Package: a4 Version: 1.4.0 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL 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 MD5sum: 35cd22093fd51bffa5faf66da960f962 source.ver: src/contrib/a4_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/a4_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/a4_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/a4_1.4.0.tgz vignettes: vignettes/a4/inst/doc/a4vignette.pdf vignetteTitles: a4vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: a4Base Version: 1.4.1 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 MD5sum: 76f70e652c627abb9761b59523aa4b21 source.ver: src/contrib/a4Base_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/a4Base_1.4.1.zip win64.binary.ver: bin/windows64/contrib/2.15/a4Base_1.4.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/a4Base_1.4.1.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: a4 Package: a4Classif Version: 1.4.0 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 MD5sum: 8d21f94114a19f4d00cd26e91111d08d source.ver: src/contrib/a4Classif_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/a4Classif_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/a4Classif_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/a4Classif_1.4.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: a4 Package: a4Core Version: 1.4.0 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 MD5sum: fd6593e7bac98a63d09d12639ac162be source.ver: src/contrib/a4Core_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/a4Core_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/a4Core_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/a4Core_1.4.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: a4, a4Base, a4Classif importsMe: a4Classif Package: a4Preproc Version: 1.4.0 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 MD5sum: b4c615ce42801a307c71404019b3556f source.ver: src/contrib/a4Preproc_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/a4Preproc_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/a4Preproc_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/a4Preproc_1.4.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: a4, a4Base, a4Classif Package: a4Reporting Version: 1.4.0 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 MD5sum: 537e5fcea693a5aaebf88e47015a423d source.ver: src/contrib/a4Reporting_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/a4Reporting_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/a4Reporting_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/a4Reporting_1.4.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: a4 Package: ABarray Version: 1.24.0 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 MD5sum: d75236c4d8ef0aaaa40c82719d8bb936 source.ver: src/contrib/ABarray_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ABarray_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ABarray_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ABarray_1.24.0.tgz 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 Package: aCGH Version: 1.34.0 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 , Peter Dimitrov Maintainer: Peter Dimitrov MD5sum: b8424335b5f80e83ee0a90b6e5fccc52 source.ver: src/contrib/aCGH_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/aCGH_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/aCGH_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/aCGH_1.34.0.tgz vignettes: vignettes/aCGH/inst/doc/aCGH.pdf vignetteTitles: aCGH Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ADaCGH2, CRImage importsMe: snapCGH suggestsMe: beadarraySNP Package: ACME Version: 2.12.0 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 Maintainer: Sean Davis URL: http://watson.nci.nih.gov/~sdavis MD5sum: b68dd8abdfb4b1463f35f4b95218e730 source.ver: src/contrib/ACME_2.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ACME_2.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ACME_2.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ACME_2.12.0.tgz vignettes: vignettes/ACME/inst/doc/ACME.pdf vignetteTitles: ACME hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ADaCGH2 Version: 1.6.0 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 , Oscar M. Rueda . Wavelet-based aCGH smoothing code from Li Hsu and Douglas Grove . Imagemap code from Barry Rowlingson . HaarSeg code from Erez Ben-Yaacov; downloaded from Maintainer: Ramon Diaz-Uriarte URL: http://launchpad.net/adacgh, http://wavicgh.bioinfo.cnio.es MD5sum: 4847d314ed4a97d7637c32ff64ff9ce6 source.ver: src/contrib/ADaCGH2_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ADaCGH2_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ADaCGH2_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ADaCGH2_1.6.0.tgz vignettes: vignettes/ADaCGH2/inst/doc/ADaCGH2.pdf vignetteTitles: ADaCGH2 Overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: adSplit Version: 1.26.0 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 URL: http://compdiag.molgen.mpg.de/software/index.shtml MD5sum: 2458d9c63172aee3d3e6ebd307c31f36 source.ver: src/contrib/adSplit_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/adSplit_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/adSplit_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/adSplit_1.26.0.tgz 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 Package: affxparser Version: 1.28.1 Depends: R (>= 2.6.0) Suggests: R.utils (>= 1.9.11), 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 MD5sum: dac9d22f2013767cbd7b833bbf1dc13f source.ver: src/contrib/affxparser_1.28.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/affxparser_1.28.1.zip win64.binary.ver: bin/windows64/contrib/2.15/affxparser_1.28.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affxparser_1.28.1.tgz 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: 1.34.0 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 , Laurent Gautier , Benjamin Milo Bolstad , and Crispin Miller with contributions from Magnus Astrand , Leslie M. Cope , Robert Gentleman, Jeff Gentry, Conrad Halling , Wolfgang Huber, James MacDonald , Benjamin I. P. Rubinstein, Christopher Workman , John Zhang Maintainer: Rafael A. Irizarry MD5sum: ecd9e2ad7fcf00305e5d366a30bce021 source.ver: src/contrib/affy_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affy_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affy_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affy_1.34.0.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 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, Cormotif, farms, ffpe, frma, gcrma, GEOsubmission, Harshlight, HTqPCR, lumi, makecdfenv, plier, plw, puma, pvac, simpleaffy, tilingArray, TurboNorm, virtualArray, vsn suggestsMe: AnnotationDbi, beadarray, beadarraySNP, BiocCaseStudies, Biostrings, BufferedMatrixMethods, categoryCompare, ExpressionView, factDesign, ffpe, GeneRegionScan, limma, made4, oneChannelGUI, PREDA, siggenes, TurboNorm Package: affycomp Version: 1.32.0 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 and Zhijin Wu with contributions from Simon Cawley Maintainer: Rafael A. Irizarry MD5sum: fd258af4e08a693ac7f18f3c2f9d3354 source.ver: src/contrib/affycomp_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affycomp_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affycomp_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affycomp_1.32.0.tgz vignettes: vignettes/affycomp/inst/doc/affycomp.pdf vignetteTitles: affycomp primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AffyCompatible Version: 1.16.0 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 MD5sum: c26b0a4dcd2c7799b551c024e4053146 source.ver: src/contrib/AffyCompatible_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/AffyCompatible_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/AffyCompatible_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AffyCompatible_1.16.0.tgz 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 importsMe: IdMappingRetrieval Package: affyContam Version: 1.14.0 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 MD5sum: 4629c42b60801e4bfb6e74387cf5e7e5 source.ver: src/contrib/affyContam_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affyContam_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affyContam_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affyContam_1.14.0.tgz vignettes: vignettes/affyContam/inst/doc/affyContam.pdf vignetteTitles: affy contamination tools hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: affycoretools Version: 1.28.0 Depends: affy, Biobase, GO.db, KEGG.db Imports: biomaRt, limma, GOstats, annotate, annaffy, genefilter, gcrma, splines, xtable, AnnotationDbi, lattice 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 MD5sum: 443cce8cef44927dc54a0a9975681c66 source.ver: src/contrib/affycoretools_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affycoretools_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affycoretools_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affycoretools_1.28.0.tgz 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 suggestsMe: Agi4x44PreProcess Package: AffyExpress Version: 1.22.0 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 , Xuejun Arthur Li Maintainer: Xuejun Arthur Li MD5sum: e076fbfb7ab7989ef306f12424ec3e89 source.ver: src/contrib/AffyExpress_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/AffyExpress_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/AffyExpress_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AffyExpress_1.22.0.tgz vignettes: vignettes/AffyExpress/inst/doc/AffyExpress.pdf vignetteTitles: 1. Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: affyILM Version: 1.8.0 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 MD5sum: dbb54c5a3b5e23e766ce63ac1bead4bb source.ver: src/contrib/affyILM_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affyILM_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affyILM_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affyILM_1.8.0.tgz vignettes: vignettes/affyILM/inst/doc/affyILM.pdf vignetteTitles: affyILM1.3.0 hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: affyio Version: 1.24.0 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 Maintainer: Benjamin Milo Bolstad MD5sum: 7b2f52916f70871ed2929b2a6f8e53ee source.ver: src/contrib/affyio_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affyio_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affyio_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affyio_1.24.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: affylmGUI, sscore importsMe: affy, crlmm, gcrma, oligo, oligoClasses suggestsMe: BufferedMatrixMethods Package: affylmGUI Version: 1.30.0 Depends: limma, tcltk, affy, Biobase, 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 URL: http://bioinf.wehi.edu.au/affylmGUI/ MD5sum: 8baefdfa8d902109d54b997d118fe68c source.ver: src/contrib/affylmGUI_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affylmGUI_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affylmGUI_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affylmGUI_1.30.0.tgz 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 dependsOnMe: oneChannelGUI Package: affyPara Version: 1.16.0 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 , Esmeralda Vicedo , Ulrich Mansmann Maintainer: Markus Schmidberger URL: http://www.ibe.med.uni-muenchen.de MD5sum: bd8d2cb31c2e7be4b0ebb1c4718962dd source.ver: src/contrib/affyPara_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affyPara_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affyPara_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affyPara_1.16.0.tgz 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 Package: affypdnn Version: 1.30.0 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 MD5sum: 1a2f47e07a63be4881d5a002d4548b4f source.ver: src/contrib/affypdnn_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affypdnn_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affypdnn_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affypdnn_1.30.0.tgz vignettes: vignettes/affypdnn/inst/doc/affypdnn.pdf vignetteTitles: affypdnn hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: affyPLM Version: 1.32.0 Depends: R (>= 2.6.0), affy (>= 1.11.0), Biobase, gcrma, stats, preprocessCore (>= 1.5.1) Imports: zlibbioc, 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 Maintainer: Ben Bolstad URL: http://bmbolstad.com MD5sum: 8324c4b90966ab75266292ad7af1893a source.ver: src/contrib/affyPLM_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affyPLM_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affyPLM_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affyPLM_1.32.0.tgz 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 dependsOnMe: RefPlus importsMe: affyQCReport, arrayQualityMetrics, virtualArray suggestsMe: AffyExpress, affylmGUI, arrayMvout, ArrayTools, BiocCaseStudies, BiocGenerics, frmaTools, ggbio, metahdep, oneChannelGUI Package: affyQCReport Version: 1.34.0 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 , Conrad Halling , Robert Gentleman Maintainer: Craig Parman MD5sum: b550ce42414b742a48872616933523d0 source.ver: src/contrib/affyQCReport_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/affyQCReport_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/affyQCReport_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/affyQCReport_1.34.0.tgz vignettes: vignettes/affyQCReport/inst/doc/affyQCReport.pdf vignetteTitles: affyQCReport: Methods for Generating Affymetrix QC Reports hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: BiocCaseStudies Package: AffyRNADegradation Version: 1.0.0 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 MD5sum: 6c5e3743a65492a92e2419cb74f5f9d1 source.ver: src/contrib/AffyRNADegradation_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/AffyRNADegradation_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/AffyRNADegradation_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AffyRNADegradation_1.0.0.tgz vignettes: vignettes/AffyRNADegradation/inst/doc/vignette.pdf vignetteTitles: AffyRNADegradation Example hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: AffyTiling Version: 1.14.0 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 Maintainer: Charles G. Danko MD5sum: 98d4b5a843ed17b89d3b11e79c8cd54b source.ver: src/contrib/AffyTiling_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/AffyTiling_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/AffyTiling_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AffyTiling_1.14.0.tgz vignettes: vignettes/AffyTiling/inst/doc/AffyTiling.pdf vignetteTitles: AffyTiling hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AGDEX Version: 1.4.0 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 ; Cuilan Lani Gao Maintainer: Cuilan lani Gao MD5sum: 6e9b2ec8f791d08099324a7b86760f97 source.ver: src/contrib/AGDEX_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/AGDEX_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/AGDEX_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AGDEX_1.4.0.tgz vignettes: vignettes/AGDEX/inst/doc/AGDEX.pdf vignetteTitles: AGDEX.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Agi4x44PreProcess Version: 1.16.0 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 Maintainer: Pedro Lopez-Romero MD5sum: 4a0d023dbe565a7b791de33e526cb63d source.ver: src/contrib/Agi4x44PreProcess_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Agi4x44PreProcess_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Agi4x44PreProcess_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Agi4x44PreProcess_1.16.0.tgz vignettes: vignettes/Agi4x44PreProcess/inst/doc/Agi4x44PreProcess.pdf vignetteTitles: Agi4x44PreProcess hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: AgiMicroRna Version: 2.6.0 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 Maintainer: Pedro Lopez-Romero MD5sum: ac0bde8c4b405f18f1c148626e431716 source.ver: src/contrib/AgiMicroRna_2.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/AgiMicroRna_2.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/AgiMicroRna_2.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AgiMicroRna_2.6.0.tgz vignettes: vignettes/AgiMicroRna/inst/doc/AgiMicroRna.pdf vignetteTitles: AgiMicroRna hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: altcdfenvs Version: 2.18.0 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 Maintainer: Laurent Gautier MD5sum: f42732f36e8f4c3cae0f67063a0a6ef7 source.ver: src/contrib/altcdfenvs_2.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/altcdfenvs_2.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/altcdfenvs_2.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/altcdfenvs_2.18.0.tgz 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 importsMe: Harshlight Package: annaffy Version: 1.28.0 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 Maintainer: Colin A. Smith MD5sum: 100fb365f9ae7f513b1caceedbc3e05e source.ver: src/contrib/annaffy_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/annaffy_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/annaffy_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/annaffy_1.28.0.tgz vignettes: vignettes/annaffy/inst/doc/annaffy.pdf vignetteTitles: annaffy Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: a4Base, a4Reporting, PGSEA, webbioc importsMe: affycoretools suggestsMe: AffyExpress, ArrayTools, BiocCaseStudies, maDB Package: annotate Version: 1.34.1 Depends: R (>= 2.10), AnnotationDbi (>= 0.1.15) Imports: Biobase, AnnotationDbi, DBI, xtable, graphics, utils, stats, methods, XML (>= 0.92-2) Suggests: Biobase, hgu95av2.db, genefilter, Biostrings (>= 2.4.4), rae230a.db, rae230aprobe, tkWidgets, XML (>= 0.92-2), GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz 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 MD5sum: 6088300ddcaf5fc4ad779779612f9d83 source.ver: src/contrib/annotate_1.34.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/annotate_1.34.1.zip win64.binary.ver: bin/windows64/contrib/2.15/annotate_1.34.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/annotate_1.34.1.tgz 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 dependsOnMe: Agi4x44PreProcess, ChromHeatMap, GeneAnswers, geneplotter, GSEABase, idiogram, macat, MLInterfaces, PCpheno, phenoTest, PREDA, RpsiXML, safe, ScISI importsMe: affycoretools, Category, categoryCompare, ChromHeatMap, codelink, GeneAnswers, genefilter, GeneGroupAnalysis, geneplotter, GlobalAncova, globaltest, GOstats, GSEABase, lumi, methylumi, phenoTest, qpgraph, safe, ScISI, splicegear, tigre suggestsMe: BiocCaseStudies, biomaRt, geneplotter, GlobalAncova, globaltest, GOstats, GSEAlm, maigesPack, MLP, oneChannelGUI, puma, siggenes, tigre Package: AnnotationDbi Version: 1.18.4 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, human.db0, hgu95av2cdf, org.Sc.sgd.db, org.At.tair.db, affy, KEGG.db, XML, RCurl, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db 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 MD5sum: 7fb590e61f6dfde6950235eeaa923a3d source.ver: src/contrib/AnnotationDbi_1.18.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/AnnotationDbi_1.18.4.zip win64.binary.ver: bin/windows64/contrib/2.15/AnnotationDbi_1.18.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AnnotationDbi_1.18.4.tgz vignettes: vignettes/AnnotationDbi/inst/doc/AnnotationDbi.pdf, vignettes/AnnotationDbi/inst/doc/databaseTypes.pdf, vignettes/AnnotationDbi/inst/doc/IntroToAnnotationPackages.pdf, vignettes/AnnotationDbi/inst/doc/makeProbePackage.pdf, vignettes/AnnotationDbi/inst/doc/NewSchema.pdf, vignettes/AnnotationDbi/inst/doc/SQLForge.pdf vignetteTitles: AnnotationDbi: How to use bimaps from the ".db" annotation packages, databaseTypes.pdf, Introduction To Bioconductor Annotation Packages, 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 dependsOnMe: a4Base, a4Preproc, annotate, AnnotationFuncs, attract, Category, categoryCompare, ChromHeatMap, eisa, GenomicFeatures, GOFunction, goProfiles, MLP, PAnnBuilder, pathRender, PGSEA, Resourcerer, RpsiXML, topGO importsMe: adSplit, affycoretools, annaffy, annotate, attract, beadarray, BioNet, CancerMutationAnalysis, Category, categoryCompare, ChIPpeakAnno, ChromHeatMap, clusterProfiler, CoCiteStats, domainsignatures, DOSE, ExpressionView, genefilter, GeneGroupAnalysis, geneplotter, GGBase, GGtools, GlobalAncova, globaltest, GOFunction, GOSemSim, goseq, GOstats, goTools, graphite, GSEABase, Gviz, HTSanalyzeR, lumi, methylumi, PAnnBuilder, PatientGeneSets, pcaGoPromoter, PCpheno, phenoTest, qpgraph, ReactomePA, REDseq, safe, ScISI, SLGI, tigre, topGO, VariantAnnotation, virtualArray suggestsMe: BiocCaseStudies, BiocGenerics, ExpressionView, GeneAnswers, GeneRegionScan, MmPalateMiRNA, oneChannelGUI, sigPathway Package: AnnotationFuncs Version: 1.6.0 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 Maintainer: Stefan McKinnon Edwards URL: http://www.iysik.com/index.php?page=annotation-functions MD5sum: 20004686577641f749ad55b8901a619a source.ver: src/contrib/AnnotationFuncs_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/AnnotationFuncs_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/AnnotationFuncs_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/AnnotationFuncs_1.6.0.tgz vignettes: vignettes/AnnotationFuncs/inst/doc/AnnotationFuncsUserguide.pdf vignetteTitles: Annotation mapping functions hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: annotationTools Version: 1.30.0 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 Maintainer: Alexandre Kuhn MD5sum: 2e7b95c0620314412ee9d5ae9024c049 source.ver: src/contrib/annotationTools_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/annotationTools_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/annotationTools_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/annotationTools_1.30.0.tgz vignettes: vignettes/annotationTools/inst/doc/annotationTools.pdf vignetteTitles: annotationTools Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: anota Version: 1.4.0 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 , Nahum Sonenberg , Robert Nadon Maintainer: Ola Larsson MD5sum: b3b38761196738c9cf1f4077cc646530 source.ver: src/contrib/anota_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/anota_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/anota_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/anota_1.4.0.tgz vignettes: vignettes/anota/inst/doc/anota.pdf vignetteTitles: ANalysis Of Translational Activity (anota) hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: apComplex Version: 2.22.0 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: Visualization, MassSpectrometry, GraphsAndNetworks Author: Denise Scholtens Maintainer: Denise Scholtens MD5sum: 5987c12f43e0f751ae500095eae4d3c6 source.ver: src/contrib/apComplex_2.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/apComplex_2.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/apComplex_2.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/apComplex_2.22.0.tgz vignettes: vignettes/apComplex/inst/doc/apComplex.pdf vignetteTitles: apComplex hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ScISI suggestsMe: BiocCaseStudies Package: aroma.light Version: 1.24.0 Depends: R.methodsS3 (>= 1.2.1) Suggests: R.oo (>= 1.8.2), R.utils (>= 1.8.2), princurve (>= 1.1-10) License: LGPL (>= 2.1) 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 Maintainer: Henrik Bengtsson URL: http://www.aroma-project.org/ MD5sum: 6a9a497e3b17fcc84fbbd20b385d90c3 source.ver: src/contrib/aroma.light_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/aroma.light_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/aroma.light_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/aroma.light_1.24.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: EDASeq suggestsMe: pcaMethods Package: ArrayExpress Version: 1.16.0 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 Maintainer: Audrey Kauffmann MD5sum: fcd02052ba84aab3eba8ba514a626bda source.ver: src/contrib/ArrayExpress_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ArrayExpress_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ArrayExpress_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ArrayExpress_1.16.0.tgz 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 Package: ArrayExpressHTS Version: 1.6.0 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 , Andrew Tikhonov MD5sum: 0d22ba3999ae8cf6b150e35744be2529 source.ver: src/contrib/ArrayExpressHTS_1.6.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ArrayExpressHTS_1.6.0.tgz vignettes: vignettes/ArrayExpressHTS/inst/doc/ArrayExpressHTS.pdf vignetteTitles: ArrayExpressHTS: RNA-Seq Pipeline for transcription profiling experiments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: arrayMvout Version: 1.14.0 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 MD5sum: 62fed33730cfde4bb8d08bcaff72477b source.ver: src/contrib/arrayMvout_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/arrayMvout_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/arrayMvout_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/arrayMvout_1.14.0.tgz 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 Package: arrayQuality Version: 1.34.0 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 Maintainer: Agnes Paquet URL: http://arrays.ucsf.edu/ MD5sum: eb7ab08e1b040eb2b1a3aca30946785f source.ver: src/contrib/arrayQuality_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/arrayQuality_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/arrayQuality_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/arrayQuality_1.34.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: arrayQualityMetrics Version: 3.12.0 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 MD5sum: 24af12132acf7be3bc478daa7be5067b source.ver: src/contrib/arrayQualityMetrics_3.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/arrayQualityMetrics_3.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/arrayQualityMetrics_3.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/arrayQualityMetrics_3.12.0.tgz 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: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ArrayTools Version: 1.16.0 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 MD5sum: 6c369979f21000e869c723ae3b9f01a5 source.ver: src/contrib/ArrayTools_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ArrayTools_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ArrayTools_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ArrayTools_1.16.0.tgz vignettes: vignettes/ArrayTools/inst/doc/ArrayTools.pdf vignetteTitles: 1. Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ASEB Version: 1.0.0 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 and Tingting Li . Maintainer: Likun Wang MD5sum: 6ea5aeee5b6b04663fb1bc305f2a818e source.ver: src/contrib/ASEB_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ASEB_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ASEB_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ASEB_1.0.0.tgz vignettes: vignettes/ASEB/inst/doc/ASEB.pdf vignetteTitles: ASEB hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: attract Version: 1.8.0 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 MD5sum: 21c1782d40b8b5384c2184a14e4da7d2 source.ver: src/contrib/attract_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/attract_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/attract_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/attract_1.8.0.tgz vignettes: vignettes/attract/inst/doc/attract.pdf vignetteTitles: Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BAC Version: 1.16.0 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 MD5sum: 9e4688f26eeb8a25335c184c4fb6ebae source.ver: src/contrib/BAC_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BAC_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BAC_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BAC_1.16.0.tgz vignettes: vignettes/BAC/inst/doc/BAC.pdf vignetteTitles: 1. Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BayesPeak Version: 1.8.0 Depends: R (>= 2.10), IRanges Imports: IRanges, graphics Enhances: multicore, snow 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 MD5sum: ef54e21fbcaa5351c9dd780130d0aa61 source.ver: src/contrib/BayesPeak_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BayesPeak_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BayesPeak_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BayesPeak_1.8.0.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 Package: baySeq Version: 1.10.0 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 MD5sum: 74e4a1f19ea7eaebd541c950b366425c source.ver: src/contrib/baySeq_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/baySeq_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/baySeq_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/baySeq_1.10.0.tgz vignettes: vignettes/baySeq/inst/doc/baySeq.pdf vignetteTitles: baySeq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: segmentSeq importsMe: segmentSeq suggestsMe: oneChannelGUI Package: BCRANK Version: 1.18.0 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: SequenceMatching Author: Adam Ameur Maintainer: Adam Ameur MD5sum: bbc886f90da8500db29b6b3514db0aa0 source.ver: src/contrib/BCRANK_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BCRANK_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BCRANK_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BCRANK_1.18.0.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 Package: beadarray Version: 2.6.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, ggplot2 Imports: BeadDataPackR, limma, AnnotationDbi, stats4, BiocGenerics, reshape2 Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db 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 MD5sum: 421fcac55ee0a327cb26b2fcabb3c58f source.ver: src/contrib/beadarray_2.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/beadarray_2.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/beadarray_2.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/beadarray_2.6.0.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 importsMe: arrayQualityMetrics suggestsMe: beadarraySNP, lumi Package: beadarraySNP Version: 1.22.0 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 MD5sum: e74b3f16f576e93519afcc7fadf410bd source.ver: src/contrib/beadarraySNP_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/beadarraySNP_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/beadarraySNP_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/beadarraySNP_1.22.0.tgz vignettes: vignettes/beadarraySNP/inst/doc/beadarraySNP.pdf vignetteTitles: beadarraySNP.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BeadDataPackR Version: 1.8.0 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 MD5sum: db1eb3ce368249a98078c24240c0b749 source.ver: src/contrib/BeadDataPackR_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BeadDataPackR_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BeadDataPackR_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BeadDataPackR_1.8.0.tgz vignettes: vignettes/BeadDataPackR/inst/doc/BeadDataPackR.pdf vignetteTitles: BeadDataPackR.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: beadarray Package: betr Version: 1.12.0 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 MD5sum: f508a6876407a0b2ad5d6bc9096ed1a3 source.ver: src/contrib/betr_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/betr_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/betr_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/betr_1.12.0.tgz vignettes: vignettes/betr/inst/doc/betr.pdf vignetteTitles: BETR Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bgafun Version: 1.18.0 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 MD5sum: 5e3585d7e65d72a596f7787c03df77a5 source.ver: src/contrib/bgafun_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/bgafun_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/bgafun_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bgafun_1.18.0.tgz vignettes: vignettes/bgafun/inst/doc/bgafun.pdf vignetteTitles: bgafun.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BGmix Version: 1.16.0 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 MD5sum: 3666ca6976798b314038b38f9450f228 source.ver: src/contrib/BGmix_1.16.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BGmix_1.16.0.tgz vignettes: vignettes/BGmix/inst/doc/BGmix.pdf vignetteTitles: BGmix Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bgx Version: 1.20.0 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 MD5sum: f37e0ad4d2bba8fb189e1f3f59936020 source.ver: src/contrib/bgx_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/bgx_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/bgx_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bgx_1.20.0.tgz vignettes: vignettes/bgx/inst/doc/bgx.pdf vignetteTitles: HowTo BGX hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BHC Version: 1.8.0 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 MD5sum: e1ab5eab969fe8528f732aaf21cc917e source.ver: src/contrib/BHC_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BHC_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BHC_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BHC_1.8.0.tgz vignettes: vignettes/BHC/inst/doc/bhc.pdf vignetteTitles: Bayesian Hierarchical Clustering hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BicARE Version: 1.14.0 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 URL: http://bioinfo.curie.fr MD5sum: 80c5b3e3541daaa45d159c43aee6a9db source.ver: src/contrib/BicARE_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BicARE_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BicARE_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BicARE_1.14.0.tgz vignettes: vignettes/BicARE/inst/doc/BicARE.pdf vignetteTitles: BicARE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Biobase Version: 2.16.0 Depends: R (>= 2.10), utils, BiocGenerics (>= 0.1.0) 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 MD5sum: 4cc0954465763fe16348f6b501626f46 source.ver: src/contrib/Biobase_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Biobase_2.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Biobase_2.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Biobase_2.16.0.tgz 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 dependsOnMe: a4Base, a4Core, ACME, affy, affycomp, affyContam, affycoretools, affylmGUI, affyPLM, affyQCReport, AGDEX, Agi4x44PreProcess, altcdfenvs, annaffy, AnnotationDbi, ArrayExpress, arrayMvout, ArrayTools, beadarray, beadarraySNP, bgx, BicARE, BiocCaseStudies, BioMVCClass, BioNet, birta, BrainStars, Category, categoryCompare, cellHTS, cellHTS2, CGHbase, CGHcall, CGHregions, charm, clippda, clusterStab, CMA, cn.farms, cn.mops, codelink, convert, copa, ddCt, DESeq, DEXSeq, DFP, 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, HELP, hopach, HTqPCR, htSeqTools, HybridMTest, idiogram, inSilicoDb, inSilicoMerging, isobar, iterativeBMA, LMGene, lumi, macat, maDB, maSigPro, MergeMaid, methylumi, Mfuzz, MiChip, minfi, MLInterfaces, MmPalateMiRNA, MSnbase, Mulcom, multtest, NormqPCR, nucleR, oneChannelGUI, OrderedList, OTUbase, OutlierD, PAnnBuilder, panp, pcaMethods, pcot2, pdInfoBuilder, pdmclass, PGSEA, phenoTest, plgem, PLPE, prada, PREDA, PROMISE, puma, qpcrNorm, R453Plus1Toolbox, RbcBook1, rbsurv, ReadqPCR, reb, RefPlus, Resourcerer, rHVDM, Ringo, Rmagpie, rMAT, RNAinteract, rnaSeqMap, RpsiXML, rqubic, RTopper, Rtreemix, safe, sigaR, siggenes, simpleaffy, SpeCond, spkTools, TDARACNE, tigre, tilingArray, topGO, tspair, VegaMC, vsn, webbioc, XDE importsMe: ABarray, aCGH, adSplit, affy, affyILM, affyQCReport, AgiMicroRna, annotate, AnnotationDbi, annotationTools, ArrayExpressHTS, arrayQualityMetrics, ArrayTools, attract, betr, biocViews, BioSeqClass, BrainStars, Category, categoryCompare, CGHnormaliter, charm, ChromHeatMap, ConsensusClusterPlus, crlmm, cycle, EBarrays, ecolitk, farms, ffpe, flowCore, flowFlowJo, flowFP, flowMeans, flowStats, flowType, flowUtils, flowViz, flowWorkspace, frma, frmaTools, gcrma, genefilter, GeneMeta, geneplotter, geneRecommender, GeneRegionScan, GeneSelectMMD, genomeIntervals, GenomicFeatures, genoset, GEOsubmission, GGBase, ggbio, GGtools, girafe, globaltest, GOFunction, GOstats, GSEABase, GSRI, GSVA, Gviz, Harshlight, HEM, HiTC, hopach, HTqPCR, IdMappingAnalysis, iFlow, imageHTS, lapmix, LiquidAssociation, lumi, maanova, makecdfenv, maSigPro, mBPCR, MCRestimate, metaArray, methylumi, MiChip, MinimumDistance, MiPP, MmPalateMiRNA, multiscan, mzR, nucleR, oligo, oligoClasses, OrderedList, PAnnBuilder, panp, pcaGoPromoter, PCpheno, plateCore, plier, ppiStats, prada, PROMISE, puma, pvac, qpgraph, R453Plus1Toolbox, randPack, ReadqPCR, Rmagpie, rMAT, rqubic, Rtreemix, safe, SAGx, ShortRead, simpleaffy, SLGI, SNPchip, spade, spkTools, splicegear, TEQC, tigre, timecourse, topGO, TSSi, twilight, VanillaICE, VariantAnnotation, virtualArray, webbioc, XDE, xmapcore suggestsMe: annotate, betr, BiocCaseStudies, BiocGenerics, biocViews, BSgenome, Category, DART, farms, genefilter, genefu, geneplotter, GlobalAncova, globaltest, Heatplus, les, nem, pkgDepTools, ROC, survcomp, tkWidgets, TypeInfo, vbmp, widgetTools Package: BiocCaseStudies Version: 1.18.0 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 (>= 2.5.0), class (>= 7.2-38), cluster (>= 1.11.9), convert (>= 1.15.0), gcrma (>= 2.11.1), genefilter (>= 1.17.6), geneplotter (>= 1.17.2), GO.db (>= 2.0.2), GOstats (>= 2.5.0), graph (>= 1.17.4), GSEABase (>= 1.1.13), hgu133a.db (>= 2.0.2), 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 MD5sum: fc85fb0518d743925eafdcf5c7988d81 source.ver: src/contrib/BiocCaseStudies_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BiocCaseStudies_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BiocCaseStudies_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BiocCaseStudies_1.18.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BiocGenerics Version: 0.2.0 Depends: methods, graphics, stats Imports: methods, graphics, stats Suggests: Biobase, IRanges, GenomicRanges, AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, 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 MD5sum: e99858faa90d26099c933712ed80dd0c source.ver: src/contrib/BiocGenerics_0.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BiocGenerics_0.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BiocGenerics_0.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BiocGenerics_0.2.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: affy, altcdfenvs, AnnotationDbi, Biobase, Biostrings, BSgenome, ChIPpeakAnno, chipseq, ChIPseqR, cn.mops, easyRNASeq, EDASeq, flowQ, flowWorkspace, genomeIntervals, GenomicFeatures, GenomicRanges, Genominator, genoset, GSEABase, htSeqTools, IRanges, KEGGSOAP, MEDIPS, minfi, MotIV, MSnbase, nucleR, PICS, R453Plus1Toolbox, REDseq, Repitools, rMAT, ShortRead, simpleaffy, TEQC, tigre importsMe: affy, AnnotationDbi, beadarray, Biobase, biocGraph, Biostrings, biovizBase, cghMCR, ChIPpeakAnno, chipseq, cn.mops, crlmm, EDASeq, fastseg, ffpe, flowCore, flowFP, flowMerge, flowQ, flowStats, frma, GenomicFeatures, GenomicRanges, genoset, GGBase, ggbio, GGtools, graph, GSEABase, Gviz, IRanges, LVSmiRNA, MEDIPS, methylumi, MinimumDistance, MotIV, nucleR, oligo, oligoClasses, pcaMethods, PICS, PING, prada, R453Plus1Toolbox, RCytoscape, REDseq, Repitools, Ringo, rMAT, Rsamtools, rtracklayer, ShortRead, simpleaffy, SLGI, tigre, VariantAnnotation, XDE suggestsMe: BiocInstaller, inSilicoMerging Package: biocGraph Version: 1.18.0 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: GraphsAndNetworks Author: Li Long , Robert Gentleman , Seth Falcon Florian Hahne Maintainer: Florian Hahne MD5sum: bb42fa1ece1cf840a2fe00f37f2b2eed source.ver: src/contrib/biocGraph_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/biocGraph_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/biocGraph_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/biocGraph_1.18.0.tgz 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 suggestsMe: BiocCaseStudies Package: BiocInstaller Version: 1.4.9 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 MD5sum: d795817cad2a5be862b6d6d600ddadd7 source.ver: src/contrib/BiocInstaller_1.4.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/BiocInstaller_1.4.9.zip win64.binary.ver: bin/windows64/contrib/2.15/BiocInstaller_1.4.