Package: ABarray Version: 1.20.0 Imports: Biobase, graphics, grDevices, methods, multtest, stats, tcltk, utils Suggests: limma, LPE License: GPL Title: Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data. Description: Automated pipline to perform gene expression analysis for Applied Biosystems Genome Survey Microarray (AB1700) data format. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A GUI interface is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used. biocViews: Microarray, OneChannel, Preprocessing Author: Yongming Andrew Sun Maintainer: Yongming Andrew Sun source.ver: src/contrib/ABarray_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ABarray_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ABarray_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ABarray_1.20.0.tgz vignettes: vignettes/ABarray/inst/doc/ABarray.pdf, vignettes/ABarray/inst/doc/ABarrayGUI.pdf Package: ACME Version: 2.8.0 Depends: Biobase (>= 2.5.5), methods Imports: graphics, stats License: GPL (>= 2) Archs: i386, x64 Title: Algorithms for Calculating Microarray Enrichment (ACME) Description: ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory. biocViews: Bioinformatics Author: Sean Davis Maintainer: Sean Davis URL: http://watson.nci.nih.gov/~sdavis source.ver: src/contrib/ACME_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ACME_2.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ACME_2.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ACME_2.8.0.tgz vignettes: vignettes/ACME/inst/doc/ACME.pdf Package: ADaCGH2 Version: 1.2.0 Depends: R (>= 2.11.0), tilingArray, aCGH, waveslim, cluster, snapCGH, snowfall, ff Suggests: GLAD, DNAcopy, CGHregions, rlecuyer Enhances: Rmpi, multicore License: GPL (>= 3) Archs: i386, x64 Title: Analysis of data from aCGH experiments using parallel computing and ff objects Description: Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized. biocViews: Microarray, CopyNumberVariants Author: Ramon Diaz-Uriarte , Oscar M. Rueda . Wavelet-based aCGH smoothing code from Li Hsu and Douglas Grove . Imagemap code from Barry Rowlingson . HaarSeg code from Erez Ben-Yaacov; downloaded from Maintainer: Ramon Diaz-Uriarte URL: http://launchpad.net/adacgh, http://wavicgh.bioinfo.cnio.es source.ver: src/contrib/ADaCGH2_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ADaCGH2_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ADaCGH2_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ADaCGH2_1.2.0.tgz vignettes: vignettes/ADaCGH2/inst/doc/ADaCGH2.pdf Package: AffyCompatible Version: 1.12.0 Depends: R (>= 2.7.0), XML (>= 2.8-1), RCurl (>= 0.8-1), methods Imports: Biostrings License: Artistic-2.0 Title: Affymetrix GeneChip software compatibility Description: This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files. biocViews: Infrastructure, Microarray, OneChannel Author: Martin Morgan, Robert Gentleman Maintainer: Martin Morgan source.ver: src/contrib/AffyCompatible_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/AffyCompatible_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/AffyCompatible_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/AffyCompatible_1.12.0.tgz vignettes: vignettes/AffyCompatible/inst/doc/MAGEAndARR.pdf, vignettes/AffyCompatible/inst/doc/NetAffxResource.pdf Package: AffyExpress Version: 1.18.0 Depends: R (>= 2.5.0), affy (>= 1.23.4), limma Suggests: simpleaffy, R2HTML, affyPLM, hgu95av2cdf, hgu95av2, test3cdf, genefilter, estrogen, annaffy, gcrma License: LGPL Title: Affymetrix Quality Assessment and Analysis Tool Description: The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data. biocViews: Microarray, OneChannel, QualityControl, Preprocessing, Bioinformatics, DifferentialExpression, Annotation, ReportWriting, Visualization Author: Xiwei Wu , Xuejun Arthur Li Maintainer: Xuejun Arthur Li source.ver: src/contrib/AffyExpress_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/AffyExpress_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/AffyExpress_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/AffyExpress_1.18.0.tgz vignettes: vignettes/AffyExpress/inst/doc/AffyExpress.pdf Package: AffyTiling Version: 1.10.0 Depends: R (>= 2.6) Imports: affxparser, affy (>= 1.16), stats, utils, preprocessCore License: GPL (>= 2) Archs: i386, x64 Title: Easy extraction of individual probes in Affymetrix tiling arrays Description: This package provides easy, fast functions for the extraction and annotation of individual probes from Affymetrix tiling arrays. biocViews: Microarray, Preprocessing Author: Charles G. Danko Maintainer: Charles G. Danko source.ver: src/contrib/AffyTiling_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/AffyTiling_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/AffyTiling_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/AffyTiling_1.10.0.tgz vignettes: vignettes/AffyTiling/inst/doc/AffyTiling.pdf Package: Agi4x44PreProcess Version: 1.12.0 Depends: R (>= 2.6.0), Biobase, limma, annotate, genefilter Suggests: vsn, affycoretools, hgug4112a.db, GO.db, marray, gplots, gtools, gdata License: GPL-3 Title: PreProcessing of Agilent 4x44 array data Description: Preprocessing of Agilent 4x44 array data biocViews: Microarray, OneChannel, Preprocessing Author: Pedro Lopez-Romero Maintainer: Pedro Lopez-Romero source.ver: src/contrib/Agi4x44PreProcess_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Agi4x44PreProcess_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Agi4x44PreProcess_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Agi4x44PreProcess_1.12.0.tgz vignettes: vignettes/Agi4x44PreProcess/inst/doc/Agi4x44PreProcess.pdf Package: AgiMicroRna Version: 2.2.0 Depends: R (>= 2.9.0),methods,Biobase,limma,affy (>= 1.22),preprocessCore,affycoretools Imports: Biobase Suggests: geneplotter,marray,gplots,gtools,gdata,codelink License: GPL-3 Title: Processing and Differential Expression Analysis of Agilent microRNA chips Description: Processing and Analysis of Agilent microRNA data biocViews: Microarray,AgilentChip,OneChannel,Preprocessing,DifferentialExpression,Bioinformatics Author: Pedro Lopez-Romero Maintainer: Pedro Lopez-Romero source.ver: src/contrib/AgiMicroRna_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/AgiMicroRna_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/AgiMicroRna_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/AgiMicroRna_2.2.0.tgz vignettes: vignettes/AgiMicroRna/inst/doc/AgiMicroRna.pdf Package: AnnotationDbi Version: 1.14.1 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, hgu95av2cdf, affy, KEGG.db, XML License: Artistic-2.0 Title: Annotation Database Interface Description: Provides user interface and database connection code for annotation data packages using SQLite data storage. biocViews: Annotation, Infrastructure Author: Herve Pages, Marc Carlson, Seth Falcon, Nianhua Li Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/AnnotationDbi_1.14.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/AnnotationDbi_1.14.1.zip win64.binary.ver: bin/windows64/contrib/2.13/AnnotationDbi_1.14.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/AnnotationDbi_1.14.1.tgz vignettes: vignettes/AnnotationDbi/inst/doc/AnnotationDbi.pdf, vignettes/AnnotationDbi/inst/doc/NewSchema.pdf, vignettes/AnnotationDbi/inst/doc/SQLForge.pdf, vignettes/AnnotationDbi/inst/doc/makeProbePackage.pdf Package: AnnotationFuncs Version: 1.0.1 Depends: R (>= 2.7.0), AnnotationDbi Suggests: org.Bt.eg.db, org.Hs.eg.db, GO.db, hom.Hs.inp.db License: GPL-2 Title: Annotation translation functions Description: Functions for handling translating between different identifieres using the Biocore Data Team data-packages (e.g. org.Bt.eg.db). biocViews: AnnotationData, Software Author: Stefan McKinnon Edwards Maintainer: Stefan McKinnon Edwards URL: http://www.iysik.com/index.php?page=annotation-functions source.ver: src/contrib/AnnotationFuncs_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/AnnotationFuncs_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.13/AnnotationFuncs_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/AnnotationFuncs_1.0.1.tgz vignettes: vignettes/AnnotationFuncs/inst/doc/AnnotationFuncsUserguide.pdf Package: ArrayExpressHTS Version: 1.2.0 Depends: sampling, Rsamtools (>= 1.3.32), snow Imports: Biobase, Biostrings, DESeq, GenomicRanges, Hmisc, IRanges, R2HTML, RColorBrewer, Rsamtools, ShortRead, XML, biomaRt, edgeR, grDevices, graphics, methods, rJava, stats, svMisc, utils LinkingTo: Rsamtools License: Artistic-2.0 Title: ArrayExpress High Throughput Sequencing Processing Pipeline Description: RNA-Seq processing pipeline for public ArrayExpress experiments or local datasets biocViews: RNAseq, Sequencing, HighThroughputSequencing Author: Angela Goncalves, Andrew Tikhonov Maintainer: Angela Goncalves , Andrew Tikhonov source.ver: src/contrib/ArrayExpressHTS_1.2.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ArrayExpressHTS_1.2.0.tgz vignettes: vignettes/ArrayExpressHTS/inst/doc/ArrayExpressHTS.pdf Package: ArrayExpress Version: 1.12.1 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: XML, affy, limma License: Artistic-2.0 Title: Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet Description: Access the ArrayExpress Repository at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet biocViews: Microarray, DataImport, OneChannel, TwoChannel Author: Audrey Kauffmann Maintainer: Audrey Kauffmann source.ver: src/contrib/ArrayExpress_1.12.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/ArrayExpress_1.12.1.zip win64.binary.ver: bin/windows64/contrib/2.13/ArrayExpress_1.12.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ArrayExpress_1.12.1.tgz vignettes: vignettes/ArrayExpress/inst/doc/ArrayExpress.pdf Package: ArrayTools Version: 1.12.0 Depends: R (>= 2.7.0), affy (>= 1.23.4), Biobase (>= 2.5.5), methods Imports: affy, Biobase, graphics, grDevices, limma, methods, stats, utils, xtable Suggests: simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy, gcrma, hugene10sttranscriptcluster.db License: LGPL (>= 2.0) Title: geneChip Analysis Package Description: This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases. biocViews: Microarray, OneChannel, QualityControl, Preprocessing, Statistics, DifferentialExpression, Annotation, ReportWriting, Visualization Author: Xiwei Wu, Arthur Li Maintainer: Arthur Li source.ver: src/contrib/ArrayTools_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ArrayTools_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ArrayTools_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ArrayTools_1.12.0.tgz vignettes: vignettes/ArrayTools/inst/doc/ArrayTools.pdf Package: BAC Version: 1.12.0 Depends: R(>= 2.6.0) License: Artistic-2.0 Archs: i386, x64 Title: Bayesian Analysis of Chip-chip experiment Description: This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments biocViews: Microarray,Transcription,Bioinformatics Author: Raphael Gottardo Maintainer: Raphael Gottardo source.ver: src/contrib/BAC_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/BAC_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/BAC_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BAC_1.12.0.tgz vignettes: vignettes/BAC/inst/doc/BAC.pdf Package: BCRANK Version: 1.14.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 Archs: i386, x64 Title: Predicting binding site consensus from ranked DNA sequences Description: Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search biocViews: SequenceMatching Author: Adam Ameur Maintainer: Adam Ameur source.ver: src/contrib/BCRANK_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/BCRANK_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/BCRANK_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BCRANK_1.14.0.tgz vignettes: vignettes/BCRANK/inst/doc/BCRANK.pdf, vignettes/BCRANK/inst/doc/BCRANK_intro_fig1.pdf, vignettes/BCRANK/inst/doc/BCRANK_intro_fig2.pdf Package: BGmix Version: 1.12.0 Depends: R (>= 2.3.1), KernSmooth License: GPL-2 Archs: i386 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 source.ver: src/contrib/BGmix_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/BGmix_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/BGmix_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BGmix_1.12.0.tgz vignettes: vignettes/BGmix/inst/doc/BGmix.pdf Package: BHC Version: 1.4.0 Imports: stats, utils Suggests: affydata, gcrma, graphics License: GPL-3 Archs: i386, x64 Title: Bayesian Hierarchical Clustering Description: The method performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) data. biocViews: Microarray, Clustering Author: Rich Savage (C++ code originally written by Yang Xu) Maintainer: Rich Savage source.ver: src/contrib/BHC_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/BHC_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/BHC_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BHC_1.4.0.tgz vignettes: vignettes/BHC/inst/doc/bhc.pdf Package: BSgenome Version: 1.20.1 Depends: R (>= 2.8.0), methods, IRanges (>= 1.9.26), GenomicRanges (>= 1.3.24), Biostrings (>= 2.19.16) Suggests: RUnit, BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.11), SNPlocs.Hsapiens.dbSNP.20100427, hgu95av2probe, Biobase License: Artistic-2.0 Title: Infrastructure for Biostrings-based genome data packages Description: Infrastructure shared by all the Biostrings-based genome data packages biocViews: Genetics, Infrastructure, DataRepresentation, SequenceMatching, Annotation, SNP Author: Herve Pages Maintainer: H. Pages source.ver: src/contrib/BSgenome_1.20.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/BSgenome_1.20.1.zip win64.binary.ver: bin/windows64/contrib/2.13/BSgenome_1.20.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BSgenome_1.20.1.tgz vignettes: vignettes/BSgenome/inst/doc/BSgenomeForge.pdf, vignettes/BSgenome/inst/doc/GenomeSearching.pdf Package: BUS Version: 1.8.0 Depends: R (>= 2.3.0), minet Imports: stats License: GPL-3 Archs: i386, x64 Title: Gene network reconstruction Description: This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical). biocViews: Preprocessing Author: Yin Jin, Hesen Peng, Lei Wang, Raffaele Fronza, Yuanhua Liu and Christine Nardini Maintainer: Yuanhua Liu source.ver: src/contrib/BUS_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/BUS_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/BUS_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BUS_1.8.0.tgz vignettes: vignettes/BUS/inst/doc/bus.pdf Package: BayesPeak Version: 1.4.3 Depends: IRanges Imports: IRanges, graphics Enhances: multicore, snow License: GPL (>= 2) Archs: i386, x64 Title: Bayesian Analysis of ChIP-seq Data Description: This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data. biocViews: ChIPseq Author: Christiana Spyrou, Jonathan Cairns, Rory Stark, Andy Lynch, Simon Tavar\\'{e}, Maintainer: Jonathan Cairns source.ver: src/contrib/BayesPeak_1.4.3.tar.gz win.binary.ver: bin/windows/contrib/2.13/BayesPeak_1.4.3.zip win64.binary.ver: bin/windows64/contrib/2.13/BayesPeak_1.4.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BayesPeak_1.4.3.tgz vignettes: vignettes/BayesPeak/inst/doc/BayesPeak.pdf, vignettes/BayesPeak/inst/doc/regionOFdiag.pdf Package: BeadDataPackR Version: 1.4.0 License: GPL-2 Archs: i386, x64 Title: Compression of Illumina BeadArray data Description: Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform biocViews: Microarray Author: Mike Smith, Andy Lynch Maintainer: Mike Smith source.ver: src/contrib/BeadDataPackR_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/BeadDataPackR_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/BeadDataPackR_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BeadDataPackR_1.4.0.tgz vignettes: vignettes/BeadDataPackR/inst/doc/BeadDataPackR.pdf Package: BicARE Version: 1.10.0 Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase License: GPL-2 Archs: i386, x64 Title: Biclustering Analysis and Results Exploration Description: Biclustering Analysis and Results Exploration biocViews: Microarray, Transcription, Bioinformatics, Clustering Author: Pierre Gestraud Maintainer: Pierre Gestraud URL: http://bioinfo.curie.fr source.ver: src/contrib/BicARE_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/BicARE_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/BicARE_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BicARE_1.10.0.tgz vignettes: vignettes/BicARE/inst/doc/BicARE.pdf Package: BioMVCClass Version: 1.20.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz License: LGPL Title: Model-View-Controller (MVC) Classes That Use Biobase Description: Creates classes used in model-view-controller (MVC) design biocViews: Visualization, Infrastructure, GraphsAndNetworks Author: Elizabeth Whalen Maintainer: Elizabeth Whalen source.ver: src/contrib/BioMVCClass_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/BioMVCClass_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/BioMVCClass_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BioMVCClass_1.20.0.tgz vignettes: vignettes/BioMVCClass/inst/doc/BioMVCClass.pdf Package: BioNet Version: 1.10.1 Depends: R (>= 2.10.0), Biobase, graph, RBGL Imports: igraph, AnnotationDbi Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML License: GPL (>= 2) Title: Routines for the functional analysis of biological networks Description: This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork. biocViews: Microarray, DataImport, GraphsAndNetworks, Visualization, Bioinformatics, GeneExpression, DifferentialExpression Author: Marcus Dittrich and Daniela Beisser Maintainer: Marcus Dittrich URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ source.ver: src/contrib/BioNet_1.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/BioNet_1.10.1.zip win64.binary.ver: bin/windows64/contrib/2.13/BioNet_1.10.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BioNet_1.10.1.tgz vignettes: vignettes/BioNet/inst/doc/Tutorial-3dplot.pdf, vignettes/BioNet/inst/doc/Tutorial.pdf, vignettes/BioNet/inst/doc/bum1.pdf, vignettes/BioNet/inst/doc/bum2.pdf, vignettes/BioNet/inst/doc/cytoscape.pdf, vignettes/BioNet/inst/doc/prec_recall_large.pdf, vignettes/BioNet/inst/doc/prec_recall_small.pdf Package: BioSeqClass Version: 1.10.0 Imports: Biostrings, ipred, e1071, klaR, randomForest, class, tree, nnet, rpart, party, foreign, Biobase, utils, stats, grDevices License: LGPL (>= 2.0) Title: Classification for Biological Sequences Description: Extracting Features from Biological Sequences and Building Classification Model biocViews: Classification Author: Li Hong sysptm@gmail.com Maintainer: Li Hong source.ver: src/contrib/BioSeqClass_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/BioSeqClass_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/BioSeqClass_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BioSeqClass_1.10.0.tgz vignettes: vignettes/BioSeqClass/inst/doc/BioSeqClass.pdf, vignettes/BioSeqClass/inst/doc/FeatureSets16.pdf, vignettes/BioSeqClass/inst/doc/cvFFSClassify0005.pdf, vignettes/BioSeqClass/inst/doc/workflow.pdf Package: Biobase Version: 2.12.2 Depends: R (>= 2.7.0), methods, utils Suggests: tools, tkWidgets, ALL License: Artistic-2.0 Archs: i386, x64 Title: Biobase: Base functions for Bioconductor Description: Functions that are needed by many other packages or which replace R functions. biocViews: Infrastructure, Bioinformatics Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/Biobase_2.12.2.tar.gz win.binary.ver: bin/windows/contrib/2.13/Biobase_2.12.2.zip win64.binary.ver: bin/windows64/contrib/2.13/Biobase_2.12.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Biobase_2.12.2.tgz vignettes: vignettes/Biobase/inst/doc/BiobaseDevelopment.pdf, vignettes/Biobase/inst/doc/Bioconductor.pdf, vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf, vignettes/Biobase/inst/doc/HowTo.pdf, vignettes/Biobase/inst/doc/Qviews.pdf, vignettes/Biobase/inst/doc/esApply.pdf Package: BiocCaseStudies Version: 1.14.0 Depends: tools, methods, utils, Biobase Suggests: affy (>= 1.17.3), affyPLM (>= 1.15.1), affyQCReport (>= 1.17.0), ALL (>= 1.4.3), annaffy (>= 1.11.1), annotate (>= 1.17.3), AnnotationDbi (>= 1.1.6), apComplex (>= 2.5.0), Biobase (>= 1.17.5), bioDist (>= 1.11.3), biocGraph (>= 1.1.1), biomaRt (>= 1.13.5), CCl4 (>= 1.0.6), CLL (>= 1.2.4), Category (>= 2.5.0), class (>= 7.2-38), cluster (>= 1.11.9), convert (>= 1.15.0), gcrma (>= 2.11.1), genefilter (>= 1.17.6), geneplotter (>= 1.17.2), GO.db (>= 2.0.2), GOstats (>= 2.5.0), graph (>= 1.17.4), GSEABase (>= 1.1.13), hgu133a.db (>= 2.0.2), hgu95av2.db, hgu95av2cdf (>= 2.0.0), hgu95av2probe (>= 2.0.0), hopach (>= 1.13.0), KEGG.db (>= 2.0.2), kohonen (>= 2.0.2), lattice (>= 0.17.2), latticeExtra (>= 0.3-1), limma (>= 2.13.1), MASS (>= 7.2-38), MLInterfaces (>= 1.13.17), multtest (>= 1.19.0), org.Hs.eg.db (>= 2.0.2), ppiStats (>= 1.5.4), randomForest (>= 4.5-20), RBGL (>= 1.15.6), RColorBrewer (>= 1.0-2), Rgraphviz (>= 1.17.11), vsn (>= 3.4.0), weaver (>= 1.5.0), xtable (>= 1.5-2), yeastExpData (>= 0.9.11) License: Artistic-2.0 Title: BiocCaseStudies: Support for the Case Studies Monograph Description: Software and data to support the case studies. biocViews: Infrastructure, Bioinformatics Author: R. Gentleman, W. Huber, F. Hahne, M. Morgan, S. Falcon Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/BiocCaseStudies_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/BiocCaseStudies_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/BiocCaseStudies_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BiocCaseStudies_1.14.0.tgz Package: Biostrings Version: 2.20.4 Depends: R (>= 2.8.0), methods, IRanges (>= 1.10.2) Imports: graphics, methods, stats, utils, IRanges LinkingTo: IRanges Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy, affydata (>= 1.11.5), RUnit Enhances: Rmpi License: Artistic-2.0 Archs: i386, x64 Title: String objects representing biological sequences, and matching algorithms Description: Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. biocViews: SequenceMatching, Genetics, Sequencing, Infrastructure, DataImport, DataRepresentation Author: H. Pages, P. Aboyoun, R. Gentleman, and S. DebRoy Maintainer: H. Pages source.ver: src/contrib/Biostrings_2.20.4.tar.gz win.binary.ver: bin/windows/contrib/2.13/Biostrings_2.20.4.zip win64.binary.ver: bin/windows64/contrib/2.13/Biostrings_2.20.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Biostrings_2.20.4.tgz vignettes: vignettes/Biostrings/inst/doc/Alignments.pdf, vignettes/Biostrings/inst/doc/Biostrings2Classes.pdf, vignettes/Biostrings/inst/doc/MultipleAlignments.pdf, vignettes/Biostrings/inst/doc/matchprobes.pdf Package: BufferedMatrixMethods Version: 1.16.0 Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods LinkingTo: BufferedMatrix Suggests: affyio, affy License: GPL (>= 2) Archs: i386, x64 Title: Microarray Data related methods that utlize BufferedMatrix objects Description: Microarray analysis methods that use BufferedMatrix objects biocViews: Infrastructure Author: B. M. Bolstad Maintainer: B. M. Bolstad URL: http://www.bmbolstad.com source.ver: src/contrib/BufferedMatrixMethods_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/BufferedMatrixMethods_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/BufferedMatrixMethods_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BufferedMatrixMethods_1.16.0.tgz Package: BufferedMatrix Version: 1.16.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) Archs: i386, x64 Title: A matrix data storage object held in temporary files Description: A tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data. biocViews: Infrastructure Author: Benjamin Milo Bolstad Maintainer: Benjamin Milo Bolstad source.ver: src/contrib/BufferedMatrix_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/BufferedMatrix_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/BufferedMatrix_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/BufferedMatrix_1.16.0.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: CALIB Version: 1.18.0 Depends: R (>= 2.6.0), limma, methods Imports: limma, methods, graphics, stats, utils License: LGPL Archs: i386, x64 Title: Calibration model for estimating absolute expression levels from microarray data Description: This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes. biocViews: Microarray,TwoChannel,Preprocessing Author: Hui Zhao, Kristof Engelen, Bart De Moor and Kathleen Marchal Maintainer: Hui Zhao source.ver: src/contrib/CALIB_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/CALIB_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/CALIB_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/CALIB_1.18.0.tgz vignettes: vignettes/CALIB/inst/doc/quickstart.pdf, vignettes/CALIB/inst/doc/readme.pdf Package: CAMERA Version: 1.8.2 Depends: R (>= 2.1.0), methods, xcms (>= 1.13.5) Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph Suggests: faahKO Enhances: Rmpi License: GPL (>= 2) Archs: i386 Title: Collection of annotation related methods for mass spectrometry data Description: Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments biocViews: MassSpectrometry Author: Carsten Kuhl, Ralf Tautenhahn, Steffen Neumann {ckuhl|rtautenh|sneumann}@ipb-halle.de Maintainer: Carsten Kuhl URL: http://msbi.ipb-halle.de/msbi/CAMERA/ source.ver: src/contrib/CAMERA_1.8.2.tar.gz win.binary.ver: bin/windows/contrib/2.13/CAMERA_1.8.2.zip win64.binary.ver: bin/windows64/contrib/2.13/CAMERA_1.8.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/CAMERA_1.8.2.tgz vignettes: vignettes/CAMERA/inst/doc/CAMERA.pdf Package: CGEN Version: 1.4.0 Depends: R (>= 2.10.1), survival License: GPL-2 Archs: i386, x64 Title: An R package for analysis of case-control studies in genetic epidemiology Description: An R package for analysis of case-control studies in genetic epidemiology biocViews: SNP, MultipleComparisons, Clustering Author: Samsiddhi Bhattacharjee, Nilanjan Chatterjee and William Wheeler Maintainer: William Wheeler source.ver: src/contrib/CGEN_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/CGEN_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/CGEN_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/CGEN_1.4.0.tgz vignettes: vignettes/CGEN/inst/doc/vignette.pdf Package: CGHbase Version: 1.10.0 Depends: R (>= 2.4.0), methods, Biobase (>= 2.5.5), marray License: GPL Title: CGHbase: Base functions and classes for arrayCGH data analysis. Description: Contains functions and classes that are needed by arrayCGH packages. biocViews: Infrastructure, Microarray, CopyNumberVariants Author: Sjoerd Vosse Maintainer: Sjoerd Vosse source.ver: src/contrib/CGHbase_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/CGHbase_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/CGHbase_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/CGHbase_1.10.0.tgz Package: CGHcall Version: 2.12.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase License: GPL (http://www.gnu.org/copyleft/gpl.html) Title: Calling aberrations for array CGH tumor profiles. Description: Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided. biocViews: Microarray,Preprocessing,Visualization Author: Sjoerd Vosse and Mark van de Wiel Maintainer: Mark van de Wiel source.ver: src/contrib/CGHcall_2.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/CGHcall_2.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/CGHcall_2.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/CGHcall_2.12.0.tgz vignettes: vignettes/CGHcall/inst/doc/CGHcall.pdf Package: CGHnormaliter Version: 1.6.0 Depends: CGHcall (>= 2.2.0), CGHbase (>= 1.2.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) Title: Normalization of array CGH data with imbalanced aberrations. Description: Normalization of array comparative genomic hybridization (aCGH) data. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs). biocViews: Microarray, Preprocessing Author: Bart P.P. van Houte, Thomas W. Binsl, Hannes Hettling Maintainer: Bart P.P. van Houte source.ver: src/contrib/CGHnormaliter_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/CGHnormaliter_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/CGHnormaliter_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/CGHnormaliter_1.6.0.tgz vignettes: vignettes/CGHnormaliter/inst/doc/CGHnormaliter-method.pdf, vignettes/CGHnormaliter/inst/doc/CGHnormaliter.pdf Package: CGHregions Version: 1.10.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase License: GPL (http://www.gnu.org/copyleft/gpl.html) Title: Dimension Reduction for Array CGH Data with Minimal Information Loss. Description: Dimension Reduction for Array CGH Data with Minimal Information Loss biocViews: Microarray,CopyNumberVariants,Visualization Author: Sjoerd Vosse & Mark van de Wiel Maintainer: Sjoerd Vosse source.ver: src/contrib/CGHregions_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/CGHregions_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/CGHregions_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/CGHregions_1.10.0.tgz vignettes: vignettes/CGHregions/inst/doc/CGHregions.pdf Package: CMA Version: 1.10.0 Depends: R (>= 2.5.1), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st License: GPL (>= 2) Title: Synthesis of microarray-based classification Description: This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment. biocViews: Classification Author: Martin Slawski , Anne-Laure Boulesteix , Christoph Bernau . Maintainer: Christoph Bernau source.ver: src/contrib/CMA_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/CMA_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/CMA_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/CMA_1.10.0.tgz vignettes: vignettes/CMA/inst/doc/CMA_vignette.pdf Package: CNTools Version: 1.8.0 Depends: methods, tools, stats, genefilter License: LGPL Archs: i386, x64 Title: Convert segment data into a region by sample matrix to allow for other high level computational analyses. Description: This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data biocViews: Microarray, CopyNumberVariants Author: Jianhua Zhang Maintainer: J. Zhang source.ver: src/contrib/CNTools_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/CNTools_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/CNTools_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/CNTools_1.8.0.tgz vignettes: vignettes/CNTools/inst/doc/HowTo.pdf Package: CNVtools Version: 1.46.0 Depends: survival License: GPL-3 Archs: i386, x64 Title: A package to test genetic association with CNV data Description: This package is meant to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies. biocViews: GeneticVariability Author: Chris Barnes and Vincent Plagnol Maintainer: Chris Barnes source.ver: src/contrib/CNVtools_1.46.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/CNVtools_1.46.0.zip win64.binary.ver: bin/windows64/contrib/2.13/CNVtools_1.46.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/CNVtools_1.46.0.tgz vignettes: vignettes/CNVtools/inst/doc/CNVtools-vignette.pdf Package: CORREP Version: 1.18.0 Imports: e1071, stats Suggests: cluster License: GPL (>= 2) Title: Multivariate Correlation Estimator and Statistical Inference Procedures. Description: Multivariate correlation estimation and statistical inference. See package vignette. biocViews: Bioinformatics, Microarray, Clustering, GraphsAndNetworks Author: Dongxiao Zhu and Youjuan Li Maintainer: Dongxiao Zhu source.ver: src/contrib/CORREP_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/CORREP_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/CORREP_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/CORREP_1.18.0.tgz vignettes: vignettes/CORREP/inst/doc/CORREP.pdf Package: CRImage Version: 1.2.0 Depends: EBImage Imports: MASS, e1071, foreach License: Artistic-2.0 Title: CRImage a package to classify cells and calculate tumour cellularity Description: CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity. biocViews: CellBiology, Classification Author: Henrik Failmezger , Yinyin Yuan , Oscar Rueda , Florian Markowetz Maintainer: Henrik Failmezger , Yinyin Yuan source.ver: src/contrib/CRImage_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/CRImage_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/CRImage_1.2.0.zip vignettes: vignettes/CRImage/inst/doc/CRImage.pdf, vignettes/CRImage/inst/doc/cellularity2.pdf, vignettes/CRImage/inst/doc/labeledImage.pdf Package: CSAR Version: 1.4.0 Depends: R(>= 2.6.0) Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 Archs: i386, x64 Title: Statistical tools for the analysis of ChIP-seq data Description: Statistical tools for ChIP-seq data analysis. The package includes the statistical method described in Kaufmann et al. (2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation. biocViews: ChIPseq,Transcription,Genetics Author: Jose M Muino Maintainer: Jose M Muino source.ver: src/contrib/CSAR_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/CSAR_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/CSAR_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/CSAR_1.4.0.tgz vignettes: vignettes/CSAR/inst/doc/CSAR.pdf Package: Category Version: 2.18.0 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 License: Artistic-2.0 Title: Category Analysis Description: A collection of tools for performing category analysis. biocViews: Bioinformatics, Annotation, GO, Pathways Author: R. Gentleman with contributions from S. Falcon and D.Sarkar Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/Category_2.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Category_2.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Category_2.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Category_2.18.0.tgz vignettes: vignettes/Category/inst/doc/Category.pdf, vignettes/Category/inst/doc/ChromBand.pdf Package: ChIPpeakAnno Version: 1.9.0 Depends: biomaRt, multtest, IRanges, Biostrings, BSgenome,BSgenome.Ecoli.NCBI.20080805, GO.db,org.Hs.eg.db,limma Imports: biomaRt, multtest, IRanges, Biostrings, BSgenome, GO.db,limma License: GPL (>= 2) Title: Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. Description: The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages biocViews: Annotation, ChIPseq, ChIPchip Author: Lihua Julie Zhu, Herve Pages, Claude Gazin, Nathan Lawson,Simon Lin, David Lapointe and Michael Green Maintainer: Lihua Julie Zhu source.ver: src/contrib/ChIPpeakAnno_1.9.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ChIPpeakAnno_1.9.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ChIPpeakAnno_1.9.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ChIPpeakAnno_1.9.0.tgz vignettes: vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.pdf Package: ChIPseqR Version: 1.6.0 Depends: R (>= 2.10.0), ShortRead, methods Imports: Biostrings, fBasics, GenomicRanges, graphics, grDevices, HilbertVis, IRanges, methods, ShortRead, stats, timsac, utils License: GPL (>= 2) Archs: i386, x64 Title: Identifying Protein Binding Sites in High-Throughput Sequencing Data Description: ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well. biocViews: ChIPseq, Bioinformatics, Infrastructure Author: Peter Humburg Maintainer: Peter Humburg source.ver: src/contrib/ChIPseqR_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ChIPseqR_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ChIPseqR_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ChIPseqR_1.6.0.tgz vignettes: vignettes/ChIPseqR/inst/doc/Introduction.pdf Package: ChIPsim Version: 1.6.0 Depends: Biostrings Imports: IRanges, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) Title: Simulation of ChIP-seq experiments Description: A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments. biocViews: Infrastructure, Bioinformatics, ChIPseq Author: Peter Humburg Maintainer: Peter Humburg source.ver: src/contrib/ChIPsim_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ChIPsim_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ChIPsim_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ChIPsim_1.6.0.tgz vignettes: vignettes/ChIPsim/inst/doc/ChIPsimIntro.pdf Package: ChemmineR Version: 2.4.4 Depends: R (>= 2.10.0), methods Imports: graphics, methods, stats, RCurl License: Artistic-2.0 Title: Analysis of Small Molecule and Screening Data Description: ChemmineR is an R package for analyzing small molecule and screening data. The new version of the package 'ChemmineR-V2' contains efficient functions and data containers for processing SDFs (structure data files), structural similarity searching, clustering/diversity analyses of compound libraries with a wide spectrum of algorithms. In addition, it offers utilities for managing complex data sets from high-throughput compound bio-assays, and visualization functions for clustering results and chemical structures. biocViews: MicrotitrePlateAssay, CellBasedAssays, Visualization, Infrastructure, DataImport, Clustering, Bioinformatics, Proteomics Author: Y. Eddie Cao, Tyler Backman, Yan Wang, Thomas Girke Maintainer: ChemmineR Team URL: http://manuals.bioinformatics.ucr.edu/home/chemminer source.ver: src/contrib/ChemmineR_2.4.4.tar.gz win.binary.ver: bin/windows/contrib/2.13/ChemmineR_2.4.4.zip win64.binary.ver: bin/windows64/contrib/2.13/ChemmineR_2.4.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ChemmineR_2.4.4.tgz vignettes: vignettes/ChemmineR/inst/doc/ChemmineR.pdf Package: ChromHeatMap Version: 1.6.0 Depends: R (>= 2.9.0), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0), hgu95av2.db Imports: annotate, AnnotationDbi, Biobase, graphics, grDevices, methods, stats, IRanges, rtracklayer Suggests: ALL License: Artistic-2.0 Title: Heat map plotting by genome coordinate Description: The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest. biocViews: Visualization Author: Tim F. Rayner Maintainer: Tim F. Rayner source.ver: src/contrib/ChromHeatMap_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ChromHeatMap_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ChromHeatMap_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ChromHeatMap_1.6.0.tgz vignettes: vignettes/ChromHeatMap/inst/doc/ChromHeatMap.pdf Package: Clonality Version: 1.0.0 Depends: R (>= 2.12.2), DNAcopy Imports: DNAcopy, grDevices, graphics, stats, utils Suggests: gdata, DNAcopy License: GPL-3 Title: Clonality testing Description: Statistical tests for clonality versus independence of tumors from the same patient based on their LOH or genomewide copy number profiles biocViews: Microarray, CopyNumberVariants, Classification, aCGH Author: Irina Ostrovnaya Maintainer: Irina Ostrovnaya source.ver: src/contrib/Clonality_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Clonality_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Clonality_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Clonality_1.0.0.tgz vignettes: vignettes/Clonality/inst/doc/Clonality.pdf Package: CoCiteStats Version: 1.24.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL Title: Different test statistics based on co-citation. Description: A collection of software tools for dealing with co-citation data. biocViews: Bioinformatics Author: B. Ding and R. Gentleman Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/CoCiteStats_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/CoCiteStats_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/CoCiteStats_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/CoCiteStats_1.24.0.tgz Package: CoGAPS Version: 1.2.0 Depends: R (>= 2.9.0), rjags(>= 2.1.0), R.utils (>= 1.2.4) Imports: graphics, grDevices, methods, stats, utils License: GPL (== 2) Title: Coordinated Gene Activity in Pattern Sets Description: Coordinated Gene Activity in Pattern Sets (CoGAPS) infers biological processes which are active in individual gene sets from corresponding microarray measurements. CoGAPS achieves this inference by combining a MCMC matrix decomposition algorithm (GAPS) with a novel statistic inferring activity on gene sets. biocViews: GeneExpression, Microarray, Bioinformatics Author: Elana J. Fertig Maintainer: Elana J. Fertig , Michael F. Ochs URL: http://www.cancerbiostats.onc.jhmi.edu/cogaps.cfm SystemRequirements: GAPS-JAGS (==1.0.2) source.ver: src/contrib/CoGAPS_1.2.0.tar.gz vignettes: vignettes/CoGAPS/inst/doc/CoGAPSUsersManual.pdf Package: ConsensusClusterPlus Version: 1.5.1 Imports: Biobase, ALL, graphics, stats, utils License: GPL version 2 Title: ConsensusClusterPlus Description: algorithm for determining cluster count and membership by stability evidence in unsupervised analysis biocViews: Software, Bioinformatics, Clustering Author: Matt Wilkerson Maintainer: Matt Wilkerson source.ver: src/contrib/ConsensusClusterPlus_1.5.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/ConsensusClusterPlus_1.5.1.zip win64.binary.ver: bin/windows64/contrib/2.13/ConsensusClusterPlus_1.5.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ConsensusClusterPlus_1.5.1.tgz vignettes: vignettes/ConsensusClusterPlus/inst/doc/ConsensusClusterPlus.pdf Package: DAVIDQuery Version: 1.12.0 Depends: RCurl (>= 1.4.0), utils License: GPL-2 Title: Retrieval from the DAVID bioinformatics data resource into R Description: Tools to retrieve data from DAVID, the Database for Annotation, Visualization and Integrated Discovery biocViews: Annotation Author: Roger Day, Alex Lisovich Maintainer: Roger Day source.ver: src/contrib/DAVIDQuery_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/DAVIDQuery_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/DAVIDQuery_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/DAVIDQuery_1.12.0.tgz vignettes: vignettes/DAVIDQuery/inst/doc/DAVIDQuery.pdf Package: DEDS Version: 1.26.0 Depends: R (>= 1.7.0) License: LGPL Archs: i386, x64 Title: Differential Expression via Distance Summary for Microarray Data Description: This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach. biocViews: Bioinformatics, Microarray, DifferentialExpression Author: Yuanyuan Xiao , Jean Yee Hwa Yang . Maintainer: Yuanyuan Xiao source.ver: src/contrib/DEDS_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/DEDS_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/DEDS_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/DEDS_1.26.0.tgz vignettes: vignettes/DEDS/inst/doc/DEDS.pdf Package: DEGraph Version: 1.4.0 Depends: R (>= 2.10.0), R.utils Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz License: GPL-3 Title: Two-sample tests on a graph Description: DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of the network to yield more powerful detection procedures. DEGraph provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results. biocViews: Microarray, Bioinformatics, DifferentialExpression, GraphsAndNetworks Author: Laurent Jacob, Pierre Neuvial and Sandrine Dudoit Maintainer: Laurent Jacob source.ver: src/contrib/DEGraph_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/DEGraph_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/DEGraph_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/DEGraph_1.4.0.tgz vignettes: vignettes/DEGraph/inst/doc/DEGraph.pdf Package: DEGseq Version: 1.6.2 Depends: R (>= 2.8.0), qvalue, ShortRead, samr, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>=2) Archs: i386, x64 Title: Identify Differentially Expressed Genes from RNA-seq data Description: DEGseq is an R package to identify differentially expressed genes from RNA-Seq data. biocViews: RNAseq, Preprocessing, GeneExpression, DifferentialExpression Author: Likun Wang and Xi Wang . Maintainer: Likun Wang source.ver: src/contrib/DEGseq_1.6.2.tar.gz win.binary.ver: bin/windows/contrib/2.13/DEGseq_1.6.2.zip win64.binary.ver: bin/windows64/contrib/2.13/DEGseq_1.6.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/DEGseq_1.6.2.tgz vignettes: vignettes/DEGseq/inst/doc/DEGseq.pdf Package: DESeq Version: 1.4.1 Depends: Biobase, locfit Imports: genefilter, geneplotter, methods License: GPL (>= 3) Archs: i386, x64 Title: Digital gene expresion analysis based on the negative binomial distribution Description: Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution biocViews: HighThroughputSequencing, ChIPseq, RNAseq, SAGE, DifferentialExpression Author: Simon Anders, EMBL Heidelberg Maintainer: Simon Anders URL: http://www-huber.embl.de/users/anders/DESeq/ source.ver: src/contrib/DESeq_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/DESeq_1.4.1.zip win64.binary.ver: bin/windows64/contrib/2.13/DESeq_1.4.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/DESeq_1.4.1.tgz vignettes: vignettes/DESeq/inst/doc/DESeq.pdf Package: DFP Version: 1.10.0 Depends: methods, Biobase (>= 2.5.5) License: GPL-2 Title: Gene Selection Description: This package provides a supervised technique able to identify differentially expressed genes, based on the construction of \emph{Fuzzy Patterns} (FPs). The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values. biocViews: Bioinformatics, Microarray, DifferentialExpression Author: R. Alvarez-Gonzalez, D. Glez-Pena, F. Diaz, F. Fdez-Riverola Maintainer: Rodrigo Alvarez-Glez source.ver: src/contrib/DFP_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/DFP_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/DFP_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/DFP_1.10.0.tgz vignettes: vignettes/DFP/inst/doc/DFP.pdf Package: DNAcopy Version: 1.26.0 License: GPL (>= 2) Archs: i386, x64 Title: DNA copy number data analysis Description: Segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number biocViews: Microarray, CopyNumberVariants Author: Venkatraman E. Seshan, Adam Olshen Maintainer: Venkatraman E. Seshan source.ver: src/contrib/DNAcopy_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/DNAcopy_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/DNAcopy_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/DNAcopy_1.26.0.tgz vignettes: vignettes/DNAcopy/inst/doc/DNAcopy.pdf Package: DynDoc Version: 1.30.0 Depends: methods, utils Imports: methods License: Artistic-2.0 Title: Dynamic document tools Description: A set of functions to create and interact with dynamic documents and vignettes. biocViews: ReportWriting, Infrastructure Author: R. Gentleman, Jeff Gentry Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/DynDoc_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/DynDoc_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/DynDoc_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/DynDoc_1.30.0.tgz Package: EBImage Version: 3.8.0 Depends: R (>= 2.8.0), methods, graphics, stats, utils, abind License: Artistic-2.0 Archs: i386 Title: Image processing toolbox for R Description: EBImage is an R package which provides general purpose functionality for the reading, writing, processing and analysis of images. Furthermore, in the context of microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors. biocViews: Visualization Author: Oleg Sklyar, Gregoire Pau, Mike Smith, Wolfgang Huber Maintainer: Gregoire Pau SystemRequirements: ImageMagick (>= 6.3.7), GTK+ (> 2.6) source.ver: src/contrib/EBImage_3.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/EBImage_3.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/EBImage_3.8.0.zip vignettes: vignettes/EBImage/inst/doc/EBImage-installation.pdf, vignettes/EBImage/inst/doc/EBImage-introduction.pdf Package: EBarrays Version: 2.16.0 Depends: R (>= 1.8.0), Biobase, lattice, methods Imports: Biobase, cluster, graphics, grDevices, lattice, methods, stats License: GPL (>= 2) Archs: i386, x64 Title: Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification Description: EBarrays provides tools for the analysis of replicated/unreplicated microarray data. biocViews: Clustering, DifferentialExpression Author: Ming Yuan, Christina Kendziorski, Michael Newton and Deepayan Sarkar Maintainer: Ming Yuan source.ver: src/contrib/EBarrays_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/EBarrays_2.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/EBarrays_2.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/EBarrays_2.16.0.tgz vignettes: vignettes/EBarrays/inst/doc/vignette.pdf Package: ENVISIONQuery Version: 1.0.0 Depends: rJava, XML, utils License: GPL-2 Title: Retrieval from the ENVISION bioinformatics data portal into R Description: Tools to retrieve data from ENVISION, the Database for Annotation, Visualization and Integrated Discovery portal biocViews: Annotation Author: Alex Lisovich, Roger Day Maintainer: Alex Lisovich , Roger Day source.ver: src/contrib/ENVISIONQuery_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ENVISIONQuery_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ENVISIONQuery_1.0.0.zip vignettes: vignettes/ENVISIONQuery/inst/doc/ENVISIONQuery.pdf Package: ExiMiR Version: 1.0.0 Depends: R (>= 2.8.0), Biobase (>= 2.5.5), affy (>= 1.26.1) Imports: affyio(>= 1.13.3), Biobase(>= 2.5.5), preprocessCore(>= 1.10.0) License: GPL-2 Title: R functions for the normalization of Exiqon miRNA array data Description: This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. biocViews: Microarray, OneChannel, DualChannel, Preprocessing, GeneExpression, Transcription Author: Sylvain Gubian , Alain Sewer , PMP SA Maintainer: Sylvain Gubian source.ver: src/contrib/ExiMiR_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ExiMiR_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ExiMiR_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ExiMiR_1.0.0.tgz vignettes: vignettes/ExiMiR/inst/doc/ExiMiR-vignette.pdf Package: ExpressionView Version: 1.4.0 Depends: caTools, bitops Imports: methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi Suggests: ALL, hgu95av2.db, biclust, GO.db, KEGG.db, AnnotationDbi, affy License: GPL (>= 2) Archs: i386, x64 Title: Visualize biclusters identified in gene expression data Description: ExpressionView visualizes possibly overlapping biclusters in a gene expression matrix. It can use the result of the ISA method (eisa package) or the algorithms in the biclust package or others. The viewer itself was developed using Adobe Flex and runs in a flash-enabled web browser. biocViews: Classification, Visualization, Microarray, GeneExpression Author: Andreas Luscher Maintainer: Gabor Csardi source.ver: src/contrib/ExpressionView_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ExpressionView_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ExpressionView_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ExpressionView_1.4.0.tgz vignettes: vignettes/ExpressionView/inst/doc/ExpressionView.format.pdf, vignettes/ExpressionView/inst/doc/ExpressionView.ordering.pdf, vignettes/ExpressionView/inst/doc/ExpressionView.tutorial.pdf Package: GEOmetadb Version: 1.12.0 Depends: GEOquery,RSQLite License: Artistic-2.0 Title: A compilation of metadata from NCBI GEO Description: The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. GEOmetadb paper: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/23/2798 . biocViews: Infrastructure Author: Jack Zhu and Sean Davis Maintainer: Jack Zhu URL: http://gbnci.abcc.ncifcrf.gov/geo/ source.ver: src/contrib/GEOmetadb_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GEOmetadb_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GEOmetadb_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GEOmetadb_1.12.0.tgz vignettes: vignettes/GEOmetadb/inst/doc/GEOmetadb.pdf, vignettes/GEOmetadb/inst/doc/GEOmetadb_diagram.pdf Package: GEOquery Version: 2.19.4 Depends: methods, Biobase Imports: XML, RCurl Suggests: limma, RUnit License: GPL-2 Title: Get data from NCBI Gene Expression Omnibus (GEO) Description: The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor. biocViews: Microarray, DataImport, OneChannel, TwoChannel, SAGE Author: Sean Davis Maintainer: Sean Davis URL: http://watson.nci.nih.gov/~sdavis source.ver: src/contrib/GEOquery_2.19.4.tar.gz win.binary.ver: bin/windows/contrib/2.13/GEOquery_2.19.4.zip win64.binary.ver: bin/windows64/contrib/2.13/GEOquery_2.19.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GEOquery_2.19.4.tgz vignettes: vignettes/GEOquery/inst/doc/GEOquery.pdf Package: GEOsubmission Version: 1.4.0 Imports: affy, Biobase, utils License: GPL (>= 2) Title: Prepares microarray data for submission to GEO Description: Helps to easily submit a microarray dataset and the associated sample information to GEO by preparing a single file for upload (direct deposit). biocViews: Microarray Author: Alexandre Kuhn Maintainer: Alexandre Kuhn source.ver: src/contrib/GEOsubmission_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GEOsubmission_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GEOsubmission_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GEOsubmission_1.4.0.tgz vignettes: vignettes/GEOsubmission/inst/doc/GEOsubmission.pdf Package: GGBase Version: 3.12.0 Depends: R (>= 2.7.0), methods, Biobase (>= 2.9.0), snpStats(>= 1.1.10), RSQLite Imports: AnnotationDbi Suggests: illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP.20090506 License: Artistic-2.0 Title: infrastructure for genetics of gene expression (c) 2008 VJ Carey Description: infrastructure for dealing with hapmap SNP reports, GWAS, etc. biocViews: SNP, GeneticVariability, Genetics, Bioinformatics Author: Vince Carey Maintainer: Vince Carey source.ver: src/contrib/GGBase_3.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GGBase_3.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GGBase_3.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GGBase_3.12.0.tgz vignettes: vignettes/GGBase/inst/doc/GGBase.pdf, vignettes/GGBase/inst/doc/makeSMLset.pdf, vignettes/GGBase/inst/doc/newSNPloc.pdf Package: GGtools Version: 3.10.2 Depends: R (>= 2.7.0), methods, Biobase (>= 1.11.26), GGBase (>= 3.7.5), snpStats(>= 1.1.10), annotate, IRanges, rtracklayer, org.Hs.eg.db, GenomicRanges (>= 1.3.38), ff Imports: AnnotationDbi, IRanges (>= 1.1.6), annaffy, GSEABase, rtracklayer Suggests: illuminaHumanv1.db, org.Hs.eg.db, SNPlocs.Hsapiens.dbSNP.20100427, rpart, rtracklayer, GSEABase, ceu1kg, ceuhm3, SNPlocs.Hsapiens.dbSNP.20090506, genefilter, hmyriB36 Enhances: multicore, Rsamtools License: Artistic-2.0 Title: software and data for genetics of gene expression (c) 2006 VJ Carey Description: dealing with hapmap SNP reports, GWAS, etc. biocViews: SNP, GeneticVariability, Genetics, Bioinformatics Author: Vince Carey Maintainer: Vince Carey source.ver: src/contrib/GGtools_3.10.2.tar.gz win.binary.ver: bin/windows/contrib/2.13/GGtools_3.10.2.zip win64.binary.ver: bin/windows64/contrib/2.13/GGtools_3.10.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GGtools_3.10.2.tgz vignettes: vignettes/GGtools/inst/doc/GGtools_2011.pdf, vignettes/GGtools/inst/doc/binf09supp.pdf, vignettes/GGtools/inst/doc/external.pdf, vignettes/GGtools/inst/doc/lab2010.pdf Package: GLAD Version: 2.14.0 Depends: R (>= 2.5.0) Suggests: aws, tcltk License: GPL-2 Archs: i386, x64 Title: Gain and Loss Analysis of DNA Description: Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified. biocViews: Microarray, CopyNumberVariants Author: Philippe Hupe Maintainer: Philippe Hupe URL: http://bioinfo.curie.fr SystemRequirements: gsl. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. source.ver: src/contrib/GLAD_2.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GLAD_2.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GLAD_2.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GLAD_2.14.0.tgz vignettes: vignettes/GLAD/inst/doc/GLAD.pdf Package: GOSemSim Version: 1.10.2 Imports: methods, AnnotationDbi, GO.db, org.Hs.eg.db, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pf.plasmo.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Sco.eg.db, org.Ss.eg.db, org.Xl.eg.db Suggests: clusterProfiler License: GPL-2 Title: GO-terms Semantic Similarity Measures Description: Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for estimating GO semantic similarities. Support many species, including Anopheles, Arabidopsis, Bovine, Canine, Chicken, Chimp, Coelicolor, E coli strain K12 and Sakai, Fly, Human, Malaria, Mouse, Pig, Rhesus, Rat, Worm, Xenopus, Yeast, and Zebrafish. biocViews: GO, Clustering, Pathways, Anopheles_gambiae, Arabidopsis_thaliana, Bos_taurus, Caenorhabditis_elegans, Canis_familiaris, Danio_rerio, Drosophila_melanogaster, Escherichia_coli, Gallus_gallus, Homo_sapiens, Mus_musculus, Pan_troglodytes, Plasmodium_falciparum, Rattus_norvegicus, Saccharomyces_cerevisiae, Streptomyces_coelicolor, Sus_scrofa, Xenopus_laevis Author: Guangchuang Yu Maintainer: Guangchuang Yu source.ver: src/contrib/GOSemSim_1.10.2.tar.gz win.binary.ver: bin/windows/contrib/2.13/GOSemSim_1.10.2.zip win64.binary.ver: bin/windows64/contrib/2.13/GOSemSim_1.10.