysis of
differential gene expression
Description: Multi-level model for cross-study detection of
differential gene expression.
biocViews: Microarray, Bioinformatics, DifferentialExpression
Author: R.B. Scharpf, G. Parmigiani, A.B. Nobel, and H. Tjelmeland
Maintainer: Robert Scharpf <rscharpf@jhsph.edu>
MD5sum: 84a1f53230a603279c54e23e70bad38b
source.ver: src/contrib/XDE_2.4.1.tar.gz
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vignettes: vignettes/XDE/inst/doc/XdeParameterClass.pdf,
vignettes/XDE/inst/doc/XDE.pdf
vignetteTitles: XdeParameterClass Vignette, XDE Vignette
hasREADME: FALSE
hasNEWS: TRUE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/XDE/inst/doc/XdeParameterClass.R,
vignettes/XDE/inst/doc/XDE.R
Package: xmapbridge
Version: 1.16.0
Depends: R (>= 2.0), methods
Suggests: RUnit, RColorBrewer
License: LGPL-3
Title: Export plotting files to the xmapBridge for visualisation in
X:Map
Description: xmapBridge can plot graphs in the X:Map genome browser.
This package exports plotting files in a suitable format.
biocViews: Annotation, ReportWriting, Visualization
Author: Tim Yates <tyates@picr.man.ac.uk> and Crispin J Miller
<cmiller@picr.man.ac.uk>
Maintainer: Tim Yates <tyates@picr.man.ac.uk>
URL: http://xmap.picr.man.ac.uk, http://www.bioconductor.org
MD5sum: 0818bf2b16c15b7cb37ec5eb595fcf59
source.ver: src/contrib/xmapbridge_1.16.0.tar.gz
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mac.binary.leopard.ver:
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vignettes: vignettes/xmapbridge/inst/doc/xmapbridge.pdf
vignetteTitles: xmapbridge primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/xmapbridge/inst/doc/xmapbridge.R
Package: xmapcore
Version: 1.12.0
Depends: R (>= 2.8.0), methods, IRanges
Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase
Suggests: RUnit
License: GPL-2
Title: Core access to the xmap database (installed separately)
Description: xmapcore is deprecated and will not be supported after
Bioconductor release 2.10. It has been superceded by a new
package 'annmap'. xmapcore allows mapping between genetic
features and any available Affymetrix Exon arrays for Homo
Sapiens, Mus Musculus, Rattus Norvegicus and
Schizosaccharomyces Pombe.
biocViews: Annotation, Bioinformatics, Microarray, OneChannel,
ReportWriting, Transcription, Visualization
Author: Tim Yates <tyates@picr.man.ac.uk>
Maintainer: Tim Yates <tyates@picr.man.ac.uk>
URL: http://xmap.picr.man.ac.uk, http://www.bioconductor.org
MD5sum: 5bc4718ca8c7a22ead3995d03afcf967
source.ver: src/contrib/xmapcore_1.12.0.tar.gz
mac.binary.leopard.ver:
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vignettes: vignettes/xmapcore/inst/doc/cookbook.pdf,
vignettes/xmapcore/inst/doc/INSTALL.pdf,
vignettes/xmapcore/inst/doc/SplicingIndexExample.pdf,
vignettes/xmapcore/inst/doc/xmapcore.pdf
vignetteTitles: cookbook.pdf, xmapcore installation instruction,
SplicingIndexExample.pdf, xmapcore primer
hasREADME: FALSE
hasNEWS: FALSE
hasINSTALL: FALSE
hasLICENSE: FALSE
Rfiles: vignettes/xmapcore/inst/doc/INSTALL.R,
vignettes/xmapcore/inst/doc/xmapcore.R
dependsOnMe: rnaSeqMap
Package: xps
Version: 1.18.1
Depends: R (>= 2.6.0), methods, utils
Suggests: tools
License: GPL (>= 2.0)
Title: Processing and Analysis of Affymetrix Oligonucleotide Arrays
including Exon Arrays, Whole Genome Arrays and Plate Arrays
Description: The package handles pre-processing, normalization,
filtering and analysis of Affymetrix GeneChip expression
arrays, including exon arrays (Exon 1.0 ST: core, extended,
full probesets), gene arrays (Gene 1.0 ST) and plate arrays on
computers with 1 GB RAM only. It imports Affymetrix .CDF, .CLF,
.PGF and .CEL as well as annotation files, and computes e.g.
