Package: ABarray Version: 1.12.0 Depends: Biobase, multtest, tcltk Suggests: limma, LPE Title: Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (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 License: GPL source.ver: src/contrib/ABarray_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/ABarray_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/ABarray_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/ABarray_1.12.0.tgz vignettes: vignettes/ABarray/inst/doc/ABarray.pdf, vignettes/ABarray/inst/doc/ABarrayGUI.pdf Package: aCGH Version: 1.18.1 Depends: R (>= 1.8.0), survival, multtest Imports: Biobase, cluster, graphics, grDevices, methods, multtest, splines, stats, survival, utils 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: DNACopyNumber, DataImport, Genetics Author: Jane Fridlyand , Peter Dimitrov Maintainer: Jane Fridlyand License: GPL source.ver: src/contrib/aCGH_1.18.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/aCGH_1.18.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/aCGH_1.18.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/aCGH_1.18.1.tgz vignettes: vignettes/aCGH/inst/doc/aCGH.pdf Package: ACME Version: 1.10.0 Depends: R (>= 2.4.0), methods 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 License: GPL version 2 or newer source.ver: src/contrib/ACME_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/ACME_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/ACME_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/ACME_1.10.0.tgz vignettes: vignettes/ACME/inst/doc/ACME.pdf Package: adSplit Version: 1.14.0 Depends: R (>= 2.1.0), methods (>= 2.1.0), graphics, stats (>= 2.1.0), cluster (>= 1.9.1), multtest (>= 1.6.0), Biobase (>= 1.5.12), affy (>= 1.6.7), GO.db (>= 1.8.1), KEGG.db (>= 1.8.1) Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) 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 License: GPL (>= 2) source.ver: src/contrib/adSplit_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/adSplit_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/adSplit_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/adSplit_1.14.0.tgz vignettes: vignettes/adSplit/inst/doc/bcb_logo.pdf, vignettes/adSplit/inst/doc/minerva_bcb.pdf, vignettes/adSplit/inst/doc/tr_2005_02.pdf Package: affxparser Version: 1.16.0 Depends: R (>= 2.6.0) Suggests: R.utils, AffymetrixDataTestFiles 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 License: LGPL-2 source.ver: src/contrib/affxparser_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/affxparser_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/affxparser_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/affxparser_1.16.0.tgz Package: affy Version: 1.22.1 Depends: R (>= 2.8.0), Biobase (>= 2.1.0) Imports: Biobase (>= 2.1.0), graphics, methods, stats, utils, affyio, preprocessCore Suggests: tkWidgets (>= 1.19.0), affydata Title: Methods for Affymetrix Oligonucleotide Arrays Description: The package contains functions for exploratory oligonucleotide array analysis. The dependance to 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 License: LGPL (>= 2.0) source.ver: src/contrib/affy_1.22.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/affy_1.22.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/affy_1.22.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/affy_1.22.1.tgz vignettes: vignettes/affy/inst/doc/affy.pdf, vignettes/affy/inst/doc/builtinMethods.pdf, vignettes/affy/inst/doc/customMethods.pdf, vignettes/affy/inst/doc/vim.pdf Package: affycomp Version: 1.20.0 Depends: R (>= 2.9.0), methods, Biobase (>= 2.3.3) Suggests: splines 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 License: GPL version 2 or newer source.ver: src/contrib/affycomp_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/affycomp_1.20.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/affycomp_1.20.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/affycomp_1.20.0.tgz vignettes: vignettes/affycomp/inst/doc/affycomp.pdf Package: AffyCompatible Version: 1.4.0 Depends: R (>= 2.7.0), XML (>= 1.99-0), RCurl (>= 0.8-1), methods Imports: Biostrings 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 License: Artistic-2.0 source.ver: src/contrib/AffyCompatible_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/AffyCompatible_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/AffyCompatible_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/AffyCompatible_1.4.0.tgz vignettes: vignettes/AffyCompatible/inst/doc/MAGEAndARR.pdf, vignettes/AffyCompatible/inst/doc/NetAffxResource.pdf Package: affyContam Version: 1.2.0 Depends: R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata 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 License: The Artistic License, Version 2.0 source.ver: src/contrib/affyContam_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/affyContam_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/affyContam_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/affyContam_1.2.0.tgz vignettes: vignettes/affyContam/inst/doc/affyContam.pdf Package: affycoretools Version: 1.16.3 Depends: affy, Biobase, GO.db, KEGG.db Imports: biomaRt, limma, GOstats, annotate, annaffy, genefilter, gcrma, splines, xtable, AnnotationDbi Suggests: affydata, hgfocuscdf 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 License: Artistic-2.0 source.ver: src/contrib/affycoretools_1.16.3.tar.gz win.binary.ver: bin/windows/contrib/2.9/affycoretools_1.16.3.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/affycoretools_1.16.3.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/affycoretools_1.16.3.tgz vignettes: vignettes/affycoretools/inst/doc/affycoretools_biomaRt.pdf, vignettes/affycoretools/inst/doc/affycoretools.pdf Package: AffyExpress Version: 1.10.0 Depends: R (>= 2.5.0), affy, limma Suggests: simpleaffy, R2HTML, affyPLM, hgu95av2cdf, hgu95av2, test3cdf, genefilter, estrogen, annaffy, gcrma 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 License: LGPL source.ver: src/contrib/AffyExpress_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/AffyExpress_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/AffyExpress_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/AffyExpress_1.10.0.tgz vignettes: vignettes/AffyExpress/inst/doc/AffyExpress.pdf Package: affyio Version: 1.12.0 Depends: R (>= 2.6.0), methods 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 License: LGPL version 2 or newer source.ver: src/contrib/affyio_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/affyio_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/affyio_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/affyio_1.12.0.tgz Package: affylmGUI Version: 1.18.0 Depends: limma, tcltk, affy, Biobase, affyio Suggests: tkrplot, affyPLM, R2HTML, xtable 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/ License: LGPL source.ver: src/contrib/affylmGUI_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/affylmGUI_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/affylmGUI_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/affylmGUI_1.18.0.tgz vignettes: vignettes/affylmGUI/inst/doc/affylmGUI.pdf, vignettes/affylmGUI/inst/doc/extract.pdf Package: affyPara Version: 1.4.0 Depends: R (>= 2.5.0), methods, affy (>= 1.20.0), snow (>= 0.2-3), vsn (>= 3.6.0) Suggests: affydata 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 License: GPL version 3 or newer source.ver: src/contrib/affyPara_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/affyPara_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/affyPara_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/affyPara_1.4.0.tgz vignettes: vignettes/affyPara/inst/doc/affyPara.pdf, vignettes/affyPara/inst/doc/speedup.pdf Package: affypdnn Version: 1.18.0 Depends: R (>= 2.3.0), affy (>= 1.5) Suggests: affydata, hgu95av2probe 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 License: LGPL source.ver: src/contrib/affypdnn_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/affypdnn_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/affypdnn_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/affypdnn_1.18.0.tgz vignettes: vignettes/affypdnn/inst/doc/affypdnn.pdf Package: affyPLM Version: 1.20.0 Depends: R (>= 2.6.0), affy (>= 1.11.0), Biobase, methods, gcrma, stats, preprocessCore (>= 1.5.1) Suggests: affydata 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 License: GPL version 2 or newer source.ver: src/contrib/affyPLM_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/affyPLM_1.20.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/affyPLM_1.20.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/affyPLM_1.20.0.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 Package: affyQCReport Version: 1.22.0 Depends: Biobase (>= 1.13.16), affy, simpleaffy, xtable, affyPLM, RColorBrewer, genefilter, lattice Suggests: tkWidgets (>= 1.5.23), affydata (>= 1.4.1) 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 License: LGPL version 2 or newer source.ver: src/contrib/affyQCReport_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/affyQCReport_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/affyQCReport_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/affyQCReport_1.22.0.tgz vignettes: vignettes/affyQCReport/inst/doc/affyQCReport.pdf Package: AffyTiling Version: 1.2.0 Depends: R (>= 2.6), Biobase, methods, utils, affy (>= 1.16), affxparser 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 License: GPL version 2 or newer source.ver: src/contrib/AffyTiling_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/AffyTiling_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/AffyTiling_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/AffyTiling_1.2.0.tgz vignettes: vignettes/AffyTiling/inst/doc/AffyTiling.pdf Package: Agi4x44PreProcess Version: 1.4.0 Depends: R (>= 2.6.0), Biobase, limma, annotate, genefilter Suggests: vsn, affycoretools, hgug4112a.db, GO.db, marray, gplots, gtools, gdata Title: PreProcessing of Agilent 4x44 array data Description: Preprocessing of Agilent 4x44 array data biocViews: Microarray, Agilent, OneChannel, Preprocessing Author: Pedro Lopez-Romero Maintainer: Pedro Lopez-Romero License: GPL v3 source.ver: src/contrib/Agi4x44PreProcess_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/Agi4x44PreProcess_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Agi4x44PreProcess_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Agi4x44PreProcess_1.4.0.tgz vignettes: vignettes/Agi4x44PreProcess/inst/doc/Agi4x44PreProcess.pdf Package: altcdfenvs Version: 2.6.0 Depends: R (>= 2.7), methods, Biobase, affy, matchprobes, makecdfenv, Biostrings, hypergraph Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer 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 License: GPL version 2 or newer source.ver: src/contrib/altcdfenvs_2.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/altcdfenvs_2.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/altcdfenvs_2.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/altcdfenvs_2.6.0.tgz vignettes: vignettes/altcdfenvs/inst/doc/altcdfenvs.pdf, vignettes/altcdfenvs/inst/doc/modify.pdf, vignettes/altcdfenvs/inst/doc/ngenomeschips.pdf Package: annaffy Version: 1.16.0 Depends: R (>= 2.5.0), methods, Biobase, GO.db, KEGG.db Imports: AnnotationDbi (>= 0.1.15) Suggests: hgu95av2.db, multtest, tcltk 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 License: LGPL source.ver: src/contrib/annaffy_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/annaffy_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/annaffy_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/annaffy_1.16.0.tgz vignettes: vignettes/annaffy/inst/doc/annaffy.pdf Package: annotate Version: 1.22.0 Depends: R (>= 2.4.0), AnnotationDbi (>= 0.1.15) Imports: Biobase, AnnotationDbi, xtable, graphics, utils, stats, methods 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 Title: Annotation for microarrays Description: Using R enviroments for annotation. biocViews: Annotation, Pathways, GO, Affymetrix Author: R. Gentleman Maintainer: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/annotate_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/annotate_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/annotate_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/annotate_1.22.0.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 Package: AnnotationDbi Version: 1.6.1 Depends: R (>= 2.7.0), methods, utils, Biobase (>= 1.17.0) Imports: methods, utils, Biobase, DBI, RSQLite Suggests: DBI (>= 0.2-4), RSQLite (>= 0.6-4), hgu95av2.db, GO.db, human.db0, mouse.db0, rat.db0, fly.db0, yeast.db0, arabidopsis.db0, zebrafish.db0, ecoliK12.db0, ecoliSakai.db0, hgu95av2cdf, affy 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: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/AnnotationDbi_1.6.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/AnnotationDbi_1.6.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/AnnotationDbi_1.6.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/AnnotationDbi_1.6.1.tgz vignettes: vignettes/AnnotationDbi/inst/doc/AnnotationDbi.pdf, vignettes/AnnotationDbi/inst/doc/makeProbePackage.pdf, vignettes/AnnotationDbi/inst/doc/SQLForge.pdf Package: annotationTools Version: 1.14.0 Depends: Biobase 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 License: GPL source.ver: src/contrib/annotationTools_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/annotationTools_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/annotationTools_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/annotationTools_1.14.0.tgz vignettes: vignettes/annotationTools/inst/doc/annotationTools.pdf Package: apComplex Version: 2.10.0 Depends: graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db 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 License: LGPL source.ver: src/contrib/apComplex_2.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/apComplex_2.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/apComplex_2.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/apComplex_2.10.0.tgz vignettes: vignettes/apComplex/inst/doc/apComplex.pdf Package: aroma.light Version: 1.12.2 Depends: R.methodsS3 Suggests: R.oo, R.utils, princurve 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, Preprocessing Author: Henrik Bengtsson Maintainer: Henrik Bengtsson URL: http://www.braju.com/R/ License: LGPL source.ver: src/contrib/aroma.light_1.12.2.tar.gz win.binary.ver: bin/windows/contrib/2.9/aroma.light_1.12.2.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/aroma.light_1.12.2.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/aroma.light_1.12.2.tgz Package: ArrayExpress Version: 1.4.3 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: XML, affy, limma 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 License: Artistic License 2.0 source.ver: src/contrib/ArrayExpress_1.4.3.tar.gz win.binary.ver: bin/windows/contrib/2.9/ArrayExpress_1.4.3.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/ArrayExpress_1.4.3.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/ArrayExpress_1.4.3.tgz vignettes: vignettes/ArrayExpress/inst/doc/ArrayExpress.pdf Package: arrayMvout Version: 1.2.0 Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy, lumi Imports: simpleaffy, mdqc, affyContam, Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf 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 License: The Artistic License, Version 2.0 source.ver: src/contrib/arrayMvout_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/arrayMvout_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/arrayMvout_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/arrayMvout_1.2.0.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 Package: arrayQuality Version: 1.22.0 Depends: R (>= 2.2.0), marray, limma, convert, hexbin, gridBase, RColorBrewer Suggests: mclust, MEEBOdata, HEEBOdata 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/ License: LGPL source.ver: src/contrib/arrayQuality_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/arrayQuality_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/arrayQuality_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/arrayQuality_1.22.0.tgz Package: arrayQualityMetrics Version: 2.2.3 Depends: affyPLM Imports: Biobase, RColorBrewer, affy, beadarray, genefilter, grDevices, graphics, hwriter, lattice, latticeExtra, limma, marray, methods, simpleaffy, stats, stats4, utils, vsn Suggests: ALLMLL, CCl4 Title: Quality metrics on microarray data sets Description: This package generates a quality metrics report on ExpressionSet, NChannelSet, AffyBatch or BeadLevelList objects containing microarray data with one or two channels. biocViews: Microarray, QualityControl, OneChannel, TwoChannel, ReportWriting Author: Audrey Kauffmann, Wolfgang Huber Maintainer: Audrey Kauffmann License: LGPL version 2 or newer source.ver: src/contrib/arrayQualityMetrics_2.2.3.tar.gz win.binary.ver: bin/windows/contrib/2.9/arrayQualityMetrics_2.2.3.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/arrayQualityMetrics_2.2.3.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/arrayQualityMetrics_2.2.3.tgz vignettes: vignettes/arrayQualityMetrics/inst/doc/aqm.pdf, vignettes/arrayQualityMetrics/inst/doc/arrayQualityMetrics.pdf Package: ArrayTools Version: 1.4.0 Depends: R (>= 2.7.0), affy, Biobase, graphics, grDevices, limma, methods, stats, utils, xtable Suggests: simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy, gcrma, hugene10sttranscriptcluster.db 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 License: LGPL(>= 2.0) source.ver: src/contrib/ArrayTools_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/ArrayTools_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/ArrayTools_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/ArrayTools_1.4.0.tgz vignettes: vignettes/ArrayTools/inst/doc/ArrayTools.pdf Package: BAC Version: 1.4.0 Depends: R(>= 2.6.0) 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 License: Artistic-2.0 source.ver: src/contrib/BAC_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/BAC_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/BAC_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/BAC_1.4.0.tgz vignettes: vignettes/BAC/inst/doc/BAC.pdf Package: BCRANK Version: 1.6.0 Depends: methods Imports: Biostrings Suggests: seqLogo 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 License: GPL, version 2 source.ver: src/contrib/BCRANK_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/BCRANK_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/BCRANK_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/BCRANK_1.6.0.tgz vignettes: vignettes/BCRANK/inst/doc/BCRANK_intro_fig1.pdf, vignettes/BCRANK/inst/doc/BCRANK_intro_fig2.pdf, vignettes/BCRANK/inst/doc/BCRANK.pdf Package: beadarray Version: 1.12.1 Depends: Biobase, methods, hwriter Imports: limma Suggests: lumi, vsn, affy 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 License: GPL source.ver: src/contrib/beadarray_1.12.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/beadarray_1.12.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/beadarray_1.12.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/beadarray_1.12.1.tgz vignettes: vignettes/beadarray/inst/doc/BASH.pdf, vignettes/beadarray/inst/doc/beadarray.pdf, vignettes/beadarray/inst/doc/beadlevel.pdf, vignettes/beadarray/inst/doc/beadsummary.pdf Package: beadarraySNP Version: 1.10.0 Depends: methods, tools, Biobase, quantsmooth Suggests: aCGH, affy, limma, snapCGH, beadarray, DNAcopy Title: Normalization and reporting of Illumina SNP bead arrays Description: Importing data from Illumina SNP experiments and performing copy number calculations and reports. biocViews: DNACopyNumber, SNPsAndGeneticVariability, TwoChannel, Preprocessing, DataImport Author: Jan Oosting Maintainer: Jan Oosting License: GPL V2 source.ver: src/contrib/beadarraySNP_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/beadarraySNP_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/beadarraySNP_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/beadarraySNP_1.10.0.tgz vignettes: vignettes/beadarraySNP/inst/doc/beadarraySNP.pdf Package: betr Version: 1.0.0 Depends: R(>= 2.6.0) Imports: Biobase, limma, mvtnorm, methods, stats Suggests: Biobase Title: Identify differentially expressed genes in microarray time-course data Description: The \pkg{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 License: LGPL source.ver: src/contrib/betr_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/betr_1.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/betr_1.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/betr_1.0.0.tgz vignettes: vignettes/betr/inst/doc/betr.pdf Package: bgafun Version: 1.6.0 Depends: made4, seqinr,ade4 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 License: Artistic License source.ver: src/contrib/bgafun_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/bgafun_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/bgafun_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/bgafun_1.6.0.tgz vignettes: vignettes/bgafun/inst/doc/bgafun.pdf Package: BGmix Version: 1.4.0 Depends: R (>= 2.3.1), KernSmooth 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 License: GPL source.ver: src/contrib/BGmix_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/BGmix_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/BGmix_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/BGmix_1.4.0.tgz vignettes: vignettes/BGmix/inst/doc/BGmix.pdf Package: bgx Version: 1.8.0 Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), gcrma (>= 2.4.1) Suggests: affydata, hgu95av2cdf 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 License: GPL source.ver: src/contrib/bgx_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/bgx_1.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/bgx_1.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/bgx_1.8.0.tgz vignettes: vignettes/bgx/inst/doc/bgx.pdf Package: BicARE Version: 1.2.0 Depends: R (>= 1.8.0), Biobase, multtest, GSEABase 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 License: GPL source.ver: src/contrib/BicARE_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/BicARE_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/BicARE_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/BicARE_1.2.0.tgz vignettes: vignettes/BicARE/inst/doc/BicARE.pdf Package: Biobase Version: 2.4.1 Depends: R (>= 2.7.0), methods, utils Suggests: tools, tkWidgets, ALL 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: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/Biobase_2.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/Biobase_2.4.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Biobase_2.4.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Biobase_2.4.1.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 Package: BiocCaseStudies Version: 1.6.1 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), Rintact (>= 1.1.4), vsn (>= 3.4.0), weaver (>= 1.5.0), xtable (>= 1.5-2), yeastExpData (>= 0.9.11) 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: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/BiocCaseStudies_1.6.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/BiocCaseStudies_1.6.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/BiocCaseStudies_1.6.