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GOSemSim_1.10.2.tgz vignettes: vignettes/GOSemSim/inst/doc/GOSemSim.pdf Package: GOstats Version: 2.18.0 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 License: Artistic-2.0 Title: Tools for manipulating GO and microarrays. Description: A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations. biocViews: Bioinformatics, Annotation, GO, MultipleComparisons Author: R. Gentleman and S. Falcon Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/GOstats_2.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GOstats_2.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GOstats_2.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GOstats_2.18.0.tgz vignettes: vignettes/GOstats/inst/doc/GOstatsForUnsupportedOrganisms.pdf, vignettes/GOstats/inst/doc/GOstatsHyperG.pdf, vignettes/GOstats/inst/doc/GOvis.pdf Package: GSEABase Version: 1.14.0 Depends: R (>= 2.6.0), Biobase, annotate, methods, graph Imports: annotate, AnnotationDbi, Biobase, graph, methods, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db License: Artistic-2.0 Title: Gene set enrichment data structures and methods Description: This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). biocViews: Infrastructure, Bioinformatics Author: Martin Morgan, Seth Falcon, Robert Gentleman Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/GSEABase_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GSEABase_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GSEABase_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GSEABase_1.14.0.tgz vignettes: vignettes/GSEABase/inst/doc/GSEABase.pdf Package: GSEAlm Version: 1.12.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 Title: Linear Model Toolset for Gene Set Enrichment Analysis Description: Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics. biocViews: Microarray, Bioinformatics Author: Assaf Oron, Robert Gentleman (with contributions from S. Falcon and Z. Jiang) Maintainer: Assaf Oron source.ver: src/contrib/GSEAlm_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GSEAlm_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GSEAlm_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GSEAlm_1.12.0.tgz vignettes: vignettes/GSEAlm/inst/doc/GSEAlm.pdf Package: GSRI Version: 2.0.0 Depends: R (>= 2.12.1), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: multicore License: GPL-3 Title: Gene Set Regulation Index Description: The GSRI package estimates the number of differentially expressed genes in gene sets, utilizing the concept of the Gene Set Regulation Index (GSRI). biocViews: Microarray, Transcription, DifferentialExpression, Genetics, Bioinformatics Author: Julian Gehring, Kilian Bartholome, Clemens Kreutz, Jens Timmer Maintainer: Julian Gehring URL: http://www.fdmold.uni-freiburg.de/~jgehring/ source.ver: src/contrib/GSRI_2.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GSRI_2.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GSRI_2.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GSRI_2.0.0.tgz vignettes: vignettes/GSRI/inst/doc/gsri.pdf Package: GSVA Version: 1.0.1 Depends: R (>= 2.13.0), methods Imports: methods, Biobase, GSEABase Suggests: limma, qpgraph, graph, Rgraphviz, RColorBrewer, genefilter, GSVAdata Enhances: snow, multicore License: GPL (>= 2) Archs: i386, x64 Title: Gene Set Variation Analysis Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. Users on all platforms must install the GNU Scientific Library; see the README file, available in the source distribution of this file, for details. biocViews: Bioinformatics, Microarray, Pathways Author: Justin Guinney (with contributions from Robert Castelo and Sonja Haenzelmann URL: http://www.sagebase.org SystemRequirements: GNU Scientific Library >= 1.12 source.ver: src/contrib/GSVA_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/GSVA_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.13/GSVA_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GSVA_1.0.1.tgz vignettes: vignettes/GSVA/inst/doc/GSVA.pdf Package: GeneAnswers Version: 1.8.0 Depends: R (>= 2.10.0), igraph, RCurl, annotate, Biobase (>= 1.12.0), methods, XML, RSQLite, MASS, rgl, Heatplus, RColorBrewer Imports: graph, Rgraphviz, RBGL, annotate Suggests: GO.db, KEGG.db, biomaRt, AnnotationDbi, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db License: LGPL (>= 2) Title: Integrated Interpretation of Genes Description: GeneAnswers provides an integrated tool for biological or medical interpretation of the given one or more groups of genes by means of statistical test. biocViews: Infrastructure, DataRepresentation, Visualization, GraphsAndNetworks Author: Gang Feng, Pan Du, Tian Xia, Warren Kibbe and Simon Lin Maintainer: Gang Feng , Pan Du and Tian Xia source.ver: src/contrib/GeneAnswers_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GeneAnswers_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GeneAnswers_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GeneAnswers_1.8.0.tgz vignettes: vignettes/GeneAnswers/inst/doc/GeneAnswersCWAnnotation.pdf, vignettes/GeneAnswers/inst/doc/geneAnswers.pdf, vignettes/GeneAnswers/inst/doc/geneFunctionSummarize.pdf Package: GeneGA Version: 1.2.0 Depends: GeneRfold, seqinr, hash, methods License: GPL version 2 Title: Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm Description: R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias, GeneGA includes the information of highly expressed genes of almost 200 genomes. biocViews: GeneExpression Author: Zhenpeng Li, Fei Li, Xiaochen Bo and Shengqi Wang Maintainer: Zhenpeng Li source.ver: src/contrib/GeneGA_1.2.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GeneGA_1.2.0.tgz vignettes: vignettes/GeneGA/inst/doc/GeneGA.pdf Package: GeneMeta Version: 1.24.0 Depends: R (>= 2.5.0), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) License: Artistic-2.0 Title: MetaAnalysis for High Throughput Experiments Description: A collection of meta-analysis tools for analysing high throughput experimental data biocViews: Bioinformatics Author: Lara Lusa , R. Gentleman, M. Ruschhaupt Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/GeneMeta_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GeneMeta_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GeneMeta_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GeneMeta_1.24.0.tgz vignettes: vignettes/GeneMeta/inst/doc/GeneMeta.pdf Package: GeneR Version: 2.22.0 Depends: R (>= 2.6.0) Imports: graphics, stats, utils License: CeCILL-2.0 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 source.ver: src/contrib/GeneR_2.22.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GeneR_2.22.0.tgz vignettes: vignettes/GeneR/inst/doc/GeneR.pdf, vignettes/GeneR/inst/doc/GeneR_address.pdf Package: GeneRegionScan Version: 1.8.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) Title: GeneRegionScan Description: A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data. biocViews: Microarray, DataImport, SNP, OneChannel, Visualization Author: Lasse Folkersen, Diego Diez Maintainer: Lasse Folkersen source.ver: src/contrib/GeneRegionScan_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GeneRegionScan_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GeneRegionScan_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GeneRegionScan_1.8.0.tgz vignettes: vignettes/GeneRegionScan/inst/doc/GeneRegionScan.pdf Package: GeneRfold Version: 1.10.0 Depends: R (>= 2.6.0), GeneR License: CeCILL-2.0 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/ source.ver: src/contrib/GeneRfold_1.10.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GeneRfold_1.10.0.tgz vignettes: vignettes/GeneRfold/inst/doc/GeneRfold.pdf, vignettes/GeneRfold/inst/doc/rnafold.pdf Package: GeneSelectMMD Version: 1.8.0 Depends: R (>= 2.9.0), Biobase Imports: Biobase, MASS, graphics, stats, survival Suggests: ALL License: GPL (>= 2) Title: Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions Description: Gene selection based on a mixture of marginal distributions biocViews: Bioinformatics, DifferentialExpression Author: Weiliang Qiu , Wenqing He , Xiaogang Wang , Ross Lazarus . Maintainer: Weiliang Qiu source.ver: src/contrib/GeneSelectMMD_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GeneSelectMMD_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GeneSelectMMD_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GeneSelectMMD_1.8.0.tgz vignettes: vignettes/GeneSelectMMD/inst/doc/gsMMD.pdf Package: GeneSelector Version: 2.2.0 Depends: R (>= 2.5.1), methods, stats, Biobase Imports: multtest, siggenes, samr, limma Suggests: multtest, siggenes, samr, limma License: GPL (>= 2) Archs: i386, x64 Title: Stability and Aggregation of ranked gene lists Description: The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various ranking methods (currently 14). In addition, the stability of the findings can be taken into account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. Given multiple ranked lists, one can use aggregation methods in order to find a synthesis. biocViews: Statistics, DifferentialExpression Author: Martin Slawski , Anne-Laure Boulesteix . Maintainer: Martin Slawski source.ver: src/contrib/GeneSelector_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GeneSelector_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GeneSelector_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GeneSelector_2.2.0.tgz vignettes: vignettes/GeneSelector/inst/doc/GeneSelector.pdf Package: GeneSpring Version: 2.26.0 Depends: R (>= 2.0.1), Biobase (>= 1.5.0), methods Imports: Biobase, methods, utils License: GPL 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 source.ver: src/contrib/GeneSpring_2.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GeneSpring_2.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GeneSpring_2.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GeneSpring_2.26.0.tgz vignettes: vignettes/GeneSpring/inst/doc/GeneSpring.pdf Package: GeneTraffic Version: 1.24.0 Depends: R (>= 1.8.1), Biobase (>= 1.4.0), methods Imports: Biobase, digest, marray (>= 1.5.10), methods, SSOAP (>= 0.1.2), utils License: GPL-2 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/ source.ver: src/contrib/GeneTraffic_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GeneTraffic_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GeneTraffic_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GeneTraffic_1.24.0.tgz vignettes: vignettes/GeneTraffic/inst/doc/GeneTraffic.pdf Package: GeneticsDesign Version: 1.20.0 Imports: gmodels, graphics, gtools (>= 2.4.0), mvtnorm, stats License: GPL-2 Title: Functions for designing genetics studies Description: This package contains functions useful for designing genetics studies, including power and sample-size calculations. biocViews: Genetics Author: Gregory Warnes David Duffy , Michael Man Weiliang Qiu Ross Lazarus Maintainer: The R Genetics Project source.ver: src/contrib/GeneticsDesign_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GeneticsDesign_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GeneticsDesign_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GeneticsDesign_1.20.0.tgz vignettes: vignettes/GeneticsDesign/inst/doc/GPC.pdf Package: GeneticsPed Version: 1.14.0 Depends: R (>= 2.4.0), gdata (>= 2.3.0), genetics (>= 1.3.0), MASS License: LGPL (>= 2.1) Archs: i386, x64 Title: Pedigree and genetic relationship functions Description: Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable. Use it with care! biocViews: Genetics Author: Gregor Gorjanc and David A. Henderson , with code contributions by Brian Kinghorn and Andrew Percy (see file COPYING) Maintainer: David Henderson URL: http://rgenetics.org source.ver: src/contrib/GeneticsPed_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GeneticsPed_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GeneticsPed_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GeneticsPed_1.14.0.tgz vignettes: vignettes/GeneticsPed/inst/doc/geneticRelatedness.pdf, vignettes/GeneticsPed/inst/doc/pedigreeHandling.pdf, vignettes/GeneticsPed/inst/doc/quanGenAnimalModel.pdf Package: GenomeGraphs Version: 1.12.0 Depends: methods, biomaRt, grid License: Artistic-2.0 Title: Plotting genomic information from Ensembl Description: Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system. biocViews: Visualization, Microarray Author: Steffen Durinck , James Bullard Maintainer: Steffen Durinck source.ver: src/contrib/GenomeGraphs_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GenomeGraphs_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GenomeGraphs_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GenomeGraphs_1.12.0.tgz vignettes: vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf Package: GenomicFeatures Version: 1.4.5 Depends: IRanges (>= 1.7.7), GenomicRanges (>= 1.3.23) Imports: methods, DBI (>= 0.2-5), RSQLite (>= 0.8-1), IRanges, GenomicRanges, Biostrings (>= 2.17.6), rtracklayer (>= 1.7.11), biomaRt, RCurl, utils Suggests: rtracklayer, biomaRt, org.Mm.eg.db, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg18 (>= 1.3.14), BSgenome.Celegans.UCSC.ce2, RUnit License: Artistic-2.0 Title: Tools for making and manipulating transcript centric annotations Description: A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format. biocViews: Genetics, Infrastructure, Annotation, HighThroughputSequencing Author: M. Carlson, H. Pages, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/GenomicFeatures_1.4.5.tar.gz win.binary.ver: bin/windows/contrib/2.13/GenomicFeatures_1.4.5.zip win64.binary.ver: bin/windows64/contrib/2.13/GenomicFeatures_1.4.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GenomicFeatures_1.4.5.tgz vignettes: vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf, vignettes/GenomicFeatures/inst/doc/examples.pdf Package: GenomicRanges Version: 1.4.8 Depends: R (>= 2.8.0), methods, IRanges (>= 1.10.6) Imports: methods, IRanges LinkingTo: IRanges Suggests: RUnit, BSgenome, GenomicFeatures, Rsamtools, EatonEtAlChIPseq (>= 0.0.2), leeBamViews, org.Sc.sgd.db, BSgenome.Scerevisiae.UCSC.sacCer2 License: Artistic-2.0 Archs: i386, x64 Title: Representation and manipulation of genomic intervals Description: The ability to efficiently store genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing data (a.k.a. NGS data). The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome. biocViews: Genetics, Sequencing, HighThroughputSequencing, Annotation Author: P. Aboyoun, H. Pages and M. Lawrence Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/GenomicRanges_1.4.8.tar.gz win.binary.ver: bin/windows/contrib/2.13/GenomicRanges_1.4.8.zip win64.binary.ver: bin/windows64/contrib/2.13/GenomicRanges_1.4.8.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GenomicRanges_1.4.8.tgz vignettes: vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.pdf, vignettes/GenomicRanges/inst/doc/GenomicRangesUseCases.pdf, vignettes/GenomicRanges/inst/doc/countGenomicOverlaps-decisiontree.pdf, vignettes/GenomicRanges/inst/doc/countGenomicOverlaps-genes.pdf, vignettes/GenomicRanges/inst/doc/countGenomicOverlaps.pdf Package: Genominator Version: 1.6.0 Depends: methods, RSQLite, DBI (>= 0.2-5), IRanges, GenomeGraphs Imports: graphics, stats, utils Suggests: biomaRt, ShortRead, yeastRNASeq License: Artistic-2.0 Title: Analyze, manage and store genomic data Description: Tools for storing, accessing, analyzing and visualizing genomic data. biocViews: Infrastructure Author: James Bullard, Kasper Daniel Hansen Maintainer: James Bullard source.ver: src/contrib/Genominator_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Genominator_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Genominator_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Genominator_1.6.0.tgz vignettes: vignettes/Genominator/inst/doc/Genominator.pdf, vignettes/Genominator/inst/doc/plotting.pdf, vignettes/Genominator/inst/doc/withShortRead.pdf Package: GlobalAncova Version: 3.20.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi Suggests: Biobase, annotate, GO.db, KEGG.db, golubEsets, hu6800.db, vsn, GSEABase License: GPL (>= 2) Archs: i386, x64 Title: Calculates a global test for differential gene expression between groups Description: We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany. biocViews: Microarray, OneChannel, Bioinformatics, DifferentialExpression, Pathways Author: U. Mansmann, R. Meister, M. Hummel, R. Scheufele, with contributions from S. Knueppel Maintainer: Manuela Hummel source.ver: src/contrib/GlobalAncova_3.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GlobalAncova_3.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GlobalAncova_3.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GlobalAncova_3.20.0.tgz vignettes: vignettes/GlobalAncova/inst/doc/GlobalAncova.pdf, vignettes/GlobalAncova/inst/doc/GlobalAncovaDecomp.pdf Package: GraphAT Version: 1.24.0 Depends: graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL Title: Graph Theoretic Association Tests Description: Functions and data used in Balasubramanian, et al. (2004) biocViews: Bioinformatics, GraphsAndNetworks Author: R. Balasubramanian, T. LaFramboise, D. Scholtens Maintainer: Thomas LaFramboise source.ver: src/contrib/GraphAT_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GraphAT_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GraphAT_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GraphAT_1.24.0.tgz Package: GraphAlignment Version: 1.14.0 License: file LICENSE Archs: i386, x64 Title: GraphAlignment Description: Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. (J. Berg and M. Laessig, "Cross-species analysis of biological networks by Bayesian alignment", PNAS 103 (29), 10967-10972 (2006)) biocViews: GraphsAndNetworks Author: Joern P. Meier , Michal Kolar, Ville Mustonen, Michael Laessig, and Johannes Berg. Maintainer: Joern P. Meier URL: http://www.thp.uni-koeln.de/~berg/GraphAlignment/ source.ver: src/contrib/GraphAlignment_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/GraphAlignment_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/GraphAlignment_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/GraphAlignment_1.14.0.tgz vignettes: vignettes/GraphAlignment/inst/doc/GraphAlignment.pdf, vignettes/GraphAlignment/inst/doc/a.pdf, vignettes/GraphAlignment/inst/doc/align_principle2b1.pdf, vignettes/GraphAlignment/inst/doc/align_principle2c1.pdf, vignettes/GraphAlignment/inst/doc/align_principle_short1.pdf, vignettes/GraphAlignment/inst/doc/binning-01a.pdf Package: HELP Version: 1.10.0 Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods License: GPL (>= 2) Title: Tools for HELP data analysis Description: The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications biocViews: CpGIsland, DNAMethylation, Microarray, TwoChannel, DataImport, QualityControl, Preprocessing, Visualization Author: Reid F. Thompson , John M. Greally , with contributions from Mark Reimers Maintainer: Reid F. Thompson source.ver: src/contrib/HELP_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/HELP_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/HELP_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/HELP_1.10.0.tgz vignettes: vignettes/HELP/inst/doc/HELP.pdf Package: HEM Version: 1.24.0 Depends: R (>= 2.1.0) Imports: Biobase, grDevices, stats, utils License: GPL (>= 2) Archs: i386, x64 Title: Heterogeneous error model for identification of differentially expressed genes under multiple conditions Description: This package fits heterogeneous error models for analysis of microarray data biocViews: Microarray, DifferentialExpression, Bioinformatics Author: HyungJun Cho and Jae K. Lee Maintainer: HyungJun Cho URL: http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/ source.ver: src/contrib/HEM_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/HEM_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/HEM_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/HEM_1.24.0.tgz vignettes: vignettes/HEM/inst/doc/HEM.pdf Package: HTSanalyzeR Version: 2.5.1 Depends: igraph, GSEABase, BioNet, cellHTS2, RankProd, methods Imports: graph, igraph, GSEABase, BioNet, cellHTS2, AnnotationDbi, biomaRt Suggests: KEGG.db, GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow License: Artistic-2.0 Title: Gene set over-representation, enrichment and network analyses for high-throughput screens Description: This package provides classes and methods for gene set over-representation, enrichment and network analyses on high-throughput screens. The over-representation analysis is performed based on hypergeometric tests. The enrichment analysis is based on the GSEA algorithm (Subramanian et al. PNAS 2005). The network analysis identifies enriched subnetworks based on algorithms from the BioNet package (Beisser et al., Bioinformatics 2010). A pipeline is also specifically designed for cellHTS2 object to perform integrative network analyses of high-throughput RNA interference screens. The users can build their own analysis pipeline for their own data set based on this package. biocViews: CellBasedAssays, Bioinformatics, MultipleComparisons Author: Xin Wang , Camille Terfve , John C. Rose , Florian Markowetz Maintainer: Xin Wang source.ver: src/contrib/HTSanalyzeR_2.5.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/HTSanalyzeR_2.5.1.zip win64.binary.ver: bin/windows64/contrib/2.13/HTSanalyzeR_2.5.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/HTSanalyzeR_2.5.1.tgz vignettes: vignettes/HTSanalyzeR/inst/doc/Figure.pdf, vignettes/HTSanalyzeR/inst/doc/HTSanalyzeR-Vignette.pdf Package: HTqPCR Version: 1.6.0 Depends: Biobase, RColorBrewer, limma Imports: affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, utils Suggests: statmod License: Artistic-2.0 Title: Automated analysis of high-throughput qPCR data Description: Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays, conventional 96- or 384-well plates, or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs). biocViews: MicrotitrePlateAssay, DifferentialExpression, GeneExpression, DataImport, QualityControl, Preprocessing, Bioinformatics, Visualization, MultipleComparisons Author: Heidi Dvinge, Paul Bertone Maintainer: Heidi Dvinge URL: http://www.ebi.ac.uk/bertone/software source.ver: src/contrib/HTqPCR_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/HTqPCR_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/HTqPCR_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/HTqPCR_1.6.0.tgz vignettes: vignettes/HTqPCR/inst/doc/HTqPCR.pdf Package: Harshlight Version: 1.24.0 Depends: R (>= 2.1.1) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) Archs: i386, x64 Title: A "corrective make-up" program for microarray chips Description: The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem. biocViews: Microarray, QualityControl, Preprocessing, AffymetrixChip, ReportWriting Author: Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkowski, Marcelo O. Magnasco Maintainer: Maurizio Pellegrino URL: http://asterion.rockefeller.edu/Harshlight/ source.ver: src/contrib/Harshlight_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Harshlight_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Harshlight_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Harshlight_1.24.0.tgz vignettes: vignettes/Harshlight/inst/doc/Harshlight.pdf Package: Heatplus Version: 1.22.0 Imports: graphics, grDevices, stats License: GPL (>= 2) 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 source.ver: src/contrib/Heatplus_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Heatplus_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Heatplus_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Heatplus_1.22.0.tgz vignettes: vignettes/Heatplus/inst/doc/Heatplus.pdf Package: HilbertVisGUI Version: 1.10.0 Depends: R (>= 2.6.0), HilbertVis (>= 1.1.6) Suggests: lattice, IRanges License: GPL (>= 3) Archs: i386 Title: HilbertVisGUI Description: An interactive tool to visualize long vectors of integer data by means of Hilbert curves biocViews: Visualization Author: Simon Anders Maintainer: Simon Anders URL: http://www.ebi.ac.uk/~anders/hilbert SystemRequirements: gtkmm-2.4 source.ver: src/contrib/HilbertVisGUI_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/HilbertVisGUI_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/HilbertVisGUI_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/HilbertVisGUI_1.10.0.tgz vignettes: vignettes/HilbertVisGUI/inst/doc/HilbertVisGUI.pdf Package: HilbertVis Version: 1.10.0 Depends: R (>= 2.6.0), grid, lattice Suggests: EBImage, IRanges License: GPL (>= 3) Archs: i386 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 source.ver: src/contrib/HilbertVis_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/HilbertVis_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/HilbertVis_1.10.0.zip vignettes: vignettes/HilbertVis/inst/doc/HilbertDisplay_GUI.pdf, vignettes/HilbertVis/inst/doc/HilbertVis.pdf, vignettes/HilbertVis/inst/doc/ThreeChTest.pdf Package: IPPD Version: 1.0.0 Depends: R (>= 2.8.0), MASS, Matrix Imports: methods, stats, graphics License: GPL (version 2 or later) Archs: i386, x64 Title: Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching Description: The package provides functionality to extract isotopic peak patterns from raw mass spectra. This is done by fitting a large set of template basis functions to the raw spectrum using either nonnegative least squares or least absolute deviation fittting. The package offers a flexible function which tries to estimate model parameters in a way tailored to the peak shapes in the data. biocViews: Proteomics Author: Martin Slawski , Rene Hussong , Matthias Hein Maintainer: Martin Slawski source.ver: src/contrib/IPPD_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/IPPD_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/IPPD_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/IPPD_1.0.0.tgz vignettes: vignettes/IPPD/inst/doc/IPPD.pdf, vignettes/IPPD/inst/doc/templatedetail.pdf, vignettes/IPPD/inst/doc/templates.pdf Package: IRanges Version: 1.10.6 Depends: R (>= 2.8.0), methods, utils, stats Imports: methods, utils, stats Suggests: RUnit License: Artistic-2.0 Archs: i386, x64 Title: Infrastructure for manipulating intervals on sequences Description: The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent "Vector API" as much as possible. biocViews: Infrastructure, DataRepresentation Author: H. Pages, P. Aboyoun and M. Lawrence Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/IRanges_1.10.6.tar.gz win.binary.ver: bin/windows/contrib/2.13/IRanges_1.10.6.zip win64.binary.ver: bin/windows64/contrib/2.13/IRanges_1.10.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/IRanges_1.10.6.tgz vignettes: vignettes/IRanges/inst/doc/IRangesOverview.pdf, vignettes/IRanges/inst/doc/RleTricks.pdf Package: ITALICS Version: 2.12.0 Depends: R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser, pd.mapping50k.xba240 Imports: affxparser, DBI, GLAD, oligo, oligoClasses, stats Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp License: GPL-2 Title: ITALICS Description: A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set biocViews: Microarray, CopyNumberVariants Author: Guillem Rigaill, Philippe Hupe Maintainer: Guillem Rigaill URL: http://bioinfo.curie.fr source.ver: src/contrib/ITALICS_2.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ITALICS_2.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ITALICS_2.