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BiocInstaller_1.4.9.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: gcrma importsMe: affy, oligoClasses suggestsMe: pkgDepTools Package: biocViews Version: 1.24.0 Depends: R (>= 2.4.0) Imports: Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools, utils, XML, RCurl 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 , BJ Harshfield , S Falcon Maintainer: Bioconductor Package Maintainer URL: http://www.bioconductor.org/packages/release/BiocViews.html MD5sum: 4391b5a081f551740bdb0a9b5c19f29d source.ver: src/contrib/biocViews_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/biocViews_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/biocViews_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/biocViews_1.24.0.tgz 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 Package: bioDist Version: 1.28.0 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 MD5sum: 2fa9f749185da4d31fbeb8d986f936e7 source.ver: src/contrib/bioDist_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/bioDist_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/bioDist_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bioDist_1.28.0.tgz vignettes: vignettes/bioDist/inst/doc/bioDist.pdf vignetteTitles: bioDist Introduction hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: flowQ suggestsMe: BiocCaseStudies Package: biomaRt Version: 2.12.0 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 , Wolfgang Huber Maintainer: Steffen Durinck MD5sum: 4259e46fc01fd0576656996ca93ef87b source.ver: src/contrib/biomaRt_2.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/biomaRt_2.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/biomaRt_2.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/biomaRt_2.12.0.tgz vignettes: vignettes/biomaRt/inst/doc/biomaRt.pdf vignetteTitles: The biomaRt users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ChIPpeakAnno, domainsignatures, easyRNASeq, gene2pathway, GenomeGraphs, VegaMC importsMe: affycoretools, ArrayExpressHTS, ChIPpeakAnno, DEXSeq, GenomicFeatures, Gviz, HTSanalyzeR, IdMappingRetrieval, phenoTest, R453Plus1Toolbox, RNAither suggestsMe: BiocCaseStudies, GeneAnswers, GenomicFeatures, Genominator, isobar, maDB, oneChannelGUI, ShortRead, SIM Package: BioMVCClass Version: 1.24.0 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 MD5sum: 0fff6e3757f2d19ede8e7268bd2fe34e source.ver: src/contrib/BioMVCClass_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BioMVCClass_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BioMVCClass_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BioMVCClass_1.24.0.tgz vignettes: vignettes/BioMVCClass/inst/doc/BioMVCClass.pdf vignetteTitles: BioMVCClass hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BioNet Version: 1.14.3 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, Visualization, Bioinformatics, GeneExpression, DifferentialExpression Author: Marcus Dittrich and Daniela Beisser Maintainer: Marcus Dittrich URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ MD5sum: 3f1391c14d69d1ad5cfe638b0c73bb6d source.ver: src/contrib/BioNet_1.14.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/BioNet_1.14.3.zip win64.binary.ver: bin/windows64/contrib/2.15/BioNet_1.14.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BioNet_1.14.3.tgz 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 dependsOnMe: HTSanalyzeR importsMe: HTSanalyzeR Package: BioSeqClass Version: 1.14.0 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 MD5sum: 3c92d1409bd6631def34fa4f683a1d7f source.ver: src/contrib/BioSeqClass_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BioSeqClass_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BioSeqClass_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BioSeqClass_1.14.0.tgz 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 Package: Biostrings Version: 2.24.1 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.1.2), IRanges (>= 1.13.6) 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), 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 MD5sum: 29fe47619dfb0e8f1ae99feb17e2bd6a source.ver: src/contrib/Biostrings_2.24.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/Biostrings_2.24.1.zip win64.binary.ver: bin/windows64/contrib/2.15/Biostrings_2.24.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Biostrings_2.24.1.tgz 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 dependsOnMe: altcdfenvs, BRAIN, BSgenome, ChIPpeakAnno, ChIPsim, DECIPHER, deepSNV, easyRNASeq, GeneRegionScan, oneChannelGUI, qrqc, R453Plus1Toolbox, REDseq, rGADEM, Rsamtools, seqbias, ShortRead importsMe: AffyCompatible, ArrayExpressHTS, BCRANK, BioSeqClass, biovizBase, charm, ChIPpeakAnno, ChIPseqR, ChIPsim, DECIPHER, gcrma, GeneRegionScan, GenomicFeatures, genoset, girafe, gwascat, HiTC, MEDIPS, MEDME, methVisual, microRNA, motifRG, oligo, oligoClasses, OTUbase, pdInfoBuilder, qrqc, R453Plus1Toolbox, REDseq, rGADEM, Rolexa, Rsamtools, rtracklayer, ShortRead, VariantAnnotation suggestsMe: annotate, CSAR, exomeCopy, GenomicFeatures, microRNA, minfi, pcaGoPromoter, procoil Package: biovizBase Version: 1.4.2 Depends: R (>= 2.10), methods Imports: methods, 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 MD5sum: 9cac35519cf7c43a7e275da331210774 source.ver: src/contrib/biovizBase_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/biovizBase_1.4.2.zip win64.binary.ver: bin/windows64/contrib/2.15/biovizBase_1.4.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/biovizBase_1.4.2.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 dependsOnMe: qrqc importsMe: qrqc Package: birta Version: 1.0.0 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 MD5sum: cff3c0b0b2a6d41dfabb2e4b679cf554 source.ver: src/contrib/birta_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/birta_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/birta_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/birta_1.0.0.tgz vignettes: vignettes/birta/inst/doc/birta.pdf vignetteTitles: Bayesian Inference of Regulation of Transcriptional Activity hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: BitSeq Version: 1.0.1 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 MD5sum: 56e47f660ebb773f167028b02aefd598 source.ver: src/contrib/BitSeq_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/BitSeq_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.15/BitSeq_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BitSeq_1.0.1.tgz vignettes: vignettes/BitSeq/inst/doc/BitSeq.pdf vignetteTitles: BitSeq User Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: BRAIN Version: 1.0.0 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, Mass spectrometry, Proteomics Author: Piotr Dittwald, with contributions of Dirk Valkenborg and Jurgen Claesen Maintainer: Piotr Dittwald MD5sum: 7ae91fae0c11c36bdb24ee5fae160191 source.ver: src/contrib/BRAIN_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BRAIN_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BRAIN_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BRAIN_1.0.0.tgz vignettes: vignettes/BRAIN/inst/doc/BRAIN-vignette.pdf vignetteTitles: BRAIN Usage hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BrainStars Version: 1.0.0 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 Maintainer: Itoshi NIKAIDO MD5sum: 9a4c6aa173dbd26a11e0dd969b45e8f9 source.ver: src/contrib/BrainStars_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BrainStars_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BrainStars_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BrainStars_1.0.0.tgz vignettes: vignettes/BrainStars/inst/doc/BrainStars.pdf vignetteTitles: BrainStars hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: bridge Version: 1.20.0 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 MD5sum: 8c37ba13252c62a8546fe2df19831ee1 source.ver: src/contrib/bridge_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/bridge_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/bridge_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/bridge_1.20.0.tgz vignettes: vignettes/bridge/inst/doc/bridge.pdf vignetteTitles: bridge Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BSgenome Version: 1.24.0 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 MD5sum: 7e8c429e1462d57d0195407d354a63ac source.ver: src/contrib/BSgenome_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BSgenome_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BSgenome_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BSgenome_1.24.0.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 dependsOnMe: ChIPpeakAnno, chipseq, easyRNASeq, htSeqTools, MEDIPS, PICS, REDseq, rGADEM importsMe: charm, ChIPpeakAnno, chipseq, genoset, ggbio, girafe, MEDIPS, PICS, PING, R453Plus1Toolbox, Repitools, rtracklayer, VariantAnnotation suggestsMe: Biostrings, biovizBase, GeneRegionScan, GenomicFeatures, GenomicRanges, oneChannelGUI, Repitools Package: BufferedMatrix Version: 1.20.0 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 Maintainer: Benjamin Milo Bolstad MD5sum: 99f7ed2653c2a41836235b2776649c03 source.ver: src/contrib/BufferedMatrix_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BufferedMatrix_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BufferedMatrix_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BufferedMatrix_1.20.0.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 dependsOnMe: BufferedMatrixMethods Package: BufferedMatrixMethods Version: 1.20.0 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 Maintainer: B. M. Bolstad URL: http://www.bmbolstad.com MD5sum: 0ab3112274e53d8eef4283445bad453b source.ver: src/contrib/BufferedMatrixMethods_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BufferedMatrixMethods_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BufferedMatrixMethods_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BufferedMatrixMethods_1.20.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: BUS Version: 1.12.0 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 MD5sum: 40df9c7d16f7e5b9870278dd07efc58a source.ver: src/contrib/BUS_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/BUS_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/BUS_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/BUS_1.12.0.tgz vignettes: vignettes/BUS/inst/doc/bus.pdf vignetteTitles: bus.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: CALIB Version: 1.22.0 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 MD5sum: 7ecf55a0c73982e0d9b5ee062dab7871 source.ver: src/contrib/CALIB_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CALIB_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CALIB_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CALIB_1.22.0.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 Package: CAMERA Version: 1.12.0 Depends: R (>= 2.1.0), methods, xcms (>= 1.13.5) 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 URL: http://msbi.ipb-halle.de/msbi/CAMERA/ MD5sum: c7293483b0ee2d142dcb9ab70928dc4a source.ver: src/contrib/CAMERA_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CAMERA_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CAMERA_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CAMERA_1.12.0.tgz vignettes: vignettes/CAMERA/inst/doc/CAMERA.pdf vignetteTitles: Molecule Identification with CAMERA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: CancerMutationAnalysis Version: 1.0.0 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. Author: Giovanni Parmigiani, Simina M. Boca Maintainer: Simina M. Boca MD5sum: d244eb925089fb52af92a5dea548651d source.ver: src/contrib/CancerMutationAnalysis_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CancerMutationAnalysis_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CancerMutationAnalysis_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CancerMutationAnalysis_1.0.0.tgz vignettes: vignettes/CancerMutationAnalysis/inst/doc/CancerMutationAnalysis.pdf vignetteTitles: CancerMutationAnalysisTutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: Category Version: 2.22.0 Depends: AnnotationDbi (>= 0.1.15), Biobase (>= 1.15.29), methods Imports: graph, methods, Biobase (>= 1.15.29), AnnotationDbi (>= 0.1.15), RBGL, GSEABase, genefilter, annotate (>= 1.15.6), stats, utils Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, Matrix, KEGG.db, GO.db, SNPchip, geneplotter, limma, lattice, graph, Biobase, genefilter, methods License: Artistic-2.0 Title: Category Analysis Description: A collection of tools for performing category analysis. biocViews: Bioinformatics, Annotation, GO, Pathways Author: R. Gentleman with contributions from S. Falcon and D.Sarkar Maintainer: Bioconductor Package Maintainer MD5sum: 43334a488c4f0c9248605384c8d3853d source.ver: src/contrib/Category_2.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Category_2.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Category_2.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Category_2.22.0.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 dependsOnMe: categoryCompare, eisa, GOstats, PCpheno importsMe: categoryCompare, cellHTS2, GOstats, PCpheno, phenoTest, ppiStats suggestsMe: BiocCaseStudies, cellHTS, MmPalateMiRNA, qpgraph Package: categoryCompare Version: 1.0.2 Depends: R (>= 2.10), Biobase (>= 1.15.29), AnnotationDbi (>= 0.1.15), Category Imports: Biobase (>= 1.15.29), AnnotationDbi (>= 0.1.15), hwriter, GSEABase, Category (>= 2.21.2), 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 Maintainer: Robert M. Flight SystemRequirements: Cytoscape (>= 2.8.0) (if used for visualization of results, heavily suggested), CytoscapeRPC plugin (>= 1.8) MD5sum: bd2432d16333b8695e9b1ebf8cf9b348 source.ver: src/contrib/categoryCompare_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/categoryCompare_1.0.2.zip win64.binary.ver: bin/windows64/contrib/2.15/categoryCompare_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/categoryCompare_1.0.2.tgz 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: 1.0.0 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 , Andreas Neudecker Maintainer: Julien Gagneur MD5sum: e3a6cd757b52acb964adad0015b52709 source.ver: src/contrib/cellGrowth_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cellGrowth_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cellGrowth_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cellGrowth_1.0.0.tgz 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 Package: cellHTS Version: 1.26.0 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 , Ligia Bras , Michael Boutros Maintainer: Ligia Bras URL: http://www.dkfz.de/signaling, http://www.ebi.ac.uk/huber MD5sum: 825f2b816077c2ad5497777f9f9b255e source.ver: src/contrib/cellHTS_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cellHTS_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cellHTS_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cellHTS_1.26.0.tgz 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 suggestsMe: prada Package: cellHTS2 Version: 2.20.0 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 , Michael Boutros , Gregoire Pau , Florian Hahne Maintainer: Joseph Barry URL: http://www.dkfz.de/signaling, http://www.ebi.ac.uk/huber MD5sum: ba391dcfb7fec39fe594f02eb94e97dc source.ver: src/contrib/cellHTS2_2.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cellHTS2_2.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cellHTS2_2.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cellHTS2_2.20.0.tgz 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 dependsOnMe: coRNAi, HTSanalyzeR, imageHTS importsMe: HTSanalyzeR, RNAinteract Package: CellNOptR Version: 1.2.0 Depends: RBGL, graph Suggests: Rgraphviz License: GPL-2 Title: R version of CellNOpt, boolean features only 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: C.Terfve, T.Cokelaer Maintainer: T.Cokelaer SystemRequirements: Graphviz version >= 2.2 MD5sum: e0d9c3f4781e4bc2515b2618d9a3b6f0 source.ver: src/contrib/CellNOptR_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CellNOptR_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CellNOptR_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CellNOptR_1.2.0.tgz 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 vignetteTitles: CellNOptR0_1flowchart.pdf, Main vignette:Playing with networks using CellNOptR, Fig2.pdf, Fig3.pdf, Fig4.pdf, Fig6.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CGEN Version: 1.8.0 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 MD5sum: 338b20a49a36bfd815e08c1baf0d85b1 source.ver: src/contrib/CGEN_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CGEN_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CGEN_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CGEN_1.8.0.tgz vignettes: vignettes/CGEN/inst/doc/vignette.pdf vignetteTitles: CGEN Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: CGHbase Version: 1.14.0 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 Maintainer: Sjoerd Vosse MD5sum: 8e541f1004917279547a312a50852e5c source.ver: src/contrib/CGHbase_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CGHbase_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CGHbase_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CGHbase_1.14.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: CGHcall, CGHnormaliter, CGHregions, sigaR importsMe: CGHnormaliter Package: CGHcall Version: 2.16.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase 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: Sjoerd Vosse and Mark van de Wiel Maintainer: Mark van de Wiel MD5sum: 1bde4d7298ab578d01dac7eee3d1585a source.ver: src/contrib/CGHcall_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CGHcall_2.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CGHcall_2.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CGHcall_2.16.0.tgz vignettes: vignettes/CGHcall/inst/doc/CGHcall.pdf vignetteTitles: CGHcall hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: CGHnormaliter importsMe: CGHnormaliter Package: cghMCR Version: 1.14.0 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 MD5sum: d00de5fbf72bd3d69b7742dbba805bd0 source.ver: src/contrib/cghMCR_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cghMCR_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cghMCR_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cghMCR_1.14.0.tgz vignettes: vignettes/cghMCR/inst/doc/findMCR.pdf vignetteTitles: cghMCR findMCR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CGHnormaliter Version: 1.10.0 Depends: CGHcall (>= 2.2.0), CGHbase (>= 1.2.0) 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 MD5sum: 7fd0e9a8f78c9506c2c9c7453c336b28 source.ver: src/contrib/CGHnormaliter_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CGHnormaliter_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CGHnormaliter_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CGHnormaliter_1.10.0.tgz 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 Package: CGHregions Version: 1.14.0 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 MD5sum: 6960a64d37e4eabae17b3a9f7dbe4f28 source.ver: src/contrib/CGHregions_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CGHregions_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CGHregions_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CGHregions_1.14.0.tgz vignettes: vignettes/CGHregions/inst/doc/CGHregions.pdf vignetteTitles: CGHcall hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: ADaCGH2 Package: charm Version: 2.2.0 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 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: Martin Aryee MD5sum: a0fa849e635a0dbcb1db670a8b3bd920 source.ver: src/contrib/charm_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/charm_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/charm_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/charm_2.2.0.tgz vignettes: vignettes/charm/inst/doc/charm.pdf vignetteTitles: charm Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: ChemmineR Version: 2.8.1 Depends: R (>= 2.10.0), methods Imports: graphics, methods, stats, RCurl License: Artistic-2.0 Title: Analysis of Small Molecule and Screening Data Description: ChemmineR is an R package for analyzing small molecule and screening data. The new version of the package 'ChemmineR-V2' contains efficient functions and data containers for processing SDFs (structure data files), structural similarity searching, clustering/diversity analyses of compound libraries with a wide spectrum of algorithms. In addition, it offers utilities for managing complex data sets from high-throughput compound bio-assays, and visualization functions for 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 URL: http://manuals.bioinformatics.ucr.edu/home/chemminer MD5sum: dcffe66328b2cbfdc9f1056ad9f9a6aa source.ver: src/contrib/ChemmineR_2.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/ChemmineR_2.8.1.zip win64.binary.ver: bin/windows64/contrib/2.15/ChemmineR_2.8.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ChemmineR_2.8.1.tgz vignettes: vignettes/ChemmineR/inst/doc/ChemmineR.pdf vignetteTitles: gpls Tutorial hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ChIPpeakAnno Version: 2.4.0 Depends: R (>= 2.10), gplots, 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 MD5sum: fc43bf1f500e7ba2441a49d7a27fa16b source.ver: src/contrib/ChIPpeakAnno_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ChIPpeakAnno_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ChIPpeakAnno_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ChIPpeakAnno_2.4.0.tgz vignettes: vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.pdf vignetteTitles: ChIPpeakAnno Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: REDseq importsMe: REDseq suggestsMe: oneChannelGUI Package: chipseq Version: 1.6.1 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 MD5sum: dadf8455fe8f501f5ba93c4c9b357dc0 source.ver: src/contrib/chipseq_1.6.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/chipseq_1.6.1.zip win64.binary.ver: bin/windows64/contrib/2.15/chipseq_1.6.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/chipseq_1.6.1.tgz vignettes: vignettes/chipseq/inst/doc/Workflow.pdf vignetteTitles: A Sample ChIP-Seq analysis workflow hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oneChannelGUI Package: ChIPseqR Version: 1.10.0 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 MD5sum: bd1d4c00f6ff601afa3f3e419b943e66 source.ver: src/contrib/ChIPseqR_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ChIPseqR_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ChIPseqR_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ChIPseqR_1.10.0.tgz vignettes: vignettes/ChIPseqR/inst/doc/Introduction.pdf vignetteTitles: Introduction to ChIPseqR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ChIPsim Version: 1.10.0 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 MD5sum: 040dee5bf831fbca398356f3988fc7e8 source.ver: src/contrib/ChIPsim_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ChIPsim_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ChIPsim_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ChIPsim_1.10.0.tgz vignettes: vignettes/ChIPsim/inst/doc/ChIPsimIntro.pdf vignetteTitles: Simulating ChIP-seq experiments hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: chopsticks Version: 1.20.5 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 Author: Hin-Tak Leung Maintainer: Hin-Tak Leung URL: http://outmodedbonsai.sourceforge.net/ MD5sum: fbb85b0d4e0bd5e0abb0b2967fcd40c4 source.ver: src/contrib/chopsticks_1.20.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/chopsticks_1.20.5.zip win64.binary.ver: bin/windows64/contrib/2.15/chopsticks_1.20.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/chopsticks_1.20.5.tgz vignettes: vignettes/chopsticks/inst/doc/chopsticks-vignette.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-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 Package: ChromHeatMap Version: 1.10.0 Depends: R (>= 2.9.0), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0), hgu95av2.db Imports: annotate, AnnotationDbi, Biobase, 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 MD5sum: fa495d6fde2c3067863f58192747bfc2 source.ver: src/contrib/ChromHeatMap_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ChromHeatMap_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ChromHeatMap_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ChromHeatMap_1.10.0.tgz vignettes: vignettes/ChromHeatMap/inst/doc/ChromHeatMap.pdf vignetteTitles: Plotting expression data with ChromHeatMap hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: clippda Version: 1.6.0 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 URL: http://www.cancerstudies.bham.ac.uk/crctu/CLIPPDA.shtml MD5sum: b5c3efc96707ce6c1cbbc206eb33e041 source.ver: src/contrib/clippda_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/clippda_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/clippda_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/clippda_1.6.0.tgz vignettes: vignettes/clippda/inst/doc/clippda.pdf vignetteTitles: Sample Size Calculation hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Clonality Version: 1.4.0 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 MD5sum: 95d67256e81e2464f7feebdc94e2edd9 source.ver: src/contrib/Clonality_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Clonality_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Clonality_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Clonality_1.4.0.tgz vignettes: vignettes/Clonality/inst/doc/Clonality.pdf vignetteTitles: Clonality hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: clst Version: 1.4.0 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 MD5sum: ccdcf0c7dd826a43fc670850394ca325 source.ver: src/contrib/clst_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/clst_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/clst_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/clst_1.4.0.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 dependsOnMe: clstutils Package: clstutils Version: 1.4.0 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 MD5sum: d4919ad82226756d4138d69bcb71dc19 source.ver: src/contrib/clstutils_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/clstutils_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/clstutils_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/clstutils_1.4.0.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 Package: clusterProfiler Version: 1.4.0 Depends: R (>= 2.10) Imports: methods, stats4, ggplot2, 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: Bioinformatics, Clustering, GO, Pathways, Visualization, MultipleComparisons Author: Guangchuang Yu, Li-Gen Wang Maintainer: Guangchuang Yu MD5sum: ac327776165967b22abbdd59a5fe99a8 source.ver: src/contrib/clusterProfiler_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/clusterProfiler_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/clusterProfiler_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/clusterProfiler_1.4.0.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 suggestsMe: DOSE, GOSemSim, ReactomePA Package: clusterStab Version: 1.28.0 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 MD5sum: fc3b7625017631ecf5430e31c0e72812 source.ver: src/contrib/clusterStab_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/clusterStab_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/clusterStab_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/clusterStab_1.28.0.tgz vignettes: vignettes/clusterStab/inst/doc/clusterStab.pdf vignetteTitles: clusterStab Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CMA Version: 1.14.0 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 , Anne-Laure Boulesteix , Christoph Bernau . Maintainer: Christoph Bernau MD5sum: cda5e7cd86d6ee83c543f1e133d48033 source.ver: src/contrib/CMA_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CMA_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CMA_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CMA_1.14.0.tgz vignettes: vignettes/CMA/inst/doc/CMA_vignette.pdf vignetteTitles: CMA_vignette.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CNAnorm Version: 1.2.0 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 , Henry M. Wood , Arief Gusnanto Maintainer: Stefano Berri URL: http://www.r-project.org, MD5sum: ceddc893ed2088fe304f57e095b75c6e source.ver: src/contrib/CNAnorm_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CNAnorm_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CNAnorm_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CNAnorm_1.2.0.tgz vignettes: vignettes/CNAnorm/inst/doc/CNAnorm.pdf vignetteTitles: CNAnorm.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: cn.farms Version: 1.4.0 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 URL: http://www.bioinf.jku.at/software/cnfarms/cnfarms.html MD5sum: b91ff797b2a6272a42a5cad78083e0dd source.ver: src/contrib/cn.farms_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cn.farms_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cn.farms_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cn.farms_1.4.0.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 Package: cn.mops Version: 1.2.6 Depends: R (>= 2.14), BiocGenerics (>= 0.1.0), Biobase, IRanges, GenomicRanges (>= 1.7.8) 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 URL: http://www.bioinf.jku.at/software/cnmops/cnmops.html MD5sum: 2554cd96aaebf9c75786db5d86770075 source.ver: src/contrib/cn.mops_1.2.6.tar.gz win.binary.ver: bin/windows/contrib/2.15/cn.mops_1.2.6.zip win64.binary.ver: bin/windows64/contrib/2.15/cn.mops_1.2.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cn.mops_1.2.6.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 Package: CNTools Version: 1.12.0 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 MD5sum: c38e2a36a06604c966f58a981c6d251f source.ver: src/contrib/CNTools_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CNTools_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CNTools_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CNTools_1.12.0.tgz vignettes: vignettes/CNTools/inst/doc/HowTo.pdf vignetteTitles: NCTools HowTo hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: cghMCR Package: cnvGSA Version: 1.0.0 Depends: methods 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 ; packaged by Robert Ziman Maintainer: Robert Ziman MD5sum: 1f427e53d3e1fe18bce9a2ad01ce9ade source.ver: src/contrib/cnvGSA_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cnvGSA_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cnvGSA_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cnvGSA_1.0.0.tgz 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 Package: CNVtools Version: 1.50.0 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 and Vincent Plagnol Maintainer: Chris Barnes MD5sum: 3a3aa8766358139a764f7270dece2b52 source.ver: src/contrib/CNVtools_1.50.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CNVtools_1.50.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CNVtools_1.50.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CNVtools_1.50.0.tgz vignettes: vignettes/CNVtools/inst/doc/CNVtools-vignette.pdf vignetteTitles: Copy Number Variation Tools hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CoCiteStats Version: 1.28.0 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 MD5sum: 392ea4226298e0181751956b7de27fef source.ver: src/contrib/CoCiteStats_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CoCiteStats_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CoCiteStats_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CoCiteStats_1.28.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: codelink Version: 1.24.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), limma Imports: annotate Suggests: genefilter Enhances: multicore 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. Author: Diego Diez Maintainer: Diego Diez URL: http://www.kuicr.kyoto-u.ac.jp/~diez MD5sum: 9672c3e2aa83d1a15cde03792419cde1 source.ver: src/contrib/codelink_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/codelink_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/codelink_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/codelink_1.24.0.tgz vignettes: vignettes/codelink/inst/doc/codelink.pdf, vignettes/codelink/inst/doc/CodelinkSet.pdf vignetteTitles: codelink, CodelinkSet hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: CoGAPS Version: 1.6.0 Depends: R (>= 2.9.0), R.utils (>= 1.2.4) 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 , Michael F. Ochs URL: http://www.cancerbiostats.onc.jhmi.edu/CoGAPS.cfm SystemRequirements: GAPS-JAGS (==1.0.2) MD5sum: 2587b4e17744a61052bae443530d78e8 source.ver: src/contrib/CoGAPS_1.6.0.tar.gz vignettes: vignettes/CoGAPS/inst/doc/CoGAPSUsersManual.pdf vignetteTitles: GAPS/CoGAPS Users Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: coGPS Version: 1.0.0 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 MD5sum: 7483512364cac16d784080c66d485fa2 source.ver: src/contrib/coGPS_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/coGPS_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/coGPS_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/coGPS_1.0.0.tgz vignettes: vignettes/coGPS/inst/doc/coGPS.pdf vignetteTitles: coGPS hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: ConsensusClusterPlus Version: 1.8.0 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 MD5sum: eb4f402e7e960cea1e0d5c0721158042 source.ver: src/contrib/ConsensusClusterPlus_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ConsensusClusterPlus_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ConsensusClusterPlus_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ConsensusClusterPlus_1.8.0.tgz vignettes: vignettes/ConsensusClusterPlus/inst/doc/ConsensusClusterPlus.pdf vignetteTitles: ConsensusClusterPlus Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: convert Version: 1.32.0 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 , James Wettenhall , Yee Hwa (Jean Yang) , Martin Morgan Martin Morgan Maintainer: Yee Hwa (Jean) Yang URL: http://bioinf.wehi.edu.au/limma/convert.html MD5sum: a6550058e688a0d71c72055bbd09086d source.ver: src/contrib/convert_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/convert_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/convert_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/convert_1.32.0.tgz vignettes: vignettes/convert/inst/doc/convert.pdf vignetteTitles: Converting Between Microarray Data Classes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: maigesPack, TurboNorm suggestsMe: BiocCaseStudies, dyebias, OLIN Package: copa Version: 1.24.0 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 MD5sum: 43d785f5db8f9a6b09451ed6dcec38a5 source.ver: src/contrib/copa_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/copa_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/copa_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/copa_1.24.0.tgz vignettes: vignettes/copa/inst/doc/copa.pdf vignetteTitles: copa Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Cormotif Version: 1.2.0 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 MD5sum: ca93c37e48376f72403467b256ae3d65 source.ver: src/contrib/Cormotif_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Cormotif_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Cormotif_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Cormotif_1.2.0.tgz vignettes: vignettes/Cormotif/inst/doc/CormotifVignette.pdf vignetteTitles: Cormotif Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: coRNAi Version: 1.6.0 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 SystemRequirements: Graphviz MD5sum: 019f04d283e4137cf995db7283242489 source.ver: src/contrib/coRNAi_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/coRNAi_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/coRNAi_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/coRNAi_1.6.0.tgz vignettes: vignettes/coRNAi/inst/doc/coRNAi.pdf vignetteTitles: coRNAi hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: CORREP Version: 1.22.0 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 MD5sum: 399c4ab814d81355e2eecc7e86e89a03 source.ver: src/contrib/CORREP_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CORREP_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CORREP_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CORREP_1.22.0.tgz vignettes: vignettes/CORREP/inst/doc/CORREP.pdf vignetteTitles: Multivariate Correlation Estimator hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cosmo Version: 1.22.0 Depends: R (>= 2.4.0), methods, utils, seqLogo Suggests: cosmoGUI License: file LICENSE Archs: i386, x64 Title: Supervised detection of conserved motifs in DNA sequences Description: cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may include bounds on the information content across certain regions of the unknown motif, for example, and can often be formulated on the basis of prior knowledge about the structure of the transcription factor in question. The unknown motif width, the distribution of motif occurrences (OOPS, ZOOPS, or TCM), as well as the appropriate constraint set can be selected data-adaptively. biocViews: SequenceMatching Author: Oliver Bembom, Fabian Gallusser, and Sandrine Dudoit Maintainer: Oliver Bembom URL: http://cosmoweb.berkeley.edu/intro.html, http://www.bepress.com/sagmb/vol6/iss1/art8 MD5sum: 99fb6aa297b7c32ee90bc3d3e746886c source.ver: src/contrib/cosmo_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cosmo_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cosmo_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cosmo_1.22.0.tgz vignettes: vignettes/cosmo/inst/doc/cosmo.pdf vignetteTitles: Supervised detection of conserved motifs in DNA sequences with cosmo hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: cosmoGUI Package: cosmoGUI Version: 1.22.0 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 URL: http://cosmoweb.berkeley.edu/intro.html, http://www.bepress.com/ucbbiostat/paper209/ MD5sum: b7c484536950c396efb1851a092a4215 source.ver: src/contrib/cosmoGUI_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cosmoGUI_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cosmoGUI_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cosmoGUI_1.22.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: cosmo Package: cqn Version: 1.2.0 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 MD5sum: 0e6ebefb87d2ead5fe91570493787ba1 source.ver: src/contrib/cqn_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cqn_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cqn_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cqn_1.2.0.tgz vignettes: vignettes/cqn/inst/doc/cqn.pdf vignetteTitles: CQN (Conditional Quantile Normalization) hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: tweeDEseq Package: CRImage Version: 1.6.0 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach 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 , Yinyin Yuan , Oscar Rueda , Florian Markowetz Maintainer: Henrik Failmezger , Yinyin Yuan MD5sum: f84ffe8c3091a520d202665c4c402180 source.ver: src/contrib/CRImage_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CRImage_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CRImage_1.6.0.zip 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 Package: crlmm Version: 1.14.3 Depends: R (>= 2.14.0), oligoClasses (>= 1.18.0) Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>= 1.23.2), ellipse, genefilter (>= 1.37.1), mvtnorm, preprocessCore (>= 1.17.7), splines, stats, SNPchip, utils, lattice, ff, foreach 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 , Robert Scharpf , Matt Ritchie MD5sum: acb21285adf3a951401f3d2bbbfd7f42 source.ver: src/contrib/crlmm_1.14.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/crlmm_1.14.3.zip win64.binary.ver: bin/windows64/contrib/2.15/crlmm_1.14.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/crlmm_1.14.3.