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/BiocCaseStudies_1.6.1.tgz Package: biocDatasets Version: 1.0.0 Depends: R (>= 2.8.0), IRanges Imports: stats, Biostrings, IRanges Suggests: Biobase Title: Synthetic datasets for bioconductor Description: Synthetic datasets to a) demonstrate the usage of bioconductor packages, b) write unit tests, while keeping dependencies and ressources usage minimal. biocViews: Infrastructure Author: L. Gautier Maintainer: L. Gautier License: GPL 3 source.ver: src/contrib/biocDatasets_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/biocDatasets_1.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/biocDatasets_1.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/biocDatasets_1.0.0.tgz vignettes: vignettes/biocDatasets/inst/doc/synthetic_arrays.pdf Package: biocGraph Version: 1.6.0 Depends: Rgraphviz, graph Imports: Rgraphviz, geneplotter, graph, methods Suggests: fibroEset, geneplotter, hgu95av2.db 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 License: Artistic-2.0 source.ver: src/contrib/biocGraph_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/biocGraph_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/biocGraph_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/biocGraph_1.6.0.tgz vignettes: vignettes/biocGraph/inst/doc/biocGraph.pdf, vignettes/biocGraph/inst/doc/layingOutPathways.pdf Package: biocViews Version: 1.12.3 Depends: R (>= 2.4.0), methods, utils Imports: tools, Biobase, graph (>= 1.9.26), RBGL (>= 1.13.5), XML Suggests: Biobase 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: Biocore Team c/o BioC user list URL: http://www.bioconductor.org/packages/release/BiocViews.html License: Artistic-2.0 source.ver: src/contrib/biocViews_1.12.3.tar.gz win.binary.ver: bin/windows/contrib/2.9/biocViews_1.12.3.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/biocViews_1.12.3.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/biocViews_1.12.3.tgz vignettes: vignettes/biocViews/inst/doc/createReposHtml.pdf, vignettes/biocViews/inst/doc/HOWTO-BCV.pdf Package: bioDist Version: 1.16.0 Depends: R (>= 2.0), methods, Biobase,KernSmooth Suggests: locfit 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: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/bioDist_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/bioDist_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/bioDist_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/bioDist_1.16.0.tgz vignettes: vignettes/bioDist/inst/doc/bioDist.pdf Package: biomaRt Version: 2.0.0 Depends: methods Imports: XML, RCurl Suggests: annotate Title: Interface to BioMart databases (e.g. Ensembl, 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, Uniprot, Gramene, Wormbase and HapMap. 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 , Sean Davis Maintainer: Steffen Durinck License: Artistic-2.0 source.ver: src/contrib/biomaRt_2.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/biomaRt_2.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/biomaRt_2.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/biomaRt_2.0.0.tgz vignettes: vignettes/biomaRt/inst/doc/biomaRt.pdf Package: BioMVCClass Version: 1.12.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz 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 License: LGPL source.ver: src/contrib/BioMVCClass_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/BioMVCClass_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/BioMVCClass_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/BioMVCClass_1.12.0.tgz vignettes: vignettes/BioMVCClass/inst/doc/BioMVCClass.pdf Package: Biostrings Version: 2.12.10 Depends: R (>= 2.8.0), methods, IRanges (>= 1.2.3) Imports: methods, utils, IRanges, Biobase Suggests: BSgenome, BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), drosophila2probe, hgu95av2probe, hgu95av2cdf, affy, affydata (>= 1.11.5), RUnit 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 set of sequences. biocViews: SequenceMatching, Genetics, Infrastructure Author: H. Pages, P. Aboyoun, R. Gentleman, and S. DebRoy Maintainer: H. Pages License: Artistic-2.0 source.ver: src/contrib/Biostrings_2.12.10.tar.gz win.binary.ver: bin/windows/contrib/2.9/Biostrings_2.12.10.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Biostrings_2.12.10.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Biostrings_2.12.10.tgz vignettes: vignettes/Biostrings/inst/doc/Alignments.pdf, vignettes/Biostrings/inst/doc/Biostrings2Classes.pdf, vignettes/Biostrings/inst/doc/DNAStringVectorization.pdf, vignettes/Biostrings/inst/doc/GenomeSearching.pdf, vignettes/Biostrings/inst/doc/matchprobes.pdf Package: bridge Version: 1.8.0 Depends: R (>= 1.9.0), rama 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 License: GPL version 2 or newer source.ver: src/contrib/bridge_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/bridge_1.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/bridge_1.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/bridge_1.8.0.tgz vignettes: vignettes/bridge/inst/doc/bridge.pdf Package: BSgenome Version: 1.12.5 Depends: R (>= 2.7.0), methods, IRanges (>= 1.1.55), Biostrings (>= 2.11.40) Suggests: BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18 (>= 1.3.11), SNPlocs.Hsapiens.dbSNP.20071016, hgu95av2probe, Biobase Title: Infrastructure for Biostrings-based genome data packages Description: Infrastructure shared by all the Biostrings-based genome data packages biocViews: Genetics, Infrastructure Author: Herve Pages Maintainer: H. Pages License: Artistic-2.0 source.ver: src/contrib/BSgenome_1.12.5.tar.gz win.binary.ver: bin/windows/contrib/2.9/BSgenome_1.12.5.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/BSgenome_1.12.5.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/BSgenome_1.12.5.tgz vignettes: vignettes/BSgenome/inst/doc/BSgenomeForge.pdf, vignettes/BSgenome/inst/doc/GenomeSearching.pdf Package: BufferedMatrix Version: 1.8.0 Depends: R (>= 2.6.0), methods 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 License: LGPL version 2 or newer source.ver: src/contrib/BufferedMatrix_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/BufferedMatrix_1.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/BufferedMatrix_1.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/BufferedMatrix_1.8.0.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 Package: BufferedMatrixMethods Version: 1.8.0 Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods Suggests: affyio, affy 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 License: GPL version 2 or later source.ver: src/contrib/BufferedMatrixMethods_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/BufferedMatrixMethods_1.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/BufferedMatrixMethods_1.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/BufferedMatrixMethods_1.8.0.tgz Package: CALIB Version: 1.10.0 Depends: R (>= 2.6.0), limma, methods 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 estiamted from external control spikes. biocViews: Microarray,TwoChannel,Preprocessing Author: Hui Zhao, Kristof Engelen, Bart De Moor and Kathleen Marchal Maintainer: Hui Zhao License: LGPL source.ver: src/contrib/CALIB_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/CALIB_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/CALIB_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/CALIB_1.10.0.tgz vignettes: vignettes/CALIB/inst/doc/quickstart.pdf, vignettes/CALIB/inst/doc/readme.pdf Package: CAMERA Version: 1.0.0 Depends: R (>= 2.1.0), methods , xcms (>= 1.13.5), Hmisc, RBGL 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: Technology,MassSpectrometry Author: Carsten Kuhl, Ralf Tautenhahn, Steffen Neumann {ckuhl|rtautenh|sneumann}@ipb-halle.de Maintainer: Carsten Kuhl URL: http://msbi.ipb-halle.de/msbi/CAMERA/ License: GPL version 2 or newer source.ver: src/contrib/CAMERA_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/CAMERA_1.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/CAMERA_1.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/CAMERA_1.0.0.tgz vignettes: vignettes/CAMERA/inst/doc/CAMERA.pdf Package: Category Version: 2.10.1 Depends: AnnotationDbi (>= 0.1.15), Biobase (>= 1.15.29) 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 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: Robert Gentleman License: Artistic-2.0 source.ver: src/contrib/Category_2.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/Category_2.10.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Category_2.10.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Category_2.10.1.tgz vignettes: vignettes/Category/inst/doc/Category.pdf, vignettes/Category/inst/doc/ChromBand.pdf Package: cellHTS Version: 1.14.0 Depends: R (>= 2.5.0), prada (>= 1.9.4), RColorBrewer, Biobase (>= 1.11.12), genefilter (>= 1.11.2) Suggests: Category, GO.db, vsn (>= 2.0.35) 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 License: Artistic License 2.0 source.ver: src/contrib/cellHTS_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/cellHTS_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/cellHTS_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/cellHTS_1.14.0.tgz vignettes: vignettes/cellHTS/inst/doc/cellhts.pdf, vignettes/cellHTS/inst/doc/Rplots.pdf, vignettes/cellHTS/inst/doc/twoChannels.pdf, vignettes/cellHTS/inst/doc/twoWay.pdf Package: cellHTS2 Version: 2.8.3 Depends: R (>= 2.6.0), RColorBrewer, Biobase (>= 1.11.12), methods, genefilter (>= 1.11.2), splots (>= 1.3.2), vsn (>= 3.0.15), hwriter (>= 0.90) Imports: prada Suggests: locfit (>= 1.5-3) Title: Analysis of cell-based screens - revised version of cellHTS Description: Analysis of cell-based RNA interference screens. See ?cellHTS2 for a brief introduction. biocViews: CellBasedAssays, Preprocessing, Visualization Author: Ligia Bras , Wolfgang Huber , Michael Boutros , Gregoire Pau , Florian Hahne Maintainer: Florian Hahne URL: http://www.dkfz.de/signaling, http://www.ebi.ac.uk/huber License: Artistic-2.0 source.ver: src/contrib/cellHTS2_2.8.3.tar.gz win.binary.ver: bin/windows/contrib/2.9/cellHTS2_2.8.3.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/cellHTS2_2.8.3.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/cellHTS2_2.8.3.tgz vignettes: vignettes/cellHTS2/inst/doc/cellhts2.pdf, vignettes/cellHTS2/inst/doc/cellhts2Complete.pdf, vignettes/cellHTS2/inst/doc/twoChannels.pdf, vignettes/cellHTS2/inst/doc/twoWay.pdf Package: CGHbase Version: 1.2.0 Depends: R (>= 2.4.0), methods, Biobase, marray Title: CGHbase: Base functions and classes for arrayCGH data analysis. Description: Contains functions and classes that are needed by arrayCGH packages. biocViews: Infrastructure, Microarray, DNACopyNumber Author: Sjoerd Vosse Maintainer: Sjoerd Vosse License: GPL (http://www.gnu.org/copyleft/gpl.html) source.ver: src/contrib/CGHbase_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/CGHbase_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/CGHbase_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/CGHbase_1.2.0.tgz Package: CGHcall Version: 2.2.0 Depends: R (>= 2.0.0), CGHbase, impute(>= 1.8.0), DNAcopy (>= 1.6.0) 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,DNACopyNumber,Preprocessing,Visualization Author: Sjoerd Vosse and Mark van de Wiel Maintainer: Sjoerd Vosse License: GPL (http://www.gnu.org/copyleft/gpl.html) source.ver: src/contrib/CGHcall_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/CGHcall_2.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/CGHcall_2.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/CGHcall_2.2.0.tgz vignettes: vignettes/CGHcall/inst/doc/CGHcall.pdf Package: cghMCR Version: 1.14.0 Depends: methods, DNAcopy, marray, arrayQuality Title: Find chromosome regions showing common gains/losses Description: Based on the algothrim proposed by Dr. Lynda Chin's lab, this package provides functions that identify chromosome regions that show gains/losses commonly observed across different samples profiled using arrayCGH platform. biocViews: Platform, Microarray Author: J. Zhang and B. Feng Maintainer: J. Zhang License: LGPL source.ver: src/contrib/cghMCR_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/cghMCR_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/cghMCR_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/cghMCR_1.14.0.tgz vignettes: vignettes/cghMCR/inst/doc/findMCR.pdf Package: CGHregions Version: 1.2.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase Title: Dimension Reduction for Array CGH Data with Minimal Information Loss. Description: Dimension Reduction for Array CGH Data with Minimal Information Loss biocViews: Microarray,DNACopyNumber,Visualization Author: Sjoerd Vosse & Mark van de Wiel Maintainer: Sjoerd Vosse License: GPL (http://www.gnu.org/copyleft/gpl.html) source.ver: src/contrib/CGHregions_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/CGHregions_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/CGHregions_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/CGHregions_1.2.0.tgz vignettes: vignettes/CGHregions/inst/doc/CGHregions.pdf Package: ChemmineR Version: 1.4.0 Title: A Compound Data Mining Framework Description: ChemMineR is an open source compound mining framework. It contains functions for atom descriptor calculation, structure similarity searching, clustering of compound libraries and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is integrated with the online ChemMine environment and allows bidirectional communications between the two services. biocViews: Clustering Author: Y. Eddie Cao, Anna Charisi, Thomas Girke Maintainer: Y. Eddie Cao License: GPL (>=2) source.ver: src/contrib/ChemmineR_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/ChemmineR_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/ChemmineR_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/ChemmineR_1.4.0.tgz vignettes: vignettes/ChemmineR/inst/doc/ChemmineR.pdf, vignettes/ChemmineR/inst/doc/overview.pdf, vignettes/ChemmineR/inst/doc/scatterplot.pdf, vignettes/ChemmineR/inst/doc/searchscreenshot.pdf, vignettes/ChemmineR/inst/doc/visualizescreenshot.pdf Package: clusterStab Version: 1.16.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter 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 License: Artistic source.ver: src/contrib/clusterStab_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/clusterStab_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/clusterStab_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/clusterStab_1.16.0.tgz vignettes: vignettes/clusterStab/inst/doc/clusterStab.pdf Package: CMA Version: 1.2.0 Depends: R (>= 2.5.1), methods, stats, Biobase Suggests: MASS, class, nnet, glmpath, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma 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: Bioinformatics, Classification Author: Martin Slawski , Anne-Laure Boulesteix . Maintainer: Martin Slawski License: GPL (version 2 or later) source.ver: src/contrib/CMA_1.2.0.tar.gz mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/CMA_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/CMA_1.2.0.tgz vignettes: vignettes/CMA/inst/doc/CMA_vignette.pdf Package: CoCiteStats Version: 1.16.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi 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: R. Gentleman License: CPL source.ver: src/contrib/CoCiteStats_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/CoCiteStats_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/CoCiteStats_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/CoCiteStats_1.16.0.tgz Package: codelink Version: 1.12.1 Depends: methods, Biobase, limma, annotate, genefilter Title: Manipulation of Codelink Bioarrays data. Description: This packages allow reading into R of Codelink bioarray data exported as text from the Codelink software. Also includes some functions to ease the manipulation and pre-processing of data, such in background correction and normalization. biocViews: Microarray, OneChannel, DataImport, Preprocessing Author: Diego Diez Maintainer: Diego Diez URL: http://www.kuicr.kyoto-u.ac.jp/~diez License: GPL source.ver: src/contrib/codelink_1.12.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/codelink_1.12.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/codelink_1.12.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/codelink_1.12.1.tgz vignettes: vignettes/codelink/inst/doc/codelink.pdf, vignettes/codelink/inst/doc/CodelinkSet.pdf Package: convert Version: 1.20.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods 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 License: LGPL source.ver: src/contrib/convert_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/convert_1.20.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/convert_1.20.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/convert_1.20.0.tgz vignettes: vignettes/convert/inst/doc/convert.pdf Package: copa Version: 1.12.0 Depends: Biobase, methods Suggests: colonCA 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 License: Artistic source.ver: src/contrib/copa_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/copa_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/copa_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/copa_1.12.0.tgz vignettes: vignettes/copa/inst/doc/copa.pdf Package: CORREP Version: 1.10.0 Depends: e1071 Suggests: cluster 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 License: GPL 2.0 or newer source.ver: src/contrib/CORREP_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/CORREP_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/CORREP_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/CORREP_1.10.0.tgz vignettes: vignettes/CORREP/inst/doc/CORREP.pdf Package: cosmo Version: 1.10.0 Depends: R (>= 2.4.0), methods, utils, seqLogo Suggests: cosmoGUI 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 License: Free for research purposes only. For details, see COPYING or type license.cosmo() in R. source.ver: src/contrib/cosmo_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/cosmo_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/cosmo_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/cosmo_1.10.0.tgz vignettes: vignettes/cosmo/inst/doc/cosmo.pdf Package: cosmoGUI Version: 1.10.0 Depends: tkWidgets, cosmo 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/ License: LGPL version 2 or newer source.ver: src/contrib/cosmoGUI_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/cosmoGUI_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/cosmoGUI_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/cosmoGUI_1.10.0.tgz Package: crlmm Version: 1.2.4 Imports: affyio, preprocessCore, utils, stats, genefilter, splines, Biobase, mvtnorm Suggests: hapmapsnp5, genomewidesnp5Crlmm (>= 1.0.2), genomewidesnp6Crlmm (>= 1.0.2), methods, GGdata, snpMatrix 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 6.0. biocViews: Microarray, Preprocessing, SNP, Bioinformatics Author: Rafael A Irizarry, Benilton S Carvalho , Robert Scharpf , Matt Ritchie Maintainer: Benilton S Carvalho , Robert Scharpf , Matt Ritchie License: Artistic-2.0 source.ver: src/contrib/crlmm_1.2.4.tar.gz win.binary.ver: bin/windows/contrib/2.9/crlmm_1.2.4.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/crlmm_1.2.4.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/crlmm_1.2.4.tgz vignettes: vignettes/crlmm/inst/doc/copynumber.pdf, vignettes/crlmm/inst/doc/crlmmDownstream.pdf, vignettes/crlmm/inst/doc/genotyping.pdf Package: ctc Version: 1.18.0 Depends: amap 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 License: GPL source.ver: src/contrib/ctc_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/ctc_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/ctc_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/ctc_1.18.0.tgz vignettes: vignettes/ctc/inst/doc/ctc.pdf Package: daMA Version: 1.16.0 Depends: MASS 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 License: GPL version 2 or newer source.ver: src/contrib/daMA_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/daMA_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/daMA_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/daMA_1.16.0.tgz Package: DAVIDQuery Version: 1.2.0 Imports: RCurl, utils 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: AnnotationData, Genomics Author: Roger Day Maintainer: Roger Day License: GPL-2 source.ver: src/contrib/DAVIDQuery_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/DAVIDQuery_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/DAVIDQuery_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/DAVIDQuery_1.2.0.tgz vignettes: vignettes/DAVIDQuery/inst/doc/DAVIDQuery.pdf Package: DEDS Version: 1.18.0 Depends: R (>= 1.7.0), methods 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 License: LGPL source.ver: src/contrib/DEDS_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/DEDS_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/DEDS_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/DEDS_1.18.0.tgz vignettes: vignettes/DEDS/inst/doc/DEDS.pdf Package: DFP Version: 1.2.0 Depends: methods, Biobase 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 License: GPL-2 source.ver: src/contrib/DFP_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/DFP_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/DFP_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/DFP_1.2.0.tgz vignettes: vignettes/DFP/inst/doc/DFP.pdf Package: diffGeneAnalysis Version: 1.26.0 Depends: minpack.lm (>= 1.0-4) Title: Performs differential gene expression Analysis Description: Analyze microarray data biocViews: Bioinformatics, Microarray, DifferentialExpression Author: Choudary Jagarlamudi Maintainer: Choudary Jagarlamudi License: GPL source.ver: src/contrib/diffGeneAnalysis_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/diffGeneAnalysis_1.26.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/diffGeneAnalysis_1.26.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/diffGeneAnalysis_1.26.0.tgz vignettes: vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf Package: DNAcopy Version: 1.18.0 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, DNACopyNumber Author: Venkatraman E. Seshan, Adam Olshen Maintainer: Venkatraman E. Seshan License: GPL version 2 or later source.ver: src/contrib/DNAcopy_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/DNAcopy_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/DNAcopy_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/DNAcopy_1.18.0.tgz vignettes: vignettes/DNAcopy/inst/doc/DNAcopy.pdf Package: domainsignatures Version: 1.4.0 Depends: R (>= 2.4.0), KEGG.db, prada, biomaRt, methods Imports: AnnotationDbi 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 License: The Artistic License, Version 2.0 source.ver: src/contrib/domainsignatures_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/domainsignatures_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/domainsignatures_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/domainsignatures_1.4.0.tgz vignettes: vignettes/domainsignatures/inst/doc/domainenrichment.pdf Package: dualKS Version: 1.4.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.0), affy, methods 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 License: LGPL (>= 2.0) source.ver: src/contrib/dualKS_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/dualKS_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/dualKS_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/dualKS_1.4.0.tgz vignettes: vignettes/dualKS/inst/doc/dualKS.pdf Package: dyebias Version: 1.2.1 Depends: R (>= 1.4.1), marray, Biobase Suggests: limma, convert, GEOquery, dyebiasexamples, methods Title: Methods to correct for gene-specific dye bias Description: Gene-specific dye-bias correction of two-color microarray data using the GASSCO method described in Margaritis et al. 2009. biocViews: Microarray, TwoChannel, QualityControl, Preprocessing Author: Philip Lijnzaad and Thanasis Margaritis Maintainer: Philip Lijnzaad URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad License: GPL v3 source.ver: src/contrib/dyebias_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/dyebias_1.2.