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ITALICS_2.12.0.tgz vignettes: vignettes/ITALICS/inst/doc/ITALICS-006.pdf, vignettes/ITALICS/inst/doc/ITALICS.pdf Package: Icens Version: 1.24.0 Depends: survival Imports: graphics License: Artistic-2.0 Title: NPMLE for Censored and Truncated Data Description: Many functions for computing the NPMLE for censored and truncated data. biocViews: Bioinformatics, Infrastructure Author: R. Gentleman and Alain Vandal Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/Icens_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Icens_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Icens_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Icens_1.24.0.tgz Package: IsoGeneGUI Version: 1.4.2 Depends: tcltk, tkrplot, IsoGene Imports: multtest, relimp, WriteXLS,gdata, RColorBrewer, geneplotter Suggests: RUnit License: GPL-2 Title: A graphical user interface to conduct a dose-response analysis of microarray data Description: The IsoGene Graphical User Interface (IsoGene-GUI) is a user friendly interface of the IsoGene package which is aimed to identify for genes with a monotonic trend in the expression levels with respect to the increasing doses using several test statistics: global likelihood ratio test (E2), Bartholomew 1961, Barlow et al. 1972 and Robertson et al. 1988), Williams (1971, 1972), Marcus (1976), the M (Hu et al. 2005) and the modified M (Lin et al. 2007). The p-values of the global likelihood ratio test (E2) are obtained using the excat distribution and permutation. The other four test statistics are obtained using permutation . Several p-values adjustment are provided: Bonferroni, Holm (1979), Hochberg (1988), and Sidak procedures for controlling the family-wise Type I error rate (FWER), and BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2001) procedures are used for controlling the FDR. the inference is based on resampling methods, which control the False Discovery Rate (FDR) (both permutations (Ge et al., 2003) and the Significance Analysis of Microarrays (SAM), Tusher et al., 2001). biocViews: Microarray, Statistics, DifferentialExpression, GUI Author: Setia Pramana, Dan Lin, Philippe Haldermans, Tobias Verbeke Maintainer: Setia Pramana URL: http://www.ibiostat.be/software/IsoGeneGUI/index.html source.ver: src/contrib/IsoGeneGUI_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.13/IsoGeneGUI_1.4.2.zip win64.binary.ver: bin/windows64/contrib/2.13/IsoGeneGUI_1.4.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/IsoGeneGUI_1.4.2.tgz vignettes: vignettes/IsoGeneGUI/inst/doc/IsoGeneGUI.pdf Package: KCsmart Version: 2.10.0 Depends: methods, siggenes, multtest, KernSmooth Enhances: Biobase, CGHbase License: GPL-3 Title: Multi sample aCGH analysis package using kernel convolution Description: Multi sample aCGH analysis package using kernel convolution biocViews: DNACopyNumber, Visualization, aCGH, Microarray Author: Jorma de Ronde, Christiaan Klijn, Arno Velds Maintainer: Jorma de Ronde source.ver: src/contrib/KCsmart_2.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/KCsmart_2.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/KCsmart_2.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/KCsmart_2.10.0.tgz vignettes: vignettes/KCsmart/inst/doc/KCS.pdf Package: KEGGSOAP Version: 1.26.1 Depends: methods Imports: XML, RCurl, SSOAP (>= 0.2-2) License: BSD 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: Biocore Team c/o BioC user list source.ver: src/contrib/KEGGSOAP_1.26.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/KEGGSOAP_1.26.1.zip win64.binary.ver: bin/windows64/contrib/2.13/KEGGSOAP_1.26.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/KEGGSOAP_1.26.1.tgz Package: KEGGgraph Version: 1.8.0 Depends: methods, XML (>= 2.3-0), graph, Rgraphviz (>= 1.22.0) Imports: methods, XML, graph Suggests: RBGL, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) Title: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor Description: KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc. biocViews: Pathways, GraphsAndNetworks Author: Jitao David Zhang and Stefan Wiemann Maintainer: Jitao David Zhang URL: http://www.dkfz.de/en/mga/index.html source.ver: src/contrib/KEGGgraph_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/KEGGgraph_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/KEGGgraph_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/KEGGgraph_1.8.0.tgz vignettes: vignettes/KEGGgraph/inst/doc/KEGGgraph.pdf, vignettes/KEGGgraph/inst/doc/KEGGgraphApp.pdf Package: LBE Version: 1.20.0 Depends: stats Imports: graphics, grDevices, methods, stats, utils Suggests: qvalue License: GPL-2 Title: Estimation of the false discovery rate. Description: LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis. biocViews: Bioinformatics, MultipleComparisons Author: Cyril Dalmasso Maintainer: Cyril Dalmasso source.ver: src/contrib/LBE_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/LBE_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/LBE_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/LBE_1.20.0.tgz vignettes: vignettes/LBE/inst/doc/LBE.pdf Package: LMGene Version: 2.8.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5), multtest, survival, affy Suggests: affydata License: LGPL Title: LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays Description: LMGene package for analysis of microarray data using a linear model and glog data transformation biocViews: Microarray, Bioinformatics, DifferentialExpression, Preprocessing Author: David Rocke, Geun Cheol Lee, John Tillinghast, Blythe Durbin-Johnson, and Shiquan Wu Maintainer: Blythe Durbin-Johnson URL: http://dmrocke.ucdavis.edu/software.html source.ver: src/contrib/LMGene_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/LMGene_2.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/LMGene_2.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/LMGene_2.8.0.tgz vignettes: vignettes/LMGene/inst/doc/LMGene.pdf Package: LPE Version: 1.26.0 Imports: stats License: LGPL Title: Methods for analyzing microarray data using Local Pooled Error (LPE) method Description: This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library. biocViews: Microarray, Bioinformatics, DifferentialExpression Author: Nitin Jain , Michael O'Connell , Jae K. Lee . Includes R source code contributed by HyungJun Cho Maintainer: Nitin Jain URL: http://www.r-project.org, http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/, http://sourceforge.net/projects/r-lpe/ source.ver: src/contrib/LPE_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/LPE_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/LPE_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/LPE_1.26.0.tgz vignettes: vignettes/LPE/inst/doc/LPE.pdf Package: LPEadj Version: 1.12.0 Depends: LPE Imports: LPE, stats License: LGPL Title: A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size. Description: Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment. biocViews: Microarray, Bioinformatics, Proteomics Author: Carl Murie , Robert Nadon Maintainer: Carl Murie source.ver: src/contrib/LPEadj_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/LPEadj_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/LPEadj_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/LPEadj_1.12.0.tgz vignettes: vignettes/LPEadj/inst/doc/LPEadj.pdf Package: LVSmiRNA Version: 1.2.0 Depends: Biobase,quantreg,splines,MASS,limma,affy,methods, SparseM, vsn Enhances: multicore,snow, Rmpi License: GPL2 Archs: i386, x64 Title: LVS normalization for Agilent miRNA data Description: Normalization of Agilent miRNA arrays. biocViews: Microarray,AgilentChip,OneChannel,Preprocessing Author: Stefano Calza, Suo Chen, Yudi Pawitam Maintainer: Stefano Calza source.ver: src/contrib/LVSmiRNA_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/LVSmiRNA_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/LVSmiRNA_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/LVSmiRNA_1.2.0.tgz vignettes: vignettes/LVSmiRNA/inst/doc/LVSmiRNA.pdf Package: LiquidAssociation Version: 1.6.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>=3) Title: LiquidAssociation Description: The package contains functions for calculate direct and model-based estimators for liquid association. It also provides functions for testing the existence of liquid association given a gene triplet data. biocViews: Pathways, GeneExpression, CellBiology, Genetics, Bioinformatics, TimeCourse Author: Yen-Yi Ho Maintainer: Yen-Yi Ho source.ver: src/contrib/LiquidAssociation_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/LiquidAssociation_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/LiquidAssociation_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/LiquidAssociation_1.6.0.tgz vignettes: vignettes/LiquidAssociation/inst/doc/LiquidAssociation.pdf Package: MANOR Version: 1.24.0 Depends: R (>= 1.8.0), GLAD Imports: GLAD, graphics, grDevices, stats, utils License: GPL-2 Archs: i386, x64 Title: CGH Micro-Array NORmalization Description: Importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments. biocViews: Microarray, TwoChannel, DataImport, QualityControl, Preprocessing, CopyNumberVariants Author: Pierre Neuvial , Philippe Hupe Maintainer: Pierre Neuvial URL: http://bioinfo.curie.fr/projects/manor/index.html source.ver: src/contrib/MANOR_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MANOR_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MANOR_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MANOR_1.24.0.tgz vignettes: vignettes/MANOR/inst/doc/MANOR.pdf Package: MBCB Version: 1.6.0 Depends: R (>= 2.9.0), tcltk, tcltk2 Imports: preprocessCore, stats, utils License: GPL (>= 2) Title: MBCB (Model-based Background Correction for Beadarray) Description: This package provides a model-based background correction method, which incorporates the negative control beads to pre-process Illumina BeadArray data. biocViews: Microarray, Preprocessing Author: Yang Xie Maintainer: Jeff Allen URL: http://www.utsouthwestern.edu source.ver: src/contrib/MBCB_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MBCB_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MBCB_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MBCB_1.6.0.tgz vignettes: vignettes/MBCB/inst/doc/MBCB.pdf Package: MCRestimate Version: 2.8.0 Depends: R (>= 2.7.2), golubEsets (>= 1.4.6) Imports: e1071 (>= 1.5-12), pamr (>= 1.22), randomForest (>= 3.9-6), RColorBrewer (>= 0.1-3), Biobase (>= 2.5.5), graphics, grDevices, stats, utils Suggests: xtable (>= 1.2-1), ROC (>= 1.8.0), genefilter (>= 1.12.0), gpls (>= 1.6.0) License: GPL (>= 2) Title: Misclassification error estimation with cross-validation Description: This package includes a function for combining preprocessing and classification methods to calculate misclassification errors biocViews: Bioinformatics, Classification Author: Marc Johannes, Markus Ruschhaupt, Holger Froehlich, Ulrich Mansmann, Andreas Buness, Patrick Warnat, Wolfgang Huber, Axel Benner, Tim Beissbarth Maintainer: Marc Johannes source.ver: src/contrib/MCRestimate_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MCRestimate_2.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MCRestimate_2.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MCRestimate_2.8.0.tgz vignettes: vignettes/MCRestimate/inst/doc/UsingMCRestimate.pdf Package: MEDIPS Version: 1.2.0 Depends: R (>= 2.12.0), BSgenome Imports: Biostrings, BSgenome, graphics, gtools, IRanges, methods, stats, utils Suggests: BSgenome, BSgenome.Hsapiens.UCSC.hg19 License: GPL (>=2) Archs: i386, x64 Title: MeDIP-Seq data analysis Description: MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-Seq). Nevertheless, functionalities like the quality controls may be applied to other types of sequencing data (e.g. ChIP-Seq). MEDIPS adresses several aspects in the context of MeDIP-Seq data analysis. biocViews: Sequencing, DNAMethylation, CpGIsland, DifferentialExpression, HighThroughputSequencing, ChIPseq, Preprocessing, QualityControl, Visualization Author: Lukas Chavez, Joern Dietrich Maintainer: Lukas Chavez source.ver: src/contrib/MEDIPS_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MEDIPS_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MEDIPS_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MEDIPS_1.2.0.tgz vignettes: vignettes/MEDIPS/inst/doc/MEDIPS.pdf Package: MEDME Version: 1.12.0 Depends: grDevices, graphics, methods, stats, utils Imports: Biostrings, MASS, drc Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 License: GPL (>= 2) Archs: i386, x64 Title: Modelling Experimental Data from MeDIP Enrichment Description: 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 source.ver: src/contrib/MEDME_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MEDME_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MEDME_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MEDME_1.12.0.tgz vignettes: vignettes/MEDME/inst/doc/MEDME.pdf Package: MLInterfaces Version: 1.32.0 Depends: R (>= 2.9), Biobase, MASS, methods, genefilter, rpart, rda, annotate, cluster Imports: mboost Suggests: class, e1071, ipred, randomForest, gpls, pamr, rpart, MASS, nnet, ALL, gbm, mlbench, hgu95av2.db, som, RColorBrewer, hu6800.db, golubEsets, ada, keggorthology, kernlab, gbm, mboost, sfsmisc, party Enhances: multicore License: LGPL Title: Uniform interfaces to R machine learning procedures for data in Bioconductor containers Description: Uniform interfaces to machine learning code for data in Bioconductor containers biocViews: Bioinformatics, Classification, Clustering Author: Vince Carey , Robert Gentleman, Jess Mar, and contributions from Jason Vertrees Maintainer: V. Carey source.ver: src/contrib/MLInterfaces_1.32.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MLInterfaces_1.32.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MLInterfaces_1.32.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MLInterfaces_1.32.0.tgz vignettes: vignettes/MLInterfaces/inst/doc/MLInterfaces.pdf, vignettes/MLInterfaces/inst/doc/MLint_devel.pdf, vignettes/MLInterfaces/inst/doc/MLprac2_2.pdf, vignettes/MLInterfaces/inst/doc/xvalComputerClusters.pdf Package: MLP Version: 1.0.0 Depends: AnnotationDbi, affy, plotrix, gplots, gmodels, gdata, gtools Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, KEGG.db, annotate, Rgraphviz, GOstats, limma, mouse4302.db, reactome.db License: GPL-3 Title: MLP Description: Mean Log P Analysis biocViews: Genetics Author: Nandini Raghavan, Tobias Verbeke, An De Bondt with contributions by Javier Cabrera, Dhammika Amaratunga, Tine Casneuf and Willem Ligtenberg Maintainer: Tobias Verbeke source.ver: src/contrib/MLP_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MLP_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MLP_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MLP_1.0.0.tgz vignettes: vignettes/MLP/inst/doc/UsingMLP.pdf Package: MSnbase Version: 1.0.7 Depends: Biobase (>= 2.11.0), methods, ggplot2 Imports: plyr, graphics, xcms, IRanges Suggests: testthat, zoo, vsn, pgfSweave License: Artistic-2.0 Title: MSnbase: Base Functions and Classes for MS-based Proteomics Description: Basic plotting, data manipulation and processing of MS-based Proteomics data biocViews: Infrastructure, Bioinformatics, Proteomics, MassSpectrometry Author: Laurent Gatto Maintainer: Laurent Gatto source.ver: src/contrib/MSnbase_1.0.7.tar.gz win.binary.ver: bin/windows/contrib/2.13/MSnbase_1.0.7.zip win64.binary.ver: bin/windows64/contrib/2.13/MSnbase_1.0.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MSnbase_1.0.7.tgz vignettes: vignettes/MSnbase/inst/doc/MSnbase-demo.pdf, vignettes/MSnbase/inst/doc/MSnbase-development.pdf Package: MVCClass Version: 1.26.0 Depends: R (>= 2.1.0), methods License: LGPL Title: Model-View-Controller (MVC) Classes Description: Creates classes used in model-view-controller (MVC) design biocViews: Visualization, Infrastructure, GraphsAndNetworks Author: Elizabeth Whalen Maintainer: Elizabeth Whalen source.ver: src/contrib/MVCClass_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MVCClass_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MVCClass_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MVCClass_1.26.0.tgz vignettes: vignettes/MVCClass/inst/doc/MVCClass.pdf Package: MantelCorr Version: 1.22.0 Depends: R (>= 2.0.0) Imports: stats License: GPL (>= 2) Title: Compute Mantel Cluster Correlations Description: Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data). biocViews: Bioinformatics, Clustering Author: Brian Steinmeyer and William Shannon Maintainer: Brian Steinmeyer source.ver: src/contrib/MantelCorr_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MantelCorr_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MantelCorr_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MantelCorr_1.22.0.tgz vignettes: vignettes/MantelCorr/inst/doc/MantelCorrVignette.pdf Package: MassArray Version: 1.4.0 Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, methods, stats, utils License: GPL (>=2) Title: Analytical Tools for MassArray Data Description: This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis. biocViews: DNAMethylation, SNP, MassSpectrometry, Genetics, DataImport, Visualization Author: Reid F. Thompson , John M. Greally Maintainer: Reid F. Thompson source.ver: src/contrib/MassArray_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MassArray_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MassArray_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MassArray_1.4.0.tgz vignettes: vignettes/MassArray/inst/doc/MassArray.pdf, vignettes/MassArray/inst/doc/conversion.pdf Package: MassSpecWavelet Version: 1.18.0 Depends: waveslim Suggests: xcms, caTools License: LGPL (>= 2) Archs: i386, x64 Title: Mass spectrum processing by wavelet-based algorithms Description: Processing Mass Spectrometry spectrum by using wavelet based algorithm biocViews: MassSpectrometry, Proteomics Author: Pan Du, Warren Kibbe, Simon Lin Maintainer: Pan Du source.ver: src/contrib/MassSpecWavelet_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MassSpecWavelet_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MassSpecWavelet_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MassSpecWavelet_1.18.0.tgz vignettes: vignettes/MassSpecWavelet/inst/doc/MassSpecWavelet.pdf Package: MeasurementError.cor Version: 1.24.0 License: LGPL Title: Measurement Error model estimate for correlation coefficient Description: Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation biocViews: Bioinformatics Author: Beiying Ding Maintainer: Beiying Ding source.ver: src/contrib/MeasurementError.cor_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MeasurementError.cor_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MeasurementError.cor_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MeasurementError.cor_1.24.0.tgz vignettes: vignettes/MeasurementError.cor/inst/doc/MeasurementError.cor.pdf Package: MergeMaid Version: 2.24.0 Depends: R (>= 2.2.0), survival, Biobase, MASS, methods License: GPL (>= 2) Title: Merge Maid Description: The functions in this R extension are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be 'list','matrix', or 'ExpressionSet'. The main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculate the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross-validate associations of gene expression data with survival. biocViews: Microarray, DifferentialExpression, Visualization Author: Xiaogang Zhong Leslie Cope Elizabeth Garrett Giovanni Parmigiani Maintainer: Xiaogang Zhong URL: http://astor.som.jhmi.edu/MergeMaid source.ver: src/contrib/MergeMaid_2.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MergeMaid_2.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MergeMaid_2.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MergeMaid_2.24.0.tgz vignettes: vignettes/MergeMaid/inst/doc/MergeMaid.pdf Package: Mfuzz Version: 2.10.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 Title: Soft clustering of time series gene expression data Description: Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface) biocViews: Microarray, Clustering, TimeCourse, Preprocessing, Visualization Author: Matthias Futschik Maintainer: Matthias Futschik URL: http://www.sysbiolab.eu source.ver: src/contrib/Mfuzz_2.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Mfuzz_2.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Mfuzz_2.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Mfuzz_2.10.0.tgz vignettes: vignettes/Mfuzz/inst/doc/Mfuzz.pdf, vignettes/Mfuzz/inst/doc/MfuzzguiScreenshot.pdf, vignettes/Mfuzz/inst/doc/yeasttable3.pdf Package: MiChip Version: 1.6.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) Title: MiChip Parsing and Summarizing Functions Description: This package takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages. biocViews: Microarray, preprocessing Author: Jonathon Blake Maintainer: Jonathon Blake source.ver: src/contrib/MiChip_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MiChip_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MiChip_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MiChip_1.6.0.tgz vignettes: vignettes/MiChip/inst/doc/MiChip.pdf Package: MiPP Version: 1.24.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) Title: Misclassification Penalized Posterior Classification Description: This package finds optimal sets of genes that seperate samples into two or more classes. biocViews: Microarray, Classification Author: HyungJun Cho , Sukwoo Kim , Mat Soukup , and Jae K. Lee Maintainer: Sukwoo Kim URL: http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/ source.ver: src/contrib/MiPP_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MiPP_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MiPP_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MiPP_1.24.0.tgz vignettes: vignettes/MiPP/inst/doc/MiPP.pdf Package: MotIV Version: 1.6.0 Imports: graphics, grid, IRanges, lattice, methods, rGADEM, stats, utils Suggests: rtracklayer License: GPL 2 Archs: i386, x64 Title: Motif Identification and Validation Description: This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs. biocViews: Microarray, ChIPchip, ChIPSeq, GenomicSequence Author: Eloi Mercier, Raphael Gottardo Maintainer: Eloi Mercier , Raphael Gottardo source.ver: src/contrib/MotIV_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/MotIV_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/MotIV_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/MotIV_1.6.0.tgz vignettes: vignettes/MotIV/inst/doc/MotIV.pdf Package: Mulcom Version: 1.2.5 Depends: R (>= 2.9.0), fields, Biobase Imports: graphics, grDevices, stats, methods License: GPL-2 Archs: i386, x64 Title: Calculates Mulcom test Description: Identification of differentially expressed genes and false discovery rate (FDR) calculation by Multiple Comparison test biocViews: Statistics, MultipleComparisons, Microarray, DifferentialExpression, GeneExpression Author: Claudio Isella Maintainer: Claudio Isella source.ver: src/contrib/Mulcom_1.2.5.tar.gz win.binary.ver: bin/windows/contrib/2.13/Mulcom_1.2.5.zip win64.binary.ver: bin/windows64/contrib/2.13/Mulcom_1.2.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Mulcom_1.2.5.tgz vignettes: vignettes/Mulcom/inst/doc/MulcomVignette.pdf Package: NCIgraph Version: 1.0.0 Depends: graph, R (>= 2.10.0) Imports: graph, KEGGgraph, methods, RBGL, RCytoscape, R.methodsS3 Suggests: Rgraphviz Enhances: DEGraph License: GPL-3 Title: Pathways from the NCI Pathways Database Description: Provides various methods to load the pathways from the NCI Pathways Database in R graph objects and to re-format them. biocViews: Bioinformatics, GraphsAndNetworks Author: Laurent Jacob Maintainer: Laurent Jacob source.ver: src/contrib/NCIgraph_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/NCIgraph_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/NCIgraph_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/NCIgraph_1.0.0.tgz vignettes: vignettes/NCIgraph/inst/doc/NCIgraph.pdf Package: NTW Version: 1.2.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 Title: Predict gene network using an Ordinary Differential Equation (ODE) based method Description: This package predicts the gene-gene interaction network and identifies the direct transcriptional targets of the perturbation using an ODE (Ordinary Differential Equation) based method. biocViews: Preprocessing Author: Wei Xiao, Yin Jin, Darong Lai, Xinyi Yang, Yuanhua Liu, Christine Nardini Maintainer: Yuanhua Liu source.ver: src/contrib/NTW_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/NTW_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/NTW_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/NTW_1.2.0.tgz vignettes: vignettes/NTW/inst/doc/NTW.pdf Package: NuPoP Version: 1.2.0 License: GPL-2 Archs: i386, x64 Title: An R package for nucleosome positioning prediction Description: NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at http://nucleosome.stats.northwestern.edu. biocViews: genetics,visualization,classification Author: Ji-Ping Wang ; Liqun Xi Maintainer: Ji-Ping Wang source.ver: src/contrib/NuPoP_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/NuPoP_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/NuPoP_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/NuPoP_1.2.0.tgz vignettes: vignettes/NuPoP/inst/doc/NuPoP-intro.pdf, vignettes/NuPoP/inst/doc/NuPoP-manual.pdf Package: OCplus Version: 1.26.0 Depends: R (>= 2.1.0), akima Imports: multtest (>= 1.7.3), graphics, grDevices, stats License: LGPL Title: Operating characteristics plus sample size and local fdr for microarray experiments Description: This package allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes). biocViews: Microarray, Bioinformatics, DifferentialExpression, MultipleComparisons Author: Yudi Pawitan and Alexander Ploner Maintainer: Alexander Ploner source.ver: src/contrib/OCplus_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/OCplus_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/OCplus_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/OCplus_1.26.0.tgz vignettes: vignettes/OCplus/inst/doc/OCplus.pdf Package: OLIN Version: 1.30.0 Depends: R (>= 2.5.0), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 Title: Optimized local intensity-dependent normalisation of two-color microarrays Description: Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data biocViews: Microarray, TwoChannel, QualityControl, Preprocessing, Visualization Author: Matthias Futschik Maintainer: Matthias Futschik URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/index.html source.ver: src/contrib/OLIN_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/OLIN_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/OLIN_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/OLIN_1.30.0.tgz vignettes: vignettes/OLIN/inst/doc/OLIN.pdf Package: OLINgui Version: 1.26.