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 importsMe: minfi, VanillaICE suggestsMe: SNPchip Package: CSAR Version: 1.8.0 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 MD5sum: 01940444eaccc52c13c22589889ce247 source.ver: src/contrib/CSAR_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/CSAR_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/CSAR_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/CSAR_1.8.0.tgz vignettes: vignettes/CSAR/inst/doc/CSAR.pdf vignetteTitles: CSAR Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: NarrowPeaks suggestsMe: NarrowPeaks Package: ctc Version: 1.30.0 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 , Laurent Gautier Maintainer: Antoine Lucas URL: http://antoinelucas.free.fr/ctc MD5sum: 6665b55b9f4ed580e539e7c137638d79 source.ver: src/contrib/ctc_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ctc_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ctc_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ctc_1.30.0.tgz vignettes: vignettes/ctc/inst/doc/ctc.pdf vignetteTitles: Introduction to ctc hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: cummeRbund Version: 1.2.0 Depends: R (>= 2.7.0), RSQLite, ggplot2, reshape2 Imports: methods Suggests: cluster 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 Maintainer: Loyal A. Goff MD5sum: ad3b5d4f0a29c89b4a90161a80f9874c source.ver: src/contrib/cummeRbund_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cummeRbund_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cummeRbund_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cummeRbund_1.2.0.tgz vignettes: vignettes/cummeRbund/inst/doc/cuffData_schema.pdf, vignettes/cummeRbund/inst/doc/cummeRbund-manual.pdf vignetteTitles: cuffData_schema.pdf, An R package for visualization and analysis of Cufflinks high-throughput sequencing data hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oneChannelGUI Package: cycle Version: 1.10.0 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 Maintainer: Matthias Futschik URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/cycle/index.html MD5sum: 08f301744bb3bd3068837cde01dd5edb source.ver: src/contrib/cycle_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/cycle_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/cycle_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/cycle_1.10.0.tgz vignettes: vignettes/cycle/inst/doc/cycle.pdf vignetteTitles: Introduction to cycle hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: daMA Version: 1.28.0 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 and Frank Bretz Maintainer: Jobst Landgrebe URL: http://www.microarrays.med.uni-goettingen.de MD5sum: 724a7527e8792966e33cfa2127d31dc7 source.ver: src/contrib/daMA_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/daMA_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/daMA_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/daMA_1.28.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DART Version: 1.2.1 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 MD5sum: bd8c4c8213c0cd94325459dc5db0d4ad source.ver: src/contrib/DART_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/DART_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/DART_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DART_1.2.1.tgz vignettes: vignettes/DART/inst/doc/DART.pdf vignetteTitles: DART Tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: DAVIDQuery Version: 1.16.0 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 MD5sum: c92b9a7935e7a77fd27e0be46876f950 source.ver: src/contrib/DAVIDQuery_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DAVIDQuery_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DAVIDQuery_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DAVIDQuery_1.16.0.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 importsMe: IdMappingRetrieval Package: ddCt Version: 1.10.0 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 MD5sum: a4e8793acbc69169e402f1f6023eb222 source.ver: src/contrib/ddCt_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ddCt_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ddCt_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ddCt_1.10.0.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 Package: DECIPHER Version: 1.2.0 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 MD5sum: 92804f106d75064c590445c5e908b0bc source.ver: src/contrib/DECIPHER_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DECIPHER_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DECIPHER_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DECIPHER_1.2.0.tgz vignettes: vignettes/DECIPHER/inst/doc/DECIPHERing.pdf, vignettes/DECIPHER/inst/doc/FindChimeras.pdf vignetteTitles: Getting Started DECIPHERing, Finding Chimeric Sequences hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DEDS Version: 1.30.0 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 , Jean Yee Hwa Yang . Maintainer: Yuanyuan Xiao MD5sum: 6441b7fb466eee79ed42f4cb43ff813a source.ver: src/contrib/DEDS_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DEDS_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DEDS_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DEDS_1.30.0.tgz vignettes: vignettes/DEDS/inst/doc/DEDS.pdf vignetteTitles: DEDS.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: deepSNV Version: 1.2.3 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: Test for 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. Author: Moritz Gerstung and Niko Beerenwinkel Maintainer: Moritz Gerstung URL: http://www.cbg.ethz.ch/software/deepSNV MD5sum: 2aa80edde446cb8614d6045923d3b08d source.ver: src/contrib/deepSNV_1.2.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/deepSNV_1.2.3.zip win64.binary.ver: bin/windows64/contrib/2.15/deepSNV_1.2.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/deepSNV_1.2.3.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 Package: DEGraph Version: 1.8.0 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, Bioinformatics, DifferentialExpression, GraphsAndNetworks Author: Laurent Jacob, Pierre Neuvial and Sandrine Dudoit Maintainer: Laurent Jacob MD5sum: bd2d79eb9b4717cd4206345775491e7e source.ver: src/contrib/DEGraph_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DEGraph_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DEGraph_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DEGraph_1.8.0.tgz vignettes: vignettes/DEGraph/inst/doc/DEGraph.pdf vignetteTitles: DEGraph: differential expression testing for gene networks hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: graphite Package: DEGseq Version: 1.10.0 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 and Xi Wang . Maintainer: Likun Wang MD5sum: 394852bc3000dc40c0685cb092f5e9aa source.ver: src/contrib/DEGseq_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DEGseq_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DEGseq_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DEGseq_1.10.0.tgz vignettes: vignettes/DEGseq/inst/doc/DEGseq.pdf vignetteTitles: DEGseq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DESeq Version: 1.8.3 Depends: Biobase (>= 2.13.11), locfit Imports: genefilter, geneplotter, methods, MASS Suggests: pasilla (>= 0.2.11), vsn 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 Maintainer: Simon Anders URL: http://www-huber.embl.de/users/anders/DESeq MD5sum: 528aefd76611c9fd986efccb89856361 source.ver: src/contrib/DESeq_1.8.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/DESeq_1.8.3.zip win64.binary.ver: bin/windows64/contrib/2.15/DESeq_1.8.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DESeq_1.8.3.tgz 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 dependsOnMe: easyRNASeq importsMe: ArrayExpressHTS, DiffBind, EDASeq, rnaSeqMap suggestsMe: DiffBind, EDASeq, GenomicRanges, oneChannelGUI Package: DEXSeq Version: 1.2.1 Depends: Biobase (>= 2.13.11) Imports: biomaRt, hwriter, methods, stringr, statmod (>= 1.4.15) Suggests: pasilla (>= 0.2.6) Enhances: multicore 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 and Alejandro Reyes , both at EMBL Heidelberg Maintainer: Alejandro Reyes MD5sum: 60a4c8ec352ea1016493ec877c5245b1 source.ver: src/contrib/DEXSeq_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/DEXSeq_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/DEXSeq_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DEXSeq_1.2.1.tgz 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 suggestsMe: GenomicRanges Package: DFP Version: 1.14.0 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 MD5sum: 8f9135a4a185ea0da0bf16e5de83a0e5 source.ver: src/contrib/DFP_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DFP_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DFP_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DFP_1.14.0.tgz vignettes: vignettes/DFP/inst/doc/DFP.pdf vignetteTitles: Howto: Discriminat Fuzzy Pattern hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DiffBind Version: 1.2.4 Depends: R (>= 2.14.0), GenomicRanges Imports: RColorBrewer, amap, edgeR (>= 2.3.58), gplots, limma, 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, Gordon Brown Maintainer: Rory Stark MD5sum: 3ef92de00fef53bdd19f77f03d02b80d source.ver: src/contrib/DiffBind_1.2.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/DiffBind_1.2.4.zip win64.binary.ver: bin/windows64/contrib/2.15/DiffBind_1.2.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DiffBind_1.2.4.tgz vignettes: vignettes/DiffBind/inst/doc/DiffBind.pdf vignetteTitles: DiffBind User's Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: diffGeneAnalysis Version: 1.38.0 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 MD5sum: 4dd978163601b294357d41086d70c463 source.ver: src/contrib/diffGeneAnalysis_1.38.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/diffGeneAnalysis_1.38.0.zip win64.binary.ver: bin/windows64/contrib/2.15/diffGeneAnalysis_1.38.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/diffGeneAnalysis_1.38.0.tgz vignettes: vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf vignetteTitles: Documentation on diffGeneAnalysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: dks Version: 1.2.0 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 Maintainer: Jeffrey T. Leek MD5sum: 7ffb027553a1dbd194a7d1f36b6ad5f0 source.ver: src/contrib/dks_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/dks_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/dks_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/dks_1.2.0.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 Package: DNAcopy Version: 1.30.0 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 MD5sum: 266b457f52aa124e982028167c415a18 source.ver: src/contrib/DNAcopy_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DNAcopy_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DNAcopy_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DNAcopy_1.30.0.tgz vignettes: vignettes/DNAcopy/inst/doc/DNAcopy.pdf vignetteTitles: DNAcopy hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: CGHcall, cghMCR, Clonality, CNAnorm, CRImage, snapCGH importsMe: Clonality, cn.farms, genoset, GWASTools, MinimumDistance, Repitools, snapCGH suggestsMe: ADaCGH2, beadarraySNP, Clonality, cn.mops, fastseg, Repitools Package: domainsignatures Version: 1.16.0 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: Bioinformatics, Annotation, Pathways Author: Florian Hahne, Tim Beissbarth Maintainer: Florian Hahne MD5sum: 1f41174b55e60a0f6aa27c03d431d6dd source.ver: src/contrib/domainsignatures_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/domainsignatures_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/domainsignatures_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/domainsignatures_1.16.0.tgz vignettes: vignettes/domainsignatures/inst/doc/domainenrichment.pdf vignetteTitles: Gene set enrichment using InterPro domain signatures hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: DOSE Version: 1.2.1 Depends: R (>= 2.10) Imports: methods, plyr, qvalue, stats4, AnnotationDbi, DO.db, org.Hs.eg.db, igraph, scales, ggplot2, graphics Suggests: clusterProfiler, GOSemSim, 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 MD5sum: 70aea2f72b57f3db5def4b9abbfeb034 source.ver: src/contrib/DOSE_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/DOSE_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/DOSE_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DOSE_1.2.1.tgz vignettes: vignettes/DOSE/inst/doc/DOSE.pdf vignetteTitles: An introduction to DOSE hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: clusterProfiler suggestsMe: GOSemSim, ReactomePA Package: DTA Version: 2.2.0 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 MD5sum: d40c528516033943ff0502d0ade9ad12 source.ver: src/contrib/DTA_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DTA_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DTA_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DTA_2.2.0.tgz vignettes: vignettes/DTA/inst/doc/DTA.pdf vignetteTitles: A guide to Dynamic Transcriptome Analysis (DTA) hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: dualKS Version: 1.16.0 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 MD5sum: b3b41e041ffc8903523e8131e83383dc source.ver: src/contrib/dualKS_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/dualKS_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/dualKS_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/dualKS_1.16.0.tgz vignettes: vignettes/dualKS/inst/doc/dualKS.pdf vignetteTitles: dualKS.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: dyebias Version: 1.14.0 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 URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad MD5sum: cfd5099b88a4177de89ceaf40110d136 source.ver: src/contrib/dyebias_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/dyebias_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/dyebias_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/dyebias_1.14.0.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 Package: DynDoc Version: 1.34.0 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 MD5sum: c5069ae6acbbe2c2c4322bf7d6177cb1 source.ver: src/contrib/DynDoc_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/DynDoc_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/DynDoc_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/DynDoc_1.34.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: tkWidgets Package: easyRNASeq Version: 1.2.5 Depends: graphics, methods, parallel, utils, genomeIntervals (>= 1.12.0), Biobase (>= 2.16.0), BiocGenerics (>= 0.2.0), biomaRt (>= 2.12.0), edgeR (>= 2.6.10), Biostrings (>= 2.24.1), BSgenome (>= 1.24.0), DESeq (>= 1.8.3), GenomicRanges (>= 1.8.12), IRanges (>= 1.14.4), Rsamtools (>= 1.8.6), ShortRead (>= 1.14.4) Suggests: BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), GenomicFeatures (>= 1.8.2), RnaSeqTutorial (>= 0.0.8) 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 MD5sum: d86aa7f517cc25f0ebb79f1d0b7148a3 source.ver: src/contrib/easyRNASeq_1.2.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/easyRNASeq_1.2.5.zip win64.binary.ver: bin/windows64/contrib/2.15/easyRNASeq_1.2.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/easyRNASeq_1.2.5.tgz vignettes: vignettes/easyRNASeq/inst/doc/easyRNASeq.pdf vignetteTitles: RNA-Seq hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: EBarrays Version: 2.20.0 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 MD5sum: 3c9b3ba8a5c1cffe9b3c44cdf568c618 source.ver: src/contrib/EBarrays_2.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/EBarrays_2.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/EBarrays_2.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/EBarrays_2.20.0.tgz vignettes: vignettes/EBarrays/inst/doc/vignette.pdf vignetteTitles: Introduction to EBarrays hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: EBcoexpress, gaga suggestsMe: Category Package: EBcoexpress Version: 1.0.0 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 MD5sum: f94186b42a44c3d37baf870cc5aceab1 source.ver: src/contrib/EBcoexpress_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/EBcoexpress_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/EBcoexpress_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/EBcoexpress_1.0.0.tgz vignettes: vignettes/EBcoexpress/inst/doc/EBcoexpressVignette.pdf vignetteTitles: EBcoexpress Demo hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: EBImage Version: 3.12.0 Depends: R (>= 2.8.0), methods, graphics, stats, utils, abind License: Artistic-2.0 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: Oleg Sklyar, Gregoire Pau, Mike Smith, Wolfgang Huber Maintainer: Gregoire Pau SystemRequirements: ImageMagick (>= 6.3.7), GTK+ (> 2.6) MD5sum: 70b87e7db3814d98dfc0cfd97883c480 source.ver: src/contrib/EBImage_3.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/EBImage_3.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/EBImage_3.12.0.zip vignettes: vignettes/EBImage/inst/doc/EBImage-installation.pdf, vignettes/EBImage/inst/doc/EBImage-introduction.pdf vignetteTitles: EBImage installation, Introduction to EBImage hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: CRImage, imageHTS suggestsMe: HilbertVis Package: ecolitk Version: 1.28.0 Depends: R (>= 2.10) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest 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 MD5sum: d6e49e5a06433e60cd91f1828ff8a680 source.ver: src/contrib/ecolitk_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ecolitk_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ecolitk_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ecolitk_1.28.0.tgz vignettes: vignettes/ecolitk/inst/doc/ecolitk.pdf vignetteTitles: ecolitk hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: EDASeq Version: 1.2.0 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 MD5sum: 7fdb9952bb083069027b693883ed2010 source.ver: src/contrib/EDASeq_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/EDASeq_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/EDASeq_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/EDASeq_1.2.0.tgz 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 suggestsMe: oneChannelGUI Package: edgeR Version: 2.6.12 Depends: R (>= 2.3.0), methods, limma Suggests: MASS, statmod, splines License: LGPL (>= 2) 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 , Davis McCarthy , Yunshun Chen , Gordon Smyth Maintainer: Mark Robinson , Davis McCarthy , Yunshun Chen , Gordon Smyth MD5sum: f402845accfd3517fdf1b6860f95f695 source.ver: src/contrib/edgeR_2.6.12.tar.gz win.binary.ver: bin/windows/contrib/2.15/edgeR_2.6.12.zip win64.binary.ver: bin/windows64/contrib/2.15/edgeR_2.6.12.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/edgeR_2.6.12.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 dependsOnMe: easyRNASeq, manta importsMe: ArrayExpressHTS, DiffBind, Repitools, rnaSeqMap, tweeDEseq suggestsMe: baySeq, cqn, EDASeq, GenomicRanges, goseq, GSVA, oneChannelGUI, Repitools Package: eisa Version: 1.8.2 Depends: methods, isa2, Biobase, AnnotationDbi, Category, genefilter, DBI 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 Maintainer: Gabor Csardi MD5sum: b3415dbb471739eb89ce09221a0d9f77 source.ver: src/contrib/eisa_1.8.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/eisa_1.8.2.zip win64.binary.ver: bin/windows64/contrib/2.15/eisa_1.8.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/eisa_1.8.2.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 importsMe: ExpressionView Package: ENVISIONQuery Version: 1.4.0 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 , Roger Day MD5sum: 9622d7da92f2790b788059dd532cec9d source.ver: src/contrib/ENVISIONQuery_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ENVISIONQuery_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ENVISIONQuery_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ENVISIONQuery_1.4.0.tgz 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 dependsOnMe: IdMappingRetrieval importsMe: IdMappingRetrieval Package: ExiMiR Version: 1.4.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.26.1) 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. biocViews: Microarray, OneChannel, DualChannel, Preprocessing, GeneExpression, Transcription Author: Sylvain Gubian , Alain Sewer , PMP SA Maintainer: Sylvain Gubian MD5sum: 9fa57c3130cca955d6562e556a6fc44b source.ver: src/contrib/ExiMiR_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ExiMiR_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ExiMiR_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ExiMiR_1.4.0.tgz vignettes: vignettes/ExiMiR/inst/doc/ExiMiR-vignette.pdf vignetteTitles: hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: exomeCopy Version: 1.2.0 Depends: IRanges, GenomicRanges, Rsamtools Imports: stats4, methods Suggests: Biostrings License: GPL (>= 2) Archs: i386, x64 Title: CNV 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 MD5sum: 98229e719d31eecf7f007e3e66d781d5 source.ver: src/contrib/exomeCopy_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/exomeCopy_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/exomeCopy_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/exomeCopy_1.2.0.tgz vignettes: vignettes/exomeCopy/inst/doc/exomeCopy.pdf vignetteTitles: CNV detection in exome sequencing data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: explorase Version: 1.20.0 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 URL: http://www.metnetdb.org/MetNet_exploRase.htm MD5sum: 01da442e6cf74fa50edad8cd7dd8ac44 source.ver: src/contrib/explorase_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/explorase_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/explorase_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/explorase_1.20.0.tgz vignettes: vignettes/explorase/inst/doc/explorase.pdf vignetteTitles: Introduction to exploRase hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ExpressionView Version: 1.8.0 Depends: caTools, bitops Imports: methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi Suggests: ALL, hgu95av2.db, biclust, GO.db, KEGG.db, AnnotationDbi, 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 Maintainer: Gabor Csardi MD5sum: 0cd5c5f461010e3602e82075da1d31e9 source.ver: src/contrib/ExpressionView_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ExpressionView_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ExpressionView_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ExpressionView_1.8.0.tgz 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 Package: externalVector Version: 1.22.0 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 MD5sum: 6f20959290f72181a1b269ad593d6545 source.ver: src/contrib/externalVector_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/externalVector_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/externalVector_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/externalVector_1.22.0.tgz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fabia Version: 2.2.2 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 Maintainer: Sepp Hochreiter URL: http://www.bioinf.jku.at/software/fabia/fabia.html MD5sum: 5df5a1e45b404c3a5ec9714cc6a53281 source.ver: src/contrib/fabia_2.2.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/fabia_2.2.2.zip win64.binary.ver: bin/windows64/contrib/2.15/fabia_2.2.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/fabia_2.2.2.tgz vignettes: vignettes/fabia/inst/doc/fabia.pdf vignetteTitles: FABIA: Manual for the R package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: factDesign Version: 1.32.0 Depends: Biobase (>= 2.5.5) Imports: stats Suggests: affy, genefilter 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 MD5sum: 8b48bd376ed74427012618e04bde2bb2 source.ver: src/contrib/factDesign_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/factDesign_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/factDesign_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/factDesign_1.32.0.tgz vignettes: vignettes/factDesign/inst/doc/factDesign.pdf vignetteTitles: factDesign hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: farms Version: 1.8.2 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 Maintainer: Djork-Arne Clevert URL: http://www.bioinf.jku.at/software/farms/farms.html MD5sum: 2019d9e8d485046be95c3675e9952d5e source.ver: src/contrib/farms_1.8.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/farms_1.8.2.zip win64.binary.ver: bin/windows64/contrib/2.15/farms_1.8.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/farms_1.8.2.tgz vignettes: vignettes/farms/inst/doc/farms.pdf vignetteTitles: hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fastseg Version: 1.2.3 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 URL: http://www.bioinf.jku.at/software/fastseg/fastseg.html MD5sum: 40c1c4ba9425ab0f29b4271b76f091fb source.ver: src/contrib/fastseg_1.2.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/fastseg_1.2.3.zip win64.binary.ver: bin/windows64/contrib/2.15/fastseg_1.2.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/fastseg_1.2.3.tgz vignettes: vignettes/fastseg/inst/doc/fastseg.pdf vignetteTitles: fastseg: Manual for the R package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: fdrame Version: 1.28.0 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 MD5sum: 741b1efb44578b508f0ef20d8249e028 source.ver: src/contrib/fdrame_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/fdrame_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/fdrame_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/fdrame_1.28.0.tgz vignettes: vignettes/fdrame/inst/doc/fdrame.pdf vignetteTitles: Annotation Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ffpe Version: 1.0.0 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 MD5sum: f50af2988b29050d9b9a605929302e6c source.ver: src/contrib/ffpe_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ffpe_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ffpe_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ffpe_1.0.0.tgz vignettes: vignettes/ffpe/inst/doc/ffpe.pdf vignetteTitles: ffpe package user guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: flagme Version: 1.12.0 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 Maintainer: Mark Robinson MD5sum: d552185866788356a3f53025c9d583d0 source.ver: src/contrib/flagme_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flagme_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flagme_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flagme_1.12.0.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 Package: flowClust Version: 2.14.0 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 , Kenneth Lo Maintainer: Raphael Gottardo MD5sum: 9384d0ecfbef4cbcdc3789a05f325bcd source.ver: src/contrib/flowClust_2.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowClust_2.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowClust_2.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowClust_2.14.0.tgz vignettes: vignettes/flowClust/inst/doc/flowClust.pdf vignetteTitles: flowClust package hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: flowMerge importsMe: flowPhyto, flowTrans, flowType suggestsMe: BiocGenerics Package: flowCore Version: 1.22.3 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 MD5sum: 77919d9e124fed8b4099ecae360c2964 source.ver: src/contrib/flowCore_1.22.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowCore_1.22.3.zip win64.binary.ver: bin/windows64/contrib/2.15/flowCore_1.22.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowCore_1.22.3.tgz vignettes: vignettes/flowCore/inst/doc/HowTo-flowCore.pdf vignetteTitles: Basic Functions for Flow Cytometry Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE 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: RchyOptimyx Package: flowFlowJo Version: 1.14.0 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 Maintainer: John J. Gosink MD5sum: c8163a25c400ae936de4878135da4dac source.ver: src/contrib/flowFlowJo_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowFlowJo_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowFlowJo_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowFlowJo_1.14.0.tgz vignettes: vignettes/flowFlowJo/inst/doc/flowFlowJo.pdf vignetteTitles: Basic Functions for working with FlowJo hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: flowFP Version: 1.14.0 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 , Wade Rogers Maintainer: Herb Holyst MD5sum: f5e47b8f885c93d0ead6390b1be4d6ff source.ver: src/contrib/flowFP_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowFP_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowFP_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowFP_1.14.0.tgz vignettes: vignettes/flowFP/inst/doc/flowFP_HowTo.pdf vignetteTitles: Fingerprinting for Flow Cytometry hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: flowMeans Version: 1.8.0 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 MD5sum: 92729c8898e06609d53aeec278c58d13 source.ver: src/contrib/flowMeans_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowMeans_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowMeans_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowMeans_1.8.0.tgz vignettes: vignettes/flowMeans/inst/doc/flowMeans.pdf vignetteTitles: flowMeans: Non-parametric Flow Cytometry Data Gating hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: flowPhyto, flowType Package: flowMerge Version: 2.4.0 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 , Raphael Gottardo Maintainer: Greg Finak MD5sum: 4454672656d15fccdfe7988b37d95d92 source.ver: src/contrib/flowMerge_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowMerge_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowMerge_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowMerge_2.4.0.tgz vignettes: vignettes/flowMerge/inst/doc/flowMerge.pdf vignetteTitles: flowMerge package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: flowType Package: flowPhyto Version: 1.8.0 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 and David M. Schruth Maintainer: David M. Schruth URL: http://seaflow.ocean.washington.edu MD5sum: ca2d713fba05070d62fa7675fcc88fce source.ver: src/contrib/flowPhyto_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowPhyto_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowPhyto_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowPhyto_1.8.0.tgz vignettes: vignettes/flowPhyto/inst/doc/flowPhyto.pdf vignetteTitles: flowPhyto hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: flowPlots Version: 1.4.0 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 MD5sum: 9e632a33fb15e16bd3d7af6237fbe6b6 source.ver: src/contrib/flowPlots_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowPlots_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowPlots_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowPlots_1.4.0.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 Package: flowQ Version: 1.16.0 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 SystemRequirements: ImageMagick MD5sum: f738d153ac3107522f266095752232b7 source.ver: src/contrib/flowQ_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowQ_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowQ_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowQ_1.16.0.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 Package: flowStats Version: 1.14.0 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 and Mike Jiang MD5sum: 9f3cf6875450b23ebdd186772c84f46a source.ver: src/contrib/flowStats_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowStats_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowStats_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowStats_1.14.0.tgz vignettes: vignettes/flowStats/inst/doc/GettingStartedWithFlowStats.pdf vignetteTitles: flowStats Overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: iFlow importsMe: iFlow suggestsMe: flowQ Package: flowTrans Version: 1.8.0 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 , Juan Manuel-Perez , Raphael Gottardo Maintainer: Greg Finak MD5sum: 07f4ee10f4b50c1ecbde8508a326dc95 source.ver: src/contrib/flowTrans_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowTrans_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowTrans_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowTrans_1.8.0.tgz vignettes: vignettes/flowTrans/inst/doc/flowTrans.pdf vignetteTitles: flowTrans package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: flowType Version: 1.2.0 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 MD5sum: 27a798afa1c4b831a6554cd4476bde24 source.ver: src/contrib/flowType_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowType_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowType_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowType_1.2.0.tgz vignettes: vignettes/flowType/inst/doc/flowType.pdf vignetteTitles: flowType package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RchyOptimyx Package: flowUtils Version: 1.16.0 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 MD5sum: f664cf076e39b6b04c2997b248f5d5bc source.ver: src/contrib/flowUtils_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowUtils_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowUtils_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowUtils_1.16.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: flowViz Version: 1.20.0 Depends: R (>= 2.7.0), flowCore (>= 1.5.17), lattice Imports: stats4, Biobase, flowCore, graphics, grDevices, grid, KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer, stats, utils Suggests: RColorBrewer, IDPmisc,colorspace License: Artistic-2.0 Archs: i386, x64 Title: Visualization for flow cytometry Description: Provides visualization tools for flow cytometry data. Author: B. Ellis, R. Gentleman, F. Hahne, N. Le Meur, D. Sarkar Maintainer: Mike Jiang MD5sum: 56fe868b10c69c79f8bab0b7d922f61e source.ver: src/contrib/flowViz_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowViz_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowViz_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowViz_1.20.0.tgz vignettes: vignettes/flowViz/inst/doc/filters.pdf vignetteTitles: Visualizing Gates with Flow Cytometry Data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: flowFP, flowQ, flowWorkspace, iFlow, plateCore importsMe: flowFP, flowQ, flowStats, flowTrans, flowUtils, iFlow suggestsMe: flowCore, flowStats, spade Package: flowWorkspace Version: 1.2.0 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 MD5sum: d10f55c8a2e49c0b6cd7596b30e9bc83 source.ver: src/contrib/flowWorkspace_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/flowWorkspace_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/flowWorkspace_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/flowWorkspace_1.2.0.tgz vignettes: vignettes/flowWorkspace/inst/doc/flowWorkspace.pdf vignetteTitles: Importing flowJo Workspaces into R hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: flowStats Package: frma Version: 1.8.0 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 , Rafael A. Irizarry , with contributions from Terry Therneau Maintainer: Matthew N. McCall URL: http://bioconductor.org MD5sum: 021027de53fb724a1639a4882d14a091 source.ver: src/contrib/frma_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/frma_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/frma_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/frma_1.8.0.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 suggestsMe: frmaTools Package: frmaTools Version: 1.8.0 Depends: R (>= 2.10.0), affy Imports: Biobase, DBI, methods, preprocessCore, stats, utils Suggests: oligo, 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 , Rafael A. Irizarry Maintainer: Matthew N. McCall URL: http://bioconductor.org MD5sum: ca11d043dd6540759c8d0e9cb5c86ae2 source.ver: src/contrib/frmaTools_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/frmaTools_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/frmaTools_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/frmaTools_1.8.0.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 Package: gaga Version: 2.2.0 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 . Maintainer: David Rossell MD5sum: 63a521a705395c5bfd1220068a6173a1 source.ver: src/contrib/gaga_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gaga_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gaga_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gaga_2.2.0.tgz vignettes: vignettes/gaga/inst/doc/gagamanual.pdf vignetteTitles: Manual for the gaga library hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gage Version: 2.6.0 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, DataRepresentation, Genetics, Bioinformatics, MultipleComparisons Author: Weijun Luo Maintainer: Weijun Luo URL: http://www.biomedcentral.com/1471-2105/10/161 MD5sum: 822306f62a3ec26cccc95e34eda186ad source.ver: src/contrib/gage_2.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gage_2.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gage_2.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gage_2.6.0.tgz vignettes: vignettes/gage/inst/doc/gage.pdf vignetteTitles: Generally Applicable Gene-set/Pathway Analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: gaggle Version: 1.24.0 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: Visualization, Annotation, GraphsAndNetworks, DataImport Author: Paul Shannon Maintainer: Christopher Bare URL: http://gaggle.systemsbiology.net/docs/geese/r/ MD5sum: 3d97cf31d52cd2dd400753aea067efa6 source.ver: src/contrib/gaggle_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gaggle_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gaggle_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gaggle_1.24.0.tgz vignettes: vignettes/gaggle/inst/doc/gaggle.pdf vignetteTitles: Gaggle Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gaia Version: 1.10.2 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, DNACopyNumber Author: Sandro Morganella et al. Maintainer: S. Morganella MD5sum: ce033b2f43d2972a4432b3c3a830ef37 source.ver: src/contrib/gaia_1.10.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/gaia_1.10.2.zip win64.binary.ver: bin/windows64/contrib/2.15/gaia_1.10.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gaia_1.10.2.tgz vignettes: vignettes/gaia/inst/doc/gaia.pdf vignetteTitles: gaia hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gcrma Version: 2.28.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils, BiocInstaller Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), IRanges, Biostrings (>= 2.11.32), splines 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 Jeff Gentry Maintainer: Z. Wu MD5sum: b77b4c06955bf0fbca196ea32994f2b4 source.ver: src/contrib/gcrma_2.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gcrma_2.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gcrma_2.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gcrma_2.28.0.tgz vignettes: vignettes/gcrma/inst/doc/gcrma2.0.pdf vignetteTitles: gcrma1.2 hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: affyILM, affyPLM, bgx, maskBAD, simpleaffy, webbioc importsMe: affycoretools, simpleaffy, virtualArray suggestsMe: AffyExpress, ArrayTools, BiocCaseStudies Package: genArise Version: 1.32.0 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 ,\\ Gustavo Corral Guille , \\ Lina Riego Ruiz ,\\ Gerardo Coello Coutino Maintainer: IFC Development Team URL: http://www.ifc.unam.mx/genarise MD5sum: c4504dd547a83deff0e1396d421fcb1f source.ver: src/contrib/genArise_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/genArise_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/genArise_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/genArise_1.32.0.tgz vignettes: vignettes/genArise/inst/doc/genArise.pdf vignetteTitles: genAriseGUI Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: gene2pathway Version: 2.10.1 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, Bioinformatics, Classification, GraphsAndNetworks, Pathways Author: Holger Froehlich Maintainer: Holger Froehlich MD5sum: 0cd5d6cc51df293d9846f99eb57d0f6b source.ver: src/contrib/gene2pathway_2.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/gene2pathway_2.10.1.zip win64.binary.ver: bin/windows64/contrib/2.15/gene2pathway_2.10.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gene2pathway_2.10.1.tgz vignettes: vignettes/gene2pathway/inst/doc/gene2pathway.pdf vignetteTitles: gene2pathway hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GeneAnswers Version: 1.12.2 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 , Pan Du and Tian Xia MD5sum: 691da41fb9ddca592bf2e615307731fe source.ver: src/contrib/GeneAnswers_1.12.