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/dyebias_1.2.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/dyebias_1.2.1.tgz vignettes: vignettes/dyebias/inst/doc/dyebias.pdf, vignettes/dyebias/inst/doc/dyebiasCompleteVignette.pdf Package: DynDoc Version: 1.22.0 Depends: methods, utils Imports: methods 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: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/DynDoc_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/DynDoc_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/DynDoc_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/DynDoc_1.22.0.tgz Package: EBarrays Version: 2.8.0 Depends: R (>= 1.8.0), Biobase, utils, lattice, cluster, methods Title: Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification Description: EBarrays provides tools for the analysis of replicated/unreplicated microarray data. Author: Ming Yuan, Christina Kendziorski, Michael Newton and Deepayan Sarkar Maintainer: Ming Yuan License: GPL (>= 2) source.ver: src/contrib/EBarrays_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/EBarrays_2.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/EBarrays_2.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/EBarrays_2.8.0.tgz vignettes: vignettes/EBarrays/inst/doc/vignette.pdf Package: EBImage Version: 3.0.5 Depends: R (>= 2.4.0), methods, graphics, stats, utils, abind 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 License: Artistic-2.0 SystemRequirements: ImageMagick (>= 6.3.7), GTK+ (> 2.6) source.ver: src/contrib/EBImage_3.0.5.tar.gz win.binary.ver: bin/windows/contrib/2.9/EBImage_3.0.5.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/EBImage_3.0.5.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/EBImage_3.0.5.tgz vignettes: vignettes/EBImage/inst/doc/EBImage-installation.pdf, vignettes/EBImage/inst/doc/EBImage-introduction.pdf Package: ecolitk Version: 1.16.0 Depends: R (>= 2.5), affy, ecoliLeucine, ecolicdf, Biobase Suggests: graph, matchprobes, multtest, vsn 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 License: GPL version 2 or newer source.ver: src/contrib/ecolitk_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/ecolitk_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/ecolitk_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/ecolitk_1.16.0.tgz vignettes: vignettes/ecolitk/inst/doc/ecolitk.pdf Package: edd Version: 1.22.0 Depends: methods, golubEsets, Biobase, class, nnet, xtable Title: expression density diagnostics Description: tools for evaluating cohort distributions of gene expression levels biocViews: Bioinformatics, DifferentialExpression Author: Vince Carey Maintainer: Vince Carey License: LGPL source.ver: src/contrib/edd_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/edd_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/edd_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/edd_1.22.0.tgz vignettes: vignettes/edd/inst/doc/eddDetails.pdf, vignettes/edd/inst/doc/HOWTO-edd.pdf Package: edgeR Version: 1.2.4 Depends: R (>= 2.3.0), methods, Biobase Suggests: MASS Title: Empirical analysis of digital gene expression data in R Description: Estimation and Testing for Differential Expression in Multiple Digital Gene Expression Libraries. biocViews: Bioinformatics, DifferentialExpression Author: Mark Robinson Maintainer: Mark Robinson , Davis McCarthy License: LGPL version 2 or newer source.ver: src/contrib/edgeR_1.2.4.tar.gz win.binary.ver: bin/windows/contrib/2.9/edgeR_1.2.4.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/edgeR_1.2.4.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/edgeR_1.2.4.tgz vignettes: vignettes/edgeR/inst/doc/edgeR.pdf Package: exonmap Version: 2.2.0 Depends: R (>= 2.0), affy, genefilter, RColorBrewer, RMySQL (>= 0.6-0), DBI, methods Title: High level analysis of Affymetrix exon array data Description: Provides fine grained annotation of Affymetrix exon arrays, including mappings between the array probes and probesets and the Ensembl exons, transcripts and genes they target. biocViews: Microarray, OneChannel, Preprocessing, Transcription, DataImport, Bioinformatics, DifferentialExpression, Annotation, ReportWriting, Visualization Author: Crispin J Miller Michal Okoniewski, Tim Yates Maintainer: Crispin Miller URL: http://www.bioconductor.org, http://bioinformatics.picr.man.ac.uk License: GPL version 2 or later source.ver: src/contrib/exonmap_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/exonmap_2.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/exonmap_2.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/exonmap_2.2.0.tgz vignettes: vignettes/exonmap/inst/doc/exonmap.example.pdf, vignettes/exonmap/inst/doc/exonmap.pdf, vignettes/exonmap/inst/doc/INSTALL.pdf Package: explorase Version: 1.8.1 Depends: R (>= 2.6.2) Imports: limma, rggobi, RGtk2 Suggests: cairoDevice Title: GUI for exploratory data analysis of systems biology data Description: explore and analyze *omics data with R and GGobi biocViews: Visualization,Microarray 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 License: GPL source.ver: src/contrib/explorase_1.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/explorase_1.8.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/explorase_1.8.1.tgz vignettes: vignettes/explorase/inst/doc/explorase.pdf Package: externalVector Version: 1.10.0 Depends: R (>= 1.8.0), methods, stats 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: Biocore Team c/o BioC user list License: LGPL source.ver: src/contrib/externalVector_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/externalVector_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/externalVector_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/externalVector_1.10.0.tgz Package: factDesign Version: 1.20.0 Depends: Biobase Imports: genefilter, stats Suggests: affy 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 License: LGPL source.ver: src/contrib/factDesign_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/factDesign_1.20.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/factDesign_1.20.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/factDesign_1.20.0.tgz vignettes: vignettes/factDesign/inst/doc/factDesign.pdf Package: fbat Version: 1.8.0 Depends: MASS, GeneticsBase Title: Family Based Association Tests for genetic data. Description: This package implements a broad class of Family Based Association Tests for genetids data, with adjustments for population admixture using the code from the 'FBAT' software program (see http://www.biostat.harvard.edu/~fbat/fbat.htm). Features include: - Uses data from nuclear families, sibships, pedigrees, or any combination; provides unbiased tests with or without founder genotypes. - Analyzes dichotomous, measured, or time-to-onset traits and multiple traits; trait definition can be optimized. - Offers bi-allelic and multi-allelic tests of association using standard genetic models (additive, dominant, recessive or genotype). - Offers large sample and Monte-Carlo exact tests of the null hypothesis: no linkage and no association; offers large sample test of H0: no association. - Estimates allele frequencies; checks Mendelian consistency. - Tests multiple markers using haplotypes; estimates haplotype frequencies and linkage disequilibrium between pairs of markers. - Offers two multi-marker tests for testing multiple markers simultaneously, without resolving phase or assuming no recombination. - Uses standard pedigree data files; phenotype file is optional. - Offers the Sibs Disequilibrium Test. biocViews: Genetics Author: Weiliang Qiu Ross Lazarus Gregory Warnes Nitin Jain Maintainer: The R Genetics Project License: LGPL source.ver: src/contrib/fbat_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/fbat_1.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/fbat_1.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/fbat_1.8.0.tgz vignettes: vignettes/fbat/inst/doc/fbat.pdf Package: fdrame Version: 1.16.0 Depends: tcltk 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 License: GPL Version 2 or later. source.ver: src/contrib/fdrame_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/fdrame_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/fdrame_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/fdrame_1.16.0.tgz vignettes: vignettes/fdrame/inst/doc/fdrame.pdf Package: flagme Version: 1.0.0 Depends: methods, graphics, xcms, SparseM, gcspikelite Suggests: gplots, MASS 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 License: LGPL version 2 or later source.ver: src/contrib/flagme_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/flagme_1.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/flagme_1.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/flagme_1.0.0.tgz vignettes: vignettes/flagme/inst/doc/flagme.pdf Package: flowClust Version: 2.2.0 Depends: R(>= 2.5.0), methods, mnormt, mclust, ellipse, Biobase, flowCore 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 Author: Raphael Gottardo , Kenneth Lo Maintainer: Raphael Gottardo License: Artistic-2.0 source.ver: src/contrib/flowClust_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/flowClust_2.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/flowClust_2.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/flowClust_2.2.0.tgz vignettes: vignettes/flowClust/inst/doc/flowClust.pdf Package: flowCore Version: 1.10.0 Depends: R (>= 2.8.1), Biobase, rrcov Imports: Biobase, feature, graph, graphics, grDevices, MASS, methods, rrcov, stats, utils Suggests: Rgraphviz, flowViz, ncdf 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: F. Hahne License: Artistic-2.0 source.ver: src/contrib/flowCore_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/flowCore_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/flowCore_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/flowCore_1.10.0.tgz vignettes: vignettes/flowCore/inst/doc/HowTo-flowCore.pdf Package: flowFlowJo Version: 1.2.0 Depends: R (>= 2.5.0), MASS, Imports: flowCore, XML (>= 1.96), methods 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 License: GPL (>=3) source.ver: src/contrib/flowFlowJo_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/flowFlowJo_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/flowFlowJo_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/flowFlowJo_1.2.0.tgz vignettes: vignettes/flowFlowJo/inst/doc/flowFlowJo.pdf Package: flowQ Version: 1.4.0 Depends: R (>= 2.4.0), outliers, lattice, flowViz, methods, mvoutlier,bioDist,parody,RColorBrewer,latticeExtra Imports: geneplotter, flowCore, flowViz Title: Qualitiy 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: F. Hahne License: Artistic-2.0 source.ver: src/contrib/flowQ_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/flowQ_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/flowQ_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/flowQ_1.4.0.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 Package: flowStats Version: 1.2.0 Depends: R (>= 2.7.0), flowCore (>= 1.9.0), fda Imports: MASS, flowCore, fda, Biobase, methods, grDevices, graphics, stats, utils, flowViz Suggests: flowViz,xtable 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 Maintainer: Florian Hahne License: Artistic-2.0 source.ver: src/contrib/flowStats_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/flowStats_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/flowStats_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/flowStats_1.2.0.tgz vignettes: vignettes/flowStats/inst/doc/GettingStartedWithFlowStats.pdf Package: flowUtils Version: 1.4.0 Depends: R (>= 2.2.0), flowCore (>= 1.2.0), methods, XML Imports: flowCore, XML, RUnit Suggests: gatingMLData 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 License: Artistic-2.0 source.ver: src/contrib/flowUtils_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/flowUtils_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/flowUtils_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/flowUtils_1.4.0.tgz Package: flowViz Version: 1.8.0 Depends: R (>= 2.7.0), flowCore (>= 1.5.17), lattice Imports: Biobase, flowCore, graphics, grDevices, grid, KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer, stats, utils Suggests: RColorBrewer Title: Visualization for flow cytometry Description: Provides visualization tools for flow cytometry data. biocViews: Infrastructure, Flowcytometry, CellBasedAssays, Visualization Author: B. Ellis, R. Gentleman, F. Hahne, N. Le Meur, D. Sarkar Maintainer: Florian Hahne License: Artistic-2.0 source.ver: src/contrib/flowViz_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/flowViz_1.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/flowViz_1.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/flowViz_1.8.0.tgz vignettes: vignettes/flowViz/inst/doc/filters.pdf Package: gaga Version: 1.4.0 Depends: R (>= 2.5.0), Biobase, coda Title: GaGa hierarchical model for microarray data analysis Description: This package fits Rossell's generalizations of the Gamma-Gamma hierarchical model for microarray data analysis, which substantially improve the quality of the fit at a low computational cost. The model can be fit via empirical Bayes (Expectation-Maximization and Simulated Annealing) and fully Bayesian techniques (Gibbs and Metropolis-Hastings posterior sampling). Routines are provided to perform differential expression analysis and class prediction. biocViews: Bioinformatics,DifferentialExpression,Classification Author: David Rossell . Maintainer: David Rossell License: GPL (>=2) source.ver: src/contrib/gaga_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/gaga_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/gaga_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/gaga_1.4.0.tgz vignettes: vignettes/gaga/inst/doc/gagamanual.pdf Package: gaggle Version: 1.12.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>= 0.4.17) Title: Broadcast data between R and other bioinformatics programs Description: this package contains functions connecting R with the Gaggle biocViews: Visualization, Annotation, GraphsAndNetworks Author: Paul Shannon Maintainer: Dan Tenenbaum URL: http://gaggle.systemsbiology.org License: GPL version 2 or newer source.ver: src/contrib/gaggle_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/gaggle_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/gaggle_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/gaggle_1.12.0.tgz vignettes: vignettes/gaggle/inst/doc/gaggle.pdf Package: gcrma Version: 2.16.0 Depends: R (>= 2.6.0), Biobase, affy (>= 1.5.0), Biostrings (>= 2.11.32) Imports: splines Suggests: affydata, matchprobes, tools, splines 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 License: LGPL source.ver: src/contrib/gcrma_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/gcrma_2.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/gcrma_2.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/gcrma_2.16.0.tgz vignettes: vignettes/gcrma/inst/doc/gcrma2.0.pdf Package: genArise Version: 1.20.0 Depends: R (>= 1.7.1), locfit, tkrplot, xtable, methods 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 License: Free for non-commercial use source.ver: src/contrib/genArise_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/genArise_1.20.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/genArise_1.20.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/genArise_1.20.0.tgz vignettes: vignettes/genArise/inst/doc/genArise.pdf Package: gene2pathway Version: 1.2.0 Depends: R (>= 2.6.0), kernlab (>= 0.9), KEGG.db (>= 2.2.0), biomaRt (>= 1.12.1), KEGGSOAP (>= 1.12.0), RBGL, AnnotationDbi,org.Dm.eg.db Imports: SSOAP, RCurl 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 , contributions by Tim Beissbarth Maintainer: Holger Froehlich License: GPL (>= 2) source.ver: src/contrib/gene2pathway_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/gene2pathway_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/gene2pathway_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/gene2pathway_1.2.0.tgz vignettes: vignettes/gene2pathway/inst/doc/gene2pathway.pdf Package: genefilter Version: 1.24.3 Imports: AnnotationDbi, annotate (>= 1.13.7), Biobase (>= 1.99.10), graphics, methods, stats, survival Suggests: Biobase (>= 1.99.10), class, hgu95av2.db, methods, tkWidgets 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: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/genefilter_1.24.3.tar.gz win.binary.ver: bin/windows/contrib/2.9/genefilter_1.24.3.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/genefilter_1.24.3.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/genefilter_1.24.3.tgz vignettes: vignettes/genefilter/inst/doc/howtogenefilter.pdf, vignettes/genefilter/inst/doc/howtogenefinder.pdf Package: GeneMeta Version: 1.16.0 Depends: R (>= 2.5.0), methods, Biobase (>= 1.15.23), genefilter Imports: methods, Biobase (>= 1.15.23) 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: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/GeneMeta_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GeneMeta_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GeneMeta_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GeneMeta_1.16.0.tgz vignettes: vignettes/GeneMeta/inst/doc/GeneMeta.pdf Package: geneplotter Version: 1.22.0 Depends: Biobase, annotate, lattice Imports: annotate, AnnotationDbi, Biobase, graphics, grDevices, grid, methods, RColorBrewer, stats, utils Suggests: Biobase, Rgraphviz, annotate, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db Title: Graphics related functions for Bioconductor Description: Some basic functions for plotting genetic data biocViews: Visualization Author: R. Gentleman, Biocore Maintainer: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/geneplotter_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/geneplotter_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/geneplotter_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/geneplotter_1.22.0.tgz vignettes: vignettes/geneplotter/inst/doc/byChroms.pdf, vignettes/geneplotter/inst/doc/visualize.pdf Package: GeneR Version: 2.14.0 Depends: R (>= 2.6.0) Title: R for genes and sequences analysis Description: Package manipulating nucleotidic sequences (Embl, Fasta, GenBank) biocViews: Annotation, Genetics Author: L. Cottret, A. Lucas, E. Marrakchi, O. Rogier, V. Lefort, P. Durosay, A. Viari, C. Thermes & Y. d'Aubenton-Carafa. Maintainer: Y. d'Aubenton-Carafa URL: http://www.cgm.cnrs-gif.fr License: CeCILL-2.0 source.ver: src/contrib/GeneR_2.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GeneR_2.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GeneR_2.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GeneR_2.14.0.tgz vignettes: vignettes/GeneR/inst/doc/GeneR_address.pdf, vignettes/GeneR/inst/doc/GeneR.pdf Package: geneRecommender Version: 1.16.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22) 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 License: GPL version 2 or newer source.ver: src/contrib/geneRecommender_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/geneRecommender_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/geneRecommender_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/geneRecommender_1.16.0.tgz vignettes: vignettes/geneRecommender/inst/doc/geneRecommender.pdf Package: GeneRegionScan Version: 1.0.0 Depends: methods, Biobase, Biostrings Imports: Biobase, affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi 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, Statistics, SNP, OneChannel, Visualization Author: Lasse Folkersen, Diego Diez Maintainer: Lasse Folkersen License: GPL version 2 or newer source.ver: src/contrib/GeneRegionScan_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GeneRegionScan_1.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GeneRegionScan_1.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GeneRegionScan_1.0.0.tgz vignettes: vignettes/GeneRegionScan/inst/doc/GeneRegionScan.pdf Package: GeneRfold Version: 1.2.0 Depends: R (>= 2.6.0), GeneR Title: R for genes and sequences, using viennaRNA package (fold) Description: Package manipulating sequences with fold routines biocViews: Annotation, Genetics Author: Y. d'Aubenton-Carafa, A. Lucas & C. Thermes Maintainer: Antoine Lucas URL: http://www.tbi.univie.ac.at/~ivo/RNA/ License: CeCILL-2.0 source.ver: src/contrib/GeneRfold_1.2.0.tar.gz mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GeneRfold_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GeneRfold_1.2.0.tgz vignettes: vignettes/GeneRfold/inst/doc/GeneRfold.pdf, vignettes/GeneRfold/inst/doc/rnafold.pdf Package: GeneSelectMMD Version: 1.0.0 Depends: R (>= 2.8.0), Biobase Imports: Biobase, MASS, graphics, stats, survival Suggests: ALL 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 License: GPL version 2 or newer source.ver: src/contrib/GeneSelectMMD_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GeneSelectMMD_1.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GeneSelectMMD_1.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GeneSelectMMD_1.0.0.tgz vignettes: vignettes/GeneSelectMMD/inst/doc/gsMMD.pdf Package: GeneSelector Version: 1.4.0 Depends: R (>= 2.5.1), methods, stats, Biobase Suggests: multtest, siggenes, samr, limma, sma Title: GeneSelector 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 featured ranking methods (currently 15). In addition, the stability of the findings can be taken in 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. biocViews: Bioinformatics, DifferentialExpression Author: Martin Slawski , Anne-Laure Boulesteix . Maintainer: Martin Slawski License: GPL (version 2 or later) source.ver: src/contrib/GeneSelector_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GeneSelector_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GeneSelector_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GeneSelector_1.4.0.tgz vignettes: vignettes/GeneSelector/inst/doc/GeneSelector.pdf Package: GeneSpring Version: 2.18.0 Depends: R (>= 2.0.1), Biobase (>= 1.5.0), methods Title: GeneSpring R Integration Functions Description: Set of functions and class definitions to be able to read and write GeneSpring specific data objects and covert them to BioConductor objects biocViews: Infrastructure Author: Thon de Boer Maintainer: Thon de Boer URL: http://www.chem.agilent.com/scripts/generic.asp?lpage=34733 License: GPL source.ver: src/contrib/GeneSpring_2.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GeneSpring_2.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GeneSpring_2.