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 Title: Graphical user interface for OLIN Description: Graphical user interface for the OLIN package biocViews: Microarray, TwoChannel, QualityControl, Preprocessing, Visualization Author: Matthias Futschik Maintainer: Matthias Futschik URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/index.html source.ver: src/contrib/OLINgui_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/OLINgui_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/OLINgui_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/OLINgui_1.26.0.tgz vignettes: vignettes/OLINgui/inst/doc/OLINgui.pdf, vignettes/OLINgui/inst/doc/OLINguiScreenshot.pdf Package: OTUbase Version: 1.2.0 Depends: R (>= 2.9.0), methods, ShortRead (>= 1.4.0), Biobase, vegan Imports: Biostrings, ShortRead, IRanges License: Artistic-2.0 Title: Provides structure and functions for the analysis of OTU data Description: Provides a platform for Operational Taxonomic Unit based analysis biocViews: Bioinformatics, HighThroughputSequencingData, DataImport Author: Daniel Beck, Matt Settles, and James A. Foster Maintainer: Daniel Beck source.ver: src/contrib/OTUbase_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/OTUbase_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/OTUbase_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/OTUbase_1.2.0.tgz vignettes: vignettes/OTUbase/inst/doc/Introduction_to_OTUbase.pdf Package: OrderedList Version: 1.24.0 Depends: R (>= 2.1.0), Biobase (>= 1.5.12), twilight (>= 1.9.2), methods Imports: Biobase, graphics, methods, stats, twilight License: GPL (>= 2) Title: Similarities of Ordered Gene Lists Description: Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively. biocViews: Microarray, DifferentialExpression, MultipleComparisons Author: Xinan Yang, Stefanie Scheid, Claudio Lottaz Maintainer: Claudio Lottaz URL: http://compdiag.molgen.mpg.de/software/index.shtml source.ver: src/contrib/OrderedList_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/OrderedList_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/OrderedList_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/OrderedList_1.24.0.tgz vignettes: vignettes/OrderedList/inst/doc/bcb_logo.pdf, vignettes/OrderedList/inst/doc/tr_2006_01.pdf Package: OutlierD Version: 1.16.0 Depends: R (>= 2.3.0), Biobase, quantreg License: GPL (>= 2) Title: Outlier detection using quantile regression on the M-A scatterplots of high-throughput data Description: This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data. biocViews: Microarray, Bioinformatics Author: HyungJun Cho Maintainer: Sukwoo Kim URL: http://www.korea.ac.kr/~stat2242/ source.ver: src/contrib/OutlierD_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/OutlierD_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/OutlierD_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/OutlierD_1.16.0.tgz vignettes: vignettes/OutlierD/inst/doc/OutlierD.pdf Package: PAnnBuilder Version: 1.16.0 Depends: R (>= 2.7.0), methods, utils, RSQLite, Biobase (>= 1.17.0), AnnotationDbi (>= 1.3.12) Imports: methods, utils, Biobase, DBI, RSQLite, AnnotationDbi Suggests: org.Hs.ipi.db License: LGPL (>= 2.0) Title: Protein annotation data package builder Description: Processing annotation data from public data repositories and building protein-centric annotation data packages. biocViews: Annotation, Proteomics Author: Li Hong lihong@sibs.ac.cn Maintainer: Li Hong URL: http://www.biosino.org/PAnnBuilder source.ver: src/contrib/PAnnBuilder_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/PAnnBuilder_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/PAnnBuilder_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/PAnnBuilder_1.16.0.tgz vignettes: vignettes/PAnnBuilder/inst/doc/PAnnBuilder.pdf, vignettes/PAnnBuilder/inst/doc/fulltext.pdf Package: PCpheno Version: 1.14.0 Depends: Category, ScISI (>= 1.3.0), SLGI, ppiStats, ppiData, annotate (>= 1.17.4) Imports: AnnotationDbi, Biobase, Category, GO.db, graph, graphics, GSEABase, KEGG.db, methods, ScISI, stats Suggests: KEGG.db, GO.db, org.Sc.sgd.db License: Artistic-2.0 Title: Phenotypes and cellular organizational units Description: Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways. biocViews: GraphsAndNetworks, Proteomics Author: Nolwenn Le Meur and Robert Gentleman Maintainer: Nolwenn Le Meur source.ver: src/contrib/PCpheno_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/PCpheno_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/PCpheno_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/PCpheno_1.14.0.tgz vignettes: vignettes/PCpheno/inst/doc/PCpheno.pdf Package: PGSEA Version: 1.26.0 Depends: GO.db, KEGG.db, AnnotationDbi, annaffy, methods, Biobase (>= 2.5.5) Suggests: GSEABase, GEOquery, org.Hs.eg.db, hgu95av2.db, limma License: GPL-2 Title: Parametric Gene Set Enrichment Analysis Description: Parametric Analysis of Gene Set Enrichment biocViews: Microarray Author: Kyle Furge and Karl Dykema Maintainer: Karl Dykema source.ver: src/contrib/PGSEA_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/PGSEA_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/PGSEA_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/PGSEA_1.26.0.tgz vignettes: vignettes/PGSEA/inst/doc/PGSEA.pdf, vignettes/PGSEA/inst/doc/PGSEA2.pdf Package: PICS Version: 1.6.0 Depends: R(>= 2.11.0), IRanges, GenomicRanges, BSgenome Imports: IRanges, GenomicRanges, BSgenome, methods, graphics, grDevices, stats Suggests: snowfall, ShortRead, rtracklayer Enhances: multicore License: Artistic-2.0 Archs: i386, x64 Title: Probabilistic inference of ChIP-seq Description: Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach. biocViews: Clustering, Visualization, Sequencing, ChIPseq Author: Xuekui Zhang , Raphael Gottardo Maintainer: Arnaud Droit , Xuekui Zhang , Raphael Gottardo source.ver: src/contrib/PICS_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/PICS_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/PICS_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/PICS_1.6.0.tgz vignettes: vignettes/PICS/inst/doc/PICS.pdf Package: PLPE Version: 1.12.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) Title: Local Pooled Error Test for Differential Expression with Paired High-throughput Data Description: This package performs tests for paired high-throughput data. biocViews: Proteomics, Microarray, DifferentialExpression Author: HyungJun Cho and Jae K. Lee Maintainer: Soo-heang Eo URL: http://www.korea.ac.kr/~stat2242/ source.ver: src/contrib/PLPE_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/PLPE_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/PLPE_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/PLPE_1.12.0.tgz vignettes: vignettes/PLPE/inst/doc/PLPE.pdf Package: PROMISE Version: 1.4.0 Depends: R (>= 2.11.0), Biobase, GSEABase Imports: Biobase, GSEABase, stats License: GPL (>= 2) Title: PRojection Onto the Most Interesting Statistical Evidence Description: A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019 biocViews: Microarray, OneChannel, Bioinformatics, MultipleComparisons, GeneExpression Author: Stan Pounds , Xueyuan Cao Maintainer: Xueyuan Cao source.ver: src/contrib/PROMISE_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/PROMISE_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/PROMISE_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/PROMISE_1.4.0.tgz vignettes: vignettes/PROMISE/inst/doc/PROMISE.pdf Package: PROcess Version: 1.28.0 Depends: Icens Imports: graphics, grDevices, Icens, stats, utils License: Artistic-2.0 Title: Ciphergen SELDI-TOF Processing Description: A package for processing protein mass spectrometry data. biocViews: MassSpectrometry, Proteomics Author: Xiaochun Li Maintainer: Xiaochun Li source.ver: src/contrib/PROcess_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/PROcess_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.13/PROcess_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/PROcess_1.28.0.tgz vignettes: vignettes/PROcess/inst/doc/howtoprocess.pdf Package: PatientGeneSets Version: 1.2.0 Depends: R (>= 2.10.0), qvalue Imports: AnnotationDbi, limma, methods, stats Suggests: KEGG.db License: GPL (>= 2.0) Archs: i386, x64 Title: Patient-oriented gene-set analysis Description: Patient-oriented analysis of mutations from cancer genome studies. biocViews: Bioinformatics Author: Simina M. Boca, Giovanni Parmigiani Maintainer: Simina M. Boca source.ver: src/contrib/PatientGeneSets_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/PatientGeneSets_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/PatientGeneSets_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/PatientGeneSets_1.2.0.tgz vignettes: vignettes/PatientGeneSets/inst/doc/PatientGeneSets.pdf Package: R453Plus1Toolbox Version: 1.2.2 Depends: R (>= 2.12.0), Biobase, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer2 Imports: Biobase, biomaRt, Biostrings, BSgenome, IRanges (>= 1.10.2), methods, R2HTML, Rsamtools, rtracklayer, ShortRead Suggests: rtracklayer, ShortRead, Rsamtools, BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 Title: A package for importing and analyzing data from Roche's Genome Sequencer System. Description: The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided. biocViews: HighThroughputSequencing, Infrastructure, DataImport, DataRepresentation, Visualization, QualityControl, ReportWriting Author: Hans-Ulrich Klein, Christoph Bartenhagen, Christian Ruckert Maintainer: Hans-Ulrich Klein source.ver: src/contrib/R453Plus1Toolbox_1.2.2.tar.gz win.binary.ver: bin/windows/contrib/2.13/R453Plus1Toolbox_1.2.2.zip win64.binary.ver: bin/windows64/contrib/2.13/R453Plus1Toolbox_1.2.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/R453Plus1Toolbox_1.2.2.tgz vignettes: vignettes/R453Plus1Toolbox/inst/doc/vignette.pdf Package: RBGL Version: 1.28.0 Depends: graph, methods Imports: methods Suggests: Rgraphviz License: Artistic-2.0 Archs: i386, x64 Title: An interface to the BOOST graph library Description: A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library. biocViews: GraphsAndNetworks Author: Vince Carey , Li Long , R. Gentleman Maintainer: Li Long URL: http://www.bioconductor.org source.ver: src/contrib/RBGL_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/RBGL_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.13/RBGL_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RBGL_1.28.0.tgz vignettes: vignettes/RBGL/inst/doc/RBGL.pdf, vignettes/RBGL/inst/doc/filedep.pdf Package: RBioinf Version: 1.12.0 Depends: graph, methods License: Artistic-2.0 Archs: i386, x64 Title: RBioinf Description: Functions and datasets and examples to accompany the monograph R For Bioinformatics. biocViews: GeneExpression, Microarray, Preprocessing, QualityControl, Classification, Clustering, MultipleComparison, Annotation Author: Robert Gentleman Maintainer: Robert Gentleman source.ver: src/contrib/RBioinf_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/RBioinf_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/RBioinf_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RBioinf_1.12.0.tgz vignettes: vignettes/RBioinf/inst/doc/RBioinf.pdf Package: RCytoscape Version: 1.2.1 Depends: R (>= 2.12.1), graph (>= 1.28.0), XMLRPC (>= 0.2.4) Imports: methods, XMLRPC Suggests: RUnit License: GPL-2 Title: Display and manipulate graphs in Cytoscape Description: Interactvive viewing and exploration of graphs, connecting R to Cytoscape. biocViews: GraphsAndNetworks Author: Paul Shannon Maintainer: Paul Shannon URL: http://rcytoscape.systemsbiology.net/versions/current/ source.ver: src/contrib/RCytoscape_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/RCytoscape_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.13/RCytoscape_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RCytoscape_1.2.1.tgz vignettes: vignettes/RCytoscape/inst/doc/RCytoscape.pdf Package: RDRToolbox Version: 1.2.0 Depends: R (>= 2.9.0),rgl Imports: graphics, grDevices, methods, stats, MASS, rgl Suggests: golubEsets License: GPL (>= 2) Title: A package for nonlinear dimension reduction with Isomap and LLE. Description: A package for nonlinear dimension reduction using the Isomap and LLE algorithm. It also includes a routine for computing the Davis-Bouldin-Index for cluster validation, a plotting tool and a data generator for microarray gene expression data and for the Swiss Roll dataset. biocViews: Dimension,DimensionReduction,FeatureExtraction,Visualization,ClusterValidation,Microarray Author: Christoph Bartenhagen Maintainer: Christoph Bartenhagen source.ver: src/contrib/RDRToolbox_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/RDRToolbox_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/RDRToolbox_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RDRToolbox_1.2.0.tgz vignettes: vignettes/RDRToolbox/inst/doc/RDRToolbox-003.pdf, vignettes/RDRToolbox/inst/doc/SwissRoll.pdf, vignettes/RDRToolbox/inst/doc/plot3D.pdf, vignettes/RDRToolbox/inst/doc/vignette.pdf Package: RLMM Version: 1.14.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) Title: A Genotype Calling Algorithm for Affymetrix SNP Arrays Description: A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now. biocViews: Microarray, OneChannel, SNP, GeneticVariability Author: Nusrat Rabbee , Gary Wong Maintainer: Nusrat Rabbee URL: http://www.stat.berkeley.edu/users/nrabbee/RLMM SystemRequirements: Internal files Xba.CQV, Xba.regions (or other regions file) source.ver: src/contrib/RLMM_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/RLMM_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/RLMM_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RLMM_1.14.0.tgz vignettes: vignettes/RLMM/inst/doc/RLMM.pdf Package: RMAGEML Version: 2.26.0 Depends: R (>= 2.6.0), methods, marray, limma, Biobase License: LGPL 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 source.ver: src/contrib/RMAGEML_2.26.0.tar.gz vignettes: vignettes/RMAGEML/inst/doc/RMAGEML.pdf Package: RMAPPER Version: 1.2.0 Depends: methods Suggests: RCurl License: Artistic 2.0 Title: R interface to the MAPPER database of transcription factor binding sites Description: The RMAPPER package allows you to retrieve a set of predicted transcription factor binding sites from the MAPPER database (http://genome.ufl.edu/mapper/) through a simple HTTP request. biocViews: Annotation, Genetics Author: VJ Carey Maintainer: Heike Sichtig , Alberto Riva source.ver: src/contrib/RMAPPER_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/RMAPPER_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/RMAPPER_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RMAPPER_1.2.0.tgz vignettes: vignettes/RMAPPER/inst/doc/readMAPPER.pdf Package: RNAinteract Version: 1.0.0 Depends: R (>= 2.12.0), abind, locfit, Biobase Imports: RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid, hwriter, lattice, latticeExtra, limma, methods, qvalue, splots (>= 1.13.12) License: Artistic-2.0 Title: Estimate Pairwise Interactions from multidimensional features Description: RNAinteract estimates genetic interactions from multi-dimensional read-outs like features extracted from images. The screen is assumed to be performed in multi-well plates or similar designs. Starting from a list of features (e.g. cell number, area, fluorescence intensity) per well, genetic interactions are estimated. The packages provides functions for reporting interacting gene pairs, plotting heatmaps and double RNAi plots. An HTML report can be written for quality control and analysis. biocViews: CellBasedAssays, QualityControl, Preprocessing, Visualization Author: Bernd Fischer Maintainer: Bernd Fischer source.ver: src/contrib/RNAinteract_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/RNAinteract_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/RNAinteract_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RNAinteract_1.0.0.tgz vignettes: vignettes/RNAinteract/inst/doc/RNAinteract.pdf Package: RNAither Version: 2.0.0 Depends: R (>= 2.7.0), topGO, RankProd, prada Imports: geneplotter, limma, biomaRt, car, splots, methods License: Artistic-2.0 Title: Statistical analysis of high-throughput RNAi screens Description: RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes. biocViews: CellBasedAssays, QualityControl, Preprocessing, Visualization, Bioinformatics, Annotation, GO Author: Nora Rieber and Lars Kaderali, University of Heidelberg, Viroquant Research Group Modeling, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany Maintainer: Nora Rieber source.ver: src/contrib/RNAither_2.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/RNAither_2.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/RNAither_2.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RNAither_2.0.0.tgz vignettes: vignettes/RNAither/inst/doc/vignetteRNAither.pdf Package: ROC Version: 1.28.0 Depends: R (>= 1.9.0), utils, methods Suggests: Biobase License: Artistic-2.0 Archs: i386, x64 Title: utilities for ROC, with uarray focus Description: utilities for ROC, with uarray focus biocViews: Bioinformatics, DifferentialExpression Author: Vince Carey , Henning Redestig for C++ language enhancements Maintainer: Vince Carey URL: http://www.bioconductor.org source.ver: src/contrib/ROC_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ROC_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ROC_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ROC_1.28.0.tgz vignettes: vignettes/ROC/inst/doc/ROCnotes.pdf Package: RPA Version: 1.8.01 Depends: R (>= 2.12.1), affy, affydata, methods License: FreeBSD Title: RPA: probe reliability and differential gene expression analysis Description: Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays. Lahti et al. "Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays", TCBB/IEEE, 2011. http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.38 biocViews: GeneExpression, Microarray, Preprocessing, QualityControl Author: Leo Lahti Maintainer: Leo Lahti source.ver: src/contrib/RPA_1.8.01.tar.gz win.binary.ver: bin/windows/contrib/2.13/RPA_1.8.01.zip win64.binary.ver: bin/windows64/contrib/2.13/RPA_1.8.01.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RPA_1.8.01.tgz vignettes: vignettes/RPA/inst/doc/RPA.pdf Package: RTCA Version: 1.4.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools License: LGPL-3 Title: Open-source toolkit to analyse data from xCELLigence System (RTCA) by Roche Description: Import, analyze and visualize data harvested from Roche(R) Xcelligence RTCA systems. The package imports the rich information in real-time cell electrical impedance data into computational and statistical environment R/Bioconductor. As an alternative to commercial software provided by Roche, the RTCA package provides more transformation (normalization) strategies and various visualization tools. biocViews: CellBasedAssays, Infrastructure, Visualization, TimeCourse Author: Jitao David Zhang, with input from Ulrich Tschulena, Özgür Sahin and Stefan Wiemann Maintainer: Jitao David Zhang URL: http://code.google.com/p/xcelligence/, http://www.xcelligence.roche.com/, http://www.nextbiomotif.com/Home/scientific-programming source.ver: src/contrib/RTCA_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/RTCA_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/RTCA_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RTCA_1.4.0.tgz vignettes: vignettes/RTCA/inst/doc/RTCAtransformation.pdf, vignettes/RTCA/inst/doc/aboutRTCA.pdf Package: RTools4TB Version: 1.8.0 Depends: R (>= 2.5.1), Biobase, limma, methods Suggests: RColorBrewer, biocGraph, ALL License: LGPL Archs: i386, x64 Title: Data mining of public microarray data through connections to the TranscriptomeBrowser database. Description: TranscriptomeBrowser (TBrowser) hosts a large collection of transcriptional signatures (TS) automatically extracted from the Gene Expression Omnibus (GEO) database. Each GEO experiment (GSE) was processed so that a subset of the original expression matrix containing the most relevant/informative genes was kept and organized into a set of homogeneous signatures. Each signature was tested for functional enrichment using annotations terms obtained from numerous ontologies or curated databases (Gene Ontology, KEGG, BioCarta, Swiss-Prot, BBID, SMART, NIH Genetic Association DB, COG/KOG...) using the DAVID knowledgebase. The RTools4TB package can be used to perform complexe queries to the database. Thereby, RTools4TB can be helpful (i) to define the biological contexts (i.e, experiments) in which a set of genes are co-expressed and (ii) to define their most frequent neighbors. In addition, RTools4TB comes with a new algoritm, "Density Based Filtering And Markov Clustering" (DBF-MCL), whose goal is to partition large and noisy datasets. DBF-MCL is a tree-step adaptative algorithm that (i) find elements located in dense areas (ie. clusters) (ii) uses selected items to construct a graph and (iii) performs graph partitioning using MCL. This algorithm is implemented in the RTools4TB package although it requires a UNIX-like systems. biocViews: Microarray, OneChannel, TwoChannel, Clustering, Classification, DataImport, Annotation, GeneExpression Author: Aurelie Bergon, Fabrice Lopez, Julien Textoris, Samuel Granjeaud and Denis Puthier Maintainer: Aurelie Bergon URL: http://tagc.univ-mrs.fr/tbrowser/ source.ver: src/contrib/RTools4TB_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/RTools4TB_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/RTools4TB_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RTools4TB_1.8.0.tgz vignettes: vignettes/RTools4TB/inst/doc/RTools4TB.pdf Package: RWebServices Version: 1.16.0 Depends: SJava (>= 0.69-4), TypeInfo, methods, tools (>= 2.10.0), R (>= 2.5.0) Imports: RCurl License: file LICENSE Title: Expose R functions as web services through Java/Axis/Apache Description: This package provides mechanisms for automatic function prototyping and exposure of R functionality in a web services environment. biocViews: Infrastructure Author: Nianhua Li, MT Morgan Maintainer: Martin Morgan source.ver: src/contrib/RWebServices_1.16.0.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/RToJava.pdf, vignettes/RWebServices/inst/doc/RelatedWork.pdf Package: RankProd Version: 2.24.0 Depends: R (>= 1.9.0) Imports: graphics License: file LICENSE Title: Rank Product method for identifying differentially expressed genes with application in meta-analysis Description: Non-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 source.ver: src/contrib/RankProd_2.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/RankProd_2.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/RankProd_2.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RankProd_2.24.0.tgz vignettes: vignettes/RankProd/inst/doc/RankProd.pdf Package: RbcBook1 Version: 1.20.0 Depends: Biobase, graph License: Artistic-2.0 Title: Support for Springer monograph on Bioconductor Description: tools for building book biocViews: Software Author: Vince Carey and Wolfgang Huber Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey source.ver: src/contrib/RbcBook1_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/RbcBook1_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/RbcBook1_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RbcBook1_1.20.0.tgz vignettes: vignettes/RbcBook1/inst/doc/RbcBook1.pdf Package: RdbiPgSQL Version: 1.26.0 Depends: R (>= 2.6.0), Rdbi License: GPL-2 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 source.ver: src/contrib/RdbiPgSQL_1.26.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RdbiPgSQL_1.26.0.tgz Package: Rdbi Version: 1.26.0 Depends: R (>= 1.2) License: GPL-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 source.ver: src/contrib/Rdbi_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Rdbi_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Rdbi_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Rdbi_1.26.0.tgz Package: Rdisop Version: 1.12.0 Depends: R (>= 2.0.0) License: GPL-2 Archs: i386, x64 Title: Decomposition of Isotopic Patterns Description: Identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists. biocViews: MassSpectrometry Author: Anton Pervukhin , Steffen Neumann Maintainer: Steffen Neumann URL: http://msbi.ipb-halle.de/ SystemRequirements: None source.ver: src/contrib/Rdisop_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Rdisop_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Rdisop_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Rdisop_1.12.0.tgz vignettes: vignettes/Rdisop/inst/doc/Rdisop-isotopes.pdf, vignettes/Rdisop/inst/doc/Rdisop.pdf Package: RefPlus Version: 1.22.0 Depends: R (>= 2.8.0), Biobase (>= 2.1.0), affy (>= 1.20.0), affyPLM (>= 1.18.0), preprocessCore (>= 1.4.0) Suggests: affydata License: GPL (>= 2) Title: A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods. Description: The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods. biocViews: Microarray, OneChannel, Preprocessing Author: Kai-Ming Chang , Chris Harbron , Marie C South Maintainer: Kai-Ming Chang source.ver: src/contrib/RefPlus_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/RefPlus_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.13/RefPlus_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RefPlus_1.22.0.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: 1.26.0 Depends: R (>= 1.9.0), Biobase, AnnotationDbi (>= 1.4.0) Suggests: human.db0, mouse.db0, rat.db0 License: LGPL Title: Reads annotation data from TIGR Resourcerer or convert the annotation data into Bioconductor data pacakge. Description: This package allows user either to read an annotation data file from TIGR Resourcerer as a matrix or convert the file into a Bioconductor annotation data package using the AnnBuilder package. biocViews: Annotation, Microarray Author: Jianhua Zhang Maintainer: Jianhua Zhang source.ver: src/contrib/Resourcerer_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Resourcerer_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Resourcerer_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Resourcerer_1.26.0.tgz vignettes: vignettes/Resourcerer/inst/doc/Resourcerer.pdf Package: Rgraphviz Version: 1.30.1 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: graph, graphics, grDevices, grid, methods, utils License: Artistic-2.0 Archs: i386 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 SystemRequirements: Graphviz version >= 2.2 source.ver: src/contrib/Rgraphviz_1.30.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/Rgraphviz_1.30.1.zip win64.binary.ver: bin/windows64/contrib/2.13/Rgraphviz_1.30.