RMA, MAS5, FARMS, DFW, FIRMA, tRMA, MAS5-calls, DABG-calls,
I/NI-calls. It is an R wrapper to XPS (eXpression Profiling
System), which is based on ROOT, an object-oriented framework
developed at CERN. Thus, the prior installation of ROOT is a
prerequisite for the usage of this package, however, no
knowledge of ROOT is required. ROOT is licensed under LGPL and
can be downloaded from http://root.cern.ch.
biocViews: ExonArray, GeneExpression, Microarray, OneChannel,
DataImport, Preprocessing, Transcription,
DifferentialExpression
Author: Christian Stratowa, Vienna, Austria
Maintainer: Christian Stratowa <cstrato@aon.at>
SystemRequirements: root_v5.32.01 <http://root.cern.ch> - See README
file for installation instructions.
MD5sum: 411babdfc161d913f62b695106145eec
source.ver: src/contrib/xps_1.18.1.tar.gz
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vignettes: vignettes/xps/inst/doc/APTvsXPS.pdf,
vignettes/xps/inst/doc/xpsClasses.pdf,
vignettes/xps/inst/doc/xps.pdf,
vignettes/xps/inst/doc/xpsPreprocess.pdf
vignetteTitles: 3. XPS Vignette: Comparison APT vs XPS, 2. XPS
Vignette: Classes, 1. XPS Vignette: Overview, 4. XPS Vignette:
Function express()
hasREADME: TRUE
hasNEWS: TRUE
hasINSTALL: FALSE
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Rfiles: vignettes/xps/inst/doc/APTvsXPS.R,
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vignettes/xps/inst/doc/xpsPreprocess.R,
vignettes/xps/inst/doc/xps.R
Package: yaqcaffy
Version: 1.18.0
Depends: simpleaffy (>= 2.19.3), methods
Imports: stats4
Suggests: MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk
License: Artistic-2.0
Title: Affymetrix expression data quality control and reproducibility
analysis
Description: Quality control of Affymetrix GeneChip expression data and
reproducibility analysis of human whole genome chips with the
MAQC reference datasets.
biocViews: Microarray,OneChannel,QualityControl,ReportWriting
Author: Laurent Gatto
Maintainer: Laurent Gatto <laurent.gatto@gmail.com>
MD5sum: b3ed0b447cd663a32b6111f2fbc47d40
source.ver: src/contrib/yaqcaffy_1.18.0.tar.gz
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vignettes: vignettes/yaqcaffy/inst/doc/yaqcaffy.pdf
vignetteTitles: yaqcaffy: Affymetrix quality control and MAQC
reproducibility
hasREADME: FALSE
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Rfiles: vignettes/yaqcaffy/inst/doc/yaqcaffy.R
Package: zlibbioc
Version: 1.4.0
License: Artistic-2.0 + file LICENSE
Archs: i386, x64
Title: An R packaged zlib-1.2.5
Description: This package uses the source code of zlib-1.2.5 to create
libraries for systems that do not have these available via
other means (most Linux and Mac users should have system-level
access to zlib, and no direct need for this package). See the
vignette for instructions on use.
biocViews: Infrastructure
Author: Martin Morgan
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
URL: http://bioconductor.org/packages/release/bioc/html/Zlibbioc.html
MD5sum: f598c1ffbc8453a4186f562fa8b86e55
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vignettes: vignettes/zlibbioc/inst/doc/UsingZlibbioc.pdf
vignetteTitles: Using zlibbioc C libraries
hasREADME: FALSE
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hasINSTALL: FALSE
hasLICENSE: TRUE
Rfiles: vignettes/zlibbioc/inst/doc/UsingZlibbioc.R
dependsOnMe: BitSeq
importsMe: affy, affyio, affyPLM, DiffBind, makecdfenv, oligo, rhdf5,
Rsamtools, rtracklayer, seqbias, ShortRead, Starr,
VariantAnnotation