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GeneSpring_2.18.0.tgz vignettes: vignettes/GeneSpring/inst/doc/GeneSpring.pdf Package: GeneticsBase Version: 1.10.0 Depends: R (>= 2.3.1), methods, combinat, xtable, mvtnorm, haplo.stats Imports: gdata (>= 2.3.0), gplots (>= 2.3.1), gtools (>= 2.2.3), MASS Title: Classes and functions for handling genetic data Description: The R Genetics Project is a collaborative effort to develop a complete set of tools for storing, accessing, manipulating, and analyzing genetics data, from small candidate-gene studies consisting of a few genetic markers to large whole-genome studies containing hundreds of thousands of markers. This package (GeneticsBase) provides a foundation of efficient data structures and easy-to-use manipulation functions. biocViews: Genetics Author: Gregory Warnes Ross Lazarus Scott D Chasalow Giovanni Montana Michael O'Connell Junsheng Cheng Nitin Jain Maintainer: The R Genetics Project License: LGPL source.ver: src/contrib/GeneticsBase_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GeneticsBase_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GeneticsBase_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GeneticsBase_1.10.0.tgz vignettes: vignettes/GeneticsBase/inst/doc/CAMP_alleleSummary_html.pdf, vignettes/GeneticsBase/inst/doc/CAMP_genotypeSummary_html.pdf, vignettes/GeneticsBase/inst/doc/CAMP_LD_html.pdf, vignettes/GeneticsBase/inst/doc/HOWTO-LoadGenotypes.pdf, vignettes/GeneticsBase/inst/doc/SummaryTables.pdf, vignettes/GeneticsBase/inst/doc/Tutorial.pdf Package: GeneticsDesign Version: 1.12.0 Depends: combinat, gdata, gmodels, gtools (>= 2.4.0), mvtnorm 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 License: GPL source.ver: src/contrib/GeneticsDesign_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GeneticsDesign_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GeneticsDesign_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GeneticsDesign_1.12.0.tgz vignettes: vignettes/GeneticsDesign/inst/doc/GPC.pdf Package: GeneticsPed Version: 1.6.0 Depends: R (>= 2.4.0), gdata (>= 2.3.0), genetics (>= 1.3.0), MASS 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: The R Genetics Project URL: http://rgenetics.org License: LGPL version 2.1 or later source.ver: src/contrib/GeneticsPed_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GeneticsPed_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GeneticsPed_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GeneticsPed_1.6.0.tgz vignettes: vignettes/GeneticsPed/inst/doc/geneticRelatedness.pdf, vignettes/GeneticsPed/inst/doc/pedigreeHandling.pdf, vignettes/GeneticsPed/inst/doc/quanGenAnimalModel.pdf Package: GeneTraffic Version: 1.16.0 Depends: R (>= 1.8.1), Biobase (>= 1.4.0), affy (>= 1.3.28), marray (>= 1.5.10), SSOAP(>= 0.1.2), XML (>= 0.95.6), digest(>= 0.1.1), methods Title: GeneTraffic R Integration Functions Description: Set of functions and class definitions to be able to read GeneTraffic specific data from a project summary zip file and covert them to BioConductor objects (for 1 color projects affy's ExpressionSet, for 2 color projects marray's marrayRaw) biocViews: Infrastructure, Microarray Author: Daniel Iordan Maintainer: Daniel Iordan URL: http://www.iobion.com/web_services/GeneTrafficAPI/ License: GPL source.ver: src/contrib/GeneTraffic_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GeneTraffic_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GeneTraffic_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GeneTraffic_1.16.0.tgz vignettes: vignettes/GeneTraffic/inst/doc/GeneTraffic.pdf Package: GenomeGraphs Version: 1.4.1 Depends: methods, biomaRt, grid 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 License: Artistic-2.0 source.ver: src/contrib/GenomeGraphs_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/GenomeGraphs_1.4.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GenomeGraphs_1.4.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GenomeGraphs_1.4.1.tgz vignettes: vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf Package: genomeIntervals Version: 1.0.1 Depends: R (>= 2.8.0), intervals (>= 0.12.2), Biobase, methods Title: Operations on genomic intervals Description: Tools for operation on genomic intervals. biocViews: DataImport, Infrastructure, Genetics Author: Julien Gagneur , Richard Bourgon Maintainer: Julien Gagneur License: Artistic-2.0 source.ver: src/contrib/genomeIntervals_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/genomeIntervals_1.0.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/genomeIntervals_1.0.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/genomeIntervals_1.0.1.tgz vignettes: vignettes/genomeIntervals/inst/doc/genomeIntervals.pdf Package: GEOmetadb Version: 1.4.0 Depends: GEOquery,RSQLite 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/ License: Artistic-2.0 source.ver: src/contrib/GEOmetadb_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GEOmetadb_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GEOmetadb_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GEOmetadb_1.4.0.tgz vignettes: vignettes/GEOmetadb/inst/doc/GEOmetadb_diagram.pdf, vignettes/GEOmetadb/inst/doc/GEOmetadb.pdf Package: GEOquery Version: 2.8.0 Depends: methods, Biobase, RCurl Suggests: limma Title: Get data from NCBI Gene Expression Omnibus (GEO) Description: The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data (>200,000 experiments). Given the rich and varied nature of these data, 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 License: GPL version 2 source.ver: src/contrib/GEOquery_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GEOquery_2.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GEOquery_2.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GEOquery_2.8.0.tgz vignettes: vignettes/GEOquery/inst/doc/GEOquery.pdf Package: GGBase Version: 3.4.0 Depends: R (>= 2.7.0), methods, Biobase (>= 1.11.26), GSEABase, snpMatrix(>= 1.7.6), RSQLite Imports: AnnotationDbi Suggests: GGtools, illuminaHumanv1.db Title: infrastructure for genetics of gene expression (c) 2008 VJ Carey Description: infrastructure for dealing with hapmap SNP reports, GWAS, etc. biocViews: SNPsAndGeneticVariability, Genetics, Bioinformatics Author: Vince Carey Maintainer: Vince Carey License: Artistic-2.0 source.ver: src/contrib/GGBase_3.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GGBase_3.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GGBase_3.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GGBase_3.4.0.tgz vignettes: vignettes/GGBase/inst/doc/GGBase.pdf, vignettes/GGBase/inst/doc/makeSMLset.pdf, vignettes/GGBase/inst/doc/newSNPloc.pdf Package: GGtools Version: 3.2.0 Depends: R (>= 2.7.0), methods, Biobase (>= 1.11.26), GGBase (>= 3.2.17), GSEABase, snpMatrix(>= 1.7.3), RColorBrewer, RSQLite, Biostrings, rpart, annaffy Imports: AnnotationDbi, IRanges (>= 1.1.6) Suggests: illuminaHumanv1.db, org.Hs.eg.db, SNPlocs.Hsapiens.dbSNP.20071016, mapLD, haplo.stats Title: software and data for genetical genomics (c) 2006 VJ Carey Description: dealing with hapmap SNP reports, GWAS, etc. biocViews: SNPsAndGeneticVariability, Genetics, Bioinformatics Author: Vince Carey Maintainer: Vince Carey License: Artistic-2.0 source.ver: src/contrib/GGtools_3.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GGtools_3.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GGtools_3.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GGtools_3.2.0.tgz vignettes: vignettes/GGtools/inst/doc/binf09supp.pdf, vignettes/GGtools/inst/doc/GGoverview2008.pdf Package: GLAD Version: 2.0.0 Depends: R (>= 1.8.0) Suggests: aws, tcltk 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 lost) to each chromosomal regions identified. biocViews: Microarray, DNACopyNumber Author: Philippe Hupe Maintainer: Philippe Hupe URL: http://bioinfo.curie.fr License: GPL source.ver: src/contrib/GLAD_2.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GLAD_2.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GLAD_2.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GLAD_2.0.0.tgz vignettes: vignettes/GLAD/inst/doc/GLAD.pdf Package: GlobalAncova Version: 3.10.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi Suggests: Biobase, GO.db, multtest, golubEsets, hu6800.db, vsn 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: R. Meister License: GPL Version 2 or newer source.ver: src/contrib/GlobalAncova_3.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GlobalAncova_3.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GlobalAncova_3.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GlobalAncova_3.10.0.tgz vignettes: vignettes/GlobalAncova/inst/doc/GlobalAncova.pdf, vignettes/GlobalAncova/inst/doc/GlobalAncovaDecomp.pdf Package: globaltest Version: 4.14.0 Depends: methods Imports: Biobase, survival, AnnotationDbi, annotate, multtest, graphics Suggests: vsn, golubEsets, KEGG.db, hu6800.db, GOstats, Rgraphviz, GO.db, annotate Title: Testing Association of Groups of Genes with a Clinical Variable Description: Testing whether sets of genes (e.g. KEGG pathways of GO terms) are significantly associated with a clinical variable of interest. biocViews: Microarray, OneChannel, Bioinformatics, DifferentialExpression, GO, Pathways Author: Jelle Goeman and Jan Oosting Maintainer: Jelle Goeman URL: http://www.msbi.nl/goeman License: GPL version 2 or newer source.ver: src/contrib/globaltest_4.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/globaltest_4.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/globaltest_4.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/globaltest_4.14.0.tgz vignettes: vignettes/globaltest/inst/doc/GlobalTest.pdf Package: goProfiles Version: 1.6.0 Depends: Biobase, AnnotationDbi, GO.db Suggests: org.Hs.eg.db 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 License: GPL source.ver: src/contrib/goProfiles_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/goProfiles_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/goProfiles_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/goProfiles_1.6.0.tgz vignettes: vignettes/goProfiles/inst/doc/goProfiles.pdf Package: GOSemSim Version: 1.2.0 Depends: AnnotationDbi, GO.db, org.Hs.eg.db, org.Dm.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Sc.sgd.db Title: GO-terms Semantic Similarity Measures Description: Methods for estimating GO semantic similarities. Implemented five methods proposed by Resnik, Schlicker(Rel), Jiang, Lin and Wang respectively. Support five species: human, rat, mouse, fly, and yeast. biocViews: GO, Clustering, Pathways Author: Guangchuang Yu Maintainer: Guangchuang Yu License: GPL version 2 source.ver: src/contrib/GOSemSim_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GOSemSim_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GOSemSim_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GOSemSim_1.2.0.tgz vignettes: vignettes/GOSemSim/inst/doc/GOSemSim.pdf Package: GOstats Version: 2.10.0 Depends: 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 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: Robert Gentleman License: Artistic-2.0 source.ver: src/contrib/GOstats_2.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GOstats_2.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GOstats_2.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GOstats_2.10.0.tgz vignettes: vignettes/GOstats/inst/doc/GOstatsHyperG.pdf, vignettes/GOstats/inst/doc/GOvis.pdf Package: goTools Version: 1.18.0 Depends: GO.db Suggests: hgu133a.db 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 License: GPL2 source.ver: src/contrib/goTools_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/goTools_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/goTools_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/goTools_1.18.0.tgz vignettes: vignettes/goTools/inst/doc/goTools.pdf Package: gpls Version: 1.16.0 Imports: stats 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: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/gpls_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/gpls_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/gpls_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/gpls_1.16.0.tgz vignettes: vignettes/gpls/inst/doc/gpls.pdf Package: graph Version: 1.22.5 Depends: R (>= 2.6.0), methods Imports: methods, stats, tools, utils Suggests: SparseM (>= 0.36), XML, RBGL 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: Robert Gentleman License: The Artistic License, Version 2.0 source.ver: src/contrib/graph_1.22.5.tar.gz win.binary.ver: bin/windows/contrib/2.9/graph_1.22.5.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/graph_1.22.5.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/graph_1.22.5.tgz vignettes: vignettes/graph/inst/doc/clusterGraph.pdf, vignettes/graph/inst/doc/graph.pdf, vignettes/graph/inst/doc/graphAttributes.pdf, vignettes/graph/inst/doc/GraphClass.pdf Package: GraphAlignment Version: 1.6.0 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/ License: file LICENSE source.ver: src/contrib/GraphAlignment_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GraphAlignment_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GraphAlignment_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GraphAlignment_1.6.0.tgz vignettes: vignettes/GraphAlignment/inst/doc/a.pdf, vignettes/GraphAlignment/inst/doc/align_principle_short1.pdf, vignettes/GraphAlignment/inst/doc/align_principle2b1.pdf, vignettes/GraphAlignment/inst/doc/align_principle2c1.pdf, vignettes/GraphAlignment/inst/doc/binning-01a.pdf, vignettes/GraphAlignment/inst/doc/GraphAlignment.pdf Package: GraphAT Version: 1.16.0 Depends: MCMCpack, graph 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 License: LGPL source.ver: src/contrib/GraphAT_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GraphAT_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GraphAT_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GraphAT_1.16.0.tgz Package: GSEABase Version: 1.6.1 Depends: R (>= 2.6.0), methods, AnnotationDbi, Biobase, annotate, graph Imports: methods, XML (>= 2.5-1) Suggests: Ruuid, hgu95av2.db, GO.db, org.Hs.eg.db 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: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/GSEABase_1.6.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/GSEABase_1.6.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GSEABase_1.6.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GSEABase_1.6.1.tgz vignettes: vignettes/GSEABase/inst/doc/GSEABase.pdf Package: GSEAlm Version: 1.4.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer 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 License: Artistic-2.0 source.ver: src/contrib/GSEAlm_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/GSEAlm_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/GSEAlm_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/GSEAlm_1.4.0.tgz vignettes: vignettes/GSEAlm/inst/doc/GSEAlm.pdf Package: Harshlight Version: 1.14.0 Depends: R (>= 2.1.1), affy , altcdfenvs 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 substitue value as whole matrix to solve the memory problem. Author: Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkowski, Marcelo O. Magnasco Maintainer: Maurizio Pellegrino URL: http://asterion.rockefeller.edu/Harshlight/ License: GPL version 2 or later source.ver: src/contrib/Harshlight_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/Harshlight_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Harshlight_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Harshlight_1.14.0.tgz vignettes: vignettes/Harshlight/inst/doc/Harshlight.pdf Package: Heatplus Version: 1.14.0 Title: A heat map displaying covariates and coloring clusters Description: Add an extra graphical display at the bottom of a heat map, indicating for each column a) whether it has one of several binary properties or not, and b) the value of a quantitative variable. A cutting threshold for the sample dendrogram can also be specified, and the resulting clustering of the columns is indicated by coloring both the dendrogram and the extra variable display. biocViews: Microarray, Visualization Author: Alexander Ploner Maintainer: Alexander Ploner License: GPL 2 or later source.ver: src/contrib/Heatplus_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/Heatplus_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Heatplus_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Heatplus_1.14.0.tgz vignettes: vignettes/Heatplus/inst/doc/Heatplus.pdf Package: HELP Version: 1.2.0 Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods 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 License: GPL version 2 or newer source.ver: src/contrib/HELP_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/HELP_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/HELP_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/HELP_1.2.0.tgz vignettes: vignettes/HELP/inst/doc/HELP.pdf Package: HEM Version: 1.16.0 Depends: R (>= 2.1.0), Biobase 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/ License: GPL version 2 or newer source.ver: src/contrib/HEM_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/HEM_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/HEM_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/HEM_1.16.0.tgz vignettes: vignettes/HEM/inst/doc/HEM.pdf Package: hexbin Version: 1.18.0 Depends: R (>= 2.0.1), methods, stats, grid, lattice Suggests: marray, cluster, affy, Biobase Title: Hexagonal Binning Routines Description: Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods. biocViews: Visualization Author: Dan Carr , ported by Nicholas Lewin-Koh and Martin Maechler Maintainer: Nicholas Lewin-Koh License: GPL 2 source.ver: src/contrib/hexbin_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/hexbin_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/hexbin_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/hexbin_1.18.0.tgz vignettes: vignettes/hexbin/inst/doc/hexagon_binning.pdf Package: HilbertVis Version: 1.2.0 Depends: R (>= 2.6.0), grid, lattice Suggests: EBImage 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 License: GPL >=3 source.ver: src/contrib/HilbertVis_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/HilbertVis_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/HilbertVis_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/HilbertVis_1.2.0.tgz vignettes: vignettes/HilbertVis/inst/doc/HilbertDisplay_GUI.pdf, vignettes/HilbertVis/inst/doc/HilbertVis.pdf, vignettes/HilbertVis/inst/doc/Rplots.pdf, vignettes/HilbertVis/inst/doc/ThreeChTest.pdf Package: HilbertVisGUI Version: 1.2.0 Depends: R (>= 2.6.0), HilbertVis (>= 1.1.6) Suggests: lattice 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 License: GPL >=3 SystemRequirements: gtkmm-2.4 source.ver: src/contrib/HilbertVisGUI_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/HilbertVisGUI_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/HilbertVisGUI_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/HilbertVisGUI_1.2.0.tgz vignettes: vignettes/HilbertVisGUI/inst/doc/HilbertVisGUI.pdf Package: hopach Version: 2.4.0 Depends: R (>= 2.6.0), cluster, Biobase, methods 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.com/ License: GPL version 2 or newer source.ver: src/contrib/hopach_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/hopach_2.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/hopach_2.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/hopach_2.4.0.tgz vignettes: vignettes/hopach/inst/doc/bootplot.pdf, vignettes/hopach/inst/doc/dplot.pdf, vignettes/hopach/inst/doc/hopach.pdf, vignettes/hopach/inst/doc/hopachManuscript.pdf, vignettes/hopach/inst/doc/MSS.pdf Package: hypergraph Version: 1.16.0 Depends: R (>= 2.1.0), methods, graph 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: Robert Gentleman License: Artistic-2.0 source.ver: src/contrib/hypergraph_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/hypergraph_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/hypergraph_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/hypergraph_1.16.0.tgz Package: Icens Version: 1.16.0 Depends: survival 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: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/Icens_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/Icens_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Icens_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Icens_1.16.0.tgz Package: idiogram Version: 1.20.0 Depends: R (>= 2.0.0), methods, Biobase, annotate, plotrix Suggests: hu6800.db, golubEsets Title: idiogram Description: A package for plotting genomic data by chromosomal location biocViews: Visualization Author: Karl J. Dykema Maintainer: Karl J. Dykema License: GPL2 source.ver: src/contrib/idiogram_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/idiogram_1.20.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/idiogram_1.20.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/idiogram_1.20.0.tgz vignettes: vignettes/idiogram/inst/doc/idiogram.pdf Package: impute Version: 1.16.0 Depends: R (>= 1.7.0) 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 License: GPL2.0 source.ver: src/contrib/impute_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/impute_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/impute_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/impute_1.16.0.tgz Package: IRanges Version: 1.2.3 Depends: R (>= 2.8.0), methods, utils, stats Imports: methods, utils, stats Suggests: RUnit Title: Infrastructure for manipulating intervals on sequences Description: The IRanges class and its extensions are low-level containers for storing sets of integer ranges. A typical use of these containers in biology is for representing a set of chromosome regions. More specific extensions of the IRanges class will typically allow the storage of additional information attached to each chromosome region as well as a hierarchical relationship between these regions. biocViews: Infrastructure, Genetics Author: H. Pages, P. Aboyoun and M. Lawrence Maintainer: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/IRanges_1.2.3.tar.gz win.binary.ver: bin/windows/contrib/2.9/IRanges_1.2.3.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/IRanges_1.2.3.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/IRanges_1.2.3.tgz vignettes: vignettes/IRanges/inst/doc/IRangesOverview.pdf Package: ITALICS Version: 2.4.0 Depends: R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser, pd.mapping50k.xba240 Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp Title: ITALICS Description: A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set biocViews: Microarray, DNACopyNumber Author: Guillem Rigaill, Philippe Hupe Maintainer: Guillem Rigaill URL: http://bioinfo.curie.fr License: GPL source.ver: src/contrib/ITALICS_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/ITALICS_2.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/ITALICS_2.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/ITALICS_2.4.0.tgz vignettes: vignettes/ITALICS/inst/doc/ITALICS-006.pdf, vignettes/ITALICS/inst/doc/ITALICS.pdf Package: iterativeBMA Version: 1.2.0 Depends: BMA, leaps, Biobase 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 License: GPL version 2 or higher source.ver: src/contrib/iterativeBMA_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/iterativeBMA_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/iterativeBMA_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/iterativeBMA_1.2.0.tgz vignettes: vignettes/iterativeBMA/inst/doc/iterativeBMA.pdf Package: iterativeBMAsurv Version: 1.2.0 Depends: BMA, leaps, survival, splines 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 License: GPL version 2 or higher source.ver: src/contrib/iterativeBMAsurv_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/iterativeBMAsurv_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/iterativeBMAsurv_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/iterativeBMAsurv_1.2.0.tgz vignettes: vignettes/iterativeBMAsurv/inst/doc/iterativeBMAsurv.pdf Package: KCsmart Version: 2.3.2 Depends: methods, siggenes, multtest Title: Multi sample aCGH analysis package using kernel convolution Description: Multi sample aCGH analysis package using kernel convolution biocViews: Visualization, CopyNumberVariants, Microarray Author: Jorma de Ronde, Christiaan Klijn, Arno Velds Maintainer: Jorma de Ronde License: GPL-3 source.ver: src/contrib/KCsmart_2.3.2.tar.gz win.binary.ver: bin/windows/contrib/2.9/KCsmart_2.3.2.