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Rgraphviz_1.30.1.tgz vignettes: vignettes/Rgraphviz/inst/doc/Rgraphviz.pdf, vignettes/Rgraphviz/inst/doc/newRgraphvizInterface.pdf Package: Ringo Version: 1.16.0 Depends: methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix, grid Imports: genefilter, limma, vsn Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0) License: Artistic-2.0 Archs: i386, x64 Title: R Investigation of ChIP-chip Oligoarrays Description: The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects, but also contains more general functions for ChIP-chip data analysis, given that the data is supplied as RGList (raw) or ExpressionSet (pre- processed). The package employs functions from various other packages of the Bioconductor project and provides additional ChIP-chip-specific and NimbleGen-specific functionalities. biocViews: Microarray,TwoChannel,DataImport,QualityControl,Preprocessing Author: Joern Toedling, Oleg Sklyar, Tammo Krueger, Matt Ritchie, Wolfgang Huber Maintainer: J. Toedling source.ver: src/contrib/Ringo_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Ringo_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Ringo_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Ringo_1.16.0.tgz vignettes: vignettes/Ringo/inst/doc/Ringo.pdf Package: Rmagpie Version: 1.8.0 Depends: R (>= 2.6.1), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab, methods, pamr, stats, utils Suggests: xtable License: GPL (>= 3) Title: MicroArray Gene-expression-based Program In Error rate estimation Description: Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. A range of modern classifiers are available, including support vector machines (SVMs), nearest shrunken centroids (NSCs)... Advanced methods are provided to estimate the predictive error rate and to report the subset of genes which appear essential in discriminating between classes. biocViews: Microarray, Classification Author: Camille Maumet , with contributions from C. Ambroise J. Zhu Maintainer: Camille Maumet URL: http://www.bioconductor.org/ source.ver: src/contrib/Rmagpie_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Rmagpie_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Rmagpie_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Rmagpie_1.8.0.tgz vignettes: vignettes/Rmagpie/inst/doc/Magpie_examples.pdf Package: RmiR Version: 1.8.0 Depends: R (>= 2.7.0), RmiR.Hs.miRNA, RSVGTipsDevice Imports: DBI, methods, stats Suggests: hgug4112a.db,org.Hs.eg.db License: Artistic-2.0 Title: Package to work with miRNAs and miRNA targets with R Description: Useful functions to merge microRNA and respective targets using differents databases biocViews: Software,GeneExpression,Microarray,TimeCourse,Visualization Author: Francesco Favero Maintainer: Francesco Favero source.ver: src/contrib/RmiR_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/RmiR_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/RmiR_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RmiR_1.8.0.tgz vignettes: vignettes/RmiR/inst/doc/RmiR.pdf Package: Rolexa Version: 1.8.0 Depends: R (>= 2.9.0), mclust, graphics, grDevices, methods, ShortRead Imports: Biostrings, graphics, grDevices, IRanges, methods, ShortRead, stats Enhances: fork License: GPL-2 Title: Statistical analysis of Solexa sequencing data Description: Provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data biocViews: Sequencing, DataImport, Preprocessing, QualityControl Author: Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef Maintainer: Jacques Rougemont source.ver: src/contrib/Rolexa_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Rolexa_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Rolexa_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Rolexa_1.8.0.tgz vignettes: vignettes/Rolexa/inst/doc/Rolexa-vignette.pdf Package: RpsiXML Version: 1.12.0 Depends: methods, annotate (>= 1.21.0), graph (>= 1.21.0), Biobase, RBGL (>= 1.17.0), XML (>= 2.4.0), hypergraph (>= 1.15.2), AnnotationDbi Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, hom.Hs.inp.db, hom.Mm.inp.db, hom.Dm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db, Rgraphviz, ppiStats License: LGPL-3 Title: R interface to PSI-MI 2.5 files Description: Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously. biocViews: Infrastructure, Proteomics Author: Jitao David Zhang, Stefan Wiemann, Marc Carlson, with contributions from Tony Chiang Maintainer: Jitao David Zhang URL: http://www.bioconductor.org source.ver: src/contrib/RpsiXML_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/RpsiXML_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/RpsiXML_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/RpsiXML_1.12.0.tgz vignettes: vignettes/RpsiXML/inst/doc/RpsiXML.pdf, vignettes/RpsiXML/inst/doc/RpsiXMLApp.pdf Package: Rredland Version: 1.18.0 Depends: R (>= 2.6.0), methods, graph License: LGPL-2.1 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 source.ver: src/contrib/Rredland_1.18.0.tar.gz vignettes: vignettes/Rredland/inst/doc/Rredland.pdf Package: Rsamtools Version: 1.4.3 Depends: methods, IRanges (>= 1.9.4), GenomicRanges (>= 0.1.0), Biostrings (>= 2.15.0) Imports: methods, utils, IRanges, GenomicRanges, Biostrings LinkingTo: Biostrings, IRanges Suggests: ShortRead, GenomicFeatures, RUnit, KEGG.db License: Artistic-2.0 + file LICENSE Archs: i386, x64 Title: Import aligned BAM file format sequences into R / Bioconductor Description: This package provides an interface to the 'samtools' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map) format files. Facilities currently available include flexible file input. biocViews: DataImport, Sequencing, HighThroughputSequencing Author: Martin Morgan, Herv\'e Pag\`es Maintainer: Biocore Team c/o BioC user list URL: http://bioconductor.org/packages/release/bioc/html/Rsamtools.html source.ver: src/contrib/Rsamtools_1.4.3.tar.gz win.binary.ver: bin/windows/contrib/2.13/Rsamtools_1.4.3.zip win64.binary.ver: bin/windows64/contrib/2.13/Rsamtools_1.4.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Rsamtools_1.4.3.tgz vignettes: vignettes/Rsamtools/inst/doc/Rsamtools-Overview.pdf, vignettes/Rsamtools/inst/doc/Rsamtools-UsingCLibraries.pdf Package: Rsubread Version: 1.1.1 License: LGPL-3 Title: Rsubread: a super fast, sensitive and accurate read aligner for mapping next-generation sequencing reads Description: This package provides an R interface to the Subread aligner (http://sourceforge.net/projects/subread/) for mapping next-gen sequencing reads. Subread aligns reads to the referenc genome by using a set of substrings(subreads) extracted from each read. The consensus location mapped by subreads directly determines the mapping location of the read. Therefore, there is no costly extension step as in the "seed-and-extend" mapping paradig. Subread achieves much higher mapping speed and mapping sensitivity than "seed-and-extend" aligners at no cost to the accuracy. Subread aligner can align reads from all the major platforms inculding Illumina GA/HiSeq, ABI SOLiD, Roche 454 and HeliScope. It supports the mapping of paired-end reads and it also allows a large number of indels in the mapping. It can be used to align long reads (>200bp) as well. biocViews: Sequencing, HighThroughputSequencing Author: Wei Shi, Yang Liao and Jenny Zhiyin Dai Maintainer: Wei Shi URL: http://bioconductor.org/packages/release/bioc/html/Rsubread.html source.ver: src/contrib/Rsubread_1.1.1.tar.gz vignettes: vignettes/Rsubread/inst/doc/Rsubread.pdf Package: Rtreemix Version: 1.14.0 Depends: R (>= 2.5.0), methods, graph, Biobase Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz License: LGPL Archs: i386, x64 Title: Rtreemix: Mutagenetic trees mixture models. Description: Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc. biocViews: Bioinformatics Author: Jasmina Bogojeska Maintainer: Jasmina Bogojeska source.ver: src/contrib/Rtreemix_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Rtreemix_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Rtreemix_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Rtreemix_1.14.0.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: 1.30.0 Depends: R (>= 2.6.0), methods Imports: methods License: Artistic-2.0 Archs: i386, x64 Title: Ruuid: Provides Universally Unique ID values Description: A package to provide UUID values in R biocViews: Infrastructure Author: R. Gentleman Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/Ruuid_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Ruuid_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Ruuid_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Ruuid_1.30.0.tgz vignettes: vignettes/Ruuid/inst/doc/Ruuid.pdf Package: SAGx Version: 1.26.0 Depends: R (>= 2.5.0), stats, multtest, methods Imports: Biobase Suggests: KEGG.db, hu6800.db License: GPL-3 Archs: i386, x64 Title: Statistical Analysis of the GeneChip Description: A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed. biocViews: Microarray, OneChannel, Preprocessing, DataImport, Bioinformatics, DifferentialExpression, Clustering, MultipleComparisons Author: Per Broberg Maintainer: Per Broberg, URL: http://home.swipnet.se/pibroberg/expression_hemsida1.html source.ver: src/contrib/SAGx_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/SAGx_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/SAGx_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/SAGx_1.26.0.tgz vignettes: vignettes/SAGx/inst/doc/samroc-ex.pdf Package: SBMLR Version: 1.48.0 Depends: XML, odesolve License: GPL-2 Title: SBML-R Interface and Analysis Tools Description: This package contains a systems biology markup language (SBML) interface and biochemical system analysis tools with illustrative examples. biocViews: GraphsAndNetworks Author: Tomas Radivoyevitch Maintainer: Tomas Radivoyevitch URL: http://epbi-radivot.cwru.edu/rpacks/ source.ver: src/contrib/SBMLR_1.48.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/SBMLR_1.48.0.zip win64.binary.ver: bin/windows64/contrib/2.13/SBMLR_1.48.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/SBMLR_1.48.0.tgz vignettes: vignettes/SBMLR/inst/doc/BMC.BioInformatics04.pdf, vignettes/SBMLR/inst/doc/manual.pdf, vignettes/SBMLR/inst/doc/quick-start.pdf Package: SIM Version: 1.20.0 Depends: R (>= 2.4), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt License: GPL (>= 2) Archs: i386, x64 Title: Integrated Analysis on two human genomic datasets Description: Finds associations between two human genomic datasets. biocViews: Microarray, Bioinformatics, Visualization Author: Renee X. de Menezes and Judith M. Boer Maintainer: Maarten van Iterson source.ver: src/contrib/SIM_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/SIM_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/SIM_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/SIM_1.20.0.tgz vignettes: vignettes/SIM/inst/doc/SIM.pdf Package: SJava Version: 0.78.0 Depends: R (>= 2.10.0), methods License: GPL (>= 2) Title: The Omegahat interface for R and Java. Description: An interface from R to Java to create and call Java objects and methods. biocViews: Infrastructure Author: Duncan Temple Lang, John Chambers Maintainer: Martin Morgan source.ver: src/contrib/SJava_0.78.0.tar.gz Package: SLGI Version: 1.12.0 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 License: Artistic-2.0 Title: Synthetic Lethal Genetic Interaction Description: A variety of data files and functions for the analysis of genetic interactions biocViews: GraphsAndNetworks, Proteomics Author: Nolwenn LeMeur, Zhen Jiang, Ting-Yuan Liu, Jess Mar and Robert Gentleman Maintainer: Nolwenn Le Meur source.ver: src/contrib/SLGI_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/SLGI_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/SLGI_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/SLGI_1.12.0.tgz vignettes: vignettes/SLGI/inst/doc/SLGI.pdf Package: SLqPCR Version: 1.18.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) Title: Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH Description: Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH biocViews: Bioinformatics Author: Matthias Kohl Maintainer: Matthias Kohl source.ver: src/contrib/SLqPCR_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/SLqPCR_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/SLqPCR_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/SLqPCR_1.18.0.tgz vignettes: vignettes/SLqPCR/inst/doc/SLqPCR.pdf Package: SMAP Version: 1.16.0 Depends: methods License: GPL-2 Archs: i386, x64 Title: A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling Description: Functions and classes for DNA copy number profiling of array-CGH data biocViews: Microarray, TwoChannel, CopyNumberVariants Author: Robin Andersson Maintainer: Robin Andersson source.ver: src/contrib/SMAP_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/SMAP_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/SMAP_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/SMAP_1.16.0.tgz vignettes: vignettes/SMAP/inst/doc/SMAP.pdf Package: SNPchip Version: 1.16.0 Depends: R (>= 2.10.0), Biobase (>= 2.7.4), methods, oligoClasses (>= 1.9.52), graphics Imports: Biobase (>= 2.7.4), graphics, grDevices, methods, oligoClasses (>= 1.9.52), stats, utils Suggests: RSQLite, VanillaICE, RColorBrewer, genefilter, pd.mapping50k.xba240 License: LGPL (>= 2) 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: CopyNumberVariants, SNP, GeneticVariability, Visualization Author: Robert Scharpf and Ingo Ruczinski Maintainer: Robert Scharpf URL: http://www.biostat.jhsph.edu/~iruczins/software/snpchip.html source.ver: src/contrib/SNPchip_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/SNPchip_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/SNPchip_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/SNPchip_1.16.0.tgz vignettes: vignettes/SNPchip/inst/doc/SNPchip.pdf Package: SPIA Version: 2.2.0 Depends: R (>= 2.8.0), graphics Imports: graphics Suggests: graph, Rgraphviz, KEGGgraph, hgu133plus2.db License: GPL (>= 2) Title: Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations Description: This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study. biocViews: Microarray, GraphsAndNetworks Author: Adi Laurentiu Tarca , Purvesh Kathri and Sorin Draghici Maintainer: Adi Laurentiu Tarca URL: http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1 source.ver: src/contrib/SPIA_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/SPIA_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/SPIA_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/SPIA_2.2.0.tgz vignettes: vignettes/SPIA/inst/doc/SPIA.pdf Package: SQUADD Version: 1.2.0 Depends: R (>= 2.11.0) Imports: graphics, grDevices, methods, RColorBrewer, stats, utils License: GPL (>=2) Title: Add-on of the SQUAD Software Description: This package SQUADD is a SQUAD add-on. It permits to generate SQUAD simulation matrix, prediction Heat-Map and Correlation Circle from PCA analysis. biocViews: GraphsAndNetworks, DataRepresentation Author: Martial Sankar, supervised by Christian Hardtke and Ioannis Xenarios Maintainer: Martial Sankar URL: http://www.unil.ch/dbmv/page21142_en.html source.ver: src/contrib/SQUADD_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/SQUADD_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/SQUADD_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/SQUADD_1.2.0.tgz vignettes: vignettes/SQUADD/inst/doc/SQUADD.pdf, vignettes/SQUADD/inst/doc/SQUADD_ERK.pdf Package: SRAdb Version: 1.6.0 Depends: RSQLite (>= 0.8-4) , graph, RCurl Imports: GEOquery Suggests: Rgraphviz License: Artistic-2.0 Title: A compilation of metadata from NCBI SRA and tools Description: The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. sra or sra-lite files can be downloaded for doing alignment locally. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata. biocViews: Infrastructure, HighThroughputSequencing, DataImport Author: Jack Zhu and Sean Davis Maintainer: Jack Zhu URL: http://watson.nci.nih.gov/ source.ver: src/contrib/SRAdb_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/SRAdb_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/SRAdb_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/SRAdb_1.6.0.tgz vignettes: vignettes/SRAdb/inst/doc/SRAdb.pdf Package: SSPA Version: 1.8.0 Depends: R (>= 2.8), methods, qvalue Imports: graphics, limma, methods, stats Suggests: multtest, quadprog, splines License: GPL (>= 2) Title: Sample Size and Power Analysis for Microarray Data Description: Sample size and power analysis for microarray data, where two groups are analysed. biocViews: Microarray Author: Maarten van Iterson Maintainer: Maarten van Iterson URL: http://www.humgen.nl/MicroarrayAnalysisGroup.html source.ver: src/contrib/SSPA_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/SSPA_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/SSPA_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/SSPA_1.8.0.tgz vignettes: vignettes/SSPA/inst/doc/SSPA.pdf, vignettes/SSPA/inst/doc/figChunk17.pdf Package: SamSPECTRAL Version: 1.6.0 Depends: R (>= 2.0.0) Imports: methods License: GPL version 2 or newer Archs: i386, x64 Title: Identifies cell population in flow cytometry data. Description: Given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting "connected components" estimate biological cell populations in the data sample. For instructions on manual installation, refer to the PDF file provided in the following documentation. biocViews: Bioinformatics, FlowCytometry, CellBiology, Clustering, Cancer, FlowCytData, StemCells, HIV Author: Habil Zare and Parisa Shooshtari Maintainer: Habil Zare source.ver: src/contrib/SamSPECTRAL_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/SamSPECTRAL_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/SamSPECTRAL_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/SamSPECTRAL_1.6.0.tgz vignettes: vignettes/SamSPECTRAL/inst/doc/Clustering_by_SamSPECTRAL.pdf Package: ScISI Version: 1.24.0 Depends: GO.db, RpsiXML, annotate, apComplex Imports: AnnotationDbi, GO.db, RpsiXML, annotate, methods, org.Sc.sgd.db, utils Suggests: ppiData, xtable License: LGPL Title: In Silico Interactome Description: Package to create In Silico Interactomes biocViews: GraphsAndNetworks, Proteomics Author: Tony Chiang Maintainer: Tony Chiang source.ver: src/contrib/ScISI_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ScISI_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ScISI_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ScISI_1.24.0.tgz vignettes: vignettes/ScISI/inst/doc/vignette.pdf Package: ShortRead Version: 1.10.4 Depends: methods, IRanges (>= 1.10.2), GenomicRanges, Biostrings (>= 2.19.0), lattice, Rsamtools Imports: IRanges, GenomicRanges, Biostrings, Biobase, hwriter, Rsamtools LinkingTo: IRanges, Biostrings Suggests: biomaRt, RUnit Enhances: Rmpi, multicore License: Artistic-2.0 Archs: i386, x64 Title: Classes and methods for high-throughput short-read sequencing data. Description: Base classes, functions, and methods for representation of high-throughput, short-read sequencing data. biocViews: DataImport, Sequencing, HighThroughputSequencing, QualityControl Author: Martin Morgan, Michael Lawrence, Simon Anders Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/ShortRead_1.10.4.tar.gz win.binary.ver: bin/windows/contrib/2.13/ShortRead_1.10.4.zip win64.binary.ver: bin/windows64/contrib/2.13/ShortRead_1.10.4.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ShortRead_1.10.4.tgz vignettes: vignettes/ShortRead/inst/doc/Overview.pdf, vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf Package: SpeCond Version: 1.6.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>=2) Title: Condition specific detection from expression data Description: This package performs a gene expression data analysis to detect condition-specific genes. Such genes are significantly up- or down-regulated in a small number of conditions. It does so by fitting a mixture of normal distributions to the expression values. Conditions can be environmental conditions, different tissues, organs or any other sources that you wish to compare in terms of gene expression. biocViews: Microarray, DifferentialExpression, Bioinformatics, MultipleComparisons, Clustering, ReportWriting Author: Florence Cavalli Maintainer: Florence Cavalli source.ver: src/contrib/SpeCond_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/SpeCond_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/SpeCond_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/SpeCond_1.6.0.tgz vignettes: vignettes/SpeCond/inst/doc/SpeCond.pdf Package: Starr Version: 1.8.1 Depends: Ringo, affy, affxparser Imports: pspline, MASS License: Artistic-2.0 Archs: i386, x64 Title: Simple tiling array analysis of Affymetrix ChIP-chip data Description: Starr facilitates the analysis of ChIP-chip data, in particular that of Affymetrix tiling arrays. The package provides functions for data import, quality assessment, data visualization and exploration. Furthermore, it includes high-level analysis features like association of ChIP signals with annotated features, correlation analysis of ChIP signals and other genomic data (e.g. gene expression), peak-finding with the CMARRT algorithm and comparative display of multiple clusters of ChIP-profiles. It uses the basic Bioconductor classes ExpressionSet and probeAnno for maximum compatibility with other software on Bioconductor. All functions from Starr can be used to investigate preprocessed data from the Ringo package, and vice versa. An important novel tool is the the automated generation of correct, up-to-date microarray probe annotation (bpmap) files, which relies on an efficient mapping of short sequences (e.g. the probe sequences on a microarray) to an arbitrary genome. biocViews: Microarray,OneChannel,DataImport,QualityControl,Preprocessing,ChIPchip Author: Benedikt Zacher, Johannes Soeding, Pei Fen Kuan, Matthias Siebert, Achim Tresch Maintainer: Benedikt Zacher source.ver: src/contrib/Starr_1.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/Starr_1.8.1.zip win64.binary.ver: bin/windows64/contrib/2.13/Starr_1.8.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Starr_1.8.1.tgz vignettes: vignettes/Starr/inst/doc/Starr.pdf Package: TDARACNE Version: 1.2.0 Depends: GenKern, Rgraphviz, Biobase License: GPL-2 Title: Network reverse engineering from time course data. Description: To infer gene networks from time-series measurements is a current challenge into bioinformatics research area. In order to detect dependencies between genes at different time delays, we propose an approach to infer gene regulatory networks from time-series measurements starting from a well known algorithm based on information theory. The proposed algorithm is expected to be useful in reconstruction of small biological directed networks from time course data. biocViews: Microarray, TimeCourse Author: Zoppoli P.,Morganella S., Ceccarelli M. Maintainer: Zoppoli Pietro source.ver: src/contrib/TDARACNE_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/TDARACNE_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/TDARACNE_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/TDARACNE_1.2.0.tgz vignettes: vignettes/TDARACNE/inst/doc/TDARACNE.pdf Package: TEQC Version: 1.0.0 Depends: IRanges Imports: Biobase, IRanges License: GPL (>= 2) Title: Quality control for target capture experiments Description: Target capture experiments combine hybridization-based (in solution or on microarrays) capture and enrichment of genomic regions of interest (e.g. the exome) with high throughput sequencing of the captured DNA fragments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on. biocViews: QualityControl, Microarray, HighThroughputSequencing, Bioinformatics, Genetics Author: M. Hummel, S. Bonnin, E. Lowy, G. Roma Maintainer: Manuela Hummel source.ver: src/contrib/TEQC_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/TEQC_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/TEQC_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/TEQC_1.0.0.tgz vignettes: vignettes/TEQC/inst/doc/TEQC.pdf Package: TargetSearch Version: 1.8.2 Depends: R (>= 2.7.0), xcms, methods Imports: graphics, grDevices, methods, stats, tcltk, utils Suggests: TargetSearchData License: GPL (>= 2) Archs: i386, x64 Title: A package for the analysis of GC-MS metabolite profiling data. Description: This packages provides a targeted pre-processing method for GC-MS data. biocViews: MassSpectrometry,Preprocessing Author: Alvaro Cuadros-Inostroza , Jan Lisec , Henning Redestig , Matt Hannah Maintainer: Alvaro Cuadros-Inostroza source.ver: src/contrib/TargetSearch_1.8.2.tar.gz win.binary.ver: bin/windows/contrib/2.13/TargetSearch_1.8.2.zip win64.binary.ver: bin/windows64/contrib/2.13/TargetSearch_1.8.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/TargetSearch_1.8.2.tgz vignettes: vignettes/TargetSearch/inst/doc/TargetSearch.pdf Package: TurboNorm Version: 1.0.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: affydata, affy, lattice License: LGPL Title: A fast scatterplot smoother suitable for microarray normalization Description: A fast scatterplot smoother based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available. biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, DNAMethylation, CpGIsland Author: Maarten van Iterson and Chantal van Leeuwen Maintainer: Maarten van Iterson URL: http://www.humgen.nl/MicroarrayAnalysisGroup.html source.ver: src/contrib/TurboNorm_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/TurboNorm_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/TurboNorm_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/TurboNorm_1.0.0.tgz vignettes: vignettes/TurboNorm/inst/doc/turbonorm.pdf Package: TypeInfo Version: 1.18.0 Depends: methods License: BSD Title: Optional Type Specification Prototype Description: A prototype for a mechanism for specifying the types of parameters and the return value for an R function. This is meta-information that can be used to generate stubs for servers and various interfaces to these functions. Additionally, the arguments in a call to a typed function can be validated using the type specifications. We allow types to be specified as either i) by class name using either inheritance - is(x, className), or strict instance of - class(x) %in% className, or ii) a dynamic test given as an R expression which is evaluated at run-time. More precise information and interesting tests can be done via ii), but it is harder to use this information as meta-data as it requires more effort to interpret it and it is of course run-time information. It is typically more meaningful. biocViews: Infrastructure Author: Duncan Temple Lang Robert Gentleman () Maintainer: Duncan Temple Lang source.ver: src/contrib/TypeInfo_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/TypeInfo_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/TypeInfo_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/TypeInfo_1.18.0.tgz vignettes: vignettes/TypeInfo/inst/doc/TypeInfoNews.pdf Package: VanillaICE Version: 1.14.0 Depends: R (>= 2.10.0), IRanges, oligoClasses (>= 1.9.53), methods Imports: SNPchip (>= 1.11.2), stats Suggests: genomewidesnp6Crlmm, hapmapsnp6, RColorBrewer, genefilter, RSQLite License: LGPL-2 Archs: i386, x64 Title: A Hidden Markov Model for high throughput genotyping arrays Description: Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays biocViews: Bioinformatics, CopyNumberVariants, SNP, GeneticVariability, Visualization Author: Robert Scharpf , Kevin Scharpf, and Ingo Ruczinski Maintainer: Robert Scharpf source.ver: src/contrib/VanillaICE_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/VanillaICE_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/VanillaICE_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/VanillaICE_1.14.0.tgz vignettes: vignettes/VanillaICE/inst/doc/VanillaICE.pdf Package: Vega Version: 1.0.0 License: GPL-2 Archs: i386, x64 Title: An R package for copy number data segmentation Description: Vega (Variational Estimator for Genomic Aberrations) is an algorithm that adapts a very popular variational model (Mumford and Shah) used in image segmentation so that chromosomal aberrant regions can be efficiently detected. biocViews: aCGH, DNACopyNumber Author: Sandro Morganella Maintainer: Sandro Morganella source.ver: src/contrib/Vega_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/Vega_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/Vega_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/Vega_1.0.0.tgz vignettes: vignettes/Vega/inst/doc/Vega.pdf Package: XDE Version: 1.12.0 Depends: R (>= 2.9.0), Biobase (>= 2.5.5), methods, graphics Imports: Biobase, genefilter, graphics, grDevices, gtools, MergeMaid, methods, stats, utils Suggests: siggenes, genefilter, MASS, RColorBrewer, GeneMeta License: LGPL-2 Archs: i386, x64 Title: XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression Description: Multi-level model for cross-study detection of differential gene expression. biocViews: Microarray, Bioinformatics, DifferentialExpression Author: R.B. Scharpf, G. Parmigiani, A.B. Nobel, and H. Tjelmeland Maintainer: Robert Scharpf source.ver: src/contrib/XDE_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/XDE_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/XDE_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/XDE_1.12.0.tgz vignettes: vignettes/XDE/inst/doc/XDE.pdf, vignettes/XDE/inst/doc/XdeParameterClass.pdf Package: a4Base Version: 1.0.1 Depends: methods, graphics, grid, Biobase, AnnotationDbi, annaffy, mpm, genefilter, limma, multtest, glmnet, a4Preproc, a4Core, gplots Suggests: Cairo, ALL Enhances: gridSVG, JavaGD License: GPL-3 Title: Automated Affymetrix Array Analysis Base Package Description: Automated Affymetrix Array Analysis biocViews: Microarray Author: Willem Talloen, Tobias Verbeke, Tine Casneuf, An De Bondt, Steven Osselaer and Hinrich Goehlmann Maintainer: Tobias Verbeke source.ver: src/contrib/a4Base_1.0.1.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/a4Base_1.0.1.tgz Package: a4Classif Version: 1.1.3 Depends: methods, a4Core, a4Preproc, MLInterfaces, ROCR, pamr, glmnet, varSelRF Imports: a4Core Suggests: ALL License: GPL-3 Title: Automated Affymetrix Array Analysis Classification Package Description: Automated Affymetrix Array Analysis Classification Package biocViews: Bioinformatics, Microarray Author: Willem Talloen, Tobias Verbeke Maintainer: Tobias Verbeke source.ver: src/contrib/a4Classif_1.1.3.tar.gz win.binary.ver: bin/windows/contrib/2.13/a4Classif_1.1.3.zip win64.binary.ver: bin/windows64/contrib/2.13/a4Classif_1.1.