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneAnswers_1.12.2.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneAnswers_1.12.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneAnswers_1.12.2.tgz 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 Package: GeneExpressionSignature Version: 1.2.0 Depends: Biobase 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 , Fei Li MD5sum: b26a546d58b1b456cf08137e6f5f5164 source.ver: src/contrib/GeneExpressionSignature_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneExpressionSignature_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneExpressionSignature_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneExpressionSignature_1.2.0.tgz vignettes: vignettes/GeneExpressionSignature/inst/doc/GeneExpressionSignature.pdf vignetteTitles: GeneExpressionSignature hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: genefilter Version: 1.38.0 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 MD5sum: 36074b4de9990cec13ac855a07bd4e1e source.ver: src/contrib/genefilter_1.38.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/genefilter_1.38.0.zip win64.binary.ver: bin/windows64/contrib/2.15/genefilter_1.38.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/genefilter_1.38.0.tgz 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 dependsOnMe: a4Base, Agi4x44PreProcess, cellHTS, cellHTS2, charm, CNTools, eisa, GeneMeta, MLInterfaces, simpleaffy importsMe: affycoretools, affyQCReport, arrayQualityMetrics, Category, crlmm, DESeq, GGBase, GSRI, 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: 1.6.1 Depends: R (>= 2.10), survcomp, mclust 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 , Markus Schroeder URL: http://compbio.dfci.harvard.edu MD5sum: f0f6e295bdb3f1c195a640d7b9ac51ba source.ver: src/contrib/genefu_1.6.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/genefu_1.6.1.zip win64.binary.ver: bin/windows64/contrib/2.15/genefu_1.6.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/genefu_1.6.1.tgz vignettes: vignettes/genefu/inst/doc/genefu.pdf vignetteTitles: genefu An Introduction (HowTo) hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GeneGA Version: 1.6.0 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 URL: http://www.tbi.univie.ac.at/~ivo/RNA/ MD5sum: 5d1cbea9125d59428ee4f68fd1c57c50 source.ver: src/contrib/GeneGA_1.6.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneGA_1.6.0.tgz vignettes: vignettes/GeneGA/inst/doc/GeneGA.pdf vignetteTitles: GeneGA hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GeneGroupAnalysis Version: 1.2.0 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 URL: http://compbio.dfci.harvard.edu/ MD5sum: bfc91cbb94d535bd2cbffe28dd150c9c source.ver: src/contrib/GeneGroupAnalysis_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneGroupAnalysis_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneGroupAnalysis_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneGroupAnalysis_1.2.0.tgz 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 Package: GeneMeta Version: 1.28.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) 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 , R. Gentleman, M. Ruschhaupt Maintainer: Bioconductor Package Maintainer MD5sum: 2fbcd600ec2566f2c5406b2f3205cf86 source.ver: src/contrib/GeneMeta_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneMeta_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneMeta_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneMeta_1.28.0.tgz vignettes: vignettes/GeneMeta/inst/doc/GeneMeta.pdf vignetteTitles: GeneMeta Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: genefu, XDE Package: geneplotter Version: 1.34.0 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 MD5sum: 59a917e6968ee0f5c8e853d020b03a07 source.ver: src/contrib/geneplotter_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/geneplotter_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/geneplotter_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/geneplotter_1.34.0.tgz 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 importsMe: biocGraph, DESeq, flowQ, IsoGeneGUI, RNAinteract, RNAither suggestsMe: BiocCaseStudies, biocGraph, Category, maDB Package: geneRecommender Version: 1.28.0 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 , with contributions from Art B. Owen and Terence P. Speed Maintainer: Greg Hather MD5sum: a92ce8d36f259c7a7b69c2d495d7ad93 source.ver: src/contrib/geneRecommender_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/geneRecommender_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/geneRecommender_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/geneRecommender_1.28.0.tgz vignettes: vignettes/geneRecommender/inst/doc/geneRecommender.pdf vignetteTitles: Using the geneRecommender Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GeneRegionScan Version: 1.12.0 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 MD5sum: ce2a729a4c20ae7be0addcca3a247d4d source.ver: src/contrib/GeneRegionScan_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneRegionScan_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneRegionScan_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneRegionScan_1.12.0.tgz vignettes: vignettes/GeneRegionScan/inst/doc/GeneRegionScan.pdf vignetteTitles: GeneRegionScan hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GeneSelectMMD Version: 1.12.0 Depends: R (>= 2.13.2), Biobase Imports: Biobase, MASS, graphics, stats, survival, limma Suggests: ALL License: GPL (>= 2) 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: Weiliang Qiu , Wenqing He , Xiaogang Wang , Ross Lazarus . Maintainer: Weiliang Qiu MD5sum: 8bd5a0f24c3d3993c79a168672cdd021 source.ver: src/contrib/GeneSelectMMD_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneSelectMMD_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneSelectMMD_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneSelectMMD_1.12.0.tgz vignettes: vignettes/GeneSelectMMD/inst/doc/gsMMD.pdf vignetteTitles: Gene Selection based on a mixture of marginal distributions hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GeneSelector Version: 2.6.0 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 , Anne-Laure Boulesteix . Maintainer: Martin Slawski MD5sum: 800537aeb48bf80990fa4540ff0a5fcf source.ver: src/contrib/GeneSelector_2.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneSelector_2.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneSelector_2.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneSelector_2.6.0.tgz vignettes: vignettes/GeneSelector/inst/doc/GeneSelector.pdf vignetteTitles: GeneSelector.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GeneticsDesign Version: 1.24.0 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 David Duffy , Michael Man Weiliang Qiu Ross Lazarus Maintainer: The R Genetics Project MD5sum: 446b0037c03e3a83cd8298e333211dcd source.ver: src/contrib/GeneticsDesign_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneticsDesign_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneticsDesign_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneticsDesign_1.24.0.tgz vignettes: vignettes/GeneticsDesign/inst/doc/GPC.pdf vignetteTitles: Package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GeneticsPed Version: 1.18.0 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 , with code contributions by Brian Kinghorn and Andrew Percy (see file COPYING) Maintainer: David Henderson URL: http://rgenetics.org MD5sum: 612ac035bb0bc61222796bd0c8b0b7f9 source.ver: src/contrib/GeneticsPed_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GeneticsPed_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GeneticsPed_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GeneticsPed_1.18.0.tgz 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 Package: genoCN Version: 1.8.0 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 MD5sum: 3d7752956cd80c8a67fd3ed239ce7b3d source.ver: src/contrib/genoCN_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/genoCN_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/genoCN_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/genoCN_1.8.0.tgz vignettes: vignettes/genoCN/inst/doc/genoCN.pdf vignetteTitles: add stuff hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: GenomeGraphs Version: 1.16.0 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 , James Bullard Maintainer: Steffen Durinck MD5sum: 18a0f5531ec5a5f7f85aea634a794cdf source.ver: src/contrib/GenomeGraphs_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GenomeGraphs_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GenomeGraphs_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GenomeGraphs_1.16.0.tgz vignettes: vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf vignetteTitles: The GenomeGraphs users guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: Genominator importsMe: PING suggestsMe: rMAT Package: genomeIntervals Version: 1.12.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.13.3), BiocGenerics (>= 0.1.11) 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 , Joern Toedling, Richard Bourgon, Nicolas Delhomme Maintainer: Julien Gagneur MD5sum: c3c85720bc1165b813698007c6bebe37 source.ver: src/contrib/genomeIntervals_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/genomeIntervals_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/genomeIntervals_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/genomeIntervals_1.12.0.tgz vignettes: vignettes/genomeIntervals/inst/doc/genomeIntervals.pdf vignetteTitles: Overview of the genomeIntervals package. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: easyRNASeq, girafe, HiTC Package: genomes Version: 2.2.0 Depends: R (>= 2.10), XML License: Artistic-2.0 Title: Genome sequencing project metadata Description: Collects genome sequencing project data from NCBI using E-utility scripts (esearch, esummary, efetch and elink) or from the ENA using the Browser REST URL. biocViews: Annotation, Genetics Author: Chris Stubben Maintainer: Chris Stubben MD5sum: 4b40f4eef5f6635edf0be756459cd3bb source.ver: src/contrib/genomes_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/genomes_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/genomes_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/genomes_2.2.0.tgz vignettes: vignettes/genomes/inst/doc/genome-tables.pdf vignetteTitles: Introduction to genome projects hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GenomicFeatures Version: 1.8.3 Depends: BiocGenerics (>= 0.1.0), IRanges (>= 1.13.10), GenomicRanges (>= 1.7.17), AnnotationDbi (>= 1.15.39) 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.Celegans.UCSC.ce2, mirbase.db, FDb.UCSC.tRNAs, RUnit, TxDb.Hsapiens.UCSC.hg18.knownGene 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 MD5sum: b246a29eeb5aa304aa79f98b86965aab source.ver: src/contrib/GenomicFeatures_1.8.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/GenomicFeatures_1.8.3.zip win64.binary.ver: bin/windows64/contrib/2.15/GenomicFeatures_1.8.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GenomicFeatures_1.8.3.tgz vignettes: vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf, vignettes/GenomicFeatures/inst/doc/spliceGraph.pdf vignetteTitles: Making and Utilizing TranscriptDb Objects, Representing Transcripts as Splice Graphs hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: biovizBase, ggbio, VariantAnnotation suggestsMe: Biostrings, chipseq, easyRNASeq, GenomicRanges, Rsamtools, ShortRead Package: GenomicRanges Version: 1.8.13 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.12), IRanges (>= 1.13.36) Imports: methods, BiocGenerics, IRanges LinkingTo: IRanges Suggests: Rsamtools (>= 1.7.42), BSgenome, rtracklayer, GenomicFeatures, EatonEtAlChIPseq (>= 0.0.3), leeBamViews, edgeR, DESeq, rtracklayer, org.Sc.sgd.db, BSgenome.Scerevisiae.UCSC.sacCer2, DEXSeq, pasilla, pasillaBamSubset, VariantAnnotation, RUnit 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 MD5sum: ae8245efa3382d22faae4318bf04c7bb source.ver: src/contrib/GenomicRanges_1.8.13.tar.gz win.binary.ver: bin/windows/contrib/2.15/GenomicRanges_1.8.13.zip win64.binary.ver: bin/windows64/contrib/2.15/GenomicRanges_1.8.13.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GenomicRanges_1.8.13.tgz 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 dependsOnMe: BSgenome, chipseq, cn.mops, CSAR, deepSNV, DiffBind, easyRNASeq, exomeCopy, fastseg, GenomicFeatures, genoset, GGtools, gwascat, htSeqTools, minfi, PICS, Repitools, Rsamtools, rtracklayer, segmentSeq, seqbias, ShortRead, VariantAnnotation importsMe: ArrayExpressHTS, biovizBase, chipseq, ChIPseqR, GenomicFeatures, genoset, ggbio, Gviz, lumi, NarrowPeaks, nucleR, PICS, PING, Repitools, rnaSeqMap, Rsamtools, rtracklayer, segmentSeq, ShortRead suggestsMe: BiocGenerics, NarrowPeaks, Repitools Package: Genominator Version: 1.10.0 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 MD5sum: 2df0b043f9f230d2a534e1cd2ee18f2f source.ver: src/contrib/Genominator_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Genominator_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Genominator_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Genominator_1.10.0.tgz 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 suggestsMe: oneChannelGUI Package: genoset Version: 1.6.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.6), Biobase (>= 2.15.1), IRanges (>= 1.13.5), bigmemory, GenomicRanges Imports: methods, BiocGenerics, Biobase, DNAcopy, graphics, IRanges, stats, GenomicRanges, Biostrings, BSgenome, bigmemory Suggests: RUnit Enhances: parallel, BSgenome.Hsapiens.UCSC.hg19 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 object from the IRanges package. This object contains feature genome location data and provides for simple 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 MD5sum: 15feaf2a40a608dfdbbea35f415d95eb source.ver: src/contrib/genoset_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/genoset_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/genoset_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/genoset_1.6.0.tgz vignettes: vignettes/genoset/inst/doc/genoset.pdf vignetteTitles: genoset hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: VegaMC importsMe: lumi Package: GEOmetadb Version: 1.16.0 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 URL: http://gbnci.abcc.ncifcrf.gov/geo/ MD5sum: b9d58b2e24df7341dfc642a771863cb7 source.ver: src/contrib/GEOmetadb_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GEOmetadb_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GEOmetadb_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GEOmetadb_1.16.0.tgz 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 Package: GEOquery Version: 2.23.5 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 Maintainer: Sean Davis URL: http://watson.nci.nih.gov/~sdavis MD5sum: f2a8e40d672f52c5f53ce51076e9cea5 source.ver: src/contrib/GEOquery_2.23.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/GEOquery_2.23.5.zip win64.binary.ver: bin/windows64/contrib/2.15/GEOquery_2.23.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GEOquery_2.23.5.tgz vignettes: vignettes/GEOquery/inst/doc/GEOquery.pdf vignetteTitles: GEOquery hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: SRAdb, virtualArray suggestsMe: dyebias, PGSEA Package: GEOsubmission Version: 1.8.0 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 Maintainer: Alexandre Kuhn MD5sum: 29639901c10735c47b241e15059b3c25 source.ver: src/contrib/GEOsubmission_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GEOsubmission_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GEOsubmission_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GEOsubmission_1.8.0.tgz vignettes: vignettes/GEOsubmission/inst/doc/GEOsubmission.pdf vignetteTitles: GEOsubmission Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GEWIST Version: 1.0.0 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 MD5sum: a7d0d8c855d238fe0223311d20c3763b source.ver: src/contrib/GEWIST_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GEWIST_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GEWIST_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GEWIST_1.0.0.tgz vignettes: vignettes/GEWIST/inst/doc/GEWIST.pdf vignetteTitles: GEWIST.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GGBase Version: 3.18.0 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 Maintainer: VJ Carey MD5sum: 28170330398348c6fd2f60df7cacc4d9 source.ver: src/contrib/GGBase_3.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GGBase_3.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GGBase_3.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GGBase_3.18.0.tgz vignettes: vignettes/GGBase/inst/doc/ggbase.pdf vignetteTitles: GGBase -- infrastructure for GGtools,, genetics of gene expression hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: GGtools importsMe: qpgraph Package: ggbio Version: 1.4.6 Depends: methods, ggplot2 (>= 0.9) Imports: methods, biovizBase(>= 1.4.2), reshape2, ggplot2(>= 0.9), BiocGenerics, Biobase, IRanges, GenomicRanges, GenomicFeatures, Rsamtools, BSgenome, gridExtra, scales, plyr, VariantAnnotation, Hmisc, rtracklayer Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, affyPLM 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 URL: http://tengfei.github.com/ggbio/ MD5sum: a9a2291a3639c510a25125b723f1cf76 source.ver: src/contrib/ggbio_1.4.6.tar.gz win.binary.ver: bin/windows/contrib/2.15/ggbio_1.4.6.zip win64.binary.ver: bin/windows64/contrib/2.15/ggbio_1.4.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ggbio_1.4.6.tgz vignettes: vignettes/ggbio/inst/doc/intro.pdf vignetteTitles: An Introduction to ggbio hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: GGtools Version: 4.4.0 Depends: R (>= 2.14), stats4, GGBase (>= 3.16.1), IRanges, GenomicRanges, Rsamtools Imports: methods, utils, stats, BiocGenerics, snpStats, ff, AnnotationDbi, Biobase, bit, VariantAnnotation Suggests: GGdata, illuminaHumanv1.db 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 Author: VJ Carey Maintainer: VJ Carey MD5sum: 651dcf4b49979c9415c7bdc1af5189a5 source.ver: src/contrib/GGtools_4.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GGtools_4.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GGtools_4.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GGtools_4.4.0.tgz vignettes: vignettes/GGtools/inst/doc/GGtools_2012.pdf vignetteTitles: GGtools 2012: efficient tools for eQTL discovery hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: girafe Version: 1.8.0 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 MD5sum: 230f3f45a0b159c38598da0d7c173eb7 source.ver: src/contrib/girafe_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/girafe_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/girafe_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/girafe_1.8.0.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 dependsOnMe: HiTC Package: GLAD Version: 2.18.0 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 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: 0f78912aa02e8417262b1dd6d6bc1571 source.ver: src/contrib/GLAD_2.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GLAD_2.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GLAD_2.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GLAD_2.18.0.tgz vignettes: vignettes/GLAD/inst/doc/GLAD.pdf vignetteTitles: GLAD hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ITALICS, MANOR importsMe: ITALICS, MANOR, snapCGH suggestsMe: ADaCGH2 Package: GlobalAncova Version: 3.24.0 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 MD5sum: 40553a37d302e2bd9e141da82abafffe source.ver: src/contrib/GlobalAncova_3.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GlobalAncova_3.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GlobalAncova_3.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GlobalAncova_3.24.0.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 Package: globaltest Version: 5.10.0 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 URL: http://www.msbi.nl/goeman MD5sum: 5e5912931a7dc48196a9aec5f98f62a8 source.ver: src/contrib/globaltest_5.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/globaltest_5.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/globaltest_5.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/globaltest_5.10.0.tgz vignettes: vignettes/globaltest/inst/doc/GlobalTest_deprecated.pdf, vignettes/globaltest/inst/doc/GlobalTest.pdf vignetteTitles: Global Test (deprecated version 4), Global Test hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: GlobalAncova importsMe: SIM suggestsMe: topGO Package: GOFunction Version: 1.2.0 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: Bioinformatics, GO, Pathways, Microarray Author: Jing Wang Maintainer: Zheng Guo MD5sum: b138835e6075e986af3e5a824c998216 source.ver: src/contrib/GOFunction_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GOFunction_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GOFunction_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GOFunction_1.2.0.tgz vignettes: vignettes/GOFunction/inst/doc/GOFunction.pdf vignetteTitles: GO-function hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: goProfiles Version: 1.18.0 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 MD5sum: 0417eb07a874fff328e5fbd87a58284b source.ver: src/contrib/goProfiles_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/goProfiles_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/goProfiles_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/goProfiles_1.18.0.tgz vignettes: vignettes/goProfiles/inst/doc/goProfiles.pdf vignetteTitles: goProfiles Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GOSemSim Version: 1.14.0 Depends: R (>= 2.10) Imports: methods, AnnotationDbi, GO.db, org.Hs.eg.db Suggests: DOSE, clusterProfiler License: GPL-2 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, Bioinformatics Author: Guangchuang Yu Maintainer: Guangchuang Yu URL: http://bioinformatics.oxfordjournals.org/content/26/7/976.full MD5sum: 966ba8118c94f87256c24a89aaba8823 source.ver: src/contrib/GOSemSim_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GOSemSim_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GOSemSim_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GOSemSim_1.14.0.tgz vignettes: vignettes/GOSemSim/inst/doc/GOSemSim.pdf vignetteTitles: An introduction to GOSemSim hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: clusterProfiler, DOSE, ReactomePA Package: goseq Version: 1.8.0 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 MD5sum: ba18a8075b1e3ac1aec25ef54773e35f source.ver: src/contrib/goseq_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/goseq_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/goseq_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/goseq_1.8.0.tgz vignettes: vignettes/goseq/inst/doc/goseq.pdf vignetteTitles: goseq User's Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oneChannelGUI Package: GOstats Version: 2.22.0 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 Suggests: hgu95av2.db (>= 1.13.0), ALL, GO.db (>= 1.13.0), annotate, multtest, genefilter, RColorBrewer, Rgraphviz, xtable, SparseM 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 MD5sum: b3b1dc526f7fd5921757b99c730be491 source.ver: src/contrib/GOstats_2.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GOstats_2.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GOstats_2.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GOstats_2.22.0.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 dependsOnMe: attract importsMe: affycoretools, attract, categoryCompare suggestsMe: BiocCaseStudies, eisa, GSEAlm, HTSanalyzeR, MLP, MmPalateMiRNA, oneChannelGUI, phenoDist, qpgraph, safe Package: goTools Version: 1.30.0 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 , Agnes Paquet Maintainer: Agnes Paquet MD5sum: ad4c314746326a0841b04f78213bf099 source.ver: src/contrib/goTools_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/goTools_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/goTools_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/goTools_1.30.0.tgz vignettes: vignettes/goTools/inst/doc/goTools.pdf vignetteTitles: goTools overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: gpls Version: 1.28.0 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 MD5sum: d75de24ee26dccdf1ef6a2b35650669e source.ver: src/contrib/gpls_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gpls_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gpls_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gpls_1.28.0.tgz vignettes: vignettes/gpls/inst/doc/gpls.pdf vignetteTitles: gpls Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MCRestimate, MLInterfaces Package: gprege Version: 1.0.0 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 Maintainer: Alfredo A. Kalaitzis URL: http://staffwww.dcs.shef.ac.uk/people/A.Kalaitzis/ MD5sum: 34d4330ffda236e462a5bfcfb8fd5924 source.ver: src/contrib/gprege_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gprege_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gprege_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gprege_1.0.0.tgz vignettes: vignettes/gprege/inst/doc/gprege_quick.pdf vignetteTitles: gprege Quick Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: graph Version: 1.34.0 Depends: R (>= 2.10), methods Imports: methods, stats, 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: Seth Falcon MD5sum: 9c82c060f35d7a25d676dd90208a7620 source.ver: src/contrib/graph_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/graph_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/graph_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/graph_1.34.0.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 dependsOnMe: apComplex, biocGraph, BioMVCClass, BioNet, CellNOptR, flowWorkspace, gage, gaggle, 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, GOFunction, GOstats, GraphAT, graphite, GSEABase, HTSanalyzeR, KEGGgraph, keggorthology, NCIgraph, nem, PCpheno, pkgDepTools, ppiStats, qpgraph, RchyOptimyx, Rgraphviz, rsbml, Rtreemix, Streamer, topGO suggestsMe: BiocCaseStudies, Category, categoryCompare, DEGraph, EBcoexpress, ecolitk, GSVA, MmPalateMiRNA, qpgraph, RedeR, SPIA Package: GraphAlignment Version: 1.18.0 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 Author: Joern P. Meier , Michal Kolar, Ville Mustonen, Michael Laessig, and Johannes Berg. Maintainer: Joern P. Meier URL: http://www.thp.uni-koeln.de/~berg/GraphAlignment/ MD5sum: 21e103d2ef713ea8562173b3b2a61940 source.ver: src/contrib/GraphAlignment_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GraphAlignment_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GraphAlignment_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GraphAlignment_1.18.0.tgz 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 Package: GraphAT Version: 1.28.0 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: Bioinformatics, GraphsAndNetworks Author: R. Balasubramanian, T. LaFramboise, D. Scholtens Maintainer: Thomas LaFramboise MD5sum: 2b1ad8b196668afb41b477cb07770849 source.ver: src/contrib/GraphAT_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GraphAT_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GraphAT_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GraphAT_1.28.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: graphite Version: 1.2.0 Depends: R (>= 2.10), graph Imports: AnnotationDbi, graph, graphics, methods, org.Hs.eg.db, stats, utils Suggests: DEGraph (>= 1.4), hgu133plus2.db, RCytoscape (>= 1.2), 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 Author: Gabriele Sales , Enrica Calura , Chiara Romualdi Maintainer: Gabriele Sales MD5sum: 39faccd7bf525b2dc75158f9f1b1092f source.ver: src/contrib/graphite_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/graphite_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/graphite_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/graphite_1.2.0.tgz vignettes: vignettes/graphite/inst/doc/graphite.pdf vignetteTitles: GRAPH Interaction from pathway Topological Environment hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE 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: Bioinformatics, TimeCourse, GraphsAndNetworks Author: Edward Morrissey Maintainer: Edward Morrissey MD5sum: 64e7dd373d30f8a9819040ab1ba7d15f 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: bin/macosx/leopard/contrib/2.15/GRENITS_1.10.0.tgz vignettes: vignettes/GRENITS/inst/doc/GRENITS_package.pdf vignetteTitles: GRENITS hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: GSEABase Version: 1.18.0 Depends: R (>= 2.6.0), BiocGenerics, Biobase, 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 MD5sum: f076a47f5b4ff011c94bc55f3d746f06 source.ver: src/contrib/GSEABase_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GSEABase_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GSEABase_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GSEABase_1.18.0.tgz vignettes: vignettes/GSEABase/inst/doc/GSEABase.pdf vignetteTitles: An introduction to GSEABase hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: AGDEX, BicARE, GSVA, HTSanalyzeR, PROMISE importsMe: Category, categoryCompare, cellHTS2, GSRI, GSVA, HTSanalyzeR, PCpheno, phenoTest, PROMISE suggestsMe: BiocCaseStudies, categoryCompare, gage, GlobalAncova, globaltest, PGSEA, phenoTest Package: GSEAlm Version: 1.16.0 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 MD5sum: 494d697a259527f2075d20a48165cf60 source.ver: src/contrib/GSEAlm_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GSEAlm_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GSEAlm_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GSEAlm_1.16.0.tgz vignettes: vignettes/GSEAlm/inst/doc/GSEAlm.pdf vignetteTitles: Linear models in GSEA hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GSRI Version: 2.4.0 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 URL: http://julian-gehring.github.com/GSRI/ MD5sum: 8849e6239a8c6d77c937359ea1c6a3b2 source.ver: src/contrib/GSRI_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/GSRI_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/GSRI_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GSRI_2.4.0.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 Package: GSVA Version: 1.4.4 Depends: R (>= 2.13.0), methods, GSEABase (>= 1.18.0) Imports: methods, Biobase, GSEABase Suggests: limma, qpgraph, RBGL, graph, Rgraphviz, RColorBrewer, genefilter, mclust, edgeR, GSVAdata Enhances: snow, parallel License: GPL (>= 2) Archs: i386, x64 Title: Gene Set Variation Analysis 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: Bioinformatics, Microarray, Pathways Author: Justin Guinney (with contributions from Robert Castelo and Sonja Haenzelmann URL: http://www.sagebase.org MD5sum: 82ca9824d5bda4aacd0db994bab6facb source.ver: src/contrib/GSVA_1.4.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/GSVA_1.4.4.zip win64.binary.ver: bin/windows64/contrib/2.15/GSVA_1.4.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GSVA_1.4.4.tgz vignettes: vignettes/GSVA/inst/doc/GSVA.pdf vignetteTitles: Gene Set Variation Analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: Gviz Version: 1.0.1 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) Suggests: xtable 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 Maintainer: Florian Hahne MD5sum: 2474c0ddc18e39e63ff8d83a02f4fc5e source.ver: src/contrib/Gviz_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/Gviz_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.15/Gviz_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Gviz_1.0.1.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: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: gwascat Version: 1.0.0 Depends: R (>= 2.14.0), methods, IRanges, GenomicRanges, snpStats, graph Imports: Biostrings Suggests: DO.db Enhances: SNPlocs.Hsapiens.dbSNP.20110815, 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 Maintainer: VJ Carey MD5sum: 797d9a3a7291f3198cf284ddb67462f2 source.ver: src/contrib/gwascat_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/gwascat_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/gwascat_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/gwascat_1.0.0.tgz vignettes: vignettes/gwascat/inst/doc/gwascat.pdf vignetteTitles: gwascat -- exploring NHGRI GWAS catalog hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: GWASTools Version: 1.2.1 Depends: Biobase, ncdf, GWASExactHW, sandwich Imports: methods, DBI, RSQLite, DNAcopy, survival, lmtest Suggests: GWASdata, RUnit, gdsfmt, SNPRelate 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, Cecilia Laurie, Caitlin McHugh, Ian Painter, Xiuwen Zheng, Jess Shen, Rohit Swarnkar Maintainer: Stephanie M. Gogarten MD5sum: 6187f6cd9a8892161476780881bbff90 source.ver: src/contrib/GWASTools_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/GWASTools_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/GWASTools_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/GWASTools_1.2.1.tgz vignettes: vignettes/GWASTools/inst/doc/DataCleaning.pdf vignetteTitles: GWAS Data Cleaning hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: Harshlight Version: 1.28.0 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 URL: http://asterion.rockefeller.edu/Harshlight/ MD5sum: 9f81738256dbb00776cf307450d70c39 source.ver: src/contrib/Harshlight_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Harshlight_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Harshlight_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Harshlight_1.28.0.tgz vignettes: vignettes/Harshlight/inst/doc/Harshlight.pdf vignetteTitles: Harshlight hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Heatplus Version: 2.2.0 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 Maintainer: Alexander Ploner MD5sum: 7d9287c5e89f5bbfe1b21a5cecfb96f6 source.ver: src/contrib/Heatplus_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Heatplus_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Heatplus_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Heatplus_2.2.0.tgz 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 dependsOnMe: GeneAnswers, phenoTest Package: HELP Version: 1.14.0 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 , John M. Greally , with contributions from Mark Reimers Maintainer: Reid F. Thompson MD5sum: fc07400acf97453f7857d4cde5241c22 source.ver: src/contrib/HELP_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HELP_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HELP_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HELP_1.14.0.tgz vignettes: vignettes/HELP/inst/doc/HELP.pdf vignetteTitles: 1. Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HEM Version: 1.28.0 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 and Jae K. Lee Maintainer: HyungJun Cho URL: http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/ MD5sum: 7655d4e4b2385ac8105527b7bb31f0ed source.ver: src/contrib/HEM_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HEM_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HEM_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HEM_1.28.0.tgz vignettes: vignettes/HEM/inst/doc/HEM.pdf vignetteTitles: HEM Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: HilbertVis Version: 1.14.0 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 Maintainer: Simon Anders URL: http://www.ebi.ac.uk/~anders/hilbert MD5sum: f2f82d696fdeb572cb87f5ed4ec407aa source.ver: src/contrib/HilbertVis_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HilbertVis_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HilbertVis_1.14.0.zip 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 dependsOnMe: HilbertVisGUI importsMe: ChIPseqR Package: HilbertVisGUI Version: 1.14.0 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 Maintainer: Simon Anders URL: http://www.ebi.ac.uk/~anders/hilbert SystemRequirements: gtkmm-2.4 MD5sum: cdea2b7465d7924e0a424cbccf289dec source.ver: src/contrib/HilbertVisGUI_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HilbertVisGUI_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HilbertVisGUI_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HilbertVisGUI_1.14.0.tgz vignettes: vignettes/HilbertVisGUI/inst/doc/HilbertVisGUI.pdf vignetteTitles: See vignette in package HilbertVis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: TRUE hasLICENSE: FALSE Package: HiTC Version: 1.0.0 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: N. Servant MD5sum: 5bea7936f165b6ce8532add254f4b6b7 source.ver: src/contrib/HiTC_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HiTC_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HiTC_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HiTC_1.0.0.tgz vignettes: vignettes/HiTC/inst/doc/HiTC.pdf vignetteTitles: Hight-Throughput Chromosome Conformation Capture analysis hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: hopach Version: 2.16.0 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 and Greg Wall Maintainer: Katherine S. Pollard URL: http://www.stat.berkeley.edu/~laan/, http://docpollard.org/ MD5sum: 3a446f08a42f0c5b11cf0d47ff1c0191 source.ver: src/contrib/hopach_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/hopach_2.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/hopach_2.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hopach_2.16.0.tgz 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 importsMe: phenoTest suggestsMe: BiocCaseStudies Package: HTqPCR Version: 1.10.0 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 URL: http://www.ebi.ac.uk/bertone/software MD5sum: 7385c497224e3afa2d71f91ccd39c572 source.ver: src/contrib/HTqPCR_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HTqPCR_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HTqPCR_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HTqPCR_1.10.0.tgz vignettes: vignettes/HTqPCR/inst/doc/HTqPCR.pdf vignetteTitles: qPCR analysis in R hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: HTSanalyzeR Version: 2.8.3 Depends: R (>= 2.10), igraph0, GSEABase, BioNet, cellHTS2, RankProd, methods Imports: graph, igraph0, GSEABase, BioNet, cellHTS2, AnnotationDbi, biomaRt 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 , Camille Terfve , John C. Rose , Florian Markowetz Maintainer: Xin Wang MD5sum: 5f022e92cfa699366c8999bc904d84aa source.ver: src/contrib/HTSanalyzeR_2.8.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/HTSanalyzeR_2.8.3.zip win64.binary.ver: bin/windows64/contrib/2.15/HTSanalyzeR_2.8.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HTSanalyzeR_2.8.3.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 importsMe: phenoTest suggestsMe: RedeR Package: htSeqTools Version: 1.2.0 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 MD5sum: 0cd33fb2542aa19d27d95696b2cd382b source.ver: src/contrib/htSeqTools_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/htSeqTools_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/htSeqTools_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/htSeqTools_1.2.0.tgz vignettes: vignettes/htSeqTools/inst/doc/htSeqTools.pdf vignetteTitles: Manual for the htSeqTools library hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: HybridMTest Version: 1.0.0 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. Author: Stan Pounds , Demba Fofana Maintainer: Demba Fofana MD5sum: e2303edaf1856005b6c1e503a1784fa9 source.ver: src/contrib/HybridMTest_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/HybridMTest_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/HybridMTest_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/HybridMTest_1.0.0.tgz vignettes: vignettes/HybridMTest/inst/doc/HybridMTest.pdf vignetteTitles: Hybrid Multiple Testing hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hyperdraw Version: 1.8.0 Depends: R (>= 2.9.0), methods, grid, graph, hypergraph, Rgraphviz Imports: stats4 License: GPL (>= 2) Title: Visualizing Hypergaphs Description: Functions for visualizing hypergraphs. biocViews: GraphsAndNetworks Author: Paul Murrell Maintainer: Paul Murrell SystemRequirements: graphviz MD5sum: 206eec54bfac982663a16438ed71e806 source.ver: src/contrib/hyperdraw_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/hyperdraw_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/hyperdraw_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hyperdraw_1.8.0.tgz vignettes: vignettes/hyperdraw/inst/doc/hyperdraw.pdf vignetteTitles: Hyperdraw hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: hypergraph Version: 1.28.0 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: Infrastructure, GraphsAndNetworks Author: Seth Falcon, Robert Gentleman Maintainer: Bioconductor Package Maintainer MD5sum: c1d4d89c3a4819224eb34a3eb1728520 source.ver: src/contrib/hypergraph_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/hypergraph_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/hypergraph_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/hypergraph_1.28.