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/KCsmart_2.3.2.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/KCsmart_2.3.2.tgz vignettes: vignettes/KCsmart/inst/doc/KCS.pdf Package: KEGGgraph Version: 1.1.0 Depends: methods, XML (>= 2.3-0), graph Suggests: RBGL, Rgraphviz (>= 1.18.0), KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA 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 and Stefan Wiemann Maintainer: Jitao David Zhang URL: http://www.dkfz.de/en/mga/index.html License: GPL (>=2) source.ver: src/contrib/KEGGgraph_1.1.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/KEGGgraph_1.1.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/KEGGgraph_1.1.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/KEGGgraph_1.1.0.tgz vignettes: vignettes/KEGGgraph/inst/doc/KEGGgraph.pdf, vignettes/KEGGgraph/inst/doc/KEGGgraphApp.pdf Package: keggorth Version: 1.6.0 Depends: R (>= 2.5.0),stats,graph,hgu95av2.db Imports: AnnotationDbi,graph,DBI, graph, grDevices, methods, RSQLite, stats, tools, utils Suggests: RBGL,ALL Title: graph support for KO, KEGG Orthology Description: test package for a pathway 'ontology' biocViews: Pathways,GraphsAndNetworks Author: VJ Carey Maintainer: VJ Carey License: Artistic source.ver: src/contrib/keggorth_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/keggorth_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/keggorth_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/keggorth_1.6.0.tgz vignettes: vignettes/keggorth/inst/doc/keggorth.pdf Package: KEGGSOAP Version: 1.18.0 Depends: methods Imports: XML, RCurl, SSOAP (>= 0.2-2) Title: Client-side SOAP access KEGG Description: A package that provides a client interface to the KEGG SOAP server biocViews: Annotation, Pathways Author: J. Zhang and R. Gentleman Maintainer: Robert Gentleman License: BSD source.ver: src/contrib/KEGGSOAP_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/KEGGSOAP_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/KEGGSOAP_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/KEGGSOAP_1.18.0.tgz Package: lapmix Version: 1.10.0 Depends: R (>= 2.6.0),stats Imports: Biobase, graphics, grDevices, methods, stats, tools, utils 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 License: GPL version 2 or newer source.ver: src/contrib/lapmix_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/lapmix_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/lapmix_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/lapmix_1.10.0.tgz vignettes: vignettes/lapmix/inst/doc/lapmix-example.pdf Package: LBE Version: 1.12.0 Depends: stats Imports: graphics, grDevices, methods, stats, utils Suggests: qvalue 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 License: GPL 2 source.ver: src/contrib/LBE_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/LBE_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/LBE_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/LBE_1.12.0.tgz vignettes: vignettes/LBE/inst/doc/LBE.pdf Package: limma Version: 2.18.3 Depends: R (>= 2.3.0), methods Suggests: affy, marray, MASS, org.Hs.eg.db, splines, sma, statmod (>= 1.2.2), vsn 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, Di Wu, Alicia Oshlack, Carolyn de Graaf, Yifang Hu and Wei Shi. Maintainer: Gordon Smyth URL: http://bioinf.wehi.edu.au/limma License: LGPL source.ver: src/contrib/limma_2.18.3.tar.gz win.binary.ver: bin/windows/contrib/2.9/limma_2.18.3.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/limma_2.18.3.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/limma_2.18.3.tgz vignettes: vignettes/limma/inst/doc/limma.pdf, vignettes/limma/inst/doc/usersguide.pdf Package: limmaGUI Version: 1.20.0 Depends: limma, tcltk Suggests: statmod, sma, R2HTML, xtable, tkrplot 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/ License: LGPL source.ver: src/contrib/limmaGUI_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/limmaGUI_1.20.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/limmaGUI_1.20.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/limmaGUI_1.20.0.tgz vignettes: vignettes/limmaGUI/inst/doc/extract.pdf, vignettes/limmaGUI/inst/doc/limmaGUI.pdf, vignettes/limmaGUI/inst/doc/LinModIntro.pdf Package: LMGene Version: 1.14.0 Depends: R (>= 2.0.0), Biobase, multtest, survival Title: LMGene Software for Date 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 in the R statistical package. biocViews: Microarray, Bioinformatics, DifferentialExpression, Preprocessing Author: David Rocke, Geun Cheol Lee, and John Tillinghast. Maintainer: John Tillinghast URL: http://www.idav.ucdavis.edu/~dmrocke/software.html License: LGPL source.ver: src/contrib/LMGene_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/LMGene_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/LMGene_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/LMGene_1.14.0.tgz vignettes: vignettes/LMGene/inst/doc/LMGene.pdf Package: logicFS Version: 1.14.0 Depends: LogicReg Suggests: genefilter, siggenes 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, FeatureSelection, Classification, Genetics Author: Holger Schwender Maintainer: Holger Schwender License: LGPL version 2 or newer source.ver: src/contrib/logicFS_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/logicFS_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/logicFS_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/logicFS_1.14.0.tgz vignettes: vignettes/logicFS/inst/doc/logicFS.pdf Package: logitT Version: 1.2.0 Depends: affy Suggests: SpikeInSubset 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 License: GPL version 2 or newer source.ver: src/contrib/logitT_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/logitT_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/logitT_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/logitT_1.2.0.tgz vignettes: vignettes/logitT/inst/doc/logitT.pdf Package: LPE Version: 1.18.0 Depends: stats Imports: grDevices, methods, stats, utils 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, License: LGPL source.ver: src/contrib/LPE_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/LPE_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/LPE_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/LPE_1.18.0.tgz vignettes: vignettes/LPE/inst/doc/LPE.pdf Package: LPEadj Version: 1.4.0 Depends: LPE 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, Differential Expression, Proteomics Author: Carl Murie , Robert Nadon Maintainer: Carl Murie License: LGPL source.ver: src/contrib/LPEadj_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/LPEadj_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/LPEadj_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/LPEadj_1.4.0.tgz vignettes: vignettes/LPEadj/inst/doc/LPEadj.pdf Package: lumi Version: 1.10.2 Depends: R (>= 2.4.0), annotate, affy, Biobase (>= 1.12.0), mgcv (>= 1.4-0), methods, preprocessCore, RSQLite Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer Title: BeadArray Specific Methods for Illumina Microarrays Description: The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. biocViews: Microarray, OneChannel, Preprocessing Author: Pan Du, Gang Feng, Warren Kibbe, Simon Lin Maintainer: Pan Du License: LGPL version 2 or newer source.ver: src/contrib/lumi_1.10.2.tar.gz win.binary.ver: bin/windows/contrib/2.9/lumi_1.10.2.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/lumi_1.10.2.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/lumi_1.10.2.tgz vignettes: vignettes/lumi/inst/doc/Bioc2007_lumi_presentation.pdf, vignettes/lumi/inst/doc/IlluminaAnnotation.pdf, vignettes/lumi/inst/doc/lumi_VST_evaluation.pdf, vignettes/lumi/inst/doc/lumi.pdf Package: maanova Version: 1.14.0 Depends: R (>= 2.7.0) Suggests: qvalue, snow Title: Tools for analyzing Micro Array experiments Description: Analysis of N-dye Micro Array experiment using mixed model effect. Containing anlysis 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 License: GPL version 2 or later source.ver: src/contrib/maanova_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/maanova_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/maanova_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/maanova_1.14.0.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 Package: macat Version: 1.18.0 Depends: Biobase, annotate Suggests: hgu95av2.db, stjudem 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 License: Artistic License 2.0 source.ver: src/contrib/macat_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/macat_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/macat_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/macat_1.18.0.tgz vignettes: vignettes/macat/inst/doc/chrom6T.pdf, vignettes/macat/inst/doc/chrom6TkNN.pdf, vignettes/macat/inst/doc/evalkNN6.pdf, vignettes/macat/inst/doc/macat.pdf, vignettes/macat/inst/doc/Slidingchrom6s3.pdf Package: maCorrPlot Version: 1.14.0 Depends: lattice 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 License: GPL2 or later source.ver: src/contrib/maCorrPlot_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/maCorrPlot_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/maCorrPlot_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/maCorrPlot_1.14.0.tgz vignettes: vignettes/maCorrPlot/inst/doc/maCorrPlot.pdf Package: maDB Version: 1.16.0 Depends: R (>= 2.6.0), Biobase (>= 1.14.0), affy (>= 1.14.0), pgUtils (>= 1.5.0), limma (>= 1.8.0), methods Suggests: annaffy (>= 1.6.2), biomaRt (>= 1.8.2) 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 License: LGPL version 2 or newer source.ver: src/contrib/maDB_1.16.0.tar.gz mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/maDB_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/maDB_1.16.0.tgz vignettes: vignettes/maDB/inst/doc/maDB.pdf Package: made4 Version: 1.18.0 Depends: ade4 Suggests: affy,RColorBrewer, gplots,scatterplot3d 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 License: Artistic-2.0 source.ver: src/contrib/made4_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/made4_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/made4_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/made4_1.18.0.tgz vignettes: vignettes/made4/inst/doc/html3D.pdf, vignettes/made4/inst/doc/introduction.pdf Package: maigesPack Version: 1.8.0 Depends: R (>= 2.0.0), convert, graph, limma, marray, methods Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML, rgl, som 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/ License: GPL version 2 or newer source.ver: src/contrib/maigesPack_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/maigesPack_1.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/maigesPack_1.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/maigesPack_1.8.0.tgz vignettes: vignettes/maigesPack/inst/doc/maigesPack_tutorial.pdf Package: makecdfenv Version: 1.22.0 Depends: R (>= 2.6.0), methods, Biobase (>= 1.4.1), affy (>= 1.4.0), utils, affyio 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 License: GPL version 2 or newer source.ver: src/contrib/makecdfenv_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/makecdfenv_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/makecdfenv_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/makecdfenv_1.22.0.tgz vignettes: vignettes/makecdfenv/inst/doc/makecdfenv.pdf Package: makePlatformDesign Version: 1.8.0 Depends: R (>= 2.6.0), affyio, oligo Title: Platform Design Package Description: makePlatformDesign creates the Platform Design environments (PDenvs) required by oligo. biocViews: OneChannel, TwoChannel, Microarray, Preprocessing, Infrastructure Author: Benilton Carvalho , Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber Maintainer: Benilton Carvalho License: LGPL version 2 or newer source.ver: src/contrib/makePlatformDesign_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/makePlatformDesign_1.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/makePlatformDesign_1.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/makePlatformDesign_1.8.0.tgz Package: MANOR Version: 1.16.0 Depends: R(>= 1.8.0), GLAD Title: CGH Micro-Array NORmalization Description: We propose importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments. biocViews: Microarray, TwoChannel, DataImport, QualityControl, Preprocessing, DNACopyNumber Author: Pierre Neuvial , Philippe Hupe Maintainer: Pierre Neuvial URL: http://bioinfo.curie.fr/projects/manor/index.html License: GPL source.ver: src/contrib/MANOR_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/MANOR_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/MANOR_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/MANOR_1.16.0.tgz vignettes: vignettes/MANOR/inst/doc/MANOR.pdf Package: MantelCorr Version: 1.14.0 Depends: R (>= 2.0.0) 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 License: GPL (>=2) source.ver: src/contrib/MantelCorr_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/MantelCorr_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/MantelCorr_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/MantelCorr_1.14.0.tgz vignettes: vignettes/MantelCorr/inst/doc/MantelCorrVignette.pdf Package: marray Version: 1.22.0 Depends: R (>= 1.9.0), limma, methods Suggests: tkWidgets 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/ License: LGPL source.ver: src/contrib/marray_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/marray_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/marray_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/marray_1.22.0.tgz vignettes: vignettes/marray/inst/doc/ExampleHTML.pdf, vignettes/marray/inst/doc/marray.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/marrayPlots.pdf, vignettes/marray/inst/doc/widget1.pdf Package: maSigPro Version: 1.16.0 Depends: R (>= 2.3.1), stats, Biobase Imports: Biobase, graphics, grDevices, limma, Mfuzz, stats, utils 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: Ana Conesa URL: http://bioinfo.cipf.es/ License: GPL (version 2 or newer) source.ver: src/contrib/maSigPro_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/maSigPro_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/maSigPro_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/maSigPro_1.16.0.tgz vignettes: vignettes/maSigPro/inst/doc/maSigPro-tutorial.pdf, vignettes/maSigPro/inst/doc/maSigPro.pdf Package: MassSpecWavelet Version: 1.10.0 Depends: waveslim Suggests: xcms, caTools 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 License: LGPL version 2 or newer source.ver: src/contrib/MassSpecWavelet_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/MassSpecWavelet_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/MassSpecWavelet_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/MassSpecWavelet_1.10.0.tgz vignettes: vignettes/MassSpecWavelet/inst/doc/MassSpecWavelet.pdf Package: matchprobes Version: 1.16.0 Depends: R (>= 2.6.0), AnnotationDbi (>= 1.5.15), Biostrings (>= 2.11.28) Imports: Biobase, affy Suggests: affy, hgu95av2cdf, hgu95av2probe, hu6800cdf, hu6800probe Title: Basic infrastructure for using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment Description: For general work with genomic sequences, this package is inadequate. Please refer to the Biostrings package for that. biocViews: Microarray, Annotation Author: Robert Gentleman, Wolfgang Huber Maintainer: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/matchprobes_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/matchprobes_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/matchprobes_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/matchprobes_1.16.0.tgz vignettes: vignettes/matchprobes/inst/doc/ Package: MCRestimate Version: 2.2.0 Depends: R (>= 2.7.2), e1071 (>= 1.5-12), pamr (>= 1.22),randomForest (>= 3.9-6), RColorBrewer (>= 0.1-3), Biobase (>= 1.4.2), golubEsets (>= 1.2), Suggests: xtable (>= 1.2-1), ROC (>= 1.8.0), genefilter (>= 1.12.0), gpls (>= 1.6.0) 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 License: GPL version 2 or newer source.ver: src/contrib/MCRestimate_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/MCRestimate_2.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/MCRestimate_2.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/MCRestimate_2.2.0.tgz vignettes: vignettes/MCRestimate/inst/doc/UsingMCRestimate.pdf Package: mdqc Version: 1.6.0 Depends: R (>= 2.2.1), cluster, MASS 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. Author: Justin Harrington Maintainer: Gabriela Cohen-Freue License: LGPL version 2 or newer source.ver: src/contrib/mdqc_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/mdqc_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/mdqc_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/mdqc_1.6.0.tgz vignettes: vignettes/mdqc/inst/doc/mdqcvignette.pdf Package: MeasurementError.cor Version: 1.16.0 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 License: LGPL source.ver: src/contrib/MeasurementError.cor_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/MeasurementError.cor_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/MeasurementError.cor_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/MeasurementError.cor_1.16.0.tgz vignettes: vignettes/MeasurementError.cor/inst/doc/MeasurementError.cor.pdf Package: MEDME Version: 1.4.0 Depends: grDevices, graphics, methods, stats, utils, MASS, drc Imports: IRanges, Biostrings Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 Title: Modelling Experimental Data from MeDIP Enrichment Description: MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments biocViews: Microarray, CpGIsland Author: Mattia Pelizzola and Annette Molinaro Maintainer: Mattia Pelizzola License: GPL>=2 source.ver: src/contrib/MEDME_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/MEDME_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/MEDME_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/MEDME_1.4.0.tgz vignettes: vignettes/MEDME/inst/doc/MEDME.pdf Package: MergeMaid Version: 2.16.0 Depends: R (>= 2.2.0), survival, Biobase, MASS, methods 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 License: GPL version 2 or higher source.ver: src/contrib/MergeMaid_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/MergeMaid_2.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/MergeMaid_2.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/MergeMaid_2.16.0.tgz vignettes: vignettes/MergeMaid/inst/doc/MergeMaid.pdf Package: metaArray Version: 1.20.1 Imports: Biobase, MergeMaid, graphics, stats 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 License: LGPL2 source.ver: src/contrib/metaArray_1.20.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/metaArray_1.20.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/metaArray_1.20.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/metaArray_1.20.1.tgz vignettes: vignettes/metaArray/inst/doc/metaArray.pdf Package: metahdep Version: 1.2.0 Depends: methods Suggests: affyPLM 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 License: GPL version 3 source.ver: src/contrib/metahdep_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/metahdep_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/metahdep_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/metahdep_1.2.0.tgz vignettes: vignettes/metahdep/inst/doc/metahdep.pdf Package: Mfuzz Version: 2.2.0 Depends: R (>= 2.5.0), Biobase, e1071 Suggests: marray, tcltk, tkWidgets 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/ License: GPL version 2 source.ver: src/contrib/Mfuzz_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/Mfuzz_2.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Mfuzz_2.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Mfuzz_2.2.0.tgz vignettes: vignettes/Mfuzz/inst/doc/Mfuzz.pdf, vignettes/Mfuzz/inst/doc/MfuzzguiScreenshot.pdf, vignettes/Mfuzz/inst/doc/yeasttable3.pdf Package: microRNA Version: 1.2.0 Depends: Biostrings (>= 2.11.32), Rlibstree 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: Robert Gentleman License: The Artistic License, Version 2.0 source.ver: src/contrib/microRNA_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/microRNA_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/microRNA_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/microRNA_1.2.0.tgz Package: minet Version: 1.4.0 Depends: R (>= 2.3.0) Title: Mutual Information Network Inference Description: This package implements various algorithms for inferring mutual information networks from data. All the algorithms compute the mutual information matrix in order to infer a network. Several mutual information estimators are implemented. biocViews: Microarray, GraphsAndNetworks Author: Patrick E. Meyer, Frederic Lafitte, Gianluca Bontempi Maintainer: Patrick E. Meyer URL: http://www.ulb.ac.be/di/mlg License: GPL (>= 3) source.ver: src/contrib/minet_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/minet_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/minet_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/minet_1.4.0.tgz vignettes: vignettes/minet/inst/doc/courbes.pdf, vignettes/minet/inst/doc/graph.pdf, vignettes/minet/inst/doc/minet.pdf Package: MiPP Version: 1.16.0 Depends: R (>= 2.4), Biobase, e1071,MASS 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/ License: GPL version 2 or newer source.ver: src/contrib/MiPP_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/MiPP_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/MiPP_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/MiPP_1.16.0.tgz vignettes: vignettes/MiPP/inst/doc/MiPP.pdf Package: miRNApath Version: 1.4.0 Depends: methods, R(>= 2.7.0) 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 License: LGPL-2.1 source.ver: src/contrib/miRNApath_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/miRNApath_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/miRNApath_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/miRNApath_1.4.0.tgz vignettes: vignettes/miRNApath/inst/doc/miRNApath.pdf Package: MLInterfaces Version: 1.24.1 Depends: R (>= 2.1), Biobase, MASS, methods, genefilter, rpart, rda, annotate, cluster Suggests: class, e1071, ipred, randomForest, gpls, pamr, rpart, MASS, nnet, ALL, gbm, mlbench, hgu95av2.db, som, RColorBrewer, hu6800.db, golubEsets, ada, keggorth, kernlab, gbm, sfsmisc 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 Maintainer: V. Carey License: LGPL source.ver: src/contrib/MLInterfaces_1.24.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/MLInterfaces_1.24.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/MLInterfaces_1.24.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/MLInterfaces_1.24.1.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 Package: multiscan Version: 1.4.0 Depends: R (>= 2.3.0) Imports: Biobase, utils 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 License: GNU General Public License (version 2 or later) source.ver: src/contrib/multiscan_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/multiscan_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/multiscan_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/multiscan_1.4.0.tgz vignettes: vignettes/multiscan/inst/doc/multiscan.pdf Package: multtest Version: 2.0.0 Depends: R (>= 2.1.0), methods, Biobase Imports: survival, MASS 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 License: LGPL source.ver: src/contrib/multtest_2.