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/a4Classif_1.1.3.tgz Package: a4Core Version: 1.1.3 Depends: methods, Biobase, glmnet License: GPL-3 Title: Automated Affymetrix Array Analysis Core Package Description: Automated Affymetrix Array Analysis Core Package biocViews: Bioinformatics, Microarray Author: Willem Talloen, Tobias Verbeke Maintainer: Tobias Verbeke source.ver: src/contrib/a4Core_1.1.3.tar.gz win.binary.ver: bin/windows/contrib/2.13/a4Core_1.1.3.zip win64.binary.ver: bin/windows64/contrib/2.13/a4Core_1.1.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/a4Core_1.1.3.tgz Package: a4Preproc Version: 1.0.1 Depends: methods, AnnotationDbi Suggests: ALL, hgu95av2.db License: GPL-3 Title: Automated Affymetrix Array Analysis Preprocessing Package Description: Automated Affymetrix Array Analysis Preprocessing Package biocViews: Microarray Author: Willem Talloen, Tobias Verbeke Maintainer: Tobias Verbeke source.ver: src/contrib/a4Preproc_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/a4Preproc_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.13/a4Preproc_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/a4Preproc_1.0.1.tgz Package: a4Reporting Version: 1.1.1 Depends: methods, annaffy Imports: xtable, utils License: GPL-3 Title: Automated Affymetrix Array Analysis Reporting Package Description: Automated Affymetrix Array Analysis Reporting Package biocViews: Microarray Author: Tobias Verbeke Maintainer: Tobias Verbeke source.ver: src/contrib/a4Reporting_1.1.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/a4Reporting_1.1.1.zip win64.binary.ver: bin/windows64/contrib/2.13/a4Reporting_1.1.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/a4Reporting_1.1.1.tgz Package: a4 Version: 1.1.2 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL License: GPL-3 Title: Automated Affymetrix Array Analysis Umbrella Package Description: Automated Affymetrix Array Analysis Umbrella Package biocViews: Bioinformatics, Microarray Author: Willem Talloen, Tobias Verbeke Maintainer: Tobias Verbeke source.ver: src/contrib/a4_1.1.2.tar.gz win.binary.ver: bin/windows/contrib/2.13/a4_1.1.2.zip win64.binary.ver: bin/windows64/contrib/2.13/a4_1.1.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/a4_1.1.2.tgz vignettes: vignettes/a4/inst/doc/a4vignette.pdf Package: aCGH Version: 1.30.0 Depends: R (>= 1.8.0), cluster, survival, multtest Imports: Biobase, cluster, grDevices, graphics, methods, multtest, stats, survival, splines, utils License: GPL-2 Archs: i386, x64 Title: Classes and functions for Array Comparative Genomic Hybridization data. Description: Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects. biocViews: CopyNumberVariants, DataImport, Genetics Author: Jane Fridlyand , Peter Dimitrov Maintainer: Peter Dimitrov source.ver: src/contrib/aCGH_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/aCGH_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/aCGH_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/aCGH_1.30.0.tgz vignettes: vignettes/aCGH/inst/doc/aCGH.pdf Package: adSplit Version: 1.22.0 Depends: R (>= 2.1.0), methods (>= 2.1.0) Imports: AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db (>= 1.8.1), graphics, grDevices, KEGG.db (>= 1.8.1), methods, multtest (>= 1.6.0), stats (>= 2.1.0) Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) License: GPL (>= 2) Archs: i386, x64 Title: Annotation-Driven Clustering Description: This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined. biocViews: Microarray, Bioinformatics, Clustering Author: Claudio Lottaz, Joern Toedling Maintainer: Claudio Lottaz URL: http://compdiag.molgen.mpg.de/software/index.shtml source.ver: src/contrib/adSplit_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/adSplit_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.13/adSplit_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/adSplit_1.22.0.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: 1.24.0 Depends: R (>= 2.6.0) Suggests: R.utils (>= 1.6.3), AffymetrixDataTestFiles License: LGPL (>= 2) Archs: i386, x64 Title: Affymetrix File Parsing SDK Description: Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure. biocViews: Infrastructure, DataImport Author: Henrik Bengtsson, James Bullard, Robert Gentleman, Kasper Daniel Hansen, Martin Morgan Maintainer: Kasper Daniel Hansen source.ver: src/contrib/affxparser_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/affxparser_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/affxparser_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/affxparser_1.24.0.tgz Package: affyContam Version: 1.10.0 Depends: R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata License: Artistic-2.0 Title: structured corruption of affymetrix cel file data Description: structured corruption of cel file data to demonstrate QA effectiveness biocViews: Infrastructure, Bioinformatics Author: V. Carey Maintainer: V. Carey source.ver: src/contrib/affyContam_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/affyContam_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/affyContam_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/affyContam_1.10.0.tgz vignettes: vignettes/affyContam/inst/doc/affyContam.pdf Package: affyILM Version: 1.4.0 Depends: R (>= 2.10.0), methods Imports: affxparser (>= 1.16.0), gcrma, affy, graphics, methods Suggests: AffymetrixDataTestFiles License: GPL-3 Archs: i386, x64 Title: Linear Model of background subtraction and the Langmuir isotherm Description: affyILM is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model. biocViews: Microarray, OneChannel, Preprocessing Author: K. Myriam Kroll, Fabrice Berger, Gerard Barkema, Enrico Carlon Maintainer: Myriam Kroll and Fabrice Berger SystemRequirements: Gnu Scientific Library version >= 1.8 source.ver: src/contrib/affyILM_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/affyILM_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/affyILM_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/affyILM_1.4.0.tgz vignettes: vignettes/affyILM/inst/doc/affyILM.pdf Package: affyPLM Version: 1.28.5 Depends: R (>= 2.6.0), affy (>= 1.11.0), Biobase, methods, gcrma, stats, preprocessCore (>= 1.5.1) LinkingTo: preprocessCore Suggests: affydata License: GPL (>= 2) Archs: i386, x64 Title: Methods for fitting probe-level models Description: A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools. biocViews: Microarray, OneChannel, Preprocessing, QualityControl Author: Ben Bolstad Maintainer: Ben Bolstad URL: http://bmbolstad.com source.ver: src/contrib/affyPLM_1.28.5.tar.gz win.binary.ver: bin/windows/contrib/2.13/affyPLM_1.28.5.zip win64.binary.ver: bin/windows64/contrib/2.13/affyPLM_1.28.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/affyPLM_1.28.5.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: affyPara Version: 1.12.0 Depends: R (>= 2.5.0), methods, affy (>= 1.20.0), snow (>= 0.2-3), vsn (>= 3.6.0), aplpack (>= 1.1.1) Suggests: affydata Enhances: affy License: GPL-3 Title: Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays Description: The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data. biocViews: Microarray, Preprocessing Author: Markus Schmidberger , Esmeralda Vicedo , Ulrich Mansmann Maintainer: Markus Schmidberger URL: http://www.ibe.med.uni-muenchen.de source.ver: src/contrib/affyPara_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/affyPara_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/affyPara_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/affyPara_1.12.0.tgz vignettes: vignettes/affyPara/inst/doc/affyPara.pdf, vignettes/affyPara/inst/doc/vsnStudy.pdf Package: affyQCReport Version: 1.30.0 Depends: Biobase (>= 1.13.16), affy, lattice Imports: affy, affyPLM, Biobase, genefilter, graphics, grDevices, lattice, RColorBrewer, simpleaffy, stats, utils, xtable Suggests: tkWidgets (>= 1.5.23), affydata (>= 1.4.1) License: LGPL (>= 2) Title: QC Report Generation for affyBatch objects Description: This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object. biocViews: Microarray,OneChannel,QualityControl Author: Craig Parman , Conrad Halling , Robert Gentleman Maintainer: Craig Parman source.ver: src/contrib/affyQCReport_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/affyQCReport_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/affyQCReport_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/affyQCReport_1.30.0.tgz vignettes: vignettes/affyQCReport/inst/doc/affyQCReport.pdf Package: affy Version: 1.30.0 Depends: R (>= 2.8.0), Biobase (>= 2.5.5) Imports: affyio (>= 1.13.3), Biobase (>= 2.5.5), graphics, grDevices, methods, preprocessCore, stats, utils LinkingTo: preprocessCore Suggests: tkWidgets (>= 1.19.0), affydata License: LGPL (>= 2.0) Archs: i386, x64 Title: Methods for Affymetrix Oligonucleotide Arrays Description: The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it. biocViews: Microarray, OneChannel, Preprocessing Author: Rafael A. Irizarry , Laurent Gautier , Benjamin Milo Bolstad , and Crispin Miller with contributions from Magnus Astrand , Leslie M. Cope , Robert Gentleman, Jeff Gentry, Conrad Halling , Wolfgang Huber, James MacDonald , Benjamin I. P. Rubinstein, Christopher Workman , John Zhang Maintainer: Rafael A. Irizarry source.ver: src/contrib/affy_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/affy_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/affy_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/affy_1.30.0.tgz vignettes: vignettes/affy/inst/doc/affy.pdf, vignettes/affy/inst/doc/builtinMethods.pdf, vignettes/affy/inst/doc/customMethods.pdf, vignettes/affy/inst/doc/vim.pdf Package: affycomp Version: 1.28.3 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycompData Suggests: splines License: GPL (>= 2) Title: Graphics Toolbox for Assessment of Affymetrix Expression Measures Description: The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays. biocViews: OneChannel, Microarray, Preprocessing Author: Rafael A. Irizarry and Zhijin Wu with contributions from Simon Cawley Maintainer: Rafael A. Irizarry source.ver: src/contrib/affycomp_1.28.3.tar.gz win.binary.ver: bin/windows/contrib/2.13/affycomp_1.28.3.zip win64.binary.ver: bin/windows64/contrib/2.13/affycomp_1.28.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/affycomp_1.28.3.tgz vignettes: vignettes/affycomp/inst/doc/affycomp.pdf Package: affycoretools Version: 1.24.0 Depends: affy, Biobase, GO.db, KEGG.db Imports: biomaRt, limma, GOstats, annotate, annaffy, genefilter, gcrma, splines, xtable, AnnotationDbi Suggests: affydata, hgfocuscdf, rgl License: Artistic-2.0 Title: Functions useful for those doing repetitive analyses with Affymetrix GeneChips. Description: Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see. biocViews: ReportWriting, Microarray, OneChannel, GeneExpression Author: James W. MacDonald Maintainer: James W. MacDonald source.ver: src/contrib/affycoretools_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/affycoretools_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/affycoretools_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/affycoretools_1.24.0.tgz vignettes: vignettes/affycoretools/inst/doc/affycoretools.pdf, vignettes/affycoretools/inst/doc/affycoretools_biomaRt.pdf Package: affyio Version: 1.20.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) Archs: i386, x64 Title: Tools for parsing Affymetrix data files Description: Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats. biocViews: Microarray, DataImport, Infrastructure Author: Benjamin Milo Bolstad Maintainer: Benjamin Milo Bolstad source.ver: src/contrib/affyio_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/affyio_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/affyio_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/affyio_1.20.0.tgz Package: affylmGUI Version: 1.26.0 Depends: limma, tcltk, affy, Biobase, affyio Suggests: tkrplot, affyPLM, R2HTML, xtable License: LGPL Title: GUI for affy analysis using limma package Description: A Graphical User Interface for affy analysis using the limma Microarray package biocViews: Microarray, OneChannel, DataImport, QualityControl, Preprocessing, Bioinformatics, DifferentialExpression, MultipleComparisons, GUI Author: James Wettenhall and Ken Simpson Division of Genetics and Bioinformatics, WEHI. Maintainer: Keith Satterley URL: http://bioinf.wehi.edu.au/affylmGUI/ source.ver: src/contrib/affylmGUI_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/affylmGUI_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/affylmGUI_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/affylmGUI_1.26.0.tgz vignettes: vignettes/affylmGUI/inst/doc/affylmGUI.pdf, vignettes/affylmGUI/inst/doc/extract.pdf Package: affypdnn Version: 1.26.0 Depends: R (>= 2.13.0), affy (>= 1.5) Suggests: affydata, hgu95av2probe License: LGPL Title: Probe Dependent Nearest Neighbours (PDNN) for the affy package Description: The package contains functions to perform the PDNN method described by Li Zhang et al. biocViews: OneChannel, Microarray, Preprocessing Author: H. Bjorn Nielsen and Laurent Gautier (Many thanks to Li Zhang early communications about the existence of the PDNN program and related publications). Maintainer: Laurent Gautier source.ver: src/contrib/affypdnn_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/affypdnn_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/affypdnn_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/affypdnn_1.26.0.tgz vignettes: vignettes/affypdnn/inst/doc/affypdnn.pdf Package: altcdfenvs Version: 2.14.0 Depends: R (>= 2.7), methods, Biobase, affy, makecdfenv, Biostrings, hypergraph Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer License: GPL (>= 2) Title: alternative CDF environments (aka probeset mappings) Description: Convenience data structures and functions to handle cdfenvs biocViews: Microarray, OneChannel, QualityControl, Preprocessing, Annotation, ProprietaryPlatforms, Transcription Author: Laurent Gautier Maintainer: Laurent Gautier source.ver: src/contrib/altcdfenvs_2.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/altcdfenvs_2.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/altcdfenvs_2.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/altcdfenvs_2.14.0.tgz vignettes: vignettes/altcdfenvs/inst/doc/altcdfenvs.pdf, vignettes/altcdfenvs/inst/doc/modify.pdf, vignettes/altcdfenvs/inst/doc/ngenomeschips.pdf Package: annaffy Version: 1.24.0 Depends: R (>= 2.5.0), methods, Biobase, GO.db, KEGG.db Imports: AnnotationDbi (>= 0.1.15) Suggests: hgu95av2.db, multtest, tcltk License: LGPL Title: Annotation tools for Affymetrix biological metadata Description: Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria. biocViews: OneChannel, Microarray, Annotation, GO, Pathways, ReportWriting Author: Colin A. Smith Maintainer: Colin A. Smith source.ver: src/contrib/annaffy_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/annaffy_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/annaffy_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/annaffy_1.24.0.tgz vignettes: vignettes/annaffy/inst/doc/annaffy.pdf Package: annotate Version: 1.30.1 Depends: R (>= 2.4.0), AnnotationDbi (>= 0.1.15) Imports: Biobase, AnnotationDbi, DBI, 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 License: Artistic-2.0 Title: Annotation for microarrays Description: Using R enviroments for annotation. biocViews: Annotation, Pathways, GO Author: R. Gentleman Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/annotate_1.30.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/annotate_1.30.1.zip win64.binary.ver: bin/windows64/contrib/2.13/annotate_1.30.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/annotate_1.30.1.tgz vignettes: vignettes/annotate/inst/doc/GOusage.pdf, vignettes/annotate/inst/doc/annotate.pdf, vignettes/annotate/inst/doc/chromLoc.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: annotationTools Version: 1.26.0 Imports: Biobase, stats License: GPL Title: Annotate microarrays and perform cross-species gene expression analyses using flat file databases. Description: Functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files). biocViews: Microarray, Annotation Author: Alexandre Kuhn Maintainer: Alexandre Kuhn source.ver: src/contrib/annotationTools_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/annotationTools_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/annotationTools_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/annotationTools_1.26.0.tgz vignettes: vignettes/annotationTools/inst/doc/annotationTools.pdf Package: anota Version: 1.0.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 Title: ANalysis Of Translational Activity (ANOTA). Description: Genome wide studies of translational control is emerging as a tool to study verious biological conditions. The output from such analysis is both the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively involved in translation (the actively translating mRNA level) for each mRNA. The standard analysis of such data strives towards identifying differential translational between two or more sample classes - i.e. differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels. This package allows for such analysis using partial variances and the random variance model. As 10s of thousands of mRNAs are analyzed in parallell the library performs a number of tests to assure that the data set is suitable for such analysis. biocViews: GeneExpression, DifferentialExpression, Microarray, HighThroughputSequencing Author: Ola Larsson , Nahum Sonenberg , Robert Nadon Maintainer: Ola Larsson source.ver: src/contrib/anota_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/anota_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/anota_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/anota_1.0.0.tgz vignettes: vignettes/anota/inst/doc/anota.pdf Package: apComplex Version: 2.18.0 Depends: graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL Title: Estimate protein complex membership using AP-MS protein data Description: Functions to estimate a bipartite graph of protein complex membership using AP-MS data. biocViews: Visualization, MassSpectrometry, GraphsAndNetworks Author: Denise Scholtens Maintainer: Denise Scholtens source.ver: src/contrib/apComplex_2.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/apComplex_2.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/apComplex_2.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/apComplex_2.18.0.tgz vignettes: vignettes/apComplex/inst/doc/apComplex.pdf Package: aroma.light Version: 1.20.0 Depends: R.methodsS3 (>= 1.2.1) Suggests: R.oo (>= 1.8.0), R.utils (>= 1.7.4), princurve (>= 1.1-10) License: LGPL (>= 2.1) Title: Light-weight methods for normalization and visualization of microarray data using only basic R data types Description: Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes. biocViews: Infrastructure, Microarray, OneChannel, TwoChannel, MultiChannel, Visualization, Preprocessing Author: Henrik Bengtsson Maintainer: Henrik Bengtsson URL: http://www.aroma-project.org/ source.ver: src/contrib/aroma.light_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/aroma.light_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/aroma.light_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/aroma.light_1.20.0.tgz Package: arrayMvout Version: 1.10.0 Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy, lumi Imports: simpleaffy, mdqc, affyContam, Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf License: Artistic-2.0 Title: multivariate outlier detection for expression array QA Description: This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate biocViews: Infrastructure, Bioinformatics, Microarray, QualityControl Author: Z. Gao, A. Asare, R. Wang, V. Carey Maintainer: V. Carey source.ver: src/contrib/arrayMvout_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/arrayMvout_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/arrayMvout_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/arrayMvout_1.10.0.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: arrayQualityMetrics Version: 3.8.0 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, Cairo (>= 1.4-6), genefilter, graphics, grDevices, grid, Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, simpleaffy, stats, SVGAnnotation (>= 0.9-0), utils, vsn, XML Suggests: ALLMLL, CCl4 License: LGPL (>= 2) Title: Quality metrics on microarray data sets Description: This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). Report contain both general and platform-specific sections. Both one and two color array platforms are supported. biocViews: Microarray, QualityControl, OneChannel, TwoChannel, ReportWriting Author: Audrey Kauffmann, Wolfgang Huber Maintainer: Audrey Kauffmann source.ver: src/contrib/arrayQualityMetrics_3.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/arrayQualityMetrics_3.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/arrayQualityMetrics_3.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/arrayQualityMetrics_3.8.0.tgz vignettes: vignettes/arrayQualityMetrics/inst/doc/aqm.pdf, vignettes/arrayQualityMetrics/inst/doc/arrayQualityMetrics.pdf Package: arrayQuality Version: 1.30.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL Title: Assessing array quality on spotted arrays Description: Functions for performing print-run and array level quality assessment. biocViews: Microarray,TwoChannel,QualityControl,Visualization Author: Agnes Paquet and Jean Yee Hwa Yang Maintainer: Agnes Paquet URL: http://arrays.ucsf.edu/ source.ver: src/contrib/arrayQuality_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/arrayQuality_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/arrayQuality_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/arrayQuality_1.30.0.tgz Package: attract Version: 1.4.0 Depends: R (>= 2.10.0), AnnotationDbi, KEGG.db, limma, cluster, GOstats, graphics, methods, stats Imports: Biobase, AnnotationDbi, KEGG.db, limma, cluster, GOstats, graphics, methods, stats Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) Title: Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape Description: This package contains the functions to find the gene expression modules that represent the drivers of Kauffman's attractor landscape. The modules are the core attractor pathways that discriminate between different cell types of groups of interest. Each pathway has a set of synexpression groups, which show transcriptionally-coordinated changes in gene expression. biocViews: Statistics, GeneExpression Author: Jessica Mar Maintainer: Jessica Mar source.ver: src/contrib/attract_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/attract_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/attract_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/attract_1.4.0.tgz vignettes: vignettes/attract/inst/doc/attract.pdf Package: baySeq Version: 1.6.0 Depends: R (>= 2.3.0), methods Suggests: snow License: GPL-3 Title: Empirical Bayesian analysis of patterns of differential expression in count data Description: This package identifies differential expression in high-throughput 'count' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods. biocViews: Bioinformatics, HighThroughputSequencing, DifferentialExpression, MultipleComparisons, SAGE Author: Thomas J. Hardcastle Maintainer: Thomas J. Hardcastle source.ver: src/contrib/baySeq_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/baySeq_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/baySeq_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/baySeq_1.6.0.tgz vignettes: vignettes/baySeq/inst/doc/baySeq.pdf Package: beadarraySNP Version: 1.18.0 Depends: methods, Biobase (>= 2.5.5), quantsmooth Suggests: aCGH, affy, limma, snapCGH, beadarray, DNAcopy License: GPL-2 Title: Normalization and reporting of Illumina SNP bead arrays Description: Importing data from Illumina SNP experiments and performing copy number calculations and reports. biocViews: CopyNumberVariants, SNP, GeneticVariability, TwoChannel, Preprocessing, DataImport Author: Jan Oosting Maintainer: Jan Oosting source.ver: src/contrib/beadarraySNP_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/beadarraySNP_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/beadarraySNP_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/beadarraySNP_1.18.0.tgz vignettes: vignettes/beadarraySNP/inst/doc/beadarraySNP.pdf Package: beadarray Version: 2.2.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods Imports: BeadDataPackR, limma Suggests: lumi, vsn, affy, hwriter License: GPL-2 Archs: i386, x64 Title: Quality assessment and low-level analysis for Illumina BeadArray data Description: The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided. biocViews: Microarray, OneChannel, QualityControl, Preprocessing Author: Mark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt Ritchie Maintainer: Mark Dunning source.ver: src/contrib/beadarray_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/beadarray_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/beadarray_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/beadarray_2.2.0.tgz vignettes: vignettes/beadarray/inst/doc/ImageProcessing.pdf, vignettes/beadarray/inst/doc/beadarray.pdf, vignettes/beadarray/inst/doc/beadlevel.pdf, vignettes/beadarray/inst/doc/beadsummary.pdf Package: betr Version: 1.8.0 Depends: R(>= 2.6.0) Imports: Biobase (>= 2.5.5), limma, mvtnorm, methods, stats Suggests: Biobase License: LGPL Title: Identify differentially expressed genes in microarray time-course data Description: The betr package implements the BETR (Bayesian Estimation of Temporal Regulation) algorithm to identify differentially expressed genes in microarray time-course data. biocViews: Microarray, Bioinformatics, DifferentialExpression, TimeCourse Author: Martin Aryee Maintainer: Martin Aryee source.ver: src/contrib/betr_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/betr_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/betr_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/betr_1.8.0.tgz vignettes: vignettes/betr/inst/doc/betr.pdf Package: bgafun Version: 1.14.0 Depends: made4, seqinr,ade4 License: Artistic-2.0 Title: BGAfun A method to identify specifity determining residues in protein families Description: A method to identify specifity determining residues in protein families using Between Group Analysis biocViews: Bioinformatics,Classification Author: Iain Wallace Maintainer: Iain Wallace source.ver: src/contrib/bgafun_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/bgafun_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/bgafun_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/bgafun_1.14.0.tgz vignettes: vignettes/bgafun/inst/doc/bgafun.pdf Package: bgx Version: 1.16.0 Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), gcrma (>= 2.4.1) Suggests: affydata, hgu95av2cdf License: GPL Archs: i386, x64 Title: Bayesian Gene eXpression Description: Bayesian integrated analysis of Affymetrix GeneChips biocViews: Microarray, DifferentialExpression Author: Ernest Turro, Graeme Ambler, Anne-Mette K Hein Maintainer: Ernest Turro source.ver: src/contrib/bgx_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/bgx_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/bgx_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/bgx_1.16.0.tgz vignettes: vignettes/bgx/inst/doc/bgx.pdf Package: bioDist Version: 1.24.1 Depends: R (>= 2.0), methods, Biobase,KernSmooth Suggests: locfit License: Artistic-2.0 Title: Different distance measures Description: A collection of software tools for calculating distance measures. biocViews: Bioinformatics Author: B. Ding, R. Gentleman and Vincent Carey Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/bioDist_1.24.