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: altcdfenvs, hyperdraw, RpsiXML Package: iASeq Version: 1.0.0 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 MD5sum: 8c1280ddc1c4999c033d55c04a44e502 source.ver: src/contrib/iASeq_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/iASeq_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/iASeq_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iASeq_1.0.0.tgz vignettes: vignettes/iASeq/inst/doc/iASeqVignette.pdf vignetteTitles: iASeq Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: iBBiG Version: 1.0.2 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: Bioinformatics, Clustering,Annotation Author: Daniel Gusenleitner, Aedin Culhane Maintainer: Aedin Culhane URL: http://bcb.dfci.harvard.edu/~aedin/publications/ MD5sum: 7de48d1a963c76d83b046dac175992cf source.ver: src/contrib/iBBiG_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/iBBiG_1.0.2.zip win64.binary.ver: bin/windows64/contrib/2.15/iBBiG_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iBBiG_1.0.2.tgz vignettes: vignettes/iBBiG/inst/doc/tutorial.pdf vignetteTitles: iBBiG User Manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ibh Version: 1.4.0 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, Bioinformatics Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin Atalay. Maintainer: Kircicegi Korkmaz MD5sum: 7c980d4b736699692311fbc8febf79ae source.ver: src/contrib/ibh_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ibh_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ibh_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ibh_1.4.0.tgz vignettes: vignettes/ibh/inst/doc/ibh.pdf vignetteTitles: hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Icens Version: 1.28.0 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 MD5sum: c1192c23c368d23af8b0290d30eac51f source.ver: src/contrib/Icens_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Icens_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Icens_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Icens_1.28.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: PROcess importsMe: PROcess Package: iChip Version: 1.10.0 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: ChIP-chip, NimbleGen, Affymetrix, Agilent,Microarray, Bioinformatics Author: Qianxing Mo Maintainer: Qianxing Mo MD5sum: c6bdcd14c73ad9018711e115b1d7188c source.ver: src/contrib/iChip_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/iChip_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/iChip_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iChip_1.10.0.tgz vignettes: vignettes/iChip/inst/doc/iChip.pdf vignetteTitles: iChip hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: idiogram Version: 1.32.0 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 Maintainer: Karl J. Dykema MD5sum: fbd6416ff926dad7fdc09707d5a0ba63 source.ver: src/contrib/idiogram_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/idiogram_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/idiogram_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/idiogram_1.32.0.tgz vignettes: vignettes/idiogram/inst/doc/idiogram.pdf vignetteTitles: HOWTO: idiogram hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: reb Package: IdMappingAnalysis Version: 1.0.1 Depends: R (>= 2.14), R.oo, 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 , Roger Day MD5sum: 857fd4c0741d8e9e726fbe60fb48fce7 source.ver: src/contrib/IdMappingAnalysis_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/IdMappingAnalysis_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.15/IdMappingAnalysis_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/IdMappingAnalysis_1.0.1.tgz 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 Package: IdMappingRetrieval Version: 1.2.0 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 , Roger Day MD5sum: ffcc987fadec6b5a0101e98f2b16a180 source.ver: src/contrib/IdMappingRetrieval_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/IdMappingRetrieval_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/IdMappingRetrieval_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/IdMappingRetrieval_1.2.0.tgz 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 Package: iFlow Version: 2.8.0 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 URL: http://www.hindawi.com/journals/abi/2009/103839.html MD5sum: d853906476d7f3356d7e4d24c2761e27 source.ver: src/contrib/iFlow_2.8.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iFlow_2.8.0.tgz vignettes: vignettes/iFlow/inst/doc/iflow.pdf vignetteTitles: How to iFlow hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: imageHTS Version: 1.6.0 Depends: R (>= 2.9.0), EBImage (>= 3.7.1), cellHTS2 (>= 2.10.0) Imports: tools, Biobase, hwriter, methods, vsn, stats, utils, e1071 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 MD5sum: 3261796a2da5b55ddee19184be98ded1 source.ver: src/contrib/imageHTS_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/imageHTS_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/imageHTS_1.6.0.zip 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 dependsOnMe: phenoDist Package: impute Version: 1.30.0 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 MD5sum: f475f7f53cf859b471004641610d8797 source.ver: src/contrib/impute_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/impute_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/impute_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/impute_1.30.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: BioNet Package: inSilicoDb Version: 1.4.0 Depends: R (>= 2.11.0), rjson, Biobase Imports: RCurl 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 Maintainer: Jonatan Taminau , David Steenhoff URL: http://insilico.ulb.ac.be MD5sum: 266d70df498d6df65c31d2fabee8022a source.ver: src/contrib/inSilicoDb_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/inSilicoDb_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/inSilicoDb_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/inSilicoDb_1.4.0.tgz vignettes: vignettes/inSilicoDb/inst/doc/inSilicoDb.pdf vignetteTitles: hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: inSilicoMerging Package: inSilicoMerging Version: 1.0.8 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 , Stijn Meganck , Cosmin Lazar Maintainer: Jonatan Taminau , Stijn Meganck , Cosmin Lazar URL: http://insilico.ulb.ac.be/insilico-project/ MD5sum: abefd18681e0b077d44716a07a426ede source.ver: src/contrib/inSilicoMerging_1.0.8.tar.gz win.binary.ver: bin/windows/contrib/2.15/inSilicoMerging_1.0.8.zip win64.binary.ver: bin/windows64/contrib/2.15/inSilicoMerging_1.0.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/inSilicoMerging_1.0.8.tgz vignettes: vignettes/inSilicoMerging/inst/doc/inSilicoMerging.pdf vignetteTitles: hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: inveRsion Version: 1.4.0 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, SNPsAndGeneticVariability Author: Alejandro Caceres Maintainer: Alejandro Caceres MD5sum: 27ec44c32ac4293fbfcac70a7c3a4198 source.ver: src/contrib/inveRsion_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/inveRsion_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/inveRsion_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/inveRsion_1.4.0.tgz 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 Package: iontree Version: 1.2.0 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 MD5sum: 10b930fab446522a982935616b5ac8d2 source.ver: src/contrib/iontree_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/iontree_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/iontree_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iontree_1.2.0.tgz vignettes: vignettes/iontree/inst/doc/iontree_doc.pdf vignetteTitles: MSn hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: IPPD Version: 1.4.0 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 , Rene Hussong , Matthias Hein Maintainer: Martin Slawski MD5sum: 2970f2ccf6af1e8c4f0851a8dd48a069 source.ver: src/contrib/IPPD_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/IPPD_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/IPPD_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/IPPD_1.4.0.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 Package: IRanges Version: 1.14.4 Depends: R (>= 2.8.0), methods, utils, stats, BiocGenerics (>= 0.1.4) Imports: methods, utils, stats, BiocGenerics, stats4 Suggests: 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 MD5sum: 30b5ee3f6ab7162bf885cf5e6de29e2d source.ver: src/contrib/IRanges_1.14.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/IRanges_1.14.4.zip win64.binary.ver: bin/windows64/contrib/2.15/IRanges_1.14.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/IRanges_1.14.4.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 dependsOnMe: BayesPeak, Biostrings, BSgenome, ChIPpeakAnno, chipseq, cn.mops, CSAR, DECIPHER, deepSNV, easyRNASeq, exomeCopy, GenomicFeatures, GenomicRanges, Genominator, genoset, GGtools, girafe, gwascat, htSeqTools, MinimumDistance, nucleR, oneChannelGUI, PICS, r3Cseq, rGADEM, rMAT, Rsamtools, segmentSeq, ShortRead, TEQC, xmapcore importsMe: AnnotationDbi, ArrayExpressHTS, BayesPeak, Biostrings, biovizBase, BitSeq, charm, ChIPpeakAnno, chipseq, ChIPseqR, ChIPsim, ChromHeatMap, cn.mops, DECIPHER, DiffBind, EDASeq, fastseg, flowQ, gcrma, GenomicFeatures, GenomicRanges, genoset, ggbio, girafe, Gviz, lumi, MEDIPS, methVisual, mosaics, motifRG, MotIV, MSnbase, NarrowPeaks, nucleR, oligoClasses, OTUbase, pdInfoBuilder, PICS, PING, R453Plus1Toolbox, REDseq, Repitools, rGADEM, rMAT, rnaSeqMap, Rolexa, Rsamtools, rtracklayer, segmentSeq, ShortRead, SNPchip, TSSi, VanillaICE, VariantAnnotation suggestsMe: BiocGenerics, HilbertVis, HilbertVisGUI, Repitools Package: iSeq Version: 1.8.0 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 or without controls. biocViews: ChIP-seq, next generation sequencing, massively parallel sequencing, bioinformatics Author: Qianxing Mo Maintainer: Qianxing Mo MD5sum: 19f0cf58fdada54723fe61959a0ac164 source.ver: src/contrib/iSeq_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/iSeq_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/iSeq_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iSeq_1.8.0.tgz vignettes: vignettes/iSeq/inst/doc/iSeq.pdf vignetteTitles: iSeq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: isobar Version: 1.2.1 Depends: R (>= 2.10.0), Biobase, stats, methods, plyr Imports: distr Suggests: MSnbase, OrgMassSpecR, XML, biomaRt, ggplot2 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 and Jacques Colinge , with contributions from Xavier Robin Maintainer: Florian P Breitwieser URL: http://bioinformatics.cemm.oeaw.ac.at MD5sum: 3f76114ef38eee2bcf0459d8d456d323 source.ver: src/contrib/isobar_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/isobar_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/isobar_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/isobar_1.2.1.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 Package: IsoGeneGUI Version: 1.12.0 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 URL: http://www.ibiostat.be/software/IsoGeneGUI/index.html MD5sum: 92fe30877ae062018be75dff7fded032 source.ver: src/contrib/IsoGeneGUI_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/IsoGeneGUI_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/IsoGeneGUI_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/IsoGeneGUI_1.12.0.tgz vignettes: vignettes/IsoGeneGUI/inst/doc/IsoGeneGUI.pdf vignetteTitles: IsoGeneGUI Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ITALICS Version: 2.16.0 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 URL: http://bioinfo.curie.fr MD5sum: 7c59500627b8b8f23d0eee0b21a2ca14 source.ver: src/contrib/ITALICS_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ITALICS_2.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ITALICS_2.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ITALICS_2.16.0.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 Package: iterativeBMA Version: 1.14.0 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 URL: http://faculty.washington.edu/kayee/research.html MD5sum: 097a39f018bf076001939a0b57a59284 source.ver: src/contrib/iterativeBMA_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/iterativeBMA_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/iterativeBMA_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iterativeBMA_1.14.0.tgz vignettes: vignettes/iterativeBMA/inst/doc/iterativeBMA.pdf vignetteTitles: The Iterative Bayesian Model Averaging Algorithm hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: iterativeBMAsurv Version: 1.14.0 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 URL: http://expression.washington.edu/ibmasurv/protected MD5sum: 29ce65bf25fde3de063b6cc8ee7822a3 source.ver: src/contrib/iterativeBMAsurv_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/iterativeBMAsurv_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/iterativeBMAsurv_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/iterativeBMAsurv_1.14.0.tgz 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 Package: joda Version: 1.4.0 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, Bioinformatics, Pathways, GraphsAnNetworks, Statistics Author: Ewa Szczurek Maintainer: Ewa Szczurek URL: http://www.bioconductor.org MD5sum: 41cd38538baae1fa90e8dd7a80d41208 source.ver: src/contrib/joda_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/joda_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/joda_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/joda_1.4.0.tgz vignettes: vignettes/joda/inst/doc/JodaVignette.pdf vignetteTitles: Introduction to joda hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: KCsmart Version: 2.14.0 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: DNACopyNumber, Visualization, aCGH, Microarray Author: Jorma de Ronde, Christiaan Klijn, Arno Velds Maintainer: Jorma de Ronde MD5sum: bd21ee8bc85a1551639d171c53ed1c4b source.ver: src/contrib/KCsmart_2.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/KCsmart_2.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/KCsmart_2.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/KCsmart_2.14.0.tgz vignettes: vignettes/KCsmart/inst/doc/KCS.pdf vignetteTitles: KCsmart example session hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: KEGGgraph Version: 1.12.0 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 Author: Jitao David Zhang Maintainer: Jitao David Zhang URL: http://www.nextbiomotif.com MD5sum: c316f1c2463864a48d29d325c6d26e8c source.ver: src/contrib/KEGGgraph_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/KEGGgraph_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/KEGGgraph_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/KEGGgraph_1.12.0.tgz 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 importsMe: DEGraph, NCIgraph suggestsMe: DEGraph, SPIA Package: keggorthology Version: 2.8.0 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 Author: VJ Carey Maintainer: VJ Carey MD5sum: 6917aa5555fbc6e5b6d2ab87e8649f2e source.ver: src/contrib/keggorthology_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/keggorthology_2.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/keggorthology_2.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/keggorthology_2.8.0.tgz vignettes: vignettes/keggorthology/inst/doc/keggorth.pdf vignetteTitles: keggorthology overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: gene2pathway suggestsMe: MLInterfaces Package: KEGGSOAP Version: 1.30.4 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 MD5sum: c51de1faa07860accaf5e5438b2a62fe source.ver: src/contrib/KEGGSOAP_1.30.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/KEGGSOAP_1.30.4.zip win64.binary.ver: bin/windows64/contrib/2.15/KEGGSOAP_1.30.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/KEGGSOAP_1.30.4.tgz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: gene2pathway Package: lapmix Version: 1.22.0 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 URL: http://www.r-project.org, http://www.bioconductor.org, http://stat.epfl.ch MD5sum: 2073c15d02f61fccc5e6329cb39c0a46 source.ver: src/contrib/lapmix_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/lapmix_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/lapmix_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/lapmix_1.22.0.tgz vignettes: vignettes/lapmix/inst/doc/lapmix-example.pdf vignetteTitles: lapmix example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LBE Version: 1.24.0 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 MD5sum: 9692eb663e76f185f02edf334d912ef2 source.ver: src/contrib/LBE_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/LBE_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/LBE_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LBE_1.24.0.tgz vignettes: vignettes/LBE/inst/doc/LBE.pdf vignetteTitles: LBE Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: les Version: 1.6.0 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 URL: http://julian-gehring.github.com/les/ MD5sum: 4d07a1084dc53e37e29542be04ebe832 source.ver: src/contrib/les_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/les_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/les_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/les_1.6.0.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 importsMe: GSRI Package: limma Version: 3.12.3 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 URL: http://bioinf.wehi.edu.au/limma MD5sum: 4ef5894345c7a9390333c7973338d894 source.ver: src/contrib/limma_3.12.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/limma_3.12.3.zip win64.binary.ver: bin/windows64/contrib/2.15/limma_3.12.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/limma_3.12.3.tgz 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 dependsOnMe: a4Base, AffyExpress, affylmGUI, Agi4x44PreProcess, attract, birta, CALIB, cghMCR, ChIPpeakAnno, codelink, convert, Cormotif, coRNAi, edgeR, HTqPCR, inSilicoMerging, limmaGUI, maDB, maigesPack, marray, MmPalateMiRNA, nem, qpcrNorm, Ringo, snapCGH, TurboNorm importsMe: affycoretools, ArrayExpress, arrayQuality, arrayQualityMetrics, ArrayTools, attract, beadarray, betr, CALIB, CancerMutationAnalysis, charm, ChIPpeakAnno, DiffBind, explorase, GeneSelectMMD, GeneSelector, GGBase, HTqPCR, iChip, maSigPro, minfi, MmPalateMiRNA, OLIN, PatientGeneSets, 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, les, lumi, methylumi, MLP, oligo, oneChannelGUI, PGSEA, plw, PREDA, puma, RTopper, rtracklayer, virtualArray Package: limmaGUI Version: 1.32.0 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 URL: http://bioinf.wehi.edu.au/limmaGUI/ MD5sum: 64937caf745b3c3ebca4cdd065b6f781 source.ver: src/contrib/limmaGUI_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/limmaGUI_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/limmaGUI_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/limmaGUI_1.32.0.tgz 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 Package: LiquidAssociation Version: 1.10.0 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, Bioinformatics, TimeCourse Author: Yen-Yi Ho Maintainer: Yen-Yi Ho MD5sum: 5af7079c511f4ca48cb7918977341e48 source.ver: src/contrib/LiquidAssociation_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/LiquidAssociation_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/LiquidAssociation_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LiquidAssociation_1.10.0.tgz vignettes: vignettes/LiquidAssociation/inst/doc/LiquidAssociation.pdf vignetteTitles: LiquidAssociation Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LMGene Version: 2.12.0 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 URL: http://dmrocke.ucdavis.edu/software.html MD5sum: 7987f07cb50e9cec451823113fdaeba0 source.ver: src/contrib/LMGene_2.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/LMGene_2.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/LMGene_2.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LMGene_2.12.0.tgz vignettes: vignettes/LMGene/inst/doc/LMGene.pdf vignetteTitles: LMGene User's Guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: logicFS Version: 1.26.0 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 MD5sum: c2029cb3077be930b86fa22c5b4c5a1f source.ver: src/contrib/logicFS_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/logicFS_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/logicFS_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/logicFS_1.26.0.tgz vignettes: vignettes/logicFS/inst/doc/logicFS.pdf vignetteTitles: logicFS Manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: logitT Version: 1.14.0 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 Maintainer: Tobias Guennel URL: http://www.bioconductor.org MD5sum: 49246e973717642d9dd890a048e08e2d source.ver: src/contrib/logitT_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/logitT_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/logitT_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/logitT_1.14.0.tgz vignettes: vignettes/logitT/inst/doc/logitT.pdf vignetteTitles: logitT primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: lol Version: 1.4.0 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 MD5sum: d8961728cfe2141ae1ac716710a693bc source.ver: src/contrib/lol_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/lol_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/lol_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/lol_1.4.0.tgz vignettes: vignettes/lol/inst/doc/lol.pdf vignetteTitles: An introduction to the lol package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: LPE Version: 1.30.0 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 , Michael O'Connell , Jae K. Lee . Includes R source code contributed by HyungJun Cho Maintainer: Nitin Jain URL: http://www.r-project.org, http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/, http://sourceforge.net/projects/r-lpe/ MD5sum: dde5eac9bad9c890108941243e90275f source.ver: src/contrib/LPE_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/LPE_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/LPE_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LPE_1.30.0.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 dependsOnMe: LPEadj, PLPE importsMe: LPEadj suggestsMe: ABarray Package: LPEadj Version: 1.16.0 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 , Robert Nadon Maintainer: Carl Murie MD5sum: 7bac7a4827a51df8907020dc08635db6 source.ver: src/contrib/LPEadj_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/LPEadj_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/LPEadj_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LPEadj_1.16.0.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 Package: lumi Version: 2.8.0 Depends: R (>= 2.10), methylumi (>= 1.7.4), Biobase (>= 2.5.5), nleqslv Imports: affy (>= 1.23.4), methylumi, genoset, GenomicRanges, IRanges, rtracklayer, annotate, Biobase (>= 2.5.5), 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, Gang Feng, Warren Kibbe, Simon Lin Maintainer: Pan Du MD5sum: 217d2a04d2e4229a0ace544b4d363416 source.ver: src/contrib/lumi_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/lumi_2.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/lumi_2.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/lumi_2.8.0.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 dependsOnMe: arrayMvout importsMe: ffpe suggestsMe: beadarray, methylumi, tigre, virtualArray Package: LVSmiRNA Version: 1.6.0 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 MD5sum: 049594483bdf8c81eff36ba526ae12a9 source.ver: src/contrib/LVSmiRNA_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/LVSmiRNA_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/LVSmiRNA_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/LVSmiRNA_1.6.0.tgz vignettes: vignettes/LVSmiRNA/inst/doc/LVSmiRNA.pdf vignetteTitles: LVSmiRNA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: maanova Version: 1.26.0 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 URL: http://research.jax.org/faculty/churchill MD5sum: 4670cd9137ab84e75d0d75cc4d86769e source.ver: src/contrib/maanova_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/maanova_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/maanova_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/maanova_1.26.0.tgz 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 Package: macat Version: 1.30.0 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 MD5sum: 0d7515f40e4b5dda8cfd3abb2e655930 source.ver: src/contrib/macat_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/macat_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/macat_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/macat_1.30.0.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 Package: maCorrPlot Version: 1.26.0 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 Maintainer: Alexander Ploner URL: http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15799785 MD5sum: 607ff0c13f7950e58dec7abb8d7174e2 source.ver: src/contrib/maCorrPlot_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/maCorrPlot_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/maCorrPlot_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/maCorrPlot_1.26.0.tgz vignettes: vignettes/maCorrPlot/inst/doc/maCorrPlot.pdf vignetteTitles: maCorrPlot Introduction hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: maDB Version: 1.28.0 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 Maintainer: Johannes Rainer MD5sum: 6a1ba77163f461e9a87e8242fa80c2a2 source.ver: src/contrib/maDB_1.28.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/maDB_1.28.0.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: 1.30.0 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 URL: http://www.hsph.harvard.edu/researchers/aculhane.html MD5sum: e9ad40d3a5e4c8e79195bb01e76746b3 source.ver: src/contrib/made4_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/made4_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/made4_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/made4_1.30.0.tgz 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 dependsOnMe: bgafun Package: maigesPack Version: 1.20.0 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, Bioinformatics, DifferentialExpression, Clustering, Classification, GraphsAndNetworks Author: Gustavo H. Esteves , with contributions from Roberto Hirata Jr , E. Jordao Neves , Elier B. Cristo , Ana C. Simoes and Lucas Fahham Maintainer: Gustavo H. Esteves URL: http://www.maiges.org/en/software/ MD5sum: 794190fd1044e73938b8a17baee1d3e8 source.ver: src/contrib/maigesPack_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/maigesPack_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/maigesPack_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/maigesPack_1.20.0.tgz vignettes: vignettes/maigesPack/inst/doc/maigesPack_tutorial.pdf vignetteTitles: maigesPack Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: makecdfenv Version: 1.34.0 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 , Laurent Gautier , Wolfgang Huber , Ben Bolstad Maintainer: James W. MacDonald MD5sum: efd326a436c29b8dcf82a88f04785d76 source.ver: src/contrib/makecdfenv_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/makecdfenv_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/makecdfenv_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/makecdfenv_1.34.0.tgz vignettes: vignettes/makecdfenv/inst/doc/makecdfenv.pdf vignetteTitles: makecdfenv primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: altcdfenvs Package: MANOR Version: 1.28.0 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 , Philippe Hupe Maintainer: Pierre Neuvial URL: http://bioinfo.curie.fr/projects/manor/index.html MD5sum: d6af6ff7ae4b92f118a7554cf89eabf8 source.ver: src/contrib/MANOR_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MANOR_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MANOR_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MANOR_1.28.0.tgz vignettes: vignettes/MANOR/inst/doc/MANOR.pdf vignetteTitles: MANOR overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: manta Version: 1.2.0 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 and Adrian Marchetti Maintainer: David M. Schruth URL: http://manta.ocean.washington.edu/ MD5sum: e34c4185153d9c7114d8461bce659c8b source.ver: src/contrib/manta_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/manta_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/manta_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/manta_1.2.0.tgz vignettes: vignettes/manta/inst/doc/manta.pdf vignetteTitles: manta hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: MantelCorr Version: 1.26.0 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 MD5sum: b047ae83447b1663b83b98e1479b14b0 source.ver: src/contrib/MantelCorr_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MantelCorr_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MantelCorr_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MantelCorr_1.26.0.tgz vignettes: vignettes/MantelCorr/inst/doc/MantelCorrVignette.pdf vignetteTitles: MantelCorrVignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: marray Version: 1.34.0 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 with contributions from Agnes Paquet and Sandrine Dudoit. Maintainer: Yee Hwa (Jean) Yang URL: http://www.maths.usyd.edu.au/u/jeany/ MD5sum: ffe660b6841ec27bbf4a181fcbd2c737 source.ver: src/contrib/marray_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/marray_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/marray_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/marray_1.34.0.tgz 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 dependsOnMe: CGHbase, convert, dyebias, maigesPack, nnNorm, OLIN, stepNorm, TurboNorm importsMe: arrayQuality, nnNorm, OLIN, OLINgui, sigaR, stepNorm, timecourse suggestsMe: Agi4x44PreProcess, DEGraph, Mfuzz Package: maSigPro Version: 1.28.0 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 , Maria Jose Nueda Maintainer: Maria Jose Nueda URL: http://bioinfo.cipf.es/ MD5sum: 612d7af5f271445913549a2ae9275d81 source.ver: src/contrib/maSigPro_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/maSigPro_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/maSigPro_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/maSigPro_1.28.0.tgz 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 suggestsMe: oneChannelGUI Package: maskBAD Version: 1.0.0 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 Maintainer: Michael Dannemann MD5sum: dc693e76a6ad24092cd3387fc159359e source.ver: src/contrib/maskBAD_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/maskBAD_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/maskBAD_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/maskBAD_1.0.0.tgz vignettes: vignettes/maskBAD/inst/doc/maskBAD.pdf vignetteTitles: Package maskBAD hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MassArray Version: 1.8.0 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 , John M. Greally Maintainer: Reid F. Thompson MD5sum: edca3f1766bfeb3ddcd4944e007ca6ac source.ver: src/contrib/MassArray_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MassArray_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MassArray_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MassArray_1.8.0.tgz 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 Package: MassSpecWavelet Version: 1.22.0 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 MD5sum: 98cc0b95dc214579ae9bde970f7f42e8 source.ver: src/contrib/MassSpecWavelet_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MassSpecWavelet_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MassSpecWavelet_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MassSpecWavelet_1.22.0.tgz vignettes: vignettes/MassSpecWavelet/inst/doc/MassSpecWavelet.pdf vignetteTitles: MassSpecWavelet hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: xcms Package: MBCB Version: 1.10.0 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 Maintainer: Jeff Allen URL: http://www.utsouthwestern.edu MD5sum: 8f3c40e67cd71a7dfb82b511318feef4 source.ver: src/contrib/MBCB_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MBCB_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MBCB_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MBCB_1.10.0.tgz vignettes: vignettes/MBCB/inst/doc/MBCB.pdf vignetteTitles: MBCB hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mBPCR Version: 1.10.0 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 , with contributions from M. Hutter Maintainer: P.M.V. Rancoita URL: http://www.idsia.ch/~paola/mBPCR MD5sum: 21e7472fd1870743f932aeeaa2709b01 source.ver: src/contrib/mBPCR_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/mBPCR_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/mBPCR_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mBPCR_1.10.0.tgz vignettes: vignettes/mBPCR/inst/doc/mBPCR.pdf vignetteTitles: mBPCR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mcaGUI Version: 1.4.0 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 URL: http://www.ibest.uidaho.edu/ibest/index.php MD5sum: ba7aa5e015e8b00dfc719406b4792a07 source.ver: src/contrib/mcaGUI_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/mcaGUI_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/mcaGUI_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mcaGUI_1.4.0.tgz 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: 2.12.0 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 MD5sum: 631814732c9966df67c3af232c7a8392 source.ver: src/contrib/MCRestimate_2.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MCRestimate_2.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MCRestimate_2.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MCRestimate_2.12.0.tgz vignettes: vignettes/MCRestimate/inst/doc/UsingMCRestimate.pdf vignetteTitles: HOW TO use MCRestimate hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mdqc Version: 1.18.0 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 MD5sum: efdfb03c7a745e7639c25d4d7b5bf9b5 source.ver: src/contrib/mdqc_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/mdqc_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/mdqc_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mdqc_1.18.0.tgz vignettes: vignettes/mdqc/inst/doc/mdqcvignette.pdf vignetteTitles: Introduction to MDQC hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: arrayMvout Package: MeasurementError.cor Version: 1.28.0 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 MD5sum: 746cd346c59c181617b83ef00cc105eb source.ver: src/contrib/MeasurementError.cor_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MeasurementError.cor_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MeasurementError.cor_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MeasurementError.cor_1.28.0.tgz vignettes: vignettes/MeasurementError.cor/inst/doc/MeasurementError.cor.pdf vignetteTitles: MeasurementError.cor Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MEDIPS Version: 1.6.0 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 MD5sum: e937cb8b70958cc848a3153782a226a5 source.ver: src/contrib/MEDIPS_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MEDIPS_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MEDIPS_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MEDIPS_1.6.0.tgz vignettes: vignettes/MEDIPS/inst/doc/MEDIPS.pdf vignetteTitles: MEDIPS hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MEDME Version: 1.16.3 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 MD5sum: e7345b3a75cce2cbc836b45b54847ba0 source.ver: src/contrib/MEDME_1.16.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/MEDME_1.16.3.zip win64.binary.ver: bin/windows64/contrib/2.15/MEDME_1.16.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MEDME_1.16.3.tgz vignettes: vignettes/MEDME/inst/doc/MEDME.pdf vignetteTitles: MEDME.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MergeMaid Version: 2.28.0 Depends: R (>= 2.2.0), 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 Leslie Cope Elizabeth Garrett Giovanni Parmigiani Maintainer: Xiaogang Zhong URL: http://astor.som.jhmi.edu/MergeMaid MD5sum: b9a319dba161dfe7b7c32c0db3e492cc source.ver: src/contrib/MergeMaid_2.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MergeMaid_2.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MergeMaid_2.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MergeMaid_2.28.0.tgz vignettes: vignettes/MergeMaid/inst/doc/MergeMaid.pdf vignetteTitles: MergeMaid primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: metaArray, XDE suggestsMe: oneChannelGUI Package: metaArray Version: 1.34.0 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 Hyungwon Choi Maintainer: Hyungwon Choi MD5sum: 1621d6c4fb9652a3d2f58eee1acd862a source.ver: src/contrib/metaArray_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/metaArray_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/metaArray_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/metaArray_1.34.0.tgz vignettes: vignettes/metaArray/inst/doc/metaArray.pdf vignetteTitles: metaArray Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oneChannelGUI Package: metahdep Version: 1.14.0 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 MD5sum: 816167e2d8517442db4944cb9f5377b7 source.ver: src/contrib/metahdep_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/metahdep_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/metahdep_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/metahdep_1.14.0.tgz vignettes: vignettes/metahdep/inst/doc/metahdep.pdf vignetteTitles: metahdep Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: methVisual Version: 1.8.0 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 MD5sum: 67085f0d604d2d7004296142adb02b9b source.ver: src/contrib/methVisual_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/methVisual_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/methVisual_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/methVisual_1.8.0.tgz vignettes: vignettes/methVisual/inst/doc/methVisual.pdf vignetteTitles: Introduction to methVisual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: methylumi Version: 2.2.0 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 MD5sum: 77249b42968df6d1857493de80a19c01 source.ver: src/contrib/methylumi_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/methylumi_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/methylumi_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/methylumi_2.2.0.tgz vignettes: vignettes/methylumi/inst/doc/methylumi.pdf vignetteTitles: An Introduction to the methylumi package hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: lumi importsMe: ffpe, lumi Package: Mfuzz Version: 2.14.0 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 Maintainer: Matthias Futschik URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/ MD5sum: 0ff3fa60c676d40b62239e1053e8ba9a source.ver: src/contrib/Mfuzz_2.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Mfuzz_2.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Mfuzz_2.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Mfuzz_2.14.0.