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/multtest_2.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/multtest_2.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/multtest_2.0.0.tgz vignettes: vignettes/multtest/inst/doc/MTP.pdf, vignettes/multtest/inst/doc/MTPALL.pdf, vignettes/multtest/inst/doc/multtest.pdf Package: MVCClass Version: 1.18.0 Depends: R (>= 2.1.0), methods 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 License: LGPL source.ver: src/contrib/MVCClass_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/MVCClass_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/MVCClass_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/MVCClass_1.18.0.tgz vignettes: vignettes/MVCClass/inst/doc/MVCClass.pdf Package: nem Version: 2.8.0 Depends: R (>= 2.0), e1071 (>= 1.5), graph (>= 1.10), Rgraphviz (>= 1.10), RBGL (>= 1.8.1), time (>= 1.0), cluster (>= 1.11), bootstrap (>= 1.0-20), RColorBrewer, plotrix Suggests: Biobase (>= 1.10) 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 or morphological profiles). The output is a directed graph representing the phenotypic hierarchy. biocViews: Microarray, Bioinformatics, GraphsAndNetworks, Pathways Author: Holger Froehlich, Florian Markowetz, Achim Tresch, Christian Bender, Matthias Maneck, Claudio Lottaz, Tim Beissbarth Maintainer: Christian Bender URL: http://www.bioconductor.org License: GPL (>= 2) source.ver: src/contrib/nem_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/nem_2.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/nem_2.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/nem_2.8.0.tgz vignettes: vignettes/nem/inst/doc/markowetz-thesis-2006.pdf, vignettes/nem/inst/doc/nem.pdf Package: nnNorm Version: 2.8.0 Depends: R(>= 2.2.0), nnet, marray 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/ License: LGPL source.ver: src/contrib/nnNorm_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/nnNorm_2.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/nnNorm_2.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/nnNorm_2.8.0.tgz vignettes: vignettes/nnNorm/inst/doc/nnNorm.pdf, vignettes/nnNorm/inst/doc/nnNormGuide.pdf Package: nudge Version: 1.10.0 Depends: stats 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 License: GPL source.ver: src/contrib/nudge_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/nudge_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/nudge_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/nudge_1.10.0.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 Package: occugene Version: 1.4.0 Depends: R (>= 2.0.0) 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 License: GPL (>= 2) source.ver: src/contrib/occugene_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/occugene_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/occugene_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/occugene_1.4.0.tgz vignettes: vignettes/occugene/inst/doc/occugene.pdf Package: OCplus Version: 1.18.0 Depends: R (>= 2.1.0), akima, multtest (>= 1.7.3) Title: Operating characteristics plus sample size and local fdr for microarray experiments Description: This package allows to characterize the operating characeristics 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 License: LGPL source.ver: src/contrib/OCplus_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/OCplus_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/OCplus_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/OCplus_1.18.0.tgz vignettes: vignettes/OCplus/inst/doc/OCplus.pdf Package: oligo Version: 1.8.3 Depends: R (>= 2.8.0), oligoClasses (>= 1.5.22), preprocessCore Imports: splines, affxparser, graphics, utils, stats, DBI, Biobase (>= 1.13.58), methods, affyio Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer Title: Tools for low-level analysis of oligonucleotide arrays. Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, DNAMethylation, ExonArray, GeneExpression, Bioinformatics, DataImport, Transcription, ChIPchip, CopyNumberVariants, CpGIsland Author: Benilton Carvalho , Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber Maintainer: Benilton Carvalho License: LGPL version 2 or newer source.ver: src/contrib/oligo_1.8.3.tar.gz win.binary.ver: bin/windows/contrib/2.9/oligo_1.8.3.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/oligo_1.8.3.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/oligo_1.8.3.tgz vignettes: vignettes/oligo/inst/doc/ClassesUsedInOligo.pdf, vignettes/oligo/inst/doc/oligo.pdf, vignettes/oligo/inst/doc/oligoNimblegenExpression.pdf Package: oligoClasses Version: 1.6.0 Depends: Biobase Imports: graphics, IRanges, Biostrings, methods, Biobase Suggests: RSQLite, oligo Title: Classes for high-throughput SNP arrays Description: This package contains class definitions, validity checks, and initialization methods for classes used by the oligo package. biocViews: Infrastructure Author: Benilton Carvalho and Robert Scharpf Maintainer: Benilton Carvalho License: GPL version 2 or newer source.ver: src/contrib/oligoClasses_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/oligoClasses_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/oligoClasses_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/oligoClasses_1.6.0.tgz vignettes: vignettes/oligoClasses/inst/doc/SnpLevelClasses.pdf Package: OLIN Version: 1.22.0 Depends: R (>= 2.5.0), methods, stats, locfit, Biobase, marray Suggests: convert, limma 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 License: GPL version 2 source.ver: src/contrib/OLIN_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/OLIN_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/OLIN_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/OLIN_1.22.0.tgz vignettes: vignettes/OLIN/inst/doc/OLIN.pdf Package: OLINgui Version: 1.18.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Suggests: tcltk, tkWidgets 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 License: GPL version 2 source.ver: src/contrib/OLINgui_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/OLINgui_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/OLINgui_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/OLINgui_1.18.0.tgz vignettes: vignettes/OLINgui/inst/doc/OLINgui.pdf, vignettes/OLINgui/inst/doc/OLINguiScreenshot.pdf Package: oneChannelGUI Version: 1.10.11 Depends: Biobase, affylmGUI, tkWidgets, GOstats, AnnotationDbi, preprocessCore Suggests: annotate, genefilter, maSigPro, pamr, pdmclass, Rgraphviz, affy ,annaffy, affyPLM, multtest, ssize, sizepower, siggenes, RankProd, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, metaArray, MergeMaid, biomaRt, GenomeGraphs, AffyCompatible, Biostrings, IRanges, rtracklayer Title: This package extends the capabilities of affylmGUI graphical interface. Affymetrix 3' IVT, gene an exon arrays are actually implemented togheter with Illumina, GEO matrix series files and tab delimited files. 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 allowing QC, filtering, statistical validation, and alternative splicing analysis. biocViews: Microarray, OneChannel, DataImport, QualityControl, Preprocessing, Statistics, DifferentialExpression, MultipleComparisons Author: Raffale A Calogero, Bioinformatics and Genomics Unit, Dept. of Clinical and Biological Sciences Torino (Italy) Maintainer: Raffaele A Calogero URL: http://www.bioinformatica.unito.it/oneChannelGUI/ License: The Artistic License, Version 2.0 source.ver: src/contrib/oneChannelGUI_1.10.11.tar.gz win.binary.ver: bin/windows/contrib/2.9/oneChannelGUI_1.10.11.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/oneChannelGUI_1.10.11.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/oneChannelGUI_1.10.11.tgz vignettes: vignettes/oneChannelGUI/inst/doc/fignew42.pdf, vignettes/oneChannelGUI/inst/doc/install.pdf, vignettes/oneChannelGUI/inst/doc/oneChannelGUI.pdf, vignettes/oneChannelGUI/inst/doc/whatIsNew.pdf Package: ontoTools Version: 1.22.0 Depends: R (>= 2.4.0), methods, graph, Biobase, AnnotationDbi, SparseM, GO.db, annotate Suggests: combinat, Iyer517, org.Hs.eg.db, KEGG.db Title: graphs and sparse matrices for working with ontologies; formal objects for nomenclatures with provenance management Description: tools for working with ontologies and graphs biocViews: GraphsAndNetworks, Infrastructure Author: Vince Carey Maintainer: Vince Carey License: GPL2 source.ver: src/contrib/ontoTools_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/ontoTools_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/ontoTools_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/ontoTools_1.22.0.tgz vignettes: vignettes/ontoTools/inst/doc/demoComp.pdf, vignettes/ontoTools/inst/doc/ontoTools.pdf, vignettes/ontoTools/inst/doc/ontoToolsArchiving.pdf, vignettes/ontoTools/inst/doc/prot2.pdf, vignettes/ontoTools/inst/doc/protlk.pdf, vignettes/ontoTools/inst/doc/sgdiOnto.pdf Package: OrderedList Version: 1.16.0 Depends: R (>= 2.1.0), Biobase (>= 1.5.12), twilight (>= 1.9.2) 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 License: GPL (>= 2) source.ver: src/contrib/OrderedList_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/OrderedList_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/OrderedList_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/OrderedList_1.16.0.tgz vignettes: vignettes/OrderedList/inst/doc/bcb_logo.pdf, vignettes/OrderedList/inst/doc/tr_2006_01.pdf Package: OutlierD Version: 1.8.0 Depends: R (>= 2.3.0), Biobase, quantreg 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/ License: GPL version 2 or newer source.ver: src/contrib/OutlierD_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/OutlierD_1.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/OutlierD_1.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/OutlierD_1.8.0.tgz vignettes: vignettes/OutlierD/inst/doc/OutlierD.pdf Package: pamr Version: 1.42.0 Depends: cluster, survival Title: Pam: prediction analysis for microarrays Description: Some functions for sample classification in microarrays biocViews: Classification, Microarray Author: T. Hastie, R. Tibshirani, Balasubramanian Narasimhan, Gil Chu Maintainer: Rob Tibshirani License: GPL2.0 source.ver: src/contrib/pamr_1.42.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/pamr_1.42.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/pamr_1.42.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/pamr_1.42.0.tgz Package: PAnnBuilder Version: 1.6.0 Depends: R (>= 2.7.0), methods, utils, RSQLite, Biobase (>= 1.17.0), AnnotationDbi (>= 1.3.12) Imports: methods, utils, Biobase, DBI, RSQLite Suggests: org.Hs.ipi.db, org.Hs.sp.db Title: Protein annotation data package builder Description: Processing annotation data from public data repositories and building annoation data packages. biocViews: Annotation, Proteomics Author: Li Hong lihong@sibs.ac.cn Maintainer: Li Hong URL: http://www.biosino.org/PAnnBuilder License: LGPL (>= 2.0) source.ver: src/contrib/PAnnBuilder_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/PAnnBuilder_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/PAnnBuilder_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/PAnnBuilder_1.6.0.tgz vignettes: vignettes/PAnnBuilder/inst/doc/fulltext.pdf, vignettes/PAnnBuilder/inst/doc/PAnnBuilder.pdf Package: panp Version: 1.14.0 Depends: affy (>= 1.14.0), R (>= 2.5.0), Biobase (>= 1.14.0) 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. Author: Peter Warren Maintainer: Peter Warren License: GPL version 2 or newer source.ver: src/contrib/panp_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/panp_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/panp_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/panp_1.14.0.tgz vignettes: vignettes/panp/inst/doc/panp.pdf Package: parody Version: 1.2.0 Depends: R (>= 2.5.0), methods, tools, utils 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 License: Artistic 2.0 source.ver: src/contrib/parody_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/parody_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/parody_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/parody_1.2.0.tgz vignettes: vignettes/parody/inst/doc/parody.pdf Package: pathRender Version: 1.12.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods Suggests: ALL, hgu95av2.db 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 License: LGPL source.ver: src/contrib/pathRender_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/pathRender_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/pathRender_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/pathRender_1.12.0.tgz vignettes: vignettes/pathRender/inst/doc/pathRender.pdf, vignettes/pathRender/inst/doc/plotExG.pdf Package: pcaMethods Version: 1.22.0 Depends: Biobase, MASS, pls, methods Suggests: aroma.light 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 estimationn 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. Developed at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany. biocViews: Bioinformatics Author: Wolfram Stacklies, Henning Redestig, Kevin Wright Maintainer: Wolfram Stacklies License: GPL version 2 (or later) source.ver: src/contrib/pcaMethods_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/pcaMethods_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/pcaMethods_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/pcaMethods_1.22.0.tgz vignettes: vignettes/pcaMethods/inst/doc/missingValues.pdf, vignettes/pcaMethods/inst/doc/outliers.pdf, vignettes/pcaMethods/inst/doc/pcaMethods.pdf Package: pcot2 Version: 1.12.0 Depends: R (>= 2.0.0), grDevices, Biobase, amap Suggests: multtest, hu6800.db, KEGG.db, mvtnorm 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 License: GPL version 2 or newer source.ver: src/contrib/pcot2_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/pcot2_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/pcot2_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/pcot2_1.12.0.tgz vignettes: vignettes/pcot2/inst/doc/HowToUseGeneLocator.pdf, vignettes/pcot2/inst/doc/pcot2.pdf Package: PCpheno Version: 1.6.0 Depends: Category, ScISI (>= 1.3.0), SLGI, ppiStats, ppiData, annotate (>= 1.17.4) Imports: AnnotationDbi, Biobase, Category, GO.db, GSEABase, KEGG.db, ScISI, graph, graphics, methods, stats Suggests: KEGG.db, GO.db, org.Sc.sgd.db 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 License: Artistic-2.0 source.ver: src/contrib/PCpheno_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/PCpheno_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/PCpheno_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/PCpheno_1.6.0.tgz vignettes: vignettes/PCpheno/inst/doc/PCpheno.pdf Package: pdInfoBuilder Version: 1.8.1 Depends: R (>= 2.6.0), methods, Biobase (>= 1.13.58), RSQLite (>= 0.4-15), affxparser (>= 1.7.2), oligo (>= 1.7.25) Imports: Biobase (>= 1.13.58), Biostrings, IRanges 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 and Matt Settles Maintainer: Benilton Carvalho License: Artistic-2.0 source.ver: src/contrib/pdInfoBuilder_1.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/pdInfoBuilder_1.8.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/pdInfoBuilder_1.8.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/pdInfoBuilder_1.8.1.tgz vignettes: vignettes/pdInfoBuilder/inst/doc/BuildingPDInfoPkgs.pdf, vignettes/pdInfoBuilder/inst/doc/howto-AffymetrixMapping.pdf Package: pdmclass Version: 1.16.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), fibroEset, mda 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 License: Artistic source.ver: src/contrib/pdmclass_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/pdmclass_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/pdmclass_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/pdmclass_1.16.0.tgz vignettes: vignettes/pdmclass/inst/doc/pdmclass.pdf Package: PGSEA Version: 1.12.0 Depends: AnnotationDbi, methods, Biobase Suggests: GO.db, GSEABase, KEGG.db, GEOquery, org.Hs.eg.db, hgu95av2.db, Ruuid Title: Parametric Gene Set Enrichment Analysis Description: Parametric Analysis of Gene Set Enrichment biocViews: Microarray Author: Kyle Furge and Karl Dykema Maintainer: Karl Dykema License: GPL2 source.ver: src/contrib/PGSEA_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/PGSEA_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/PGSEA_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/PGSEA_1.12.0.tgz vignettes: vignettes/PGSEA/inst/doc/PGSEA.pdf, vignettes/PGSEA/inst/doc/PGSEA2.pdf Package: pgUtils Version: 1.16.0 Depends: R (>= 1.8.0), Rdbi (>= 1.0.2), RdbiPgSQL (>= 1.0.2), methods Title: Utility functions for PostgreSQL databases Description: Functions for creating PostgreSQL database tables, with auto incrementing primary keys, selection of foreign keys to allow referencial integrity and a logging mechanism. biocViews: Infrastructure Author: Johannes Rainer Maintainer: Johannes Rainer License: LGPL version 2 or newer source.ver: src/contrib/pgUtils_1.16.0.tar.gz mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/pgUtils_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/pgUtils_1.16.0.tgz vignettes: vignettes/pgUtils/inst/doc/pgUtils.pdf Package: pickgene Version: 1.16.0 Depends: MASS 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 License: GPL version 2 or newer source.ver: src/contrib/pickgene_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/pickgene_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/pickgene_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/pickgene_1.16.0.tgz vignettes: vignettes/pickgene/inst/doc/pickgene.pdf Package: pkgDepTools Version: 1.10.0 Depends: methods, graph, RBGL Imports: graph, RBGL Suggests: Biobase, Rgraphviz, RCurl 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 License: GPL2 source.ver: src/contrib/pkgDepTools_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/pkgDepTools_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/pkgDepTools_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/pkgDepTools_1.10.0.tgz vignettes: vignettes/pkgDepTools/inst/doc/pkgDepTools.pdf Package: plgem Version: 1.16.1 Depends: R (>= 2.6.0), Biobase, MASS Imports: utils Title: Power Law Global Error Model Description: PLGEM is useful for detecting differential expression in microarray and proteomics datasets. biocViews: Microarray, DifferentialExpression, Proteomics Author: Mattia Pelizzola and Norman Pavelka Maintainer: Norman Pavelka URL: http://www.genopolis.it License: GPL source.ver: src/contrib/plgem_1.16.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/plgem_1.16.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/plgem_1.16.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/plgem_1.16.1.tgz vignettes: vignettes/plgem/inst/doc/plgem.pdf Package: plier Version: 1.14.0 Depends: R (>= 2.0), affy, methods 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. Author: Affymetrix Inc., Crispin J Miller, PICR Maintainer: Crispin Miller License: GPL version 2 or later source.ver: src/contrib/plier_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/plier_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/plier_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/plier_1.14.0.tgz Package: PLPE Version: 1.4.0 Depends: R (>= 2.6.2), Biobase, LPE, MASS, methods 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/ License: GPL (>=2) source.ver: src/contrib/PLPE_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/PLPE_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/PLPE_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/PLPE_1.4.0.tgz vignettes: vignettes/PLPE/inst/doc/PLPE.pdf Package: plw Version: 1.4.0 Depends: MASS, affy, splines Suggests: limma 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 License: GPL source.ver: src/contrib/plw_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/plw_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/plw_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/plw_1.4.0.tgz vignettes: vignettes/plw/inst/doc/HowToPLW.pdf Package: ppiStats Version: 1.10.0 Depends: ScISI (>= 1.13.2), lattice, ppiData (>= 0.1.6) Imports: Biobase, Category, graph, graphics, grDevices, lattice, methods, RColorBrewer, stats Suggests: yeastExpData, xtable 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 License: Artistic-2.0 source.ver: src/contrib/ppiStats_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/ppiStats_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/ppiStats_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/ppiStats_1.10.0.tgz vignettes: vignettes/ppiStats/inst/doc/ppiStats.pdf Package: prada Version: 1.20.0 Depends: R (>= 2.1.0), Biobase, RColorBrewer, grid, methods, rrcov Imports: Biobase, graphics, grDevices, grid, MASS, methods, RColorBrewer, rrcov, utils Suggests: cellHTS, rflowcyt, tcltk 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 License: LGPL source.ver: src/contrib/prada_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/prada_1.20.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/prada_1.20.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/prada_1.20.0.tgz vignettes: vignettes/prada/inst/doc/norm2.pdf, vignettes/prada/inst/doc/prada2cellHTS.pdf Package: preprocessCore Version: 1.6.0 Depends: methods Title: A collection of pre-processing functions Description: A library of core preprocessing routines biocViews: Infrastructure Author: Benjamin Milo Bolstad Maintainer: Benjamin Milo Bolstad License: LGPL version 2 or newer source.ver: src/contrib/preprocessCore_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/preprocessCore_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/preprocessCore_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/preprocessCore_1.6.0.tgz Package: PROcess Version: 1.20.0 Depends: Icens Title: Ciphergen SELDI-TOF Processing Description: A package for processing protein mass spectrometry data. biocViews: MassSpectrometry, Proteomics Author: Xiaochun Li Maintainer: Xiaochun Li License: Artistic source.ver: src/contrib/PROcess_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/PROcess_1.20.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/PROcess_1.20.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/PROcess_1.20.0.tgz vignettes: vignettes/PROcess/inst/doc/howtoprocess.pdf Package: puma Version: 1.10.1 Depends: R (>= 2.6.0), Biobase, affy, graphics, grDevices, methods, stats, utils Suggests: pumadata, affydata, snow, limma, annotate, ROCR 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 Maintainer: Richard Pearson URL: http://umber.sbs.man.ac.uk/resources/puma License: LGPL excluding donlp2 source.ver: src/contrib/puma_1.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/puma_1.10.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/puma_1.10.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/puma_1.10.1.tgz vignettes: vignettes/puma/inst/doc/puma.pdf Package: qpcrNorm Version: 1.2.0 Depends: methods, limma, affy, Biobase 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 License: LGPL (>= 2) source.ver: src/contrib/qpcrNorm_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/qpcrNorm_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/qpcrNorm_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/qpcrNorm_1.2.0.tgz vignettes: vignettes/qpcrNorm/inst/doc/qpcrNorm.pdf Package: qpgraph Version: 1.0.0 Depends: methods, Biobase, AnnotationDbi Imports: methods, Biobase, AnnotationDbi Suggests: mvtnorm, graph, Rgraphviz, annotate, genefilter, Category (>= 2.9.7), org.EcK12.eg.db (>= 2.2.6), GOstats 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 that represent 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 License: GPL version 2 or newer source.ver: src/contrib/qpgraph_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/qpgraph_1.