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/bioDist_1.24.1.zip win64.binary.ver: bin/windows64/contrib/2.13/bioDist_1.24.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/bioDist_1.24.1.tgz vignettes: vignettes/bioDist/inst/doc/bioDist.pdf Package: biocGraph Version: 1.14.0 Depends: Rgraphviz, graph Imports: Rgraphviz, geneplotter, graph, methods Suggests: fibroEset, geneplotter, hgu95av2.db License: Artistic-2.0 Title: Graph examples and use cases in Bioinformatics Description: This package provides examples and code that make use of the different graph related packages produced by Bioconductor. biocViews: GraphsAndNetworks Author: Li Long , Robert Gentleman , Seth Falcon Florian Hahne Maintainer: Florian Hahne source.ver: src/contrib/biocGraph_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/biocGraph_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/biocGraph_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/biocGraph_1.14.0.tgz vignettes: vignettes/biocGraph/inst/doc/biocGraph.pdf, vignettes/biocGraph/inst/doc/layingOutPathways.pdf Package: biocViews Version: 1.20.3 Depends: R (>= 2.4.0) Imports: Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools, utils, XML Suggests: Biobase License: Artistic-2.0 Title: Categorized views of R package repositories Description: structures for vocabularies and narratives of views biocViews: Infrastructure Author: VJ Carey , BJ Harshfield , S Falcon Maintainer: Biocore Team c/o BioC user list URL: http://www.bioconductor.org/packages/release/BiocViews.html source.ver: src/contrib/biocViews_1.20.3.tar.gz win.binary.ver: bin/windows/contrib/2.13/biocViews_1.20.3.zip win64.binary.ver: bin/windows64/contrib/2.13/biocViews_1.20.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/biocViews_1.20.3.tgz vignettes: vignettes/biocViews/inst/doc/HOWTO-BCV.pdf, vignettes/biocViews/inst/doc/createReposHtml.pdf Package: biomaRt Version: 2.8.1 Depends: methods Imports: XML, RCurl Suggests: annotate License: Artistic-2.0 Title: Interface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase and Gramene) Description: In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining. biocViews: Annotation Author: Steffen Durinck , Wolfgang Huber Maintainer: Steffen Durinck source.ver: src/contrib/biomaRt_2.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/biomaRt_2.8.1.zip win64.binary.ver: bin/windows64/contrib/2.13/biomaRt_2.8.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/biomaRt_2.8.1.tgz vignettes: vignettes/biomaRt/inst/doc/biomaRt.pdf Package: bridge Version: 1.16.0 Depends: R (>= 1.9.0), rama License: GPL (>= 2) Archs: i386, x64 Title: Bayesian Robust Inference for Differential Gene Expression Description: Test for differentially expressed genes with microarray data. This package can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. Our model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space. biocViews: Microarray,OneChannel,TwoChannel,DifferentialExpression Author: Raphael Gottardo Maintainer: Raphael Gottardo source.ver: src/contrib/bridge_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/bridge_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/bridge_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/bridge_1.16.0.tgz vignettes: vignettes/bridge/inst/doc/bridge.pdf Package: cellHTS2 Version: 2.16.0 Depends: RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid Imports: prada, GSEABase, Category License: Artistic-2.0 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 source.ver: src/contrib/cellHTS2_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/cellHTS2_2.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/cellHTS2_2.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/cellHTS2_2.16.0.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: cellHTS Version: 1.22.0 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) License: Artistic-2.0 Title: Analysis of cell-based screens Description: Analysis of cell-based RNA interference screens biocViews: CellBasedAssays, Visualization Author: Wolfgang Huber , Ligia Bras , Michael Boutros Maintainer: Ligia Bras URL: http://www.dkfz.de/signaling, http://www.ebi.ac.uk/huber source.ver: src/contrib/cellHTS_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/cellHTS_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.13/cellHTS_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/cellHTS_1.22.0.tgz vignettes: vignettes/cellHTS/inst/doc/cellhts.pdf, vignettes/cellHTS/inst/doc/twoChannels.pdf, vignettes/cellHTS/inst/doc/twoWay.pdf Package: cghMCR Version: 1.10.0 Depends: methods, DNAcopy, CNTools, limma License: LGPL Title: Find chromosome regions showing common gains/losses Description: This package provides functions to identify genomic regions of interests based on segmented copy number data from multiple samples. biocViews: Microarray, CopyNumberVariants Author: J. Zhang and B. Feng Maintainer: J. Zhang source.ver: src/contrib/cghMCR_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/cghMCR_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/cghMCR_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/cghMCR_1.10.0.tgz vignettes: vignettes/cghMCR/inst/doc/findMCR.pdf Package: charm Version: 1.4.0 Depends: R (>= 2.11.0), Biobase, SQN, fields, RColorBrewer, genefilter Imports: BSgenome, Biobase, oligo (>= 1.11.31), oligoClasses(>= 1.9.42), ff, preprocessCore, methods, stats, Biostrings, IRanges, siggenes, nor1mix, gtools, grDevices, graphics, utils Suggests: charmData, BSgenome.Hsapiens.UCSC.hg18 License: LGPL (>= 2) Title: Analysis of DNA methylation data from CHARM microarrays Description: This package implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. It finds differentially methylated regions between samples, calculates percentage methylation estimates and includes array quality assessment tools. biocViews: Microarray, Bioinformatics, DNAMethylation Author: Martin Aryee, Peter Murakami, Harris Jaffee, Srinivasan Yegnasubramanian, Rafael Irizarry Maintainer: Martin Aryee source.ver: src/contrib/charm_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/charm_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/charm_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/charm_1.4.0.tgz vignettes: vignettes/charm/inst/doc/charm.pdf Package: chipseq Version: 1.2.0 Depends: methods, IRanges (>= 1.7.13), GenomicRanges (>= 1.3.4), BSgenome, ShortRead Imports: BSgenome, GenomicRanges, IRanges, lattice, methods, ShortRead, stats Suggests: GenomicFeatures, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 Archs: i386, x64 Title: chipseq: A package for analyzing chipseq data Description: Tools for helping process short read data for chipseq experiments biocViews: ChIPseq Author: Deepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/chipseq_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/chipseq_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/chipseq_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/chipseq_1.2.0.tgz vignettes: vignettes/chipseq/inst/doc/Workflow.pdf Package: chopsticks Version: 1.16.0 Depends: R(>= 2.3.0), survival, methods Imports: graphics, grDevices, methods, stats, survival, utils Suggests: hexbin License: GPL-3 Archs: i386, x64 Title: The snp.matrix and X.snp.matrix classes Description: Implements classes and methods for large-scale SNP association studies biocViews: Microarray, SNP, GeneticVariability Author: Hin-Tak Leung Maintainer: Hin-Tak Leung URL: http://sourceforge.net/projects/outmodedbonsai/ source.ver: src/contrib/chopsticks_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/chopsticks_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/chopsticks_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/chopsticks_1.16.0.tgz vignettes: vignettes/chopsticks/inst/doc/chopsticks-vignette.pdf, vignettes/chopsticks/inst/doc/clustering-comparison-vignette.pdf, vignettes/chopsticks/inst/doc/imputation-vignette.pdf, vignettes/chopsticks/inst/doc/pca-vignette.pdf, vignettes/chopsticks/inst/doc/snpMatrix-paper-HumanHeridity2007.pdf, vignettes/chopsticks/inst/doc/tdt-vignette.pdf Package: clippda Version: 1.2.0 Depends: R (>= 2.10.0),limma, statmod, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>=2) Title: A package for the clinical proteomic profiling data analysis Description: Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations. biocViews: Proteomics, OneChannel, DataPreprocessing,Bioinformatics,DifferentialExpression, MultipleComparisons, SampleSize Author: Stephen Nyangoma Maintainer: Stephen Nyangoma URL: http://www.cancerstudies.bham.ac.uk/crctu/CLIPPDA.shtml source.ver: src/contrib/clippda_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/clippda_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/clippda_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/clippda_1.2.0.tgz vignettes: vignettes/clippda/inst/doc/clippda.pdf Package: clst Version: 1.0.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 Title: Classification by local similarity threshold Description: Package for modified nearest-neighbor classification based on calculation of a similarity threshold distinguishing within-group from between-group comparisons. biocViews: Classification Author: Noah Hoffman Maintainer: Noah Hoffman source.ver: src/contrib/clst_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/clst_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/clst_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/clst_1.0.0.tgz vignettes: vignettes/clst/inst/doc/clstDemo.pdf, vignettes/clst/inst/doc/matchtypes.pdf Package: clstutils Version: 1.0.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit, RSVGTipsDevice License: GPL-3 Title: Tools for performing taxonomic assignment. Description: Tools for performing taxonomic assignment based on phylogeny using pplacer and clst. biocViews: HighThroughputSequencing, Classification, Visualization, QualityControl Author: Noah Hoffman Maintainer: Noah Hoffman source.ver: src/contrib/clstutils_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/clstutils_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/clstutils_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/clstutils_1.0.0.tgz vignettes: vignettes/clstutils/inst/doc/pplacerDemo.pdf, vignettes/clstutils/inst/doc/refSet.pdf Package: clusterProfiler Version: 1.0.6 Depends: stats, plyr, ggplot2 Imports: methods, qvalue, AnnotationDbi, GO.db, KEGG.db, org.Hs.eg.db, org.Mm.eg.db, org.Sc.sgd.db Suggests: GOSemSim License: Artistic-2.0 Title: statistical analysis and visulization of functional profiles for genes and gene clusters Description: The package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters. biocViews: Bioinformatics, Clustering, GO, Pathways, Visualization, MultipleComparisons Author: Guangchuang Yu Maintainer: Guangchuang Yu source.ver: src/contrib/clusterProfiler_1.0.6.tar.gz win.binary.ver: bin/windows/contrib/2.13/clusterProfiler_1.0.6.zip win64.binary.ver: bin/windows64/contrib/2.13/clusterProfiler_1.0.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/clusterProfiler_1.0.6.tgz vignettes: vignettes/clusterProfiler/inst/doc/clusterProfiler.pdf Package: clusterStab Version: 1.24.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 Title: Compute cluster stability scores for microarray data Description: This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters. biocViews: Clustering Author: James W. MacDonald, Debashis Ghosh, Mark Smolkin Maintainer: James W. MacDonald source.ver: src/contrib/clusterStab_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/clusterStab_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/clusterStab_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/clusterStab_1.24.0.tgz vignettes: vignettes/clusterStab/inst/doc/clusterStab.pdf Package: cn.farms Version: 1.1.12 Depends: R (>= 2.11), Biobase, methods, ff, oligoClasses, snowfall Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 License: LGPL (>= 2.0) Archs: i386, x64 Title: cn.farms - Factor Analysis for copy number estimation Description: This package implements the cn.FARMS algorithm for copy number variation (CNV) analysis. cn.FARMS allows to analyze all existing Affymetrix (10K-SNP6.0) array types, supports high-performance computing using snow and ff. biocViews: Microarray, Bioinformatics, CopyNumberVariants Author: Andreas Mitterecker , Djork-Arne Clevert Maintainer: Andreas Mitterecker , Djork-Arne Clevert URL: http://www.bioinf.jku.at/software/cnfarms/cnfarms.html source.ver: src/contrib/cn.farms_1.1.12.tar.gz win.binary.ver: bin/windows/contrib/2.13/cn.farms_1.1.12.zip win64.binary.ver: bin/windows64/contrib/2.13/cn.farms_1.1.12.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/cn.farms_1.1.12.tgz vignettes: vignettes/cn.farms/inst/doc/cn.farms.pdf Package: coRNAi Version: 1.2.0 Depends: cellHTS2, limma, locfit Imports: MASS, gplots, lattice, grDevices, graphics, stats License: Artistic-2.0 Title: Analysis of co-knock-down RNAi data Description: Analysis of combinatorial cell-based RNAi screens biocViews: CellBasedAssays Author: Elin Axelsson Maintainer: Elin Axelsson SystemRequirements: Graphviz source.ver: src/contrib/coRNAi_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/coRNAi_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/coRNAi_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/coRNAi_1.2.0.tgz vignettes: vignettes/coRNAi/inst/doc/coRNAi.pdf Package: codelink Version: 1.20.0 Depends: methods, Biobase (>= 2.5.5), limma Imports: annotate Suggests: genefilter Enhances: multicore License: GPL-2 Title: Manipulation of Codelink Bioarrays data. Description: This packages allow reading into R of Codelink bioarray data exported as text from the Codelink software. Also includes some functions to ease the manipulation and pre-processing of data, such in background correction and normalization. biocViews: Microarray, OneChannel, DataImport, Preprocessing Author: Diego Diez Maintainer: Diego Diez URL: http://www.kuicr.kyoto-u.ac.jp/~diez source.ver: src/contrib/codelink_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/codelink_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/codelink_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/codelink_1.20.0.tgz vignettes: vignettes/codelink/inst/doc/CodelinkSet.pdf, vignettes/codelink/inst/doc/codelink.pdf Package: convert Version: 1.28.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL Title: Convert Microarray Data Objects Description: Define coerce methods for microarray data objects. biocViews: Infrastructure, Microarray, TwoChannel Author: Gordon Smyth , James Wettenhall , Yee Hwa (Jean Yang) , Martin Morgan Martin Morgan Maintainer: Yee Hwa (Jean) Yang URL: http://bioinf.wehi.edu.au/limma/convert.html source.ver: src/contrib/convert_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/convert_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.13/convert_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/convert_1.28.0.tgz vignettes: vignettes/convert/inst/doc/convert.pdf Package: copa Version: 1.20.0 Depends: Biobase, methods Suggests: colonCA License: Artistic-2.0 Archs: i386, x64 Title: Functions to perform cancer outlier profile analysis. Description: COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles. biocViews: OneChannel, TwoChannel, DifferentialExpression, Visualization Author: James W. MacDonald Maintainer: James W. MacDonald source.ver: src/contrib/copa_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/copa_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/copa_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/copa_1.20.0.tgz vignettes: vignettes/copa/inst/doc/copa.pdf Package: cosmoGUI Version: 1.18.0 Depends: tkWidgets, cosmo License: LGPL (>= 2) Title: GUI for constructing constraint sets used by the cosmo package Description: cosmoGUI allows the user to interactively define constraint sets that can be used by the cosmo package to supervise the search for shared motifs in a set of DNA sequences. The constraints can be either adapted from a set of commonly used templates or defined from scratch. biocViews: SequenceMatching, GUI Author: Fabian Gallusser, Oliver Bembom, and Sandrine Dudoit Maintainer: Oliver Bembom URL: http://cosmoweb.berkeley.edu/intro.html, http://www.bepress.com/ucbbiostat/paper209/ source.ver: src/contrib/cosmoGUI_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/cosmoGUI_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/cosmoGUI_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/cosmoGUI_1.18.0.tgz Package: cosmo Version: 1.18.0 Depends: R (>= 2.4.0), methods, utils, seqLogo Suggests: cosmoGUI License: file LICENSE Archs: i386, x64 Title: Supervised detection of conserved motifs in DNA sequences Description: cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may include bounds on the information content across certain regions of the unknown motif, for example, and can often be formulated on the basis of prior knowledge about the structure of the transcription factor in question. The unknown motif width, the distribution of motif occurrences (OOPS, ZOOPS, or TCM), as well as the appropriate constraint set can be selected data-adaptively. biocViews: SequenceMatching Author: Oliver Bembom, Fabian Gallusser, and Sandrine Dudoit Maintainer: Oliver Bembom URL: http://cosmoweb.berkeley.edu/intro.html, http://www.bepress.com/sagmb/vol6/iss1/art8 source.ver: src/contrib/cosmo_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/cosmo_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/cosmo_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/cosmo_1.18.0.tgz vignettes: vignettes/cosmo/inst/doc/cosmo.pdf Package: crlmm Version: 1.10.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.11.9), oligoClasses (>= 1.13.22) Imports: affyio (>= 1.19.2), ellipse, ff (>= 2.2-1), genefilter (>= 1.33.0), mvtnorm, preprocessCore (>= 1.13.4), splines, stats, SNPchip, utils Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.4), snpMatrix, ellipse, RUnit License: Artistic-2.0 Archs: i386, x64 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms biocViews: Microarray, Preprocessing, SNP, Bioinformatics, CopyNumberVariants Author: Benilton S Carvalho , Robert Scharpf , Matt Ritchie , Ingo Ruczinski , Rafael A Irizarry Maintainer: Benilton S Carvalho , Robert Scharpf , Matt Ritchie source.ver: src/contrib/crlmm_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/crlmm_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/crlmm_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/crlmm_1.10.0.tgz vignettes: vignettes/crlmm/inst/doc/AffymetrixPreprocessCN.pdf, vignettes/crlmm/inst/doc/IlluminaPreprocessCN.pdf, vignettes/crlmm/inst/doc/Infrastructure.pdf, vignettes/crlmm/inst/doc/copynumber.pdf, vignettes/crlmm/inst/doc/crlmmDownstream.pdf, vignettes/crlmm/inst/doc/crlmmIllumina.pdf, vignettes/crlmm/inst/doc/illumina_copynumber.pdf Package: ctc Version: 1.26.0 Depends: amap License: GPL-2 Title: Cluster and Tree Conversion. Description: Tools for export and import classification trees and clusters to other programs biocViews: Microarray, Clustering, Classification, DataImport, Visualization Author: Antoine Lucas , Laurent Gautier Maintainer: Antoine Lucas URL: http://antoinelucas.free.fr/ctc source.ver: src/contrib/ctc_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ctc_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ctc_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ctc_1.26.0.tgz vignettes: vignettes/ctc/inst/doc/ctc.pdf Package: cycle Version: 1.6.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 Title: Significance of periodic expression pattern in time-series data Description: Package for assessing the statistical significance of periodic expression based on Fourier analysis and comparison with data generated by different background models biocViews: Microarray, Bioinformatics,TimeCourse Author: Matthias Futschik Maintainer: Matthias Futschik URL: http://itb.biologie.hu-berlin.de/~futschik/software/R/cycle/index.html source.ver: src/contrib/cycle_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/cycle_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/cycle_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/cycle_1.6.0.tgz vignettes: vignettes/cycle/inst/doc/cycle.pdf Package: daMA Version: 1.24.0 Imports: MASS, stats License: GPL (>= 2) Title: Efficient design and analysis of factorial two-colour microarray data Description: This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. Statistical details are described in Bretz et al. (2003, submitted) biocViews: Microarray, TwoChannel, Bioinformatics, DifferentialExpression Author: Jobst Landgrebe and Frank Bretz Maintainer: Jobst Landgrebe URL: http://www.microarrays.med.uni-goettingen.de source.ver: src/contrib/daMA_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/daMA_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/daMA_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/daMA_1.24.0.tgz Package: ddCt Version: 1.6.0 Depends: R (>= 2.3.0), Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, methods License: LGPL-3 Title: The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR) Description: The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions. biocViews: GeneExpression, DifferentialExpression, RT-PCR Author: Jitao David Zhang, Rudolf Biczok and Markus Ruschhaupt Maintainer: Jitao David Zhang source.ver: src/contrib/ddCt_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ddCt_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ddCt_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ddCt_1.6.0.tgz vignettes: vignettes/ddCt/inst/doc/RT-PCR-Script-ddCt.pdf, vignettes/ddCt/inst/doc/rtPCR-usage.pdf, vignettes/ddCt/inst/doc/rtPCR.pdf Package: diffGeneAnalysis Version: 1.34.0 Imports: graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils License: GPL Title: Performs differential gene expression Analysis Description: Analyze microarray data biocViews: Bioinformatics, Microarray, DifferentialExpression Author: Choudary Jagarlamudi Maintainer: Choudary Jagarlamudi source.ver: src/contrib/diffGeneAnalysis_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/diffGeneAnalysis_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.13/diffGeneAnalysis_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/diffGeneAnalysis_1.34.0.tgz vignettes: vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf Package: domainsignatures Version: 1.12.0 Depends: R (>= 2.4.0), KEGG.db, prada, biomaRt, methods Imports: AnnotationDbi License: Artistic-2.0 Title: Geneset enrichment based on InterPro domain signatures Description: Find significantly enriched gene classifications in a list of functionally undescribed genes based on their InterPro domain structure. biocViews: Bioinformatics, Annotation, Pathways Author: Florian Hahne, Tim Beissbarth Maintainer: Florian Hahne source.ver: src/contrib/domainsignatures_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/domainsignatures_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/domainsignatures_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/domainsignatures_1.12.0.tgz vignettes: vignettes/domainsignatures/inst/doc/domainenrichment.pdf Package: dualKS Version: 1.12.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.0), affy, methods License: LGPL (>= 2.0) Title: Dual KS Discriminant Analysis and Classification Description: This package implements a Kolmogorov Smirnov rank-sum based algorithm for training (i.e. discriminant analysis--identification of genes that discriminate between classes) and classification of gene expression data sets. One of the chief strengths of this approach is that it is amenable to the "multiclass" problem. That is, it can discriminate between more than 2 classes. biocViews: Microarray, Bioinformatics Author: Eric J. Kort, Yarong Yang Maintainer: Eric J. Kort source.ver: src/contrib/dualKS_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/dualKS_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/dualKS_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/dualKS_1.12.0.tgz vignettes: vignettes/dualKS/inst/doc/dualKS.pdf Package: dyebias Version: 1.10.0 Depends: R (>= 1.4.1), marray, Biobase Suggests: limma, convert, GEOquery, dyebiasexamples, methods License: GPL-3 Title: The GASSCO method for correcting for slide-dependent gene-specific dye bias Description: Many two-colour hybridizations suffer from a dye bias that is both gene-specific and slide-specific. The former depends on the content of the nucleotide used for labeling; the latter depends on the labeling percentage. The slide-dependency was hitherto not recognized, and made addressing the artefact impossible. Given a reasonable number of dye-swapped pairs of hybridizations, or of same vs. same hybridizations, both the gene- and slide-biases can be estimated and corrected using the GASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009), doi:10.1038/msb.2009.21) biocViews: Microarray, TwoChannel, QualityControl, Preprocessing Author: Philip Lijnzaad and Thanasis Margaritis Maintainer: Philip Lijnzaad URL: http://www.holstegelab.nl/publications/margaritis_lijnzaad source.ver: src/contrib/dyebias_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/dyebias_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/dyebias_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/dyebias_1.10.0.tgz vignettes: vignettes/dyebias/inst/doc/dyebias-vignette.pdf, vignettes/dyebias/inst/doc/dyebiasCompleteVignette.pdf, vignettes/dyebias/inst/doc/gassco.pdf Package: ecolitk Version: 1.24.0 Depends: R (>= 2.5) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest License: GPL (>= 2) Title: Meta-data and tools for E. coli Description: Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids. biocViews: Annotation, Visualization Author: Laurent Gautier Maintainer: Laurent Gautier source.ver: src/contrib/ecolitk_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ecolitk_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ecolitk_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ecolitk_1.24.0.tgz vignettes: vignettes/ecolitk/inst/doc/ecolitk.pdf Package: edd Version: 1.30.0 Depends: methods, golubEsets, Biobase, class, nnet, xtable License: LGPL Title: expression density diagnostics Description: tools for evaluating cohort distributions of gene expression levels biocViews: Bioinformatics, DifferentialExpression Author: Vince Carey Maintainer: Vince Carey source.ver: src/contrib/edd_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/edd_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/edd_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/edd_1.30.0.tgz vignettes: vignettes/edd/inst/doc/HOWTO-edd.pdf, vignettes/edd/inst/doc/eddDetails.pdf Package: edgeR Version: 2.2.6 Depends: R (>= 2.3.0), methods Imports: limma Suggests: MASS, statmod, splines License: LGPL (>= 2) Title: Empirical analysis of digital gene expression data in R Description: Differential expression analysis of RNA-seq and digital gene expression profiles with biological replication. Uses empirical Bayes estimation and exact tests based on the negative binomial distribution. Also useful for differential signal analysis with other types of genome-scale count data. biocViews: Bioinformatics, DifferentialExpression, SAGE, HighThroughputSequencing, RNAseq Author: Mark Robinson , Davis McCarthy , Gordon Smyth Maintainer: Mark Robinson , Davis McCarthy , Gordon Smyth source.ver: src/contrib/edgeR_2.2.6.tar.gz win.binary.ver: bin/windows/contrib/2.13/edgeR_2.2.6.zip win64.binary.ver: bin/windows64/contrib/2.13/edgeR_2.2.6.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/edgeR_2.2.6.tgz vignettes: vignettes/edgeR/inst/doc/edgeR.pdf, vignettes/edgeR/inst/doc/edgeR_case_study_Li_MDSplot.pdf, vignettes/edgeR/inst/doc/edgeR_case_study_Tuch_MDSplot.pdf, vignettes/edgeR/inst/doc/edgeR_case_study_longSAGE_MDSplot.