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 dependsOnMe: cycle importsMe: maSigPro Package: mgsa Version: 1.4.0 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 Author: Sebastian Bauer , Julien Gagneur Maintainer: Sebastian Bauer MD5sum: 7cdd4c33dcb0684545b0299403a8ef04 source.ver: src/contrib/mgsa_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/mgsa_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/mgsa_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mgsa_1.4.0.tgz vignettes: vignettes/mgsa/inst/doc/mgsa.pdf vignetteTitles: Overview of the mgsa package. hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MiChip Version: 1.10.0 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 Maintainer: Jonathon Blake MD5sum: 21886e0b911ae1927ffcf83fbdd1d8b6 source.ver: src/contrib/MiChip_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MiChip_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MiChip_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MiChip_1.10.0.tgz vignettes: vignettes/MiChip/inst/doc/MiChip.pdf vignetteTitles: MiChip miRNA Microarray Processing hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: microRNA Version: 1.14.0 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" MD5sum: f4786ac22baf948f3c25bb51f6afac59 source.ver: src/contrib/microRNA_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/microRNA_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/microRNA_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/microRNA_1.14.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: MmPalateMiRNA, rtracklayer Package: minet Version: 3.10.0 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 Author: Patrick E. Meyer, Frederic Lafitte, Gianluca Bontempi Maintainer: Patrick E. Meyer URL: http://minet.meyerp.com MD5sum: c049d75948d310d3d165e332a73ad8ca source.ver: src/contrib/minet_3.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/minet_3.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/minet_3.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/minet_3.10.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: BUS, netresponse suggestsMe: predictionet Package: minfi Version: 1.2.0 Depends: methods, BiocGenerics (>= 0.1.0), Biobase (>= 2.15.1), lattice, reshape, GenomicRanges Imports: beanplot, RColorBrewer, nor1mix, siggenes, limma, preprocessCore, crlmm, matrixStats, mclust Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), minfiData (>= 0.2.0), Biostrings 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 MD5sum: 6267bb0b4a9e097c632e3c6a26a34e30 source.ver: src/contrib/minfi_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/minfi_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/minfi_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/minfi_1.2.0.tgz vignettes: vignettes/minfi/inst/doc/minfi.pdf vignetteTitles: Minfi Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: MinimumDistance Version: 1.0.0 Depends: R (>= 2.14), IRanges (>= 1.13.30) Imports: methods, DNAcopy, utils, msm, lattice, BiocGenerics, VanillaICE (>= 1.17.22), ff, SNPchip (>= 2.0.3), Biobase, foreach, oligoClasses (>= 1.17.38) 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 Maintainer: Moiz Bootwalla , Robert B Scharpf MD5sum: 6fd68cae28c94ae9ac1b0fa1771249de source.ver: src/contrib/MinimumDistance_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MinimumDistance_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MinimumDistance_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MinimumDistance_1.0.0.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 Package: MiPP Version: 1.28.0 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 , Sukwoo Kim , Mat Soukup , and Jae K. Lee Maintainer: Sukwoo Kim URL: http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/ MD5sum: b7379ef94886c897f8cfa05c86929740 source.ver: src/contrib/MiPP_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MiPP_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MiPP_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MiPP_1.28.0.tgz vignettes: vignettes/MiPP/inst/doc/MiPP.pdf vignetteTitles: MiPP Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: miRNApath Version: 1.16.0 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, Bioinformatics, DifferentialExpression Author: James M. Ward with contributions from Yunling Shi, Cindy Richards, John P. Cogswell Maintainer: James M. Ward MD5sum: e1c59b9d9116b172f01d6b0d3ca597c4 source.ver: src/contrib/miRNApath_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/miRNApath_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/miRNApath_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/miRNApath_1.16.0.tgz vignettes: vignettes/miRNApath/inst/doc/miRNApath.pdf vignetteTitles: miRNApath: Pathway Enrichment for miRNA Expression Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: MLInterfaces Version: 1.36.1 Depends: R (>= 2.9), Biobase, MASS, methods, genefilter, rpart, rda, annotate, cluster, sfsmisc Imports: mboost, gdata 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 , Robert Gentleman, Jess Mar, and contributions from Jason Vertrees and Laurent Gatto Maintainer: V. Carey MD5sum: bcaa3391f800082032c1c6229195b5ae source.ver: src/contrib/MLInterfaces_1.36.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/MLInterfaces_1.36.1.zip win64.binary.ver: bin/windows64/contrib/2.15/MLInterfaces_1.36.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MLInterfaces_1.36.1.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: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: a4Classif suggestsMe: BiocCaseStudies Package: MLP Version: 1.4.2 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 MD5sum: e06e8cef480990b75b3ce0a502eb10a0 source.ver: src/contrib/MLP_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/MLP_1.4.2.zip win64.binary.ver: bin/windows64/contrib/2.15/MLP_1.4.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MLP_1.4.2.tgz vignettes: vignettes/MLP/inst/doc/UsingMLP.pdf vignetteTitles: UsingMLP hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: a4 Package: MmPalateMiRNA Version: 1.4.0 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 , Partha Mukhopadhyay , Vasyl Pihur , Robert M. Greene , and M. Michele Pisano Maintainer: Guy Brock MD5sum: 726beca463348dfac3f26e35992f1551 source.ver: src/contrib/MmPalateMiRNA_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MmPalateMiRNA_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MmPalateMiRNA_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MmPalateMiRNA_1.4.0.tgz vignettes: vignettes/MmPalateMiRNA/inst/doc/MmPalateMiRNA.pdf vignetteTitles: Palate miRNA Analysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: mosaics Version: 1.4.1 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 URL: http://groups.google.com/group/mosaics_user_group SystemRequirements: Perl MD5sum: 3e71c3a4a0e419ae32678a5b5c203580 source.ver: src/contrib/mosaics_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/mosaics_1.4.1.zip win64.binary.ver: bin/windows64/contrib/2.15/mosaics_1.4.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mosaics_1.4.1.tgz vignettes: vignettes/mosaics/inst/doc/mosaics-example.pdf vignetteTitles: MOSAiCS hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: motifRG Version: 1.0.0 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 Author: Zizhen Yao Maintainer: Zizhen Yao MD5sum: 20eb49010beb9b4a6b14656e72700f14 source.ver: src/contrib/motifRG_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/motifRG_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/motifRG_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/motifRG_1.0.0.tgz vignettes: vignettes/motifRG/inst/doc/motifRG.pdf vignetteTitles: motifRG: regression-based discriminative motif discovery hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MotIV Version: 1.10.0 Depends: R (>= 2.10), BiocGenerics (>= 0.1.0) Imports: graphics, grid, methods, BiocGenerics, IRanges (>= 1.13.5), 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 Author: Eloi Mercier, Raphael Gottardo Maintainer: Eloi Mercier , Raphael Gottardo MD5sum: 27b451cfdde7abeb4bc2e1a48ec510ca source.ver: src/contrib/MotIV_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MotIV_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MotIV_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MotIV_1.10.0.tgz vignettes: vignettes/MotIV/inst/doc/MotIV.pdf vignetteTitles: The MotIV users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: MSnbase Version: 1.4.1 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.3), Biobase (>= 2.15.2), ggplot2, mzR Imports: graphics, plyr, IRanges, preprocessCore, vsn, grid, reshape Suggests: testthat, zoo, pgfSweave, Rdisop Enhances: foreach, doMC 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 with contributions from Guangchuang Yu Maintainer: Laurent Gatto MD5sum: 03457105e31a4d146f20ebcbeb7533ef source.ver: src/contrib/MSnbase_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/MSnbase_1.4.1.zip win64.binary.ver: bin/windows64/contrib/2.15/MSnbase_1.4.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MSnbase_1.4.1.tgz 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 suggestsMe: isobar Package: Mulcom Version: 1.6.0 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 MD5sum: 5945ebce8dcfa21bc807725c710442c9 source.ver: src/contrib/Mulcom_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Mulcom_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Mulcom_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Mulcom_1.6.0.tgz vignettes: vignettes/Mulcom/inst/doc/MulcomVignette.pdf vignetteTitles: Mulcom Manual hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: multiscan Version: 1.16.0 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 , Chris Glasbey, Bruce Worton. Maintainer: Mizanur Khondoker MD5sum: 116170acda1e38058c087fbae35889be source.ver: src/contrib/multiscan_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/multiscan_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/multiscan_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/multiscan_1.16.0.tgz 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 Package: multtest Version: 2.12.0 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 MD5sum: deefabe11ab9763565377a8e8cbf1108 source.ver: src/contrib/multtest_2.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/multtest_2.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/multtest_2.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/multtest_2.12.0.tgz 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, KCsmart, LMGene, PREDA, REDseq, SAGx, siggenes, webbioc importsMe: ABarray, aCGH, adSplit, anota, ChIPpeakAnno, GeneSelector, globaltest, IsoGeneGUI, OCplus, phyloseq, REDseq, RTopper, webbioc suggestsMe: annaffy, BiocCaseStudies, ecolitk, GeneSelector, GOstats, GSEAlm, maigesPack, MmPalateMiRNA, oneChannelGUI, pcot2, safe, SSPA, topGO, xcms Package: MVCClass Version: 1.30.0 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 MD5sum: 6eb2550c2ff4e04399edb734acd29782 source.ver: src/contrib/MVCClass_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/MVCClass_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/MVCClass_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/MVCClass_1.30.0.tgz vignettes: vignettes/MVCClass/inst/doc/MVCClass.pdf vignetteTitles: MVCClass hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: BioMVCClass Package: mzR Version: 1.2.2 Depends: Rcpp (>= 0.9.4), methods Imports: Biobase LinkingTo: Rcpp Suggests: msdata, 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 , Steffen Neumann , Laurent Gatto SystemRequirements: GNU make, NetCDF, zlib MD5sum: e608949fe217c4928288dd516c192e51 source.ver: src/contrib/mzR_1.2.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/mzR_1.2.2.zip win64.binary.ver: bin/windows64/contrib/2.15/mzR_1.2.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/mzR_1.2.2.tgz vignettes: vignettes/mzR/inst/doc/mzR.pdf vignetteTitles: mzR,, Ramp,, mzXML,, mzData,, mzML hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: MSnbase, TargetSearch, xcms Package: NarrowPeaks Version: 1.0.1 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 , with contributions from Pawel Krajewski Maintainer: Pedro Madrigal MD5sum: 6826b2306d54854c890b2e0cc238ad01 source.ver: src/contrib/NarrowPeaks_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/NarrowPeaks_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.15/NarrowPeaks_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/NarrowPeaks_1.0.1.tgz vignettes: vignettes/NarrowPeaks/inst/doc/NarrowPeaks.pdf vignetteTitles: NarrowPeaks Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ncdfFlow Version: 1.2.1 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 SystemRequirements: netcdf 4.0.1, hdf5 MD5sum: 604ab1be7ec78034da31364c4f965f55 source.ver: src/contrib/ncdfFlow_1.2.1.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ncdfFlow_1.2.1.tgz vignettes: vignettes/ncdfFlow/inst/doc/ncdfFlow.pdf vignetteTitles: Basic Functions for Flow Cytometry Data hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: NCIgraph Version: 1.4.0 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: Bioinformatics, GraphsAndNetworks Author: Laurent Jacob Maintainer: Laurent Jacob MD5sum: a0356b2d865369eed2b289c7e5c884c1 source.ver: src/contrib/NCIgraph_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/NCIgraph_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/NCIgraph_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/NCIgraph_1.4.0.tgz 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 importsMe: DEGraph suggestsMe: DEGraph Package: nem Version: 2.32.1 Depends: R (>= 2.0), e1071 (>= 1.5), graph (>= 1.24), Rgraphviz (>= 1.22), plotrix, limma, cluster (>= 1.11), statmod, Hmisc Imports: boot, e1071, graph, graphics, grDevices, methods, RBGL (>= 1.8.1), RColorBrewer, Rgraphviz, stats, utils Suggests: Biobase (>= 1.10) Enhances: doMC 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 URL: http://www.bioconductor.org MD5sum: 9ffb691fafa54a3f427b51486268139d source.ver: src/contrib/nem_2.32.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/nem_2.32.1.zip win64.binary.ver: bin/windows64/contrib/2.15/nem_2.32.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/nem_2.32.1.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 Package: netresponse Version: 1.8.0 Depends: R (>= 2.14.1), methods, igraph, graph, minet, qvalue, parallel, RColorBrewer, Rgraphviz, ggplot2 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, GraphsAndNetworks, DifferentialExpression, Microarray, Transcription Author: Leo Lahti, Olli-Pekka Huovilainen, Antonio Gusmao and Juuso Parkkinen Maintainer: Leo Lahti URL: http://netpro.r-forge.r-project.org/ MD5sum: d8e97af1ea7c4153174528f9964b3df6 source.ver: src/contrib/netresponse_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/netresponse_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/netresponse_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/netresponse_1.8.0.tgz vignettes: vignettes/netresponse/inst/doc/netresponse.pdf vignetteTitles: netresponse hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: nnNorm Version: 2.20.0 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 Maintainer: Adi Laurentiu Tarca URL: http://bioinformaticsprb.med.wayne.edu/tarca/ MD5sum: 54b869b5ca2f4b9fa4ff393326f39292 source.ver: src/contrib/nnNorm_2.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/nnNorm_2.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/nnNorm_2.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/nnNorm_2.20.0.tgz 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 Package: NormqPCR Version: 1.2.0 Depends: R(>= 2.10.0), 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. Author: Matthias Kohl, James Perkins Maintainer: James Perkins URL: www.bioconductor.org/packages/release/bioc/html/NormqPCR.html MD5sum: b0382b6a684bcf83eada03d8c86a61a0 source.ver: src/contrib/NormqPCR_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/NormqPCR_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/NormqPCR_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/NormqPCR_1.2.0.tgz vignettes: vignettes/NormqPCR/inst/doc/NormqPCR.pdf vignetteTitles: NormqPCR: Functions for normalisation of RT-qPCR data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: NTW Version: 1.6.0 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 MD5sum: 5a46b8b32502bb38401512faa6de026d source.ver: src/contrib/NTW_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/NTW_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/NTW_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/NTW_1.6.0.tgz vignettes: vignettes/NTW/inst/doc/NTW.pdf vignetteTitles: NTW vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: nucleR Version: 1.4.0 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 MD5sum: a456b3a01a0db5c2df745a2495399e33 source.ver: src/contrib/nucleR_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/nucleR_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/nucleR_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/nucleR_1.4.0.tgz vignettes: vignettes/nucleR/inst/doc/nucleR.pdf vignetteTitles: Quick analysis of nucleosome positioning experiments hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: nudge Version: 1.22.0 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 and A. E. Raftery Maintainer: N. Dean MD5sum: 59a9e429e191d0a82e52cdfbe4e20354 source.ver: src/contrib/nudge_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/nudge_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/nudge_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/nudge_1.22.0.tgz 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 Package: NuPoP Version: 1.6.0 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 ; Liqun Xi Maintainer: Ji-Ping Wang MD5sum: 07fe4a6288e374057e4d1f486d9df9ac source.ver: src/contrib/NuPoP_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/NuPoP_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/NuPoP_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/NuPoP_1.6.0.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 Package: occugene Version: 1.16.0 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 Maintainer: Oliver Will MD5sum: 42dcd16e799f2586d6902b7d4f2c6bbd source.ver: src/contrib/occugene_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/occugene_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/occugene_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/occugene_1.16.0.tgz vignettes: vignettes/occugene/inst/doc/occugene.pdf vignetteTitles: occugene hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: OCplus Version: 1.30.0 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 and Alexander Ploner Maintainer: Alexander Ploner MD5sum: 125d211609b40a084b22da9457879c67 source.ver: src/contrib/OCplus_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/OCplus_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/OCplus_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OCplus_1.30.0.tgz vignettes: vignettes/OCplus/inst/doc/OCplus.pdf vignetteTitles: OCplus Introduction hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: oligo Version: 1.20.4 Depends: R (>= 2.14.0), oligoClasses (>= 1.17.35) Imports: affyio (>= 1.23.2), affxparser (>= 1.27.5), Biobase (>= 2.15.4), Biostrings (>= 2.23.6), BiocGenerics (>= 0.1.14), DBI (>= 0.2-5), ff, graphics, methods, preprocessCore (>= 1.17.7), 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 MD5sum: aad2af9a12ffe4650396dbdfd972692d source.ver: src/contrib/oligo_1.20.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/oligo_1.20.4.zip win64.binary.ver: bin/windows64/contrib/2.15/oligo_1.20.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/oligo_1.20.4.tgz vignettes: vignettes/oligo/inst/doc/primer.pdf vignetteTitles: oligo - Primer hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ITALICS, pdInfoBuilder importsMe: charm, cn.farms, frma, ITALICS suggestsMe: BiocGenerics, frmaTools Package: oligoClasses Version: 1.18.0 Depends: R (>= 2.14) Imports: Biobase (>= 2.15.1), methods, graphics, BiocGenerics (>= 0.1.14), IRanges (>= 1.13.30), 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, VanillaICE, RUnit 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 and Robert Scharpf MD5sum: 7b60ae30b78bfc38d96ba6bcdab89d06 source.ver: src/contrib/oligoClasses_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/oligoClasses_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/oligoClasses_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/oligoClasses_1.18.0.tgz hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: cn.farms, crlmm, mBPCR, oligo importsMe: frma, ITALICS, MinimumDistance, SNPchip, VanillaICE suggestsMe: BiocGenerics Package: OLIN Version: 1.34.0 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 Maintainer: Matthias Futschik URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/index.html MD5sum: 1bf72fbcc63153a593fd22c164a2ea9b source.ver: src/contrib/OLIN_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/OLIN_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/OLIN_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OLIN_1.34.0.tgz vignettes: vignettes/OLIN/inst/doc/OLIN.pdf vignetteTitles: Introduction to OLIN hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: OLINgui importsMe: OLINgui suggestsMe: maigesPack Package: OLINgui Version: 1.30.0 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 Maintainer: Matthias Futschik URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/index.html MD5sum: 3ce7bc2c2471e1305f7206e3858552f9 source.ver: src/contrib/OLINgui_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/OLINgui_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/OLINgui_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OLINgui_1.30.0.tgz 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 Package: oneChannelGUI Version: 1.22.12 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, cummeRbund, 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 License: The Artistic License, Version 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 URL: http://www.bioinformatica.unito.it/oneChannelGUI/ MD5sum: 4de434e321793fcdd76be29fe9fa27e7 source.ver: src/contrib/oneChannelGUI_1.22.12.tar.gz win.binary.ver: bin/windows/contrib/2.15/oneChannelGUI_1.22.12.zip win64.binary.ver: bin/windows64/contrib/2.15/oneChannelGUI_1.22.12.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/oneChannelGUI_1.22.12.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 Package: ontoCAT Version: 1.8.0 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 MD5sum: 4c967eaa2d307e10afeb6345828f6290 source.ver: src/contrib/ontoCAT_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ontoCAT_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ontoCAT_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ontoCAT_1.8.0.tgz vignettes: vignettes/ontoCAT/inst/doc/ontoCAT.pdf vignetteTitles: ontoCAT package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: OrderedList Version: 1.28.0 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 URL: http://compdiag.molgen.mpg.de/software/index.shtml MD5sum: 103228b3085f6f854195d0f8a871736c source.ver: src/contrib/OrderedList_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/OrderedList_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/OrderedList_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OrderedList_1.28.0.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 Package: OTUbase Version: 1.6.0 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 MD5sum: d78cf0afcb918e8833277c52f0b89b81 source.ver: src/contrib/OTUbase_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/OTUbase_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/OTUbase_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OTUbase_1.6.0.tgz vignettes: vignettes/OTUbase/inst/doc/Introduction_to_OTUbase.pdf vignetteTitles: An introduction to OTUbase hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: mcaGUI Package: OutlierD Version: 1.20.0 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 Maintainer: Sukwoo Kim URL: http://www.korea.ac.kr/~stat2242/ MD5sum: 5f18cbd54da12b2e693564a1a7601aa5 source.ver: src/contrib/OutlierD_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/OutlierD_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/OutlierD_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/OutlierD_1.20.0.tgz vignettes: vignettes/OutlierD/inst/doc/OutlierD.pdf vignetteTitles: Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PAnnBuilder Version: 1.20.0 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 URL: http://www.biosino.org/PAnnBuilder MD5sum: 2926406dc0745a59ed0b2810e1a708f4 source.ver: src/contrib/PAnnBuilder_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PAnnBuilder_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PAnnBuilder_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PAnnBuilder_1.20.0.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 Package: panp Version: 1.26.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) Imports: Biobase, methods, stats, utils 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 MD5sum: 82623ca5360c8cf606f4351732ded019 source.ver: src/contrib/panp_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/panp_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/panp_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/panp_1.26.0.tgz vignettes: vignettes/panp/inst/doc/panp.pdf vignetteTitles: gene presence/absence calls hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PANR Version: 1.2.3 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: Visualization, GraphsAndNetworks, Clustering, CellBasedAssays Author: Xin Wang Maintainer: Xin Wang MD5sum: 59dae5b209e51c222fa40bf6d830cea8 source.ver: src/contrib/PANR_1.2.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/PANR_1.2.3.zip win64.binary.ver: bin/windows64/contrib/2.15/PANR_1.2.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PANR_1.2.3.tgz vignettes: vignettes/PANR/inst/doc/fullPAN.pdf, vignettes/PANR/inst/doc/pvmodule.pdf, vignettes/PANR/inst/doc/sigmod.pdf vignetteTitles: fullPAN.pdf, pvmodule.pdf, sigmod.pdf hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: RedeR Package: parody Version: 1.14.0 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 Maintainer: VJ Carey MD5sum: 702ab7128d2ab9642427642896614e1a source.ver: src/contrib/parody_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/parody_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/parody_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/parody_1.14.0.tgz vignettes: vignettes/parody/inst/doc/parody.pdf vignetteTitles: parody: parametric and resistant outlier detection hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: arrayMvout, flowQ Package: pathRender Version: 1.24.0 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 Author: Li Long Maintainer: Li Long URL: http://www.bioconductor.org MD5sum: eb1a6433e72c4ff3c7a00f30158667ef source.ver: src/contrib/pathRender_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pathRender_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pathRender_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pathRender_1.24.0.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 Package: PatientGeneSets Version: 1.6.0 Depends: R (>= 2.10.0), qvalue Imports: AnnotationDbi, limma, methods, stats Suggests: KEGG.db License: GPL (>= 2.0) Archs: i386, x64 Title: Patient-oriented gene-set analysis Description: Patient-oriented analysis of mutations from cancer genome studies. biocViews: Bioinformatics Author: Simina M. Boca, Giovanni Parmigiani Maintainer: Simina M. Boca MD5sum: 82a6073e30d1f40cf53eea1f53d91775 source.ver: src/contrib/PatientGeneSets_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PatientGeneSets_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PatientGeneSets_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PatientGeneSets_1.6.0.tgz vignettes: vignettes/PatientGeneSets/inst/doc/PatientGeneSets.pdf vignetteTitles: PatientGeneSetsTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaGoPromoter Version: 1.0.0 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 MD5sum: 35df30fe74fbaf7716eaacf0654373f6 source.ver: src/contrib/pcaGoPromoter_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pcaGoPromoter_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pcaGoPromoter_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pcaGoPromoter_1.0.0.tgz vignettes: vignettes/pcaGoPromoter/inst/doc/pcaGoPromoter.pdf vignetteTitles: pcaGoPromoter hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pcaMethods Version: 1.42.0 Depends: Biobase, MASS, pls, methods, Rcpp (>= 0.8.7) Imports: BiocGenerics LinkingTo: Rcpp Suggests: aroma.light 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 unique interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany. Now developed at CAS-MPG Partner Institute for Computational Biology (PICB) Shanghai, P.R. China and RIKEN Plant Science Center, Yokohama Japan. biocViews: Bioinformatics Author: Wolfram Stacklies, Henning Redestig, Kevin Wright Maintainer: Wolfram Stacklies SystemRequirements: Rcpp MD5sum: 4cdeb7e4658043a90b56343997cf6d93 source.ver: src/contrib/pcaMethods_1.42.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pcaMethods_1.42.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pcaMethods_1.42.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pcaMethods_1.42.0.tgz 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 Package: pcot2 Version: 1.24.0 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 MD5sum: 3e3cfcf84b15914de69541d6d4d07c2a source.ver: src/contrib/pcot2_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pcot2_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pcot2_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pcot2_1.24.0.tgz 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 Package: PCpheno Version: 1.18.0 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 Author: Nolwenn Le Meur and Robert Gentleman Maintainer: Nolwenn Le Meur MD5sum: 544d570c4c84b7940f5b059f9bb0be2c source.ver: src/contrib/PCpheno_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PCpheno_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PCpheno_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PCpheno_1.18.0.tgz vignettes: vignettes/PCpheno/inst/doc/PCpheno.pdf vignetteTitles: PCpheno Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: pdInfoBuilder Version: 1.20.0 Depends: R (>= 2.11.0), methods, Biobase (>= 2.5.5), RSQLite (>= 0.7-1), affxparser (>= 1.7.3), oligo (>= 1.9.19) Imports: Biostrings (>= 2.13.50), IRanges (>= 1.3.89) 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 MD5sum: 75ca4de7bd16b1564976fd51eb5c1dab source.ver: src/contrib/pdInfoBuilder_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pdInfoBuilder_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pdInfoBuilder_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pdInfoBuilder_1.20.0.tgz 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 Package: pdmclass Version: 1.28.0 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 MD5sum: 5d54d5d7cf17078de8978b460dfcac34 source.ver: src/contrib/pdmclass_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pdmclass_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pdmclass_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pdmclass_1.28.0.tgz vignettes: vignettes/pdmclass/inst/doc/pdmclass.pdf vignetteTitles: pdmclass Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oneChannelGUI Package: PGSEA Version: 1.30.0 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 and Karl Dykema Maintainer: Karl Dykema MD5sum: 590766f1b4de5e469978447434ebd03b source.ver: src/contrib/PGSEA_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PGSEA_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PGSEA_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PGSEA_1.30.0.tgz 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 Package: pgUtils Version: 1.28.0 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 Maintainer: Johannes Rainer MD5sum: 971beb59e3c0b34d7fcb1cd8558bd052 source.ver: src/contrib/pgUtils_1.28.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pgUtils_1.28.0.tgz vignettes: vignettes/pgUtils/inst/doc/pgUtils.pdf vignetteTitles: pgUtils.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: maDB Package: phenoDist Version: 1.4.0 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 URL: http://www.dkfz.de/signaling, http://www.embl.de/research/units/genome_biology/huber/ MD5sum: 9008f074562e3c037519988fc8e30f54 source.ver: src/contrib/phenoDist_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/phenoDist_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/phenoDist_1.4.0.zip vignettes: vignettes/phenoDist/inst/doc/phenoDist.pdf vignetteTitles: Introduction to phenoDist hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: phenoTest Version: 1.4.0 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 MD5sum: 76d447effd5847b0322f71749b3c52e8 source.ver: src/contrib/phenoTest_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/phenoTest_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/phenoTest_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/phenoTest_1.4.0.tgz vignettes: vignettes/phenoTest/inst/doc/phenoTest.pdf vignetteTitles: Manual for the phenoTest library hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: phyloseq Version: 1.0.3 Depends: R (>= 2.15.0), methods, ade4 (>= 1.4), ape (>= 2.8), ggplot2 (>= 0.9.2), picante (>= 1.3), reshape (>= 0.8.4) Imports: foreach (>= 1.3), igraph0 (>= 0.5), multtest (>= 2.8), plyr (>= 1.7), RJSONIO (>= 0.98), vegan (>= 2.0) Suggests: genefilter Enhances: doParallel (>= 1.0) License: AGPL-3 Title: Handling and analysis of high-throughput phylogenetic sequence data. Description: phyloseq is 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 , Susan Holmes Maintainer: Paul J. McMurdie MD5sum: 75d924f6e363077b6e56035f07facd2b source.ver: src/contrib/phyloseq_1.0.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/phyloseq_1.0.3.zip win64.binary.ver: bin/windows64/contrib/2.15/phyloseq_1.0.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/phyloseq_1.0.3.tgz 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 Package: pickgene Version: 1.28.0 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 Maintainer: Brian S. Yandell URL: http://www.stat.wisc.edu/~yandell/statgen MD5sum: 836544cd44b97b54d41d6e1fc427f849 source.ver: src/contrib/pickgene_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pickgene_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pickgene_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pickgene_1.28.0.tgz vignettes: vignettes/pickgene/inst/doc/pickgene.pdf vignetteTitles: Adaptive Gene Picking for Microarray Expression Data Analysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: PICS Version: 1.10.0 Depends: R (>= 2.11.0), BiocGenerics (>= 0.1.3), IRanges (>= 1.13.10), GenomicRanges, BSgenome Imports: methods, BiocGenerics, stats4, IRanges, GenomicRanges, BSgenome, graphics, grDevices, stats Suggests: snowfall, ShortRead, rtracklayer Enhances: multicore 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 , Raphael Gottardo Maintainer: Arnaud Droit MD5sum: 9edc193f8f107541a4d0fc63e44dff85 source.ver: src/contrib/PICS_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PICS_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PICS_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PICS_1.10.0.tgz vignettes: vignettes/PICS/inst/doc/PICS.pdf vignetteTitles: The PICS users guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: PING Version: 1.0.0 Depends: R(>= 2.11.0),chipseq Imports: methods, graphics, grDevices, stats, GenomeGraphs, fda , IRanges, GenomicRanges, BSgenome, stats4, BiocGenerics Suggests: snowfall, ShortRead, rtracklayer Enhances: parallel 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 , Raphael Gottardo , Sangsoon Woo, Maintainer: Xuekui Zhang , Raphael Gottardo , Sangsoon Woo, MD5sum: 3fcfe766638908c61a232d3eed487c82 source.ver: src/contrib/PING_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PING_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PING_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PING_1.0.0.tgz vignettes: vignettes/PING/inst/doc/PING.pdf vignetteTitles: The PING users guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: pint Version: 1.8.0 Depends: mvtnorm, methods, graphics, Matrix, dmt License: FreeBSD Title: Pairwise INTegration of functional genomics data Description: Pairwise data integration for functional genomics. In particular, tools to screen functionally active chromosomal aberrations from paired copy number, gene expression and miRNA measurements from the same patients. biocViews: aCGH, GeneExpression, Genetics, DifferentialExpression, Microarray Author: Olli-Pekka Huovilainen and Leo Lahti Maintainer: Olli-Pekka Huovilainen MD5sum: 5912daaf4114c59a61a77ea022634cae source.ver: src/contrib/pint_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pint_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pint_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pint_1.8.0.tgz vignettes: vignettes/pint/inst/doc/depsearch.pdf vignetteTitles: pint hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: pkgDepTools Version: 1.22.0 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 MD5sum: 4a07be5d978f3c163a381bc0fac27ef4 source.ver: src/contrib/pkgDepTools_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pkgDepTools_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pkgDepTools_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pkgDepTools_1.22.0.tgz vignettes: vignettes/pkgDepTools/inst/doc/pkgDepTools.pdf vignetteTitles: How to Use pkgDepTools hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: plateCore Version: 1.14.0 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 URL: http://www.bioconductor.org MD5sum: 729e20bfbaac62139308f72a43268997 source.ver: src/contrib/plateCore_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/plateCore_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/plateCore_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/plateCore_1.14.0.tgz 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 Package: plgem Version: 1.28.0 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 and Norman Pavelka Maintainer: Norman Pavelka URL: http://www.genopolis.it MD5sum: d7a19b719529e35b47705aff2698e03e source.ver: src/contrib/plgem_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/plgem_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/plgem_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/plgem_1.28.0.tgz vignettes: vignettes/plgem/inst/doc/plgem.pdf vignetteTitles: An introduction to PLGEM hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: plier Version: 1.26.0 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 MD5sum: a592ea978bc0204fbcab61e2092cc24b source.ver: src/contrib/plier_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/plier_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/plier_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/plier_1.26.0.tgz hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: virtualArray Package: PLPE Version: 1.16.0 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 and Jae K. Lee Maintainer: Soo-heang Eo URL: http://www.korea.ac.kr/~stat2242/ MD5sum: cef8202328378d4f5f1b624781e16b39 source.ver: src/contrib/PLPE_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PLPE_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PLPE_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PLPE_1.16.0.tgz vignettes: vignettes/PLPE/inst/doc/PLPE.pdf vignetteTitles: PLPE Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: plw Version: 1.16.0 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 MD5sum: 1ebc3caf2cf37f18d46575fb65061ce6 source.ver: src/contrib/plw_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/plw_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/plw_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/plw_1.16.0.tgz vignettes: vignettes/plw/inst/doc/HowToPLW.pdf vignetteTitles: HowTo plw hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ppiStats Version: 1.22.0 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 Author: T. Chiang and D. Scholtens with contributions from W. Huber and L. Wang Maintainer: Tony Chiang MD5sum: 4e26b1333d6b8f597e225bdc5e38bb0a source.ver: src/contrib/ppiStats_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ppiStats_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ppiStats_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ppiStats_1.22.0.tgz vignettes: vignettes/ppiStats/inst/doc/ppiStats.pdf vignetteTitles: ppiStats hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: PCpheno suggestsMe: BiocCaseStudies, RpsiXML Package: prada Version: 1.32.0 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 , Wolfgang Huber , Markus Ruschhaupt, Joern Toedling Maintainer: Florian Hahne URL: http://www.dkfz.de/mga/whuber, http://www.dkfz.de/LIFEdb MD5sum: 4076d5d2d9aa8301a191a7a5d98e04d8 source.ver: src/contrib/prada_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/prada_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/prada_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/prada_1.32.0.tgz 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 dependsOnMe: cellHTS, domainsignatures, RNAither importsMe: cellHTS2 Package: PREDA Version: 1.2.0 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 Maintainer: Francesco Ferrari MD5sum: f6902f5c7efd846945a1b19d2f8a3068 source.ver: src/contrib/PREDA_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PREDA_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PREDA_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PREDA_1.2.0.