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/qpgraph_1.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/qpgraph_1.0.0.tgz vignettes: vignettes/qpgraph/inst/doc/qpPCCdistbyTF.pdf, vignettes/qpgraph/inst/doc/qpPreRecComparison.pdf, vignettes/qpgraph/inst/doc/qpPreRecComparisonFullRecall.pdf, vignettes/qpgraph/inst/doc/qpTRnet50pctpre.pdf, vignettes/qpgraph/inst/doc/qpTxRegNet.pdf Package: quantsmooth Version: 1.10.0 Depends: quantreg, lodplot, grid 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, DNACopyNumber Author: Jan Oosting, Paul Eilers, Renee Menezes Maintainer: Jan Oosting License: GPL V2 source.ver: src/contrib/quantsmooth_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/quantsmooth_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/quantsmooth_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/quantsmooth_1.10.0.tgz vignettes: vignettes/quantsmooth/inst/doc/quantsmooth.pdf Package: qvalue Version: 1.18.0 Depends: tcltk 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 License: LGPL source.ver: src/contrib/qvalue_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/qvalue_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/qvalue_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/qvalue_1.18.0.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-002.pdf, vignettes/qvalue/inst/doc/qvalue-004.pdf, vignettes/qvalue/inst/doc/qvalue-006.pdf, vignettes/qvalue/inst/doc/qvalue.pdf Package: rama Version: 1.18.0 Depends: R(>= 2.5.0) 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 License: GPL version 2 or newer source.ver: src/contrib/rama_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/rama_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/rama_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/rama_1.18.0.tgz vignettes: vignettes/rama/inst/doc/rama.pdf Package: RankProd Version: 2.16.0 Depends: R (>= 1.9.0) Title: Rank Product method for identifying differentially expressed genes with application in meta-analysis Description: Non-paramteric 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 and Colin Smith Maintainer: Fangxin Hong License: free for non-commercial users. Non-academic users MUST have requested from the author source.ver: src/contrib/RankProd_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/RankProd_2.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/RankProd_2.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/RankProd_2.16.0.tgz vignettes: vignettes/RankProd/inst/doc/RankProd.pdf Package: RbcBook1 Version: 1.12.0 Depends: Biobase, graph Title: Support for Springer monograph on Bioconductor Description: tools for building book Author: Vince Carey and Wolfgang Huber Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey License: Artistic-2.0 source.ver: src/contrib/RbcBook1_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/RbcBook1_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/RbcBook1_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/RbcBook1_1.12.0.tgz vignettes: vignettes/RbcBook1/inst/doc/RbcBook1.pdf Package: RBGL Version: 1.20.0 Depends: graph, methods Imports: methods 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: Li Long URL: http://www.bioconductor.org License: The Artistic License, Version 2.0 source.ver: src/contrib/RBGL_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/RBGL_1.20.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/RBGL_1.20.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/RBGL_1.20.0.tgz vignettes: vignettes/RBGL/inst/doc/filedep.pdf, vignettes/RBGL/inst/doc/RBGL.pdf Package: RBioinf Version: 1.4.0 Depends: graph, methods Title: RBioinf Description: Functions and datasets and examples to accompany the monograph R For Bioinformatics. Author: Robert Gentleman Maintainer: Robert Gentleman License: Artistic-2.0 source.ver: src/contrib/RBioinf_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/RBioinf_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/RBioinf_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/RBioinf_1.4.0.tgz vignettes: vignettes/RBioinf/inst/doc/RBioinf.pdf Package: rbsurv Version: 2.2.0 Depends: R (>= 2.5.0), Biobase, survival 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/ License: GPL (>=2) source.ver: src/contrib/rbsurv_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/rbsurv_2.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/rbsurv_2.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/rbsurv_2.2.0.tgz vignettes: vignettes/rbsurv/inst/doc/rbsurv.pdf Package: Rdbi Version: 1.18.0 Depends: R (>= 1.2) Title: Generic database methods Description: Generic framework for database access in R. Code written by Timothy H. Keitt and modified by Jianhua Zhang biocViews: Infrastructure Author: Timothy H. Keitt Maintainer: Jianhua Zhang License: GPL source.ver: src/contrib/Rdbi_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/Rdbi_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Rdbi_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Rdbi_1.18.0.tgz Package: RdbiPgSQL Version: 1.18.1 Depends: R (>= 2.6.0), Rdbi Title: PostgreSQL access Description: Provides methods for accessing data stored in PostgreSQL tables. Code written by Timothy H. Keitt and modified by Jianhua Zhang biocViews: Infrastructure Author: Timothy H. Keitt Maintainer: Jianhua Zhang License: GPL source.ver: src/contrib/RdbiPgSQL_1.18.1.tar.gz mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/RdbiPgSQL_1.18.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/RdbiPgSQL_1.18.1.tgz Package: Rdisop Version: 1.4.0 Depends: R (>= 2.0.0) 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: Technology,MassSpectrometry Author: Anton Pervukhin , Steffen Neumann Maintainer: Steffen Neumann URL: http://msbi.ipb-halle.de/ License: GPL SystemRequirements: None source.ver: src/contrib/Rdisop_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/Rdisop_1.4.0.zip vignettes: vignettes/Rdisop/inst/doc/Rdisop-isotopes.pdf, vignettes/Rdisop/inst/doc/Rdisop.pdf Package: reb Version: 1.18.0 Depends: R (>= 2.0), Biobase, idiogram (>= 1.5.3) Title: Regional Expression Biases Description: A set of functions to dentify regional expression biases biocViews: Microarray, DNACopyNumber, Visualization Author: Kyle A. Furge and Karl Dykema Maintainer: Karl J. Dykema License: VAI, Free for non-commercial, academic use. source.ver: src/contrib/reb_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/reb_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/reb_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/reb_1.18.0.tgz vignettes: vignettes/reb/inst/doc/reb.pdf Package: RefPlus Version: 1.14.0 Depends: R (>= 2.8.0), Biobase (>= 2.1.0), affy (>= 1.20.0), affyPLM (>= 1.18.0), preprocessCore (>= 1.4.0) Suggests: affydata 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 License: GPL version 2 or newer source.ver: src/contrib/RefPlus_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/RefPlus_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/RefPlus_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/RefPlus_1.14.0.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 Package: Resourcerer Version: 1.18.0 Depends: R (>= 1.9.0), Biobase, AnnotationDbi (>= 1.4.0) 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 License: LGPL source.ver: src/contrib/Resourcerer_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/Resourcerer_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Resourcerer_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Resourcerer_1.18.0.tgz vignettes: vignettes/Resourcerer/inst/doc/Resourcerer.pdf Package: rflowcyt Version: 1.16.0 Depends: R (>= 2.3.0), fields, hexbin, lattice, locfit, methods, prada, rfcdmin (>= 0.9.0), splancs, stats, survival, xgobi, xtable Imports: Biobase, KernSmooth, grDevices, graphics, hexbin, lattice, methods, prada, stats, survival, utils Title: Statistical tools and data structures for analytic flow cytometry Description: Provides basic S4 data structures and routines for analysing flow cytometry data. biocViews: Bioinformatics, Infrastructure, CellBasedAssays Author: A.J. Rossini, J.Y. Wan, N. LeMeur and Zoe Moodie Maintainer: N. LeMeur License: GNU General Public License 2.0. source.ver: src/contrib/rflowcyt_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/rflowcyt_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/rflowcyt_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/rflowcyt_1.16.0.tgz vignettes: vignettes/rflowcyt/inst/doc/rflowcyt.pdf Package: Rgraphviz Version: 1.22.2 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: graph, graphics, grDevices, grid, methods, utils 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 Falcon , Florian Hahne , Deepayan Sarkar , Kasper Hansen Maintainer: Kasper Hansen License: Artistic-2.0 SystemRequirements: Graphviz version >= 2.2 source.ver: src/contrib/Rgraphviz_1.22.2.tar.gz win.binary.ver: bin/windows/contrib/2.9/Rgraphviz_1.22.2.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Rgraphviz_1.22.2.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Rgraphviz_1.22.2.tgz vignettes: vignettes/Rgraphviz/inst/doc/newRgraphvizInterface.pdf, vignettes/Rgraphviz/inst/doc/Rgraphviz.pdf Package: rHVDM Version: 1.10.1 Depends: R (>= 2.3), R2HTML (>= 1.5), affy (>= 1.5), minpack.lm (>= 1.0-5), Biobase 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 License: GPL version 2.0 or later source.ver: src/contrib/rHVDM_1.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/rHVDM_1.10.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/rHVDM_1.10.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/rHVDM_1.10.1.tgz vignettes: vignettes/rHVDM/inst/doc/rHVDM.pdf Package: Ringo Version: 1.8.0 Depends: methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix Imports: genefilter, limma, vsn Suggests: rtracklayer (>= 1.3.1), mclust 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 License: Artistic License 2.0 source.ver: src/contrib/Ringo_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/Ringo_1.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Ringo_1.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Ringo_1.8.0.tgz vignettes: vignettes/Ringo/inst/doc/Ringo.pdf Package: Rintact Version: 1.6.0 Depends: XML (>= 1.9) Imports: Biobase, RBGL, XML (>= 1.9), graph, hypergraph, methods, utils Title: Interface to EBI Intact protein interaction data base Description: Queries and data structures for protein interactions biocViews: Infrastructure, Proteomics Author: Tony Chiang , Nianhua Li, Vincent J. Carey, R. Gentleman Maintainer: Tony Chiang URL: http://www.bioconductor.org License: Artistic-2.0 source.ver: src/contrib/Rintact_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/Rintact_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Rintact_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Rintact_1.6.0.tgz vignettes: vignettes/Rintact/inst/doc/SuppMat.pdf Package: RLMM Version: 1.6.0 Depends: R (>= 2.1.0), MASS 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, SNPsAndGeneticVariability Author: Nusrat Rabbee , Gary Wong Maintainer: Nusrat Rabbee URL: http://www.stat.berkeley.edu/users/nrabbee/RLMM License: LGPL version 2 or newer SystemRequirements: Internal files Xba.CQV, Xba.regions (or other regions file) source.ver: src/contrib/RLMM_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/RLMM_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/RLMM_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/RLMM_1.6.0.tgz vignettes: vignettes/RLMM/inst/doc/RLMM.pdf Package: RMAGEML Version: 2.18.0 Depends: R (>= 2.6.0), methods, marray, limma, Biobase Title: Handling MAGEML documents Description: This package can be used to handle MAGEML documents in Bioconductor biocViews: Microarray Author: Steffen Durinck , Joke Allemeersch and Vincent Carey Maintainer: Steffen Durinck URL: http://www.esat.kuleuven.ac.be/~jallemee,http://www.esat.kuleuven.ac.be/~sdurinck License: LGPL source.ver: src/contrib/RMAGEML_2.18.0.tar.gz vignettes: vignettes/RMAGEML/inst/doc/RMAGEML.pdf Package: Rmagpie Version: 1.0.0 Depends: R (>= 2.6.1), Biobase (>= 1.16.3) Imports: Biobase, e1071, graphics, grDevices, kernlab, methods, pamr, stats, utils Suggests: xtable 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/ License: GPL (>= 3) source.ver: src/contrib/Rmagpie_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/Rmagpie_1.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Rmagpie_1.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Rmagpie_1.0.0.tgz vignettes: vignettes/Rmagpie/inst/doc/Magpie_examples.pdf Package: rMAT Version: 1.1.2 Imports: Biobase,affxparser,methods Suggests: GenomeGraphs 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 anf GenomeGraphs installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. biocViews: Microarray, Preprocessing, Statistics Author: Charles Cheung and Arnaud Droit and Raphael Gottardo Maintainer: Arnaud Droit and Raphael Gottardo URL: http://www.rglab.org License: Artistic-2.0 source.ver: src/contrib/rMAT_1.1.2.tar.gz win.binary.ver: bin/windows/contrib/2.9/rMAT_1.1.2.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/rMAT_1.1.2.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/rMAT_1.1.2.tgz vignettes: vignettes/rMAT/inst/doc/rMAT.pdf Package: RNAither Version: 1.4.2 Depends: R (>= 2.7.0), topGO, RankProd, prada Imports: geneplotter, limma, biomaRt 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 License: Artistic License 2.0 source.ver: src/contrib/RNAither_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.9/RNAither_1.4.2.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/RNAither_1.4.2.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/RNAither_1.4.2.tgz vignettes: vignettes/RNAither/inst/doc/vignetteRNAither.pdf Package: ROC Version: 1.18.0 Depends: R (>= 1.9.0), utils, methods Suggests: Biobase 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 License: LGPL source.ver: src/contrib/ROC_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/ROC_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/ROC_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/ROC_1.18.0.tgz vignettes: vignettes/ROC/inst/doc/ROCnotes.pdf Package: RpsiXML Version: 1.4.1 Depends: annotate (>= 1.21.0), graph (>= 1.21.0), Biobase, RBGL (>= 1.17.0), methods, hypergraph (>= 1.15.0) Imports: Biobase, annotate, graph, RBGL, XML 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 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 License: LGPL-3 source.ver: src/contrib/RpsiXML_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/RpsiXML_1.4.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/RpsiXML_1.4.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/RpsiXML_1.4.1.tgz vignettes: vignettes/RpsiXML/inst/doc/RpsiXML.pdf, vignettes/RpsiXML/inst/doc/RpsiXMLApp.pdf Package: Rredland Version: 1.10.0 Depends: R (>= 2.6.0), methods, graph Title: interface to redland RDF utilities Description: interface to redland RDF utilities; assumes librdf, possibly berkeley DB; include OWL files from www.biopax.org, and RDF serializations of various resources from ISB-SIB.CH; redland is a production of Dave Beckett (see librdf.org) biocViews: Infrastructure Author: VJ Carey Maintainer: VJ Carey URL: http://www.bioconductor.org License: LGPL version 2.1 source.ver: src/contrib/Rredland_1.10.0.tar.gz mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Rredland_1.10.0.tgz vignettes: vignettes/Rredland/inst/doc/Rredland.pdf Package: rsbml Version: 2.2.1 Depends: R (>= 2.6.0), methods Imports: graph, utils 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 License: Artistic-2.0 SystemRequirements: libsbml (=2.3.4, >=3.0.3) source.ver: src/contrib/rsbml_2.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/rsbml_2.2.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/rsbml_2.2.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/rsbml_2.2.1.tgz vignettes: vignettes/rsbml/inst/doc/quick-start.pdf Package: rtracklayer Version: 1.4.1 Depends: R (>= 2.7.0), methods, RCurl Imports: XML (>= 1.98-0), IRanges (>= 1.1.34), Biostrings (>= 2.11.14), BSgenome (>= 1.11.9) Suggests: humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db 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 and WIG 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 Maintainer: Michael Lawrence License: Artistic-2.0 source.ver: src/contrib/rtracklayer_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/rtracklayer_1.4.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/rtracklayer_1.4.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/rtracklayer_1.4.1.tgz vignettes: vignettes/rtracklayer/inst/doc/rtracklayer.pdf Package: Rtreemix Version: 1.6.0 Depends: R (>= 2.5.0), methods, graph, Biobase Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz 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 License: LGPL source.ver: src/contrib/Rtreemix_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/Rtreemix_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Rtreemix_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Rtreemix_1.6.0.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 Package: Ruuid Version: 1.22.0 Depends: R (>= 2.6.0), methods Imports: methods Title: Ruuid: Provides Universally Unique ID values Description: A package to provide UUID values in R biocViews: Infrastructure, Technology Author: R. Gentleman Maintainer: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/Ruuid_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/Ruuid_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/Ruuid_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/Ruuid_1.22.0.tgz vignettes: vignettes/Ruuid/inst/doc/Ruuid.pdf Package: RWebServices Version: 1.8.0 Depends: SJava (>= 0.69-4), TypeInfo, methods, tools, R (>= 2.5.0) Imports: RCurl 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 License: caBIG source.ver: src/contrib/RWebServices_1.8.0.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 Package: safe Version: 2.4.0 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 Title: Significance Analysis of Function and Expression Description: SAFE is a resampling-based method for testing functional categories is 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. Author: William T. Barry Maintainer: William T. Barry URL: http://www.duke.edu/~dinbarry/SAFE/ License: GPL version 2 or newer source.ver: src/contrib/safe_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/safe_2.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/safe_2.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/safe_2.4.0.tgz vignettes: vignettes/safe/inst/doc/SAFEmanual2.pdf Package: sagenhaft Version: 1.14.0 Depends: R (>= 2.5), SparseM (>= 0.73) Title: Collection of functions for reading and comparing SAGE libraries Description: This package implements several functions useful for analysis of SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison. biocViews: SAGE Author: Tim Beissbarth , with contributions from Gordon Smyth and Lavinia Hyde . Maintainer: Tim Beissbarth URL: http://tagcalling.mbgproject.org License: GPL version 2 or newer source.ver: src/contrib/sagenhaft_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/sagenhaft_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/sagenhaft_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/sagenhaft_1.14.0.tgz vignettes: vignettes/sagenhaft/inst/doc/SAGEnhaft.pdf Package: SAGx Version: 1.18.0 Depends: R (>= 2.5.0), stats, multtest, methods Imports: Biobase Suggests: KEGG.db, hu6800.db 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 License: LGPL source.ver: src/contrib/SAGx_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/SAGx_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/SAGx_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/SAGx_1.18.0.tgz vignettes: vignettes/SAGx/inst/doc/samroc-ex.pdf Package: SBMLR Version: 1.38.0 Depends: XML, odesolve 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/ License: GPL-2 source.ver: src/contrib/SBMLR_1.38.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/SBMLR_1.38.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/SBMLR_1.38.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/SBMLR_1.38.0.tgz vignettes: vignettes/SBMLR/inst/doc/BMC.BioInformatics04.pdf, vignettes/SBMLR/inst/doc/manual.pdf Package: ScISI Version: 1.16.0 Depends: GO.db, RpsiXML, annotate, apComplex Imports: AnnotationDbi, GO.db, RpsiXML, annotate, methods, org.Sc.sgd.db, utils Suggests: ppiData, xtable Title: In Silico Interactome Description: Package to create In Silico Interactomes biocViews: GraphsAndNetworks, Proteomics Author: Tony Chiang Maintainer: Tony Chiang License: LGPL source.ver: src/contrib/ScISI_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/ScISI_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/ScISI_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/ScISI_1.16.0.tgz vignettes: vignettes/ScISI/inst/doc/vignette.pdf Package: seqLogo Version: 1.10.0 Depends: methods, grid 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 License: LGPL version 2 or newer source.ver: src/contrib/seqLogo_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/seqLogo_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/seqLogo_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/seqLogo_1.10.0.tgz vignettes: vignettes/seqLogo/inst/doc/seqLogo.pdf Package: ShortRead Version: 1.2.1 Depends: methods, IRanges (>= 1.1.55), Biostrings (>= 2.11.25), BSgenome (>= 1.1.14), lattice Imports: IRanges, Biostrings, Biobase, BSgenome, hwriter Suggests: biomaRt Title: Base 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: Infrastructure Author: Martin Morgan, Michael Lawrence, Simon Anders Maintainer: Biocore Team c/o BioC user list License: Artistic-2.0 source.ver: src/contrib/ShortRead_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/ShortRead_1.2.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/ShortRead_1.2.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/ShortRead_1.2.1.tgz vignettes: vignettes/ShortRead/inst/doc/Overview.pdf, vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf Package: siggenes Version: 1.18.0 Depends: methods, multtest, Biobase, splines Suggests: affy, annotate, genefilter, KernSmooth, scrime (>= 1.1.2) 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: Statistics, MultipleComparisons, Microarray, GeneExpression, SNP, ExonArray, DifferentialExpression Author: Holger Schwender Maintainer: Holger Schwender License: LGPL version 2 or newer source.ver: src/contrib/siggenes_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/siggenes_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/siggenes_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/siggenes_1.18.0.tgz vignettes: vignettes/siggenes/inst/doc/siggenes.pdf, vignettes/siggenes/inst/doc/siggenesRnews.pdf Package: sigPathway Version: 1.12.1 Depends: R (>= 2.0.0) Suggests: hgu133a.db (>= 1.10.0), XML (>= 1.6-3), AnnotationDbi (>= 1.3.12) 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 License: GPL 2 source.ver: src/contrib/sigPathway_1.12.1.tar.gz win.binary.ver: bin/windows/contrib/2.9/sigPathway_1.12.1.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/sigPathway_1.12.1.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/sigPathway_1.12.1.tgz vignettes: vignettes/sigPathway/inst/doc/sigPathway-vignette.pdf Package: SIM Version: 1.12.0 Depends: R (>= 2.4), fields, globaltest, marray, quantsmooth, clac, multtest Title: Integrated Analysis of gene expression and copynumber data Description: Finds associations between DNA copy number and gene expression. biocViews: Microarray, DNACopyNumber, Bioinformatics, Visualization Author: Renee X. de Menezes and Judith M. Boer Maintainer: Maarten van Iterson URL: http://www.humgen.nl/MicroarrayAnalysisGroup.html License: GPL (>= 2) source.ver: src/contrib/SIM_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/SIM_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/SIM_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/SIM_1.12.0.tgz vignettes: vignettes/SIM/inst/doc/SIM.pdf Package: simpleaffy Version: 2.20.0 Depends: R (>= 2.0.0), affy, genefilter, Biobase, methods, utils, gcrma Imports: affy, Biobase, gcrma, genefilter, graphics, grDevices, methods, stats, utils 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/ License: GPL version 2 or later source.ver: src/contrib/simpleaffy_2.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/simpleaffy_2.20.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/simpleaffy_2.20.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/simpleaffy_2.20.0.tgz vignettes: vignettes/simpleaffy/inst/doc/QCandSimpleaffy.pdf, vignettes/simpleaffy/inst/doc/simpleAffy.pdf Package: simulatorAPMS Version: 1.16.0 Depends: ScISI, apComplex Imports: ScISI Title: Computationally simulates the AP-MS technology. Description: Functions to computationally simulate the AP-MS technology based on wet-lab data. biocViews: MassSpectrometry, GraphsAndNetworks Author: Tony Chiang Maintainer: Tony Chiang License: LGPL source.ver: src/contrib/simulatorAPMS_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/simulatorAPMS_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/simulatorAPMS_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/simulatorAPMS_1.16.0.tgz vignettes: vignettes/simulatorAPMS/inst/doc/simulatorAPMS.pdf Package: sizepower Version: 1.14.0 Depends: stats 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 License: LGPL source.ver: src/contrib/sizepower_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/sizepower_1.14.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/sizepower_1.14.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/sizepower_1.14.0.tgz vignettes: vignettes/sizepower/inst/doc/sizepower.pdf Package: SLGI Version: 1.4.0 Depends: R (>= 2.6.0), ScISI, lattice Imports: AnnotationDbi, Biobase, GO.db, ScISI, graphics, lattice, methods, stats Suggests: Biostrings, GO.db, org.Sc.sgd.db 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 License: Artistic-2.0 source.ver: src/contrib/SLGI_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/SLGI_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/SLGI_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/SLGI_1.4.0.tgz vignettes: vignettes/SLGI/inst/doc/SLGI.pdf Package: SLqPCR Version: 1.10.0 Depends: R(>= 2.4.0), stats, RColorBrewer 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 Author: Matthias Kohl Maintainer: Matthias Kohl License: GPL (version 2 or later) source.ver: src/contrib/SLqPCR_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/SLqPCR_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/SLqPCR_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/SLqPCR_1.10.0.tgz vignettes: vignettes/SLqPCR/inst/doc/SLqPCR.pdf Package: SMAP Version: 1.8.0 Depends: methods 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, DNACopyNumber Author: Robin Andersson Maintainer: Robin Andersson License: GPL, version 2 source.ver: src/contrib/SMAP_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/SMAP_1.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/SMAP_1.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/SMAP_1.8.0.tgz vignettes: vignettes/SMAP/inst/doc/SMAP.pdf Package: snapCGH Version: 1.12.0 Depends: limma,tilingArray,DNAcopy,GLAD,cluster,methods,aCGH 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, DNACopyNumber, TwoChannel, Preprocessing Author: Mike L. Smith, John C. Marioni, Steven McKinney, Thomas Hardcastle, Natalie P. Thorne Maintainer: John Marioni License: GPL source.ver: src/contrib/snapCGH_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/snapCGH_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/snapCGH_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/snapCGH_1.12.0.tgz vignettes: vignettes/snapCGH/inst/doc/snapCGHguide.pdf Package: SNPchip Version: 1.8.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.19), methods, oligoClasses (>= 1.1.13), graphics Suggests: RSQLite, geneplotter, stats, graphics, VanillaICE, RColorBrewer Title: Classes and Methods for high throughput SNP chip data Description: This package defines classes and functions for plotting copy number and genotype in high throughput SNP platforms such as Affymetrix and Illumina. In particular, SNPchip is a useful add-on to the oligo package for visualizing SNP-level estimates after pre-processing. biocViews: DNACopyNumber, SNPsAndGeneticVariability, Visualization Author: Robert Scharpf and Ingo Ruczinski Maintainer: Robert Scharpf URL: http://www.biostat.jhsph.edu/~iruczins/software/snpchip.html License: LGPL version 2 or newer source.ver: src/contrib/SNPchip_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/SNPchip_1.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/SNPchip_1.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/SNPchip_1.8.0.tgz vignettes: vignettes/SNPchip/inst/doc/oligoHowTo.pdf, vignettes/SNPchip/inst/doc/SNPchip.pdf Package: snpMatrix Version: 1.8.0 Depends: R(>= 2.3.0), survival, methods Suggests: hexbin Title: The snp.matrix and X.snp.matrix classes Description: Implements classes and methods for large-scale SNP association studies biocViews: Microarray, SNPsAndGeneticVariability Author: David Clayton and Hin-Tak Leung Maintainer: David Clayton URL: http://www-gene.cimr.cam.ac.uk/clayton/software/ License: GNU General Public Licence (GPLv3) source.ver: src/contrib/snpMatrix_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/snpMatrix_1.8.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/snpMatrix_1.8.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/snpMatrix_1.8.0.tgz vignettes: vignettes/snpMatrix/inst/doc/imputation-vignette.pdf, vignettes/snpMatrix/inst/doc/pca-vignette.pdf, vignettes/snpMatrix/inst/doc/snpMatrix-paper-HumanHeridity2007.pdf, vignettes/snpMatrix/inst/doc/snpMatrix-vignette.pdf, vignettes/snpMatrix/inst/doc/tdt-vignette.pdf Package: SPIA Version: 1.0.0 Depends: R (>= 2.8.0), graphics,RCurl Imports: graphics,RCurl Suggests: graph, Rgraphviz, KEGGgraph 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 License: GPL (>=2) source.ver: src/contrib/SPIA_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/SPIA_1.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/SPIA_1.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/SPIA_1.0.0.tgz vignettes: vignettes/SPIA/inst/doc/SPIA.pdf Package: spikeLI Version: 2.4.0 Depends: utils 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 License: GPL source.ver: src/contrib/spikeLI_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/spikeLI_2.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/spikeLI_2.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/spikeLI_2.4.0.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 Package: spkTools Version: 1.0.0 Depends: R (>= 2.7.0), Biobase Imports: Biobase, graphics, grDevices, gtools, methods, RColorBrewer, stats, utils Suggests: xtable 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 License: GPL version 2 or newer source.ver: src/contrib/spkTools_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/spkTools_1.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/spkTools_1.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/spkTools_1.0.0.tgz vignettes: vignettes/spkTools/inst/doc/spkDoc.pdf Package: splicegear Version: 1.16.0 Depends: R (>= 2.6.0), methods, Biobase(>= 1.15) Imports: annotate, Biobase, graphics, grDevices, grid, methods, utils, XML Title: splicegear Description: A set of tools to work with alternative splicing biocViews: Infrastructure, Transcription Author: Laurent Gautier Maintainer: Laurent Gautier License: LGPL source.ver: src/contrib/splicegear_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/splicegear_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/splicegear_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/splicegear_1.16.0.tgz vignettes: vignettes/splicegear/inst/doc/splicegear.pdf Package: splots Version: 1.10.0 Depends: grid Title: Visualization of high-throughput assays in microtitre plate or chamber slide format Description: The splots package provides the plotScreen function for the visualization of for high-throughput assays in microtitre plate or chamber slide format. Author: Oleg Sklyar Maintainer: Oleg Sklyar License: LGPL source.ver: src/contrib/splots_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/splots_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/splots_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/splots_1.10.0.tgz vignettes: vignettes/splots/inst/doc/splotsHOWTO.pdf Package: spotSegmentation Version: 1.18.0 Depends: R (>= 1.7.0), mclust 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 License: GPL version 2 or higher source.ver: src/contrib/spotSegmentation_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/spotSegmentation_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/spotSegmentation_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/spotSegmentation_1.18.0.tgz vignettes: vignettes/spotSegmentation/inst/doc/spotsegdoc.pdf Package: sscore Version: 1.16.0 Depends: R (>= 1.8.0), affy, affyio Suggests: affydata 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 License: GPL version 2 or newer source.ver: src/contrib/sscore_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/sscore_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/sscore_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/sscore_1.16.0.tgz vignettes: vignettes/sscore/inst/doc/sscore.pdf Package: ssize Version: 1.18.0 Depends: gdata, xtable 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 License: LGPL source.ver: src/contrib/ssize_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/ssize_1.18.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/ssize_1.18.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/ssize_1.18.0.tgz vignettes: vignettes/ssize/inst/doc/ssize.pdf Package: SSPA Version: 1.0.0 Depends: R (>= 2.8), methods, qvalue Imports: graphics, limma, methods, stats Suggests: multtest, quadprog, splines 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, Statistics Author: Maarten van Iterson Maintainer: Maarten van Iterson URL: http://www.humgen.nl/MicroarrayAnalysisGroup.html License: GPL (>= 2) source.ver: src/contrib/SSPA_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/SSPA_1.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/SSPA_1.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/SSPA_1.0.0.tgz vignettes: vignettes/SSPA/inst/doc/SSPA.pdf Package: stam Version: 1.12.0 Depends: R (>= 2.7.0), GO.db (>= 2.1.3), Biobase (>= 1.99.5), pamr (>= 1.37.0), cluster (>= 1.11.10), annaffy (>= 1.11.5), methods (>= 2.7.0), utils (>= 2.7.0) Imports: Biobase (>= 1.99.5), methods (>= 2.7.0), pamr (>= 1.37.0), cluster (>= 1.11.10) Suggests: golubEsets (>= 1.4.4), hu6800.db (>= 2.1.4) Title: Structured Analysis of Microarray Data Description: The stam package performs a biologically structured classification of microarray profiles according to clinical phenotypes. GO terms are used to link classification results to biological aspects. We call biologically focused signatures corresponding to these class predictions molecular symptoms. Thus, stam allows for molecular stratification of patients with complex phenotypes according to presence/absence patterns of molecular symptoms. biocViews: Microarray, Bioinformatics, Classification Author: Claudio Lottaz Maintainer: Claudio Lottaz URL: http://compdiag.uni-regensburg.de/software/index.shtml License: GPL (>= 2) source.ver: src/contrib/stam_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/stam_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/stam_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/stam_1.12.0.tgz vignettes: vignettes/stam/inst/doc/bcb_logo.pdf, vignettes/stam/inst/doc/minerva_bcb.pdf, vignettes/stam/inst/doc/server_scheme.pdf, vignettes/stam/inst/doc/tr_2004_03.pdf Package: stepNorm Version: 1.16.0 Depends: R (>= 1.8.0), marray, MASS, methods 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/ License: LGPL source.ver: src/contrib/stepNorm_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/stepNorm_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/stepNorm_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/stepNorm_1.16.0.tgz Package: TargetSearch Version: 1.0.0 Depends: R (>= 2.7.0), xcms, methods Imports: methods Suggests: TargetSearchData 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: Technology,MassSpectrometry,Preprocessing Author: Alvaro Cuadros-Inostroza , Henning Redestig , Matt Hannah Maintainer: Alvaro Cuadros-Inostroza License: GPL version 2 or newer source.ver: src/contrib/TargetSearch_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/TargetSearch_1.0.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/TargetSearch_1.0.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/TargetSearch_1.0.0.tgz vignettes: vignettes/TargetSearch/inst/doc/TargetSearch.pdf Package: tilingArray Version: 1.22.0 Depends: Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid 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 License: The Artistic License, Version 2.0 source.ver: src/contrib/tilingArray_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/tilingArray_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/tilingArray_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/tilingArray_1.22.0.tgz vignettes: vignettes/tilingArray/inst/doc/assessNorm.pdf, vignettes/tilingArray/inst/doc/costMatrix.pdf, vignettes/tilingArray/inst/doc/findsegments.pdf, vignettes/tilingArray/inst/doc/segmentation.pdf Package: timecourse Version: 1.16.0 Depends: R (>= 2.1.1), limma (>= 1.8.6), MASS, Biobase, methods 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 License: LGPL source.ver: src/contrib/timecourse_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/timecourse_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/timecourse_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/timecourse_1.16.0.tgz vignettes: vignettes/timecourse/inst/doc/timecourse.pdf Package: tkWidgets Version: 1.22.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase 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 License: Artistic-2.0 source.ver: src/contrib/tkWidgets_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/tkWidgets_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/tkWidgets_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/tkWidgets_1.22.0.tgz vignettes: vignettes/tkWidgets/inst/doc/importWizard.pdf, vignettes/tkWidgets/inst/doc/tkWidgets.pdf Package: topGO Version: 1.12.0 Depends: R (>= 2.9.0), methods, graph (>= 1.14.0), Biobase (>= 1.99.0), GO.db (>= 2.1.4), AnnotationDbi (>= 1.1.35), SparseM (>= 0.73) Imports: methods, graph (>= 1.14.0), Biobase (>= 1.99.0), SparseM (>= 0.73), AnnotationDbi (>= 1.1.35), lattice Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest 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 License: LGPL source.ver: src/contrib/topGO_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/topGO_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/topGO_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/topGO_1.12.0.tgz vignettes: vignettes/topGO/inst/doc/topGO.pdf Package: tspair Version: 1.2.0 Depends: R (>= 2.2.1), Biobase, time 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 License: GPL source.ver: src/contrib/tspair_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/tspair_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/tspair_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/tspair_1.2.0.tgz vignettes: vignettes/tspair/inst/doc/tsp.pdf, vignettes/tspair/inst/doc/tsp1.pdf Package: twilight Version: 1.20.0 Depends: R (>= 2.1.0), splines (>= 2.2.0), stats (>= 2.2.0),Biobase(>= 1.12.0) Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) 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 License: GPL version 2.0 or newer source.ver: src/contrib/twilight_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/twilight_1.20.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/twilight_1.20.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/twilight_1.20.0.tgz vignettes: vignettes/twilight/inst/doc/bcb_logo.pdf, vignettes/twilight/inst/doc/Rplots.pdf, vignettes/twilight/inst/doc/tr_2004_01.pdf Package: TypeInfo Version: 1.10.0 Depends: methods 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 License: BSD source.ver: src/contrib/TypeInfo_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/TypeInfo_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/TypeInfo_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/TypeInfo_1.10.0.tgz vignettes: vignettes/TypeInfo/inst/doc/TypeInfoNews.pdf Package: VanillaICE Version: 1.6.0 Depends: R (>= 2.8.0) Imports: SNPchip (>= 1.7.2), stats Suggests: genomewidesnp6Crlmm, hapmapsnp6, RColorBrewer, genefilter, RSQLite, oligoClasses (>= 1.5.15), Biobase, methods 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, DNACopyNumber, SNPsAndGeneticVariability, Visualization Author: Robert Scharpf , Kevin Scharpf, and Ingo Ruczinski Maintainer: Robert Scharpf License: LGPL-2 source.ver: src/contrib/VanillaICE_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/VanillaICE_1.6.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/VanillaICE_1.6.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/VanillaICE_1.6.0.tgz vignettes: vignettes/VanillaICE/inst/doc/VanillaICE.pdf Package: vbmp Version: 1.12.0 Depends: R (>= 2.5) Suggests: Biobase, statmod 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 License: GPL version 2 or newer source.ver: src/contrib/vbmp_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/vbmp_1.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/vbmp_1.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/vbmp_1.12.0.tgz vignettes: vignettes/vbmp/inst/doc/vbmp.pdf Package: vsn Version: 3.12.0 Depends: Biobase (>= 2.3.1) Imports: methods, affy, limma, lattice Suggests: affydata, hgu95av2cdf 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 License: Artistic-2.0, see http://www.opensource.org/licenses/artistic-license-2.0.php source.ver: src/contrib/vsn_3.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/vsn_3.12.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/vsn_3.12.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/vsn_3.12.0.tgz vignettes: vignettes/vsn/inst/doc/convergence2.pdf, vignettes/vsn/inst/doc/likelihoodcomputations.pdf, vignettes/vsn/inst/doc/vsn.pdf Package: weaver Version: 1.10.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools 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 License: GPL2 source.ver: src/contrib/weaver_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/weaver_1.10.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/weaver_1.10.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/weaver_1.10.0.tgz vignettes: vignettes/weaver/inst/doc/weaver_howTo.pdf Package: webbioc Version: 1.16.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue 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/ License: GPL version 2 or newer SystemRequirements: Unix, Perl (>= 5.6.0), Netpbm source.ver: src/contrib/webbioc_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/webbioc_1.16.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/webbioc_1.16.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/webbioc_1.16.0.tgz vignettes: vignettes/webbioc/inst/doc/demoscript.pdf, vignettes/webbioc/inst/doc/webbioc.pdf Package: widgetTools Version: 1.22.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase 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 License: LGPL source.ver: src/contrib/widgetTools_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/widgetTools_1.22.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/widgetTools_1.22.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/widgetTools_1.22.0.tgz vignettes: vignettes/widgetTools/inst/doc/widget.pdf, vignettes/widgetTools/inst/doc/widgetTools.pdf Package: xcms Version: 1.16.3 Depends: R (>= 1.9.0), methods Suggests: faahKO, msdata, multtest, ncdf, rgl, MassSpecWavelet (>= 1.5.2), Rgraphviz 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, and mzData files. Preprocesses data for high-throughput, untargeted analyte profiling. biocViews: Technology,MassSpectrometry Author: Colin A. Smith , Ralf Tautenhahn Maintainer: Colin A. Smith URL: http://metlin.scripps.edu/download/ License: GPL version 2 or newer SystemRequirements: NetCDF, zlib source.ver: src/contrib/xcms_1.16.3.tar.gz win.binary.ver: bin/windows/contrib/2.9/xcms_1.16.3.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/xcms_1.16.3.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/xcms_1.16.3.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 Package: XDE Version: 1.4.0 Depends: R (>= 2.6.0), Biobase, methods, graphics Imports: genefilter, gtools Suggests: MergeMaid, siggenes, genefilter, MASS, RColorBrewer, GeneMeta 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 License: LGPL-2 source.ver: src/contrib/XDE_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/XDE_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/XDE_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/XDE_1.4.0.tgz vignettes: vignettes/XDE/inst/doc/XDE.pdf, vignettes/XDE/inst/doc/XdeParameterClass.pdf Package: xmapbridge Version: 1.2.0 Depends: R (>= 2.0), methods 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 License: LGPL-v3 source.ver: src/contrib/xmapbridge_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/xmapbridge_1.2.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/xmapbridge_1.2.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/xmapbridge_1.2.0.tgz vignettes: vignettes/xmapbridge/inst/doc/xmapbridge.pdf Package: xps Version: 1.4.10 Depends: R (>= 2.6.0), methods 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, 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 Author: Christian Stratowa, Vienna, Austria Maintainer: Christian Stratowa License: GPL (>= 2.0) SystemRequirements: root_v5.22.00 - See README file for installation instructions. source.ver: src/contrib/xps_1.4.10.tar.gz win.binary.ver: bin/windows/contrib/2.9/xps_1.4.10.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/xps_1.4.10.tgz vignettes: vignettes/xps/inst/doc/APTvsXPS.pdf, vignettes/xps/inst/doc/xps.pdf, vignettes/xps/inst/doc/xpsClasses.pdf Package: yaqcaffy Version: 1.4.0 Depends: simpleaffy (>= 2.19.3), methods Imports: simpleaffy, methods Suggests: MAQCsubsetAFX, affydata, xtable 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 URL: http://www.slashhome.be/yaqcaffy.php License: Artistic-2.0 source.ver: src/contrib/yaqcaffy_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.9/yaqcaffy_1.4.0.zip mac.binary.universal.ver: bin/macosx/universal/contrib/2.9/yaqcaffy_1.4.0.tgz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.9/yaqcaffy_1.4.0.tgz vignettes: vignettes/yaqcaffy/inst/doc/yaqcaffy.pdf