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 Package: predictionet Version: 1.2.2 Depends: igraph0, catnet Imports: penalized 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. Author: Benjamin Haibe-Kains, Catharina Olsen, Gianluca Bontempi, John Quackenbush Maintainer: Benjamin Haibe-Kains , Catharina Olsen URL: http://compbio.dfci.harvard.edu, http://www.ulb.ac.be/di/mlg MD5sum: 061dd2f55d2c3968441208fd3b8fd0db source.ver: src/contrib/predictionet_1.2.2.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/predictionet_1.2.2.tgz vignettes: vignettes/predictionet/inst/doc/predictionet.pdf vignetteTitles: predictionet hasREADME: TRUE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: preprocessCore Version: 1.18.0 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 Maintainer: Benjamin Milo Bolstad MD5sum: 98e4aff20ffbff77c632597d25dda183 source.ver: src/contrib/preprocessCore_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/preprocessCore_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/preprocessCore_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/preprocessCore_1.18.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: affyPLM, cqn, RefPlus, virtualArray importsMe: affy, AffyTiling, charm, cn.farms, crlmm, frma, frmaTools, lumi, MBCB, minfi, MSnbase, oligo suggestsMe: oneChannelGUI Package: PROcess Version: 1.32.0 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 MD5sum: 0a8e5a08def7f04b659664c28640e810 source.ver: src/contrib/PROcess_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PROcess_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PROcess_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PROcess_1.32.0.tgz vignettes: vignettes/PROcess/inst/doc/howtoprocess.pdf vignetteTitles: HOWTO PROcess hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: procoil Version: 1.6.0 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 URL: http://www.bioinf.jku.at/software/procoil/ MD5sum: 76905744f7bf5be150d180b933ab3f1d source.ver: src/contrib/procoil_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/procoil_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/procoil_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/procoil_1.6.0.tgz 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 Package: PROMISE Version: 1.8.0 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 , Xueyuan Cao Maintainer: Stan Pounds , Xueyuan Cao MD5sum: c24b87e148f6e388d3c5756c74eea59d source.ver: src/contrib/PROMISE_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/PROMISE_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/PROMISE_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/PROMISE_1.8.0.tgz vignettes: vignettes/PROMISE/inst/doc/PROMISE.pdf vignetteTitles: An introduction to PROMISE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: puma Version: 2.8.0 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 URL: http://umber.sbs.man.ac.uk/resources/puma MD5sum: 5559a868126d2bf12ecfbd9c4e6a862d source.ver: src/contrib/puma_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/puma_2.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/puma_2.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/puma_2.8.0.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: 1.4.0 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 , Pierre R. Bushel MD5sum: e912e84270ffed1e7cf6fe2aec696fed source.ver: src/contrib/pvac_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/pvac_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/pvac_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/pvac_1.4.0.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 Package: qpcrNorm Version: 1.14.0 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 MD5sum: 9ed533f5f7d5b7fc7af7030e0beaa08d source.ver: src/contrib/qpcrNorm_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/qpcrNorm_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/qpcrNorm_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/qpcrNorm_1.14.0.tgz vignettes: vignettes/qpcrNorm/inst/doc/qpcrNorm.pdf vignetteTitles: qPCR Normalization Example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: qpgraph Version: 1.12.2 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, Bioinformatics, GraphsAndNetworks Author: R. Castelo and A. Roverato Maintainer: Robert Castelo URL: http://functionalgenomics.upf.edu/qpgraph MD5sum: 5d5eb3607317ad027b8b4ac5878ee612 source.ver: src/contrib/qpgraph_1.12.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/qpgraph_1.12.2.zip win64.binary.ver: bin/windows64/contrib/2.15/qpgraph_1.12.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/qpgraph_1.12.2.tgz 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 suggestsMe: GSVA Package: qrqc Version: 1.10.0 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 URL: http://github.com/vsbuffalo/qrqc MD5sum: 1f7ea852bb3ecf2f4347323204e9c630 source.ver: src/contrib/qrqc_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/qrqc_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/qrqc_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/qrqc_1.10.0.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 Package: QUALIFIER Version: 1.0.2 Depends: R (>= 2.14.0),reshape,flowWorkspace, Imports: MASS,hwriter,RSVGTipsDevice,lattice,stats4,flowCore,flowViz,methods 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 MD5sum: 7ac0387378cb57d4dd369ad2a4063158 source.ver: src/contrib/QUALIFIER_1.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/QUALIFIER_1.0.2.zip win64.binary.ver: bin/windows64/contrib/2.15/QUALIFIER_1.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/QUALIFIER_1.0.2.tgz vignettes: vignettes/QUALIFIER/inst/doc/QUALIFIER.pdf vignetteTitles: Quality assessment for gated Flow Cytometry Data hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: quantsmooth Version: 1.22.2 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 MD5sum: 9ff0f2315899754088a94779bac60ed2 source.ver: src/contrib/quantsmooth_1.22.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/quantsmooth_1.22.2.zip win64.binary.ver: bin/windows64/contrib/2.15/quantsmooth_1.22.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/quantsmooth_1.22.2.tgz vignettes: vignettes/quantsmooth/inst/doc/quantsmooth.pdf vignetteTitles: quantsmooth hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: beadarraySNP importsMe: SIM suggestsMe: PREDA Package: qvalue Version: 1.30.0 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 and John D. Storey , with assistance from Gregory R. Warnes Maintainer: John D. Storey MD5sum: 6a44785bc3096f241ae3fb7bb4f323d2 source.ver: src/contrib/qvalue_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/qvalue_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/qvalue_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/qvalue_1.30.0.tgz 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 dependsOnMe: anota, CancerMutationAnalysis, DEGseq, netresponse, PatientGeneSets, SSPA, webbioc importsMe: anota, DOSE, ReactomePA, trigger, webbioc suggestsMe: LBE, maanova, PREDA Package: r3Cseq Version: 1.2.0 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 Maintainer: Supat Thongjuea MD5sum: 15296adfd2aa65890f4d165939c37bdd source.ver: src/contrib/r3Cseq_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/r3Cseq_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/r3Cseq_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/r3Cseq_1.2.0.tgz vignettes: vignettes/r3Cseq/inst/doc/r3Cseq.pdf vignetteTitles: r3Cseq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: R453Plus1Toolbox Version: 1.6.1 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 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 MD5sum: cc28be1e661c40ffdb4a4ab876b227d2 source.ver: src/contrib/R453Plus1Toolbox_1.6.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/R453Plus1Toolbox_1.6.1.zip win64.binary.ver: bin/windows64/contrib/2.15/R453Plus1Toolbox_1.6.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/R453Plus1Toolbox_1.6.1.tgz 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 Package: rama Version: 1.30.0 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 MD5sum: 73e9e745a75832dce29027115a2f55f3 source.ver: src/contrib/rama_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/rama_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/rama_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rama_1.30.0.tgz vignettes: vignettes/rama/inst/doc/rama.pdf vignetteTitles: rama Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: bridge Package: RamiGO Version: 1.2.0 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, Visualization, GraphsAndNetworks, Classification Author: Markus Schroeder, Daniel Gusenleitner, Aedin Culhane, Benjamin Haibe-Kains, John Quackenbush Maintainer: Markus Schroeder MD5sum: 9cc1a46e324e1e4ce36e9827bd557cc2 source.ver: src/contrib/RamiGO_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RamiGO_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RamiGO_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RamiGO_1.2.0.tgz vignettes: vignettes/RamiGO/inst/doc/RamiGO.pdf vignetteTitles: RamiGO: An Introduction (HowTo) hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: randPack Version: 1.2.0 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 and Robert Gentleman Maintainer: Robert Gentleman MD5sum: 028a03c640e1ea812a7c8c914c6a4a5d source.ver: src/contrib/randPack_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/randPack_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/randPack_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/randPack_1.2.0.tgz vignettes: vignettes/randPack/inst/doc/randPack.pdf vignetteTitles: Clinical trial randomization infrastructure hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RankProd Version: 2.28.0 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 and Ben Wittner with contribution from Rainer Breitling , Colin Smith , and Florian Battke Maintainer: Fangxin Hong MD5sum: 485cf54f1fda22122bdded41e81060e6 source.ver: src/contrib/RankProd_2.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RankProd_2.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RankProd_2.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RankProd_2.28.0.tgz vignettes: vignettes/RankProd/inst/doc/RankProd.pdf vignetteTitles: RankProd Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: HTSanalyzeR, RNAither suggestsMe: oneChannelGUI Package: RbcBook1 Version: 1.24.0 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 and Wolfgang Huber Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey MD5sum: 59c10123498ca240f9287ecde13b63f2 source.ver: src/contrib/RbcBook1_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RbcBook1_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RbcBook1_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RbcBook1_1.24.0.tgz vignettes: vignettes/RbcBook1/inst/doc/RbcBook1.pdf vignetteTitles: RbcBook1 Primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RBGL Version: 1.32.1 Depends: graph, methods Imports: methods Suggests: Rgraphviz 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 Author: Vince Carey , Li Long , R. Gentleman Maintainer: Bioconductor Package Maintainer URL: http://www.bioconductor.org MD5sum: a6285aa23a6489a897f32130e7023a7c source.ver: src/contrib/RBGL_1.32.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/RBGL_1.32.1.zip win64.binary.ver: bin/windows64/contrib/2.15/RBGL_1.32.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RBGL_1.32.1.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 dependsOnMe: apComplex, BioNet, CellNOptR, flowWorkspace, gene2pathway, joda, pkgDepTools, RpsiXML importsMe: biocViews, CAMERA, Category, DEGraph, GeneAnswers, GOstats, NCIgraph, nem, pkgDepTools suggestsMe: BiocCaseStudies, DEGraph, graph, GSVA, KEGGgraph Package: RBioinf Version: 1.16.0 Depends: graph, methods 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 MD5sum: 22353da13c4cb63fa2386cc7d81d6b86 source.ver: src/contrib/RBioinf_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RBioinf_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RBioinf_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RBioinf_1.16.0.tgz vignettes: vignettes/RBioinf/inst/doc/RBioinf.pdf vignetteTitles: RBioinf Introduction hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: rbsurv Version: 2.14.0 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 , Sukwoo Kim , Soo-heang Eo , Jaewoo Kang Maintainer: Soo-heang Eo URL: http://www.korea.ac.kr/~stat2242/ MD5sum: 157ee824da83f0273e8b29ad753db497 source.ver: src/contrib/rbsurv_2.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/rbsurv_2.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/rbsurv_2.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rbsurv_2.14.0.tgz vignettes: vignettes/rbsurv/inst/doc/rbsurv.pdf vignetteTitles: Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RCASPAR Version: 1.2.0 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 , Lars Kaderali MD5sum: 99415a121bd36fdc2e3e12987f59ab83 source.ver: src/contrib/RCASPAR_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RCASPAR_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RCASPAR_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RCASPAR_1.2.0.tgz 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 Package: RchyOptimyx Version: 1.0.0 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 , Nima Aghaeepour MD5sum: e62df35e988cb7f433e9ca08c3d6ca25 source.ver: src/contrib/RchyOptimyx_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RchyOptimyx_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RchyOptimyx_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RchyOptimyx_1.0.0.tgz vignettes: vignettes/RchyOptimyx/inst/doc/RchyOptimyx.pdf vignetteTitles: flowType package hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RCytoscape Version: 1.6.5 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: GraphsAndNetworks Author: Paul Shannon Maintainer: Paul Shannon URL: http://rcytoscape.systemsbiology.net MD5sum: 0a9f67bc4de9fd4f4ced46bf73bdd78f source.ver: src/contrib/RCytoscape_1.6.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/RCytoscape_1.6.5.zip win64.binary.ver: bin/windows64/contrib/2.15/RCytoscape_1.6.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RCytoscape_1.6.5.tgz vignettes: vignettes/RCytoscape/inst/doc/RCytoscape.pdf vignetteTitles: RCytoscape Overview hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: categoryCompare, NCIgraph suggestsMe: graphite Package: Rdisop Version: 1.16.0 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 , Steffen Neumann Maintainer: Steffen Neumann URL: http://msbi.ipb-halle.de/ SystemRequirements: None MD5sum: 130b6dbd6268de9e243997579ee9dbb5 source.ver: src/contrib/Rdisop_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Rdisop_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Rdisop_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Rdisop_1.16.0.tgz vignettes: vignettes/Rdisop/inst/doc/Rdisop.pdf vignetteTitles: \\ hasREADME: FALSE hasNEWS: FALSE hasINSTALL: TRUE hasLICENSE: FALSE suggestsMe: MSnbase Package: RDRToolbox Version: 1.6.0 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 MD5sum: 95f50bac74d03288118daa5d10bca17c source.ver: src/contrib/RDRToolbox_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RDRToolbox_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RDRToolbox_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RDRToolbox_1.6.0.tgz 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 Package: ReactomePA Version: 1.0.1 Imports: methods, AnnotationDbi, reactome.db, stats4, plyr, igraph0, qvalue, graphics, org.Hs.eg.db Suggests: clusterProfiler, DOSE, GOSemSim 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 Maintainer: Guangchuang Yu MD5sum: 62e41ccea004ff1a17efadb86d337ace source.ver: src/contrib/ReactomePA_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/ReactomePA_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.15/ReactomePA_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ReactomePA_1.0.1.tgz 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 suggestsMe: clusterProfiler, DOSE Package: ReadqPCR Version: 1.2.0 Depends: R(>= 2.10.0), 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. Author: James Perkins, Matthias Kohl Maintainer: James Perkins URL: http://qpcr.r-forge.r-project.org/ MD5sum: a38bdcd781942682620d747d29973ee2 source.ver: src/contrib/ReadqPCR_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ReadqPCR_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ReadqPCR_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ReadqPCR_1.2.0.tgz vignettes: vignettes/ReadqPCR/inst/doc/ReadqPCR.pdf vignetteTitles: Functions to load RT-qPCR data into R hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: NormqPCR importsMe: NormqPCR Package: reb Version: 1.32.0 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 and Karl Dykema Maintainer: Karl J. Dykema MD5sum: a3c47c72c28b49e44c78cb32cb93547d source.ver: src/contrib/reb_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/reb_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/reb_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/reb_1.32.0.tgz vignettes: vignettes/reb/inst/doc/reb.pdf vignetteTitles: Smoothing of Microarray Data hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RedeR Version: 1.2.5 Depends: R (>= 2.15), igraph0, RCurl, XML, XMLRPC Imports: rJava, methods Suggests: PANR, HTSanalyzeR, pvclust, graph License: GPL (>= 2) Title: Bridging the gap between hierarchical network representation and functional analysis. Description: RedeR is an R-based package combined with a stand-alone Java application for dynamic network visualization and manipulation. 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: for R Developers, it allows the development of Java plug-ins exclusively using R codes; for Java Users, it runs R methods implemented in a stand-alone application, and for R Users RedeR interactively displays R graphs using a robust Java graphic engine embedded in this package. biocViews: GraphsAndNetworks, Visualization, GUI Author: Mauro Castro, Xin Wang, Florian Markowetz Maintainer: Mauro Castro URL: http://www.markowetzlab.org/software/networks.html MD5sum: eb5111d5486d45f1218767af6344893a source.ver: src/contrib/RedeR_1.2.5.tar.gz win.binary.ver: bin/windows/contrib/2.15/RedeR_1.2.5.zip win64.binary.ver: bin/windows64/contrib/2.15/RedeR_1.2.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RedeR_1.2.5.tgz 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, fig5b.pdf, fig5c.pdf, fig6.pdf, Main vignette: RedeR Overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: PANR Package: REDseq Version: 1.2.0 Depends: R (>= 2.14.0), 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 MD5sum: a2dde31c1bd6e47e19fb2ae1c149ab91 source.ver: src/contrib/REDseq_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/REDseq_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/REDseq_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/REDseq_1.2.0.tgz vignettes: vignettes/REDseq/inst/doc/REDseq.pdf vignetteTitles: REDseq Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RefPlus Version: 1.26.0 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 , Chris Harbron , Marie C South Maintainer: Kai-Ming Chang MD5sum: 5f2613864631bc19376bd7662dd828a4 source.ver: src/contrib/RefPlus_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RefPlus_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RefPlus_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RefPlus_1.26.0.tgz vignettes: vignettes/RefPlus/inst/doc/An_Exploration_of_Extensions_to_the_RMA_Algorithm.pdf, 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 Package: Repitools Version: 1.2.0 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, 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 , Dario Strbenac , Aaron Statham Maintainer: Mark Robinson MD5sum: 511577f86afaeed5170d4abac6c66ff2 source.ver: src/contrib/Repitools_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Repitools_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Repitools_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Repitools_1.2.0.tgz 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 Package: ReQON Version: 1.3.9 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 SystemRequirements: Java version >= 1.6 MD5sum: 0a1225a5cf38ff9d1ee2f65595bc05d1 source.ver: src/contrib/ReQON_1.3.9.tar.gz win.binary.ver: bin/windows/contrib/2.15/ReQON_1.3.9.zip win64.binary.ver: bin/windows64/contrib/2.15/ReQON_1.3.9.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ReQON_1.3.9.tgz vignettes: vignettes/ReQON/inst/doc/ReQON.pdf vignetteTitles: ReQON Tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: Resourcerer Version: 1.30.0 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 MD5sum: 7001246065f8595ac6323ec38a616fd9 source.ver: src/contrib/Resourcerer_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Resourcerer_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Resourcerer_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Resourcerer_1.30.0.tgz vignettes: vignettes/Resourcerer/inst/doc/Resourcerer.pdf vignetteTitles: Resourcerer Resourcerer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: rGADEM Version: 2.4.0 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 Author: Arnaud Droit, Raphael Gottardo, Gordon Robertson and Leiping Li Maintainer: Arnaud Droit MD5sum: 77a857cf238a8fc92f1a7536347fc93a source.ver: src/contrib/rGADEM_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/rGADEM_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/rGADEM_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rGADEM_2.4.0.tgz vignettes: vignettes/rGADEM/inst/doc/rGADEM.pdf vignetteTitles: The rGADEM users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MotIV Package: Rgraphviz Version: 1.34.2 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: stats4, graph, graphics, grDevices, grid, methods, utils License: Artistic-2.0 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 Author: Jeff Gentry, Li Long, Robert Gentleman, Seth, Florian Hahne, Deepayan Sarkar, Kasper Hansen Maintainer: Kasper Hansen SystemRequirements: Graphviz version >= 2.2 MD5sum: 10c0a5d73743cd584d888d4d12822798 source.ver: src/contrib/Rgraphviz_1.34.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/Rgraphviz_1.34.2.zip win64.binary.ver: bin/windows64/contrib/2.15/Rgraphviz_1.34.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Rgraphviz_1.34.2.tgz 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: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: biocGraph, BioMVCClass, flowMerge, GOFunction, hyperdraw, nem, netresponse, pathRender, TDARACNE importsMe: apComplex, biocGraph, DEGraph, GeneAnswers, GOFunction, nem, RchyOptimyx suggestsMe: altcdfenvs, annotate, BiocCaseStudies, Category, CellNOptR, DEGraph, flowCore, flowMerge, flowWorkspace, geneplotter, GlobalAncova, globaltest, GOstats, GSEABase, GSVA, KEGGgraph, MLP, NCIgraph, oneChannelGUI, pcaGoPromoter, pkgDepTools, RBGL, Rtreemix, safe, SPIA, SRAdb, topGO Package: rhdf5 Version: 2.0.2 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 SystemRequirements: GNU make MD5sum: 1fdb4909fead378cb21e3eabd8457b98 source.ver: src/contrib/rhdf5_2.0.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/rhdf5_2.0.2.zip win64.binary.ver: bin/windows64/contrib/2.15/rhdf5_2.0.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rhdf5_2.0.2.tgz 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 Package: rHVDM Version: 1.22.0 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 Author: Martino Barenco Maintainer: Martino Barenco MD5sum: 0ba99376849d9f6fdc8b5ded948099b4 source.ver: src/contrib/rHVDM_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/rHVDM_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/rHVDM_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rHVDM_1.22.0.tgz vignettes: vignettes/rHVDM/inst/doc/rHVDM.pdf vignetteTitles: rHVDM primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Ringo Version: 1.20.0 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 MD5sum: 83f97f13ae53f7a4a1e951cfaaebee6c source.ver: src/contrib/Ringo_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Ringo_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Ringo_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Ringo_1.20.0.tgz vignettes: vignettes/Ringo/inst/doc/Ringo.pdf vignetteTitles: R Investigation of NimbleGen Oligoarrays hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: Starr importsMe: Repitools suggestsMe: Repitools Package: RLMM Version: 1.18.0 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 , Gary Wong Maintainer: Nusrat Rabbee URL: http://www.stat.berkeley.edu/users/nrabbee/RLMM SystemRequirements: Internal files Xba.CQV, Xba.regions (or other regions file) MD5sum: 73bf7900f324b1a1ca7cf94a0e27f0d4 source.ver: src/contrib/RLMM_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RLMM_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RLMM_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RLMM_1.18.0.tgz vignettes: vignettes/RLMM/inst/doc/RLMM.pdf vignetteTitles: RLMM Doc hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Rmagpie Version: 1.12.0 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 , with contributions from C. Ambroise J. Zhu Maintainer: Camille Maumet URL: http://www.bioconductor.org/ MD5sum: 8d38203263777c6354136a90e980d271 source.ver: src/contrib/Rmagpie_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Rmagpie_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Rmagpie_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Rmagpie_1.12.0.tgz vignettes: vignettes/Rmagpie/inst/doc/Magpie_examples.pdf vignetteTitles: Rmagpie Examples hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RMAPPER Version: 1.6.0 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 Maintainer: Heike Sichtig , Alberto Riva MD5sum: 8cee65ea26596b136d19fb1116f3a8f8 source.ver: src/contrib/RMAPPER_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RMAPPER_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RMAPPER_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RMAPPER_1.6.0.tgz vignettes: vignettes/RMAPPER/inst/doc/readMAPPER.pdf vignetteTitles: Interface to MAPPER TFBS database hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: rMAT Version: 3.6.0 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 and Raphael Gottardo URL: http://www.rglab.org MD5sum: 9dc6914ec17a0302cb9798dc3507c064 source.ver: src/contrib/rMAT_3.6.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rMAT_3.6.0.tgz vignettes: vignettes/rMAT/inst/doc/rMAT.pdf vignetteTitles: The rMAT users guide hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RmiR Version: 1.12.0 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 MD5sum: 3927a510caf760d5dc774a5246e4969f source.ver: src/contrib/RmiR_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RmiR_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RmiR_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RmiR_1.12.0.tgz vignettes: vignettes/RmiR/inst/doc/RmiR.pdf vignetteTitles: RmiR Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oneChannelGUI Package: RNAinteract Version: 1.4.0 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 Maintainer: Bernd Fischer MD5sum: d9bfe56b4396caa8f0eb42db5fc126f7 source.ver: src/contrib/RNAinteract_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RNAinteract_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RNAinteract_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RNAinteract_1.4.0.tgz vignettes: vignettes/RNAinteract/inst/doc/RNAinteract.pdf vignetteTitles: RNAinteract hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RNAither Version: 2.4.0 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 MD5sum: 285357de27d4c28d5bf9b82af96ec1bb source.ver: src/contrib/RNAither_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RNAither_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RNAither_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RNAither_2.4.0.tgz 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 Package: rnaSeqMap Version: 2.10.0 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: Provides means of analysis for RNAseq data, used together with genomic annotation. Requires a set of BAM files on the input or alternatively, an xmapcore database in MySQL as a back-end, which is also a storage for sequencing reads. Front-end analyses include transformations of the coverage function, splicing analysis, finding irreducible regions with the two-sliding-windows algorithm and genomic region visualizations. biocViews: Annotation, Bioinformatics, ReportWriting, Transcription, GeneExpression, DifferentialExpression, HighThroughputSequencing, RNAseq, SAGE, Visualization Author: Anna Lesniewska ; Michal Okoniewski Maintainer: Michal Okoniewski MD5sum: 8cda2799a33eb5f99bee8a67860f13a0 source.ver: src/contrib/rnaSeqMap_2.10.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rnaSeqMap_2.10.0.tgz vignettes: vignettes/rnaSeqMap/inst/doc/rnaSeqMap.pdf vignetteTitles: rnaSeqMap primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ROC Version: 1.32.0 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 , Henning Redestig for C++ language enhancements Maintainer: Vince Carey URL: http://www.bioconductor.org MD5sum: 8713b81de20f2fde95167f8359c39418 source.ver: src/contrib/ROC_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ROC_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ROC_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ROC_1.32.0.tgz vignettes: vignettes/ROC/inst/doc/ROCnotes.pdf vignetteTitles: ROC notes hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: clst suggestsMe: genefilter, MCRestimate Package: Rolexa Version: 1.12.0 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 MD5sum: eca6532594af02d395d39b4958db8383 source.ver: src/contrib/Rolexa_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Rolexa_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Rolexa_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Rolexa_1.12.0.tgz vignettes: vignettes/Rolexa/inst/doc/Rolexa-vignette.pdf vignetteTitles: Rolexa hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: RPA Version: 1.12.0 Depends: R (>= 2.14.1), 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 Maintainer: Leo Lahti MD5sum: 7448fa348007e437e96611e411c9ada3 source.ver: src/contrib/RPA_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RPA_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RPA_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RPA_1.12.0.tgz vignettes: vignettes/RPA/inst/doc/RPA.pdf vignetteTitles: RPA hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: TRUE Package: RpsiXML Version: 1.16.0 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 URL: http://www.bioconductor.org MD5sum: 7d9082289d5bbc2717b38efcd1287ccd source.ver: src/contrib/RpsiXML_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RpsiXML_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RpsiXML_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RpsiXML_1.16.0.tgz 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 dependsOnMe: ScISI importsMe: ScISI Package: rqubic Version: 1.2.0 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 MD5sum: 879bf0400b2f8ae35432155dafcc165e source.ver: src/contrib/rqubic_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/rqubic_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/rqubic_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rqubic_1.2.0.tgz vignettes: vignettes/rqubic/inst/doc/rqubic.pdf vignetteTitles: Qualitative Biclustering with Bioconductor Package rqubic hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: Rsamtools Version: 1.8.6 Depends: methods, IRanges (>= 1.13.30), GenomicRanges (>= 1.7.43), Biostrings (>= 2.21.12) Imports: methods, utils, IRanges, GenomicRanges, Biostrings, zlibbioc, bitops, BiocGenerics (>= 0.1.3) LinkingTo: Biostrings, IRanges Suggests: ShortRead (>= 1.13.19), GenomicFeatures, RUnit, KEGG.db 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 URL: http://bioconductor.org/packages/release/bioc/html/Rsamtools.html MD5sum: 83d77a6e9a2689138c6262011647b199 source.ver: src/contrib/Rsamtools_1.8.6.tar.gz win.binary.ver: bin/windows/contrib/2.15/Rsamtools_1.8.6.zip win64.binary.ver: bin/windows64/contrib/2.15/Rsamtools_1.8.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Rsamtools_1.8.6.tgz 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 dependsOnMe: ArrayExpressHTS, BitSeq, deepSNV, easyRNASeq, EDASeq, exomeCopy, GGtools, girafe, oneChannelGUI, qrqc, ReQON, rnaSeqMap, ShortRead, TEQC, VariantAnnotation importsMe: ArrayExpressHTS, biovizBase, deepSNV, ggbio, R453Plus1Toolbox, rtracklayer, ShortRead, VariantAnnotation suggestsMe: GenomicRanges, R453Plus1Toolbox, seqbias, Streamer Package: rsbml Version: 2.14.4 Depends: R (>= 2.6.0), methods, utils Imports: 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 Author: Michael Lawrence Maintainer: Michael Lawrence URL: http://www.sbml.org SystemRequirements: libsbml (>=3.0.3) MD5sum: 865f74318de2896abc33489c39e0d7c0 source.ver: src/contrib/rsbml_2.14.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/rsbml_2.14.4.zip win64.binary.ver: bin/windows64/contrib/2.15/rsbml_2.14.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rsbml_2.14.4.tgz vignettes: vignettes/rsbml/inst/doc/quick-start.pdf vignetteTitles: Quick start for rsbml hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: Rsubread Version: 1.6.4 License: LGPL-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, which is entirely different from the "seed-and-extent" paradigm. 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 and Jenny Zhiyin Dai Maintainer: Wei Shi URL: http://bioconductor.org/packages/release/bioc/html/Rsubread.html MD5sum: 3cb065060c708d3335c07836af810396 source.ver: src/contrib/Rsubread_1.6.4.tar.gz vignettes: vignettes/Rsubread/inst/doc/Rsubread.pdf vignetteTitles: Rsubread Vignette hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: RTCA Version: 1.8.0 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 URL: http://code.google.com/p/xcelligence/, http://www.xcelligence.roche.com/, http://www.nextbiomotif.com/Home/scientific-programming MD5sum: 5680d0fc164a4a10108d713b04fb7032 source.ver: src/contrib/RTCA_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RTCA_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RTCA_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RTCA_1.8.0.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 Package: RTopper Version: 1.2.0 Depends: R (>= 2.11.0), Biobase Imports: limma, multtest Suggests: limma, org.Hs.eg.db, KEGG.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 , Svitlana Tyekucheva Maintainer: Luigi Marchionni MD5sum: 14147f5ea23d1ed5d6225185d159e2c2 source.ver: src/contrib/RTopper_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/RTopper_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/RTopper_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/RTopper_1.2.0.tgz vignettes: vignettes/RTopper/inst/doc/RTopper.pdf vignetteTitles: RTopper user's manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: rtracklayer Version: 1.16.3 Depends: R (>= 2.10), methods, GenomicRanges Imports: XML (>= 1.98-0), BiocGenerics (>= 0.1.0), IRanges (>= 1.13.14), GenomicRanges (>= 1.7.28), Biostrings (>= 2.23.2), 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 MD5sum: b8417413876f872f9bc70dc76c44137c source.ver: src/contrib/rtracklayer_1.16.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/rtracklayer_1.16.3.zip win64.binary.ver: bin/windows64/contrib/2.15/rtracklayer_1.16.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/rtracklayer_1.16.3.tgz vignettes: vignettes/rtracklayer/inst/doc/rtracklayer.pdf vignetteTitles: rtracklayer hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: r3Cseq importsMe: ChromHeatMap, GenomicFeatures, ggbio, Gviz, lumi, R453Plus1Toolbox suggestsMe: biovizBase, GenomicFeatures, GenomicRanges, MotIV, NarrowPeaks, oneChannelGUI, PICS, PING, R453Plus1Toolbox, Ringo, rMAT, TSSi Package: Rtreemix Version: 1.18.0 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 MD5sum: 5615f8405b3b9b32412f29de12f1d19a source.ver: src/contrib/Rtreemix_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Rtreemix_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Rtreemix_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Rtreemix_1.18.0.tgz 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 Package: RWebServices Version: 1.20.0 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 MD5sum: dfb0d68fd29db2971b64093313d42b03 source.ver: src/contrib/RWebServices_1.20.0.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 Package: safe Version: 2.16.0 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 URL: http://www.duke.edu/~dinbarry/SAFE/ MD5sum: 82d1f1f43d936b03135b1ec38015d41f source.ver: src/contrib/safe_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/safe_2.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/safe_2.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/safe_2.16.0.tgz vignettes: vignettes/safe/inst/doc/SAFEmanual2.pdf vignetteTitles: SAFE manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: sagenhaft Version: 1.26.0 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 , with contributions from Gordon Smyth and Lavinia Hyde . Maintainer: Tim Beissbarth URL: http://tagcalling.mbgproject.org MD5sum: f48b8539023d62a359a93a853a4345c1 source.ver: src/contrib/sagenhaft_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/sagenhaft_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/sagenhaft_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/sagenhaft_1.26.0.tgz vignettes: vignettes/sagenhaft/inst/doc/SAGEnhaft.pdf vignetteTitles: SAGEnhaft hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SAGx Version: 1.30.0 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, URL: http://home.swipnet.se/pibroberg/expression_hemsida1.html MD5sum: 4183cca6790b524f760eaa7603a85e92 source.ver: src/contrib/SAGx_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SAGx_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SAGx_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SAGx_1.30.0.tgz vignettes: vignettes/SAGx/inst/doc/samroc-ex.pdf vignetteTitles: samroc - example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SamSPECTRAL Version: 1.10.0 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 MD5sum: ff12159c3296ff9bd90a5a2c6c478686 source.ver: src/contrib/SamSPECTRAL_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SamSPECTRAL_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SamSPECTRAL_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SamSPECTRAL_1.10.0.tgz 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 Package: SBMLR Version: 1.52.0 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 Author: Tomas Radivoyevitch Maintainer: Tomas Radivoyevitch URL: http://epbi-radivot.cwru.edu/SBMLR/SBMLR.html MD5sum: 5ffa3268328c0226eead495014614543 source.ver: src/contrib/SBMLR_1.52.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SBMLR_1.52.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SBMLR_1.52.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SBMLR_1.52.0.tgz 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 Package: ScISI Version: 1.28.0 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 Author: Tony Chiang Maintainer: Tony Chiang MD5sum: 5064c6d587ec540c5179e31f0b262eaa source.ver: src/contrib/ScISI_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ScISI_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ScISI_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ScISI_1.28.0.tgz vignettes: vignettes/ScISI/inst/doc/vignette.pdf vignetteTitles: ScISI Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: PCpheno, ppiStats, SLGI importsMe: PCpheno, SLGI suggestsMe: RpsiXML Package: segmentSeq Version: 1.8.0 Depends: R (>= 2.3.0), methods, baySeq (>= 1.8.1), 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 MD5sum: 67089c21f6e249852359a09e621ac8b7 source.ver: src/contrib/segmentSeq_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/segmentSeq_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/segmentSeq_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/segmentSeq_1.8.0.tgz vignettes: vignettes/segmentSeq/inst/doc/segmentSeq.pdf vignetteTitles: segmentSeq hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: seqbias Version: 1.4.0 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 Maintainer: Daniel Jones MD5sum: 70558605f7a35cb48a3cd2d3d8f70bf8 source.ver: src/contrib/seqbias_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/seqbias_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/seqbias_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/seqbias_1.4.0.tgz vignettes: vignettes/seqbias/inst/doc/overview.pdf vignetteTitles: hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ReQON Package: seqLogo Version: 1.22.0 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 MD5sum: 5837ae912e5e67a945445928b84a0765 source.ver: src/contrib/seqLogo_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/seqLogo_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/seqLogo_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/seqLogo_1.22.0.tgz vignettes: vignettes/seqLogo/inst/doc/seqLogo.pdf vignetteTitles: Sequence logos for DNA sequence alignments hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: cosmo, rGADEM importsMe: motifRG, rGADEM suggestsMe: BCRANK Package: ShortRead Version: 1.14.4 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.4), GenomicRanges (>= 1.7.43), Biostrings (>= 2.23.2), 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 MD5sum: 6de73dce7e748165f04acddbe30ebcc4 source.ver: src/contrib/ShortRead_1.14.4.tar.gz win.binary.ver: bin/windows/contrib/2.15/ShortRead_1.14.4.zip win64.binary.ver: bin/windows64/contrib/2.15/ShortRead_1.14.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ShortRead_1.14.4.tgz 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 dependsOnMe: chipseq, ChIPseqR, easyRNASeq, EDASeq, girafe, nucleR, OTUbase, Rolexa, segmentSeq importsMe: ArrayExpressHTS, chipseq, ChIPseqR, ChIPsim, HiTC, nucleR, OTUbase, R453Plus1Toolbox, Rolexa suggestsMe: CSAR, Genominator, PICS, PING, R453Plus1Toolbox, Repitools, Rsamtools Package: sigaR Version: 1.0.0 Depends: Biobase, CGHbase, corpcor (>= 1.6.2), methods Imports: graphics, marray, MASS, mvtnorm, quadprog, 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 Maintainer: Wessel N. van Wieringen URL: http://www.few.vu.nl/~wvanwie MD5sum: b09dd8e2750c2259c95325a625623f02 source.ver: src/contrib/sigaR_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/sigaR_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/sigaR_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/sigaR_1.0.0.tgz vignettes: vignettes/sigaR/inst/doc/sigaR.pdf vignetteTitles: sigaR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: siggenes Version: 1.30.0 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 MD5sum: c58400ce10419692512fccd8e0aabfe8 source.ver: src/contrib/siggenes_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/siggenes_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/siggenes_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/siggenes_1.30.0.tgz 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 dependsOnMe: KCsmart, oneChannelGUI importsMe: charm, GeneSelector, minfi suggestsMe: GeneSelector, logicFS, XDE Package: sigPathway Version: 1.24.0 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 URL: http://www.pnas.org/cgi/doi/10.1073/pnas.0506577102, http://www.chip.org/~ppark/Supplements/PNAS05.html MD5sum: 2f4b488ed5a9199b34a159de383e34af source.ver: src/contrib/sigPathway_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/sigPathway_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/sigPathway_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/sigPathway_1.24.0.tgz vignettes: vignettes/sigPathway/inst/doc/sigPathway-vignette.pdf vignetteTitles: sigPathway hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SIM Version: 1.26.0 Depends: R (>= 2.4), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt 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: Maarten van Iterson MD5sum: 3b601d9a44fcf4d53fd8b8fb81ad638b source.ver: src/contrib/SIM_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SIM_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SIM_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SIM_1.26.0.tgz vignettes: vignettes/SIM/inst/doc/SIM.pdf vignetteTitles: SIM vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: simpleaffy Version: 2.32.0 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 URL: http://www.bioconductor.org, http://bioinformatics.picr.man.ac.uk/simpleaffy/ MD5sum: 0507387405aefd893cd4d433418c0a19 source.ver: src/contrib/simpleaffy_2.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/simpleaffy_2.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/simpleaffy_2.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/simpleaffy_2.32.0.tgz 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 dependsOnMe: yaqcaffy importsMe: affyQCReport, arrayMvout, arrayQualityMetrics suggestsMe: AffyExpress, ArrayTools Package: sizepower Version: 1.26.0 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 and Mei-Ling Ting Lee and George Alex Whitmore Maintainer: Weiliang Qiu MD5sum: 9339a83bf8dd103a93a5523c1998795f source.ver: src/contrib/sizepower_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/sizepower_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/sizepower_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/sizepower_1.26.0.tgz vignettes: vignettes/sizepower/inst/doc/sizepower.pdf vignetteTitles: package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oneChannelGUI Package: SJava Version: 0.82.0 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 MD5sum: e4b56292ba2f8ad3669f8c7fe44222ed source.ver: src/contrib/SJava_0.82.0.tar.gz hasREADME: TRUE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: RWebServices Package: SLGI Version: 1.16.0 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 Author: Nolwenn LeMeur, Zhen Jiang, Ting-Yuan Liu, Jess Mar and Robert Gentleman Maintainer: Nolwenn Le Meur MD5sum: 60550aee6045e60047113a3abc3a6444 source.ver: src/contrib/SLGI_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SLGI_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SLGI_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SLGI_1.16.0.tgz vignettes: vignettes/SLGI/inst/doc/SLGI.pdf vignetteTitles: SLGI Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: PCpheno Package: SLqPCR Version: 1.22.0 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 MD5sum: 93e3ee774d220765467c6f17c0dc9989 source.ver: src/contrib/SLqPCR_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SLqPCR_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SLqPCR_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SLqPCR_1.22.0.tgz vignettes: vignettes/SLqPCR/inst/doc/SLqPCR.pdf vignetteTitles: SLqPCR hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SMAP Version: 1.20.0 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 Maintainer: Robin Andersson MD5sum: 8242ffaa45143e6e42f210d963627f1c source.ver: src/contrib/SMAP_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SMAP_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SMAP_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SMAP_1.20.0.tgz vignettes: vignettes/SMAP/inst/doc/SMAP.pdf vignetteTitles: SMAP hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: snapCGH Version: 1.26.0 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 MD5sum: 1dc9ef2a16fec4427dfc9732864f45eb source.ver: src/contrib/snapCGH_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/snapCGH_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.15/snapCGH_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/snapCGH_1.26.0.tgz vignettes: vignettes/snapCGH/inst/doc/snapCGHguide.pdf vignetteTitles: Segmentation Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: ADaCGH2 suggestsMe: beadarraySNP Package: snm Version: 1.4.0 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 and John D. Storey Maintainer: Brig Mecham MD5sum: dc9ed8494a22293319e238142e85b15b source.ver: src/contrib/snm_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/snm_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/snm_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/snm_1.4.0.tgz vignettes: vignettes/snm/inst/doc/snm.pdf vignetteTitles: snm Tutorial hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: SNPchip Version: 2.2.0 Depends: R (>= 2.14.0) Imports: graphics, lattice, grid, foreach, IRanges, utils, methods, oligoClasses (>= 1.17.25), Biobase Suggests: crlmm 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 and Ingo Ruczinski Maintainer: Robert Scharpf URL: http://www.biostat.jhsph.edu/~iruczins/software/snpchip.html MD5sum: de0e7f97f7020692c34176c2e3adc2d4 source.ver: src/contrib/SNPchip_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SNPchip_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SNPchip_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SNPchip_2.2.0.tgz vignettes: vignettes/SNPchip/inst/doc/PlottingIdiograms.pdf vignetteTitles: Plotting Idiograms hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: mBPCR importsMe: crlmm, MinimumDistance, phenoTest suggestsMe: Category, VanillaICE Package: snpStats Version: 1.6.0 Depends: R(>= 2.10.0), survival, methods, Matrix Imports: graphics, grDevices, methods, stats, survival, utils, Matrix 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 Maintainer: David Clayton URL: http://www-gene.cimr.cam.ac.uk/clayton MD5sum: d19e6ee44e2514b410251515dafc20ca source.ver: src/contrib/snpStats_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/snpStats_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/snpStats_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/snpStats_1.6.0.tgz 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 dependsOnMe: GGBase, gwascat importsMe: GGtools, VariantAnnotation suggestsMe: crlmm Package: spade Version: 1.2.0 Depends: R (>= 2.11), igraph 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. Bjornsen Maintainer: Michael Linderman URL: http://cytospade.org MD5sum: 036263fc4a2c3df2bf22ffdbae6dae19 source.ver: src/contrib/spade_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/spade_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/spade_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/spade_1.2.0.tgz vignettes: vignettes/spade/inst/doc/SPADE.pdf vignetteTitles: spade package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE Package: SpeCond Version: 1.10.0 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 MD5sum: 3005ffc4504ea8e87a3548b95dd02c38 source.ver: src/contrib/SpeCond_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SpeCond_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SpeCond_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SpeCond_1.10.0.tgz vignettes: vignettes/SpeCond/inst/doc/SpeCond.pdf vignetteTitles: SpeCond hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SPIA Version: 2.6.0 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 Author: Adi Laurentiu Tarca , Purvesh Kathri and Sorin Draghici Maintainer: Adi Laurentiu Tarca URL: http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1 MD5sum: b471d3b900d4dc372507e3e426f7019d source.ver: src/contrib/SPIA_2.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SPIA_2.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SPIA_2.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SPIA_2.6.0.tgz vignettes: vignettes/SPIA/inst/doc/SPIA.pdf vignetteTitles: SPIA hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: graphite, KEGGgraph Package: spikeLI Version: 2.16.0 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 , Sarah Ternisien, Thomas Heim, Enrico Carlon Maintainer: Enrico Carlon MD5sum: 6da17d3d75f40b0d55ad3f240803a71d source.ver: src/contrib/spikeLI_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/spikeLI_2.16.0.zip win64.binary.ver: bin/windows64/contrib/2.15/spikeLI_2.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/spikeLI_2.16.0.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 Package: spkTools Version: 1.12.0 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 , Rafael A Irizarry Maintainer: Matthew N McCall URL: http://bioconductor.org MD5sum: 5b0d4341b8c0a8aca04f5e5b7aa7aec8 source.ver: src/contrib/spkTools_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/spkTools_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/spkTools_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/spkTools_1.12.0.tgz vignettes: vignettes/spkTools/inst/doc/spkDoc.pdf vignetteTitles: spkTools: Spike-in Data Analysis and Visualization hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: splicegear Version: 1.28.0 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 Maintainer: Laurent Gautier MD5sum: 6648a9024cae7eee3cc590c6f4cd31b6 source.ver: src/contrib/splicegear_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/splicegear_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/splicegear_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/splicegear_1.28.0.tgz vignettes: vignettes/splicegear/inst/doc/splicegear.pdf vignetteTitles: splicegear Introduction hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: splots Version: 1.22.0 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 MD5sum: b3371b72f4e7aaa9714f94d796a8959f source.ver: src/contrib/splots_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/splots_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/splots_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/splots_1.22.0.tgz 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 dependsOnMe: cellHTS2 importsMe: RNAinteract, RNAither Package: spotSegmentation Version: 1.30.0 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 URL: http://www.stat.washington.edu/fraley MD5sum: a68bbfa36c78816c631c6881ab7c47e9 source.ver: src/contrib/spotSegmentation_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/spotSegmentation_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.15/spotSegmentation_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/spotSegmentation_1.30.0.tgz vignettes: vignettes/spotSegmentation/inst/doc/spotsegdoc.pdf vignetteTitles: spotsegdoc.pdf hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: SQUADD Version: 1.6.0 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, DataRepresentation Author: Martial Sankar, supervised by Christian Hardtke and Ioannis Xenarios Maintainer: Martial Sankar URL: http://www.unil.ch/dbmv/page21142_en.html MD5sum: 160b0f3ae6c4e3333936215e393dc8d1 source.ver: src/contrib/SQUADD_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SQUADD_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SQUADD_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SQUADD_1.6.0.tgz 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 Package: SRAdb Version: 1.10.0 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 URL: http://watson.nci.nih.gov/ MD5sum: d9d141effbe267b2322a71c0c4d3d06f source.ver: src/contrib/SRAdb_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SRAdb_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SRAdb_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SRAdb_1.10.0.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 Package: sscore Version: 1.28.0 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 , based on C++ code from Li Zhang and Borland Delphi code from Robnet Kerns . Maintainer: Richard Kennedy URL: http://home.att.net/~richard-kennedy/professional.html MD5sum: 93f72217d0e4c5811745f8a8426ca49f source.ver: src/contrib/sscore_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/sscore_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/sscore_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/sscore_1.28.0.tgz vignettes: vignettes/sscore/inst/doc/sscore.pdf vignetteTitles: SScore primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: ssize Version: 1.30.2 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 MD5sum: e6da36b245a33091bbb55b535915f1b5 source.ver: src/contrib/ssize_1.30.2.tar.gz win.binary.ver: bin/windows/contrib/2.15/ssize_1.30.2.zip win64.binary.ver: bin/windows64/contrib/2.15/ssize_1.30.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ssize_1.30.2.tgz vignettes: vignettes/ssize/inst/doc/ssize.pdf vignetteTitles: package hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: oneChannelGUI Package: SSPA Version: 1.12.0 Depends: R (>= 2.8), methods, qvalue Imports: graphics, limma, methods, stats Suggests: multtest, quadprog, splines License: GPL (>= 2) 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 URL: http://www.humgen.nl/MicroarrayAnalysisGroup.html MD5sum: 5f5a5905d0792ac8eef216d501f83212 source.ver: src/contrib/SSPA_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/SSPA_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/SSPA_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/SSPA_1.12.0.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 Package: Starr Version: 1.12.0 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 MD5sum: f280955e027d505ed7eb4e4511f95b80 source.ver: src/contrib/Starr_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Starr_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Starr_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Starr_1.12.0.tgz vignettes: vignettes/Starr/inst/doc/Starr.pdf vignetteTitles: Simple tiling array analysis hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: stepNorm Version: 1.28.0 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 , Yee Hwa (Jean) Yang Maintainer: Yuanyuan Xiao URL: http://www.biostat.ucsf.edu/jean/ MD5sum: 5035832ec4d7ce1f979488d3a7e81e49 source.ver: src/contrib/stepNorm_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/stepNorm_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/stepNorm_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/stepNorm_1.28.0.tgz hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: stepwiseCM Version: 1.2.1 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 MD5sum: 02c36f5eb0fc5a6131bfe52cbd2ac4c0 source.ver: src/contrib/stepwiseCM_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/stepwiseCM_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/stepwiseCM_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/stepwiseCM_1.2.1.tgz vignettes: vignettes/stepwiseCM/inst/doc/stepwiseCM.pdf vignetteTitles: stepwiseCM hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Streamer Version: 1.2.1 Imports: methods, graph Suggests: RUnit, Rsamtools (>= 1.5.53) Enhances: multicore 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. Author: Martin Morgan, Nishant Gopalakrishnan Maintainer: Martin Morgan MD5sum: 347fb98e558c9710de387bdeba375593 source.ver: src/contrib/Streamer_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/Streamer_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/Streamer_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Streamer_1.2.1.tgz vignettes: vignettes/Streamer/inst/doc/Streamer.pdf vignetteTitles: Streamer: A simple example hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: survcomp Version: 1.6.0 Depends: R (>= 2.10), survival, prodlim Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta Suggests: Hmisc, CPE, clinfun, survJamda, Biobase 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 , Markus Schroeder , Catharina Olsen URL: http://compbio.dfci.harvard.edu MD5sum: bffa60d90437c057a357689082457752 source.ver: src/contrib/survcomp_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/survcomp_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/survcomp_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/survcomp_1.6.0.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 dependsOnMe: genefu Package: sva Version: 3.2.1 Depends: R (>= 2.8), corpcor, mgcv 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 , W. Evan Johnson , Hilary S. Parker , Andrew E. Jaffe , John D. Storey , Maintainer: Jeffrey T. Leek MD5sum: 8fc5557d4c43bae7689a16a308b4ceac source.ver: src/contrib/sva_3.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/sva_3.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/sva_3.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/sva_3.2.1.tgz vignettes: vignettes/sva/inst/doc/sva.pdf vignetteTitles: bladderbatchTutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: trigger Package: TargetSearch Version: 1.12.3 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 , Jan Lisec , Henning Redestig , Matt Hannah Maintainer: Alvaro Cuadros-Inostroza MD5sum: a9f236fef96479f69d96f093d221be65 source.ver: src/contrib/TargetSearch_1.12.3.tar.gz win.binary.ver: bin/windows/contrib/2.15/TargetSearch_1.12.3.zip win64.binary.ver: bin/windows64/contrib/2.15/TargetSearch_1.12.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TargetSearch_1.12.3.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 Package: TDARACNE Version: 1.6.0 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 MD5sum: 3f553099a2c8eb1d3be27abb95d84d0c source.ver: src/contrib/TDARACNE_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/TDARACNE_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.15/TDARACNE_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TDARACNE_1.6.0.tgz vignettes: vignettes/TDARACNE/inst/doc/TDARACNE.pdf vignetteTitles: TDARACNE hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: TEQC Version: 2.4.0 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 MD5sum: 3e14e6c02f78349f08b5abc71ba53ffe source.ver: src/contrib/TEQC_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/TEQC_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/TEQC_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TEQC_2.4.0.tgz vignettes: vignettes/TEQC/inst/doc/TEQC.pdf vignetteTitles: TEQC hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: ternarynet Version: 1.0.0 Depends: R (>= 2.10.0), methods 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 , Anthony Almudevar Maintainer: Matthew N. McCall MD5sum: c201ccc86b74066689702d2a3cdbf3fd source.ver: src/contrib/ternarynet_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/ternarynet_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/ternarynet_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/ternarynet_1.0.0.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 Package: tigre Version: 1.10.0 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 URL: http://www.bioinf.manchester.ac.uk/resources/tiger/ MD5sum: 84f434df914c8e5e2642a9b7e5fad1fa source.ver: src/contrib/tigre_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/tigre_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.15/tigre_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/tigre_1.10.0.tgz vignettes: vignettes/tigre/inst/doc/tigre-009.pdf, vignettes/tigre/inst/doc/tigre-010.pdf, vignettes/tigre/inst/doc/tigre-011.pdf, vignettes/tigre/inst/doc/tigre.pdf, vignettes/tigre/inst/doc/tigre_quick.pdf vignetteTitles: tigre-009.pdf, tigre-010.pdf, tigre-011.pdf, tigre User Guide, tigre Quick Guide hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: tilingArray Version: 1.34.0 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 MD5sum: 519954b5451fd854513eeeac752fb47b source.ver: src/contrib/tilingArray_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/tilingArray_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/tilingArray_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/tilingArray_1.34.0.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 dependsOnMe: ADaCGH2 importsMe: snapCGH Package: timecourse Version: 1.28.0 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 URL: http://www.bioconductor.org MD5sum: ce727a65af72909ea6c5e7d25f30c315 source.ver: src/contrib/timecourse_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/timecourse_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/timecourse_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/timecourse_1.28.0.tgz vignettes: vignettes/timecourse/inst/doc/timecourse.pdf vignetteTitles: timecourse manual hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: tkWidgets Version: 1.34.0 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 Maintainer: J. Zhang MD5sum: ee817c0da3607fc2aac51c0affe2a3d3 source.ver: src/contrib/tkWidgets_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/tkWidgets_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/tkWidgets_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/tkWidgets_1.34.0.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 dependsOnMe: cosmoGUI, oneChannelGUI importsMe: Mfuzz, OLINgui suggestsMe: affy, affyQCReport, annotate, Biobase, genefilter, marray Package: topGO Version: 2.8.0 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 MD5sum: 1c76cdc95412fe85cade247919ca7ff3 source.ver: src/contrib/topGO_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/topGO_2.8.0.zip win64.binary.ver: bin/windows64/contrib/2.15/topGO_2.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/topGO_2.8.0.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 dependsOnMe: RNAither suggestsMe: Ringo Package: trigger Version: 1.2.0 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 , Dipen P. Sangurdekar and John D. Storey Maintainer: John D. Storey MD5sum: 28cdc9f917ea75b5a0329c7cae6614b3 source.ver: src/contrib/trigger_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/trigger_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/trigger_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/trigger_1.2.0.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 Package: tspair Version: 1.14.1 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 Maintainer: Jeffrey T. Leek MD5sum: cf8be5daaf619302e8fa3c07c02b83bb source.ver: src/contrib/tspair_1.14.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/tspair_1.14.1.zip win64.binary.ver: bin/windows64/contrib/2.15/tspair_1.14.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/tspair_1.14.1.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 dependsOnMe: stepwiseCM Package: TSSi Version: 1.2.0 Depends: R (>= 2.13.2) Imports: methods, Hmisc, minqa, stats, Biobase, 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 URL: http://julian-gehring.github.com/TSSi/ MD5sum: 641fa849de2dde06586cd6904a04232c source.ver: src/contrib/TSSi_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/TSSi_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/TSSi_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TSSi_1.2.0.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 Package: TurboNorm Version: 1.4.0 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 URL: http://www.humgen.nl/MicroarrayAnalysisGroup.html MD5sum: c410aff9bc7647f3ff177924dd96a2a2 source.ver: src/contrib/TurboNorm_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/TurboNorm_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/TurboNorm_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TurboNorm_1.4.0.tgz vignettes: vignettes/TurboNorm/inst/doc/turbonorm.pdf vignetteTitles: TurboNorm Overview hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: tweeDEseq Version: 1.2.1 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 and Mikel Esnaola (with contributions from Robert Castelo ) Maintainer: Juan R Gonzalez URL: http://www.creal.cat/jrgonzalez/software.htm MD5sum: 8bd30018e7ff471028abba606a19994c source.ver: src/contrib/tweeDEseq_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/tweeDEseq_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.15/tweeDEseq_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/tweeDEseq_1.2.1.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 Package: twilight Version: 1.32.0 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 Maintainer: Stefanie Scheid URL: http://compdiag.molgen.mpg.de/software/twilight.shtml MD5sum: 296a12d6b1bff115a6142a991b7ff96c source.ver: src/contrib/twilight_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/twilight_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/twilight_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/twilight_1.32.0.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 dependsOnMe: OrderedList importsMe: OrderedList Package: TypeInfo Version: 1.22.0 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 () Maintainer: Duncan Temple Lang MD5sum: 760f397134ad67c9e9fcfd2bdf2145b3 source.ver: src/contrib/TypeInfo_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/TypeInfo_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/TypeInfo_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/TypeInfo_1.22.0.tgz vignettes: vignettes/TypeInfo/inst/doc/TypeInfoNews.pdf vignetteTitles: TypeInfo R News hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: RWebServices Package: VanillaICE Version: 1.18.0 Depends: R (>= 2.14.0) Imports: stats, utils, methods, Biobase, oligoClasses (>= 1.17.36), lattice, IRanges (>= 1.13.22), grid, msm, crlmm (>= 1.13.12), foreach Suggests: genomewidesnp6Crlmm, hapmapsnp6, RColorBrewer, genefilter, RSQLite, foreach, RUnit, pd.mapping50k.hind240, SNPchip (>= 2.0.3) 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 , Kevin Scharpf, and Ingo Ruczinski Maintainer: Robert Scharpf MD5sum: 7d4f7f1ab1c85f49901fa9d073049ac5 source.ver: src/contrib/VanillaICE_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/VanillaICE_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.15/VanillaICE_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/VanillaICE_1.18.0.tgz vignettes: vignettes/VanillaICE/inst/doc/crlmmDownstream.pdf, vignettes/VanillaICE/inst/doc/VanillaICE.pdf vignetteTitles: crlmmDownstream, VanillaICE Vignette hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: MinimumDistance suggestsMe: oligoClasses Package: VariantAnnotation Version: 1.2.11 Depends: R (>= 2.8.0), methods, GenomicRanges (>= 1.8.13), Rsamtools (>= 1.7.41) Imports: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Biobase (>= 2.15.1), Rsamtools (>= 1.7.41), AnnotationDbi (>= 1.17.11), Biostrings (>= 2.23.4), zlibbioc, BSgenome, GenomicFeatures, snpStats, 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 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 MD5sum: e79b631bb8bcc79a7f9e95fdcfe55d63 source.ver: src/contrib/VariantAnnotation_1.2.11.tar.gz win.binary.ver: bin/windows/contrib/2.15/VariantAnnotation_1.2.11.zip win64.binary.ver: bin/windows64/contrib/2.15/VariantAnnotation_1.2.11.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/VariantAnnotation_1.2.11.tgz vignettes: vignettes/VariantAnnotation/inst/doc/VariantAnnotation.pdf vignetteTitles: Introduction to VariantAnnotation hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE importsMe: ggbio, GGtools suggestsMe: GenomicRanges Package: vbmp Version: 1.24.0 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 , Mark Girolami Maintainer: Nicola Lama URL: http://bioinformatics.oxfordjournals.org/cgi/content/short/btm535v1 MD5sum: 2492570243913ac1e17b5427ef52a982 source.ver: src/contrib/vbmp_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/vbmp_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/vbmp_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/vbmp_1.24.0.tgz vignettes: vignettes/vbmp/inst/doc/vbmp.pdf vignetteTitles: vbmp Tutorial hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: Vega Version: 1.4.0 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, DNACopyNumber Author: Sandro Morganella Maintainer: Sandro Morganella MD5sum: 9bd2f633d47f5b5b6a2a4fa0c3024624 source.ver: src/contrib/Vega_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/Vega_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.15/Vega_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/Vega_1.4.0.tgz vignettes: vignettes/Vega/inst/doc/Vega.pdf vignetteTitles: Vega hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: VegaMC Version: 2.0.0 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, DNACopyNumber Author: S. Morganella and M. Ceccarelli Maintainer: Sandro Morganella MD5sum: ee682456b512b787dbc11a1733c13ac9 source.ver: src/contrib/VegaMC_2.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/VegaMC_2.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/VegaMC_2.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/VegaMC_2.0.0.tgz vignettes: vignettes/VegaMC/inst/doc/VegaMC.pdf vignetteTitles: VegaMC hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: virtualArray Version: 1.0.0 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: multicore 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 MD5sum: a6ea9f587f824f1b56171df1cc770bcd source.ver: src/contrib/virtualArray_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/virtualArray_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.15/virtualArray_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/virtualArray_1.0.0.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 Package: vsn Version: 3.24.0 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 URL: http://www.r-project.org, http://www.ebi.ac.uk/huber MD5sum: 159c049811647699bafb28cb486ed2e2 source.ver: src/contrib/vsn_3.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/vsn_3.24.0.zip win64.binary.ver: bin/windows64/contrib/2.15/vsn_3.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/vsn_3.24.0.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 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: weaver Version: 1.22.0 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 MD5sum: de390b8703f96c5e9e24457e9bf5be92 source.ver: src/contrib/weaver_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/weaver_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.15/weaver_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/weaver_1.22.0.tgz vignettes: vignettes/weaver/inst/doc/weaver_howTo.pdf vignetteTitles: Using weaver to process Sweave documents hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE suggestsMe: BiocCaseStudies Package: webbioc Version: 1.28.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: Biobase, multtest, qvalue, stats, utils 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 Maintainer: Colin A. Smith URL: http://www.bioconductor.org/ SystemRequirements: Unix, Perl (>= 5.6.0), Netpbm MD5sum: e09134b43f0c4fe6023d093c4290e52c source.ver: src/contrib/webbioc_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/webbioc_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.15/webbioc_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/webbioc_1.28.0.tgz vignettes: vignettes/webbioc/inst/doc/demoscript.pdf, vignettes/webbioc/inst/doc/webbioc.pdf vignetteTitles: webbioc Demo Script, webbioc Overview hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: widgetTools Version: 1.34.0 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 MD5sum: f33b2b0e04b7186369ad849474167ac5 source.ver: src/contrib/widgetTools_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/widgetTools_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.15/widgetTools_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/widgetTools_1.34.0.tgz vignettes: vignettes/widgetTools/inst/doc/widget.pdf, vignettes/widgetTools/inst/doc/widgetTools.pdf vignetteTitles: widget.pdf, widgetTools Introduction hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE dependsOnMe: tkWidgets importsMe: OLINgui suggestsMe: affy Package: xcms Version: 1.32.0 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 Author: Colin A. Smith , Ralf Tautenhahn , Steffen Neumann , Paul Benton Maintainer: Ralf Tautenhahn URL: http://metlin.scripps.edu/download/ MD5sum: cd9c2cb991bd62121d132d888f8364ed source.ver: src/contrib/xcms_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/xcms_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.15/xcms_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/xcms_1.32.0.tgz 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 dependsOnMe: CAMERA, flagme importsMe: CAMERA suggestsMe: MassSpecWavelet Package: XDE Version: 2.2.0 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 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 MD5sum: 7e3b4a8e1d1b17e53828a7a8e8094f1a source.ver: src/contrib/XDE_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/XDE_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/XDE_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/XDE_2.2.0.tgz 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 Package: xmapbridge Version: 1.14.0 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 and Crispin J Miller Maintainer: Tim Yates URL: http://xmap.picr.man.ac.uk, http://www.bioconductor.org MD5sum: eac88e58499b1c1ec2d71dda98486b01 source.ver: src/contrib/xmapbridge_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/xmapbridge_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.15/xmapbridge_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/xmapbridge_1.14.0.tgz vignettes: vignettes/xmapbridge/inst/doc/xmapbridge.pdf vignetteTitles: xmapbridge primer hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: FALSE Package: xmapcore Version: 1.10.0 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 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 Maintainer: Tim Yates URL: http://xmap.picr.man.ac.uk, http://www.bioconductor.org MD5sum: c85a17fd3ec25eb45b1ca3650c994455 source.ver: src/contrib/xmapcore_1.10.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/xmapcore_1.10.0.tgz 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 dependsOnMe: rnaSeqMap Package: xps Version: 1.16.0 Depends: R (>= 2.6.0), methods 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 SystemRequirements: root_v5.32.01 - See README file for installation instructions. MD5sum: a0add6886bd4927523f6382462c58e0f source.ver: src/contrib/xps_1.16.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/xps_1.16.0.tgz 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 hasLICENSE: FALSE Package: yaqcaffy Version: 1.16.1 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 MD5sum: cc21902783e00e7ff9a8e99f3fcb2ea8 source.ver: src/contrib/yaqcaffy_1.16.1.tar.gz win.binary.ver: bin/windows/contrib/2.15/yaqcaffy_1.16.1.zip win64.binary.ver: bin/windows64/contrib/2.15/yaqcaffy_1.16.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/yaqcaffy_1.16.1.tgz vignettes: vignettes/yaqcaffy/inst/doc/yaqcaffy.pdf vignetteTitles: yaqcaffy: Affymetrix quality control and MAQC reproducibility hasREADME: FALSE hasNEWS: TRUE hasINSTALL: FALSE hasLICENSE: FALSE Package: zlibbioc Version: 1.2.0 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 URL: http://bioconductor.org/packages/release/bioc/html/Zlibbioc.html MD5sum: a74eaf384f87a81900882695361b401a source.ver: src/contrib/zlibbioc_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.15/zlibbioc_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.15/zlibbioc_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.15/zlibbioc_1.2.0.tgz vignettes: vignettes/zlibbioc/inst/doc/UsingZlibbioc.pdf vignetteTitles: Using zlibbioc C libraries hasREADME: FALSE hasNEWS: FALSE hasINSTALL: FALSE hasLICENSE: TRUE dependsOnMe: BitSeq importsMe: affy, affyio, affyPLM, DiffBind, makecdfenv, oligo, rhdf5, Rsamtools, rtracklayer, seqbias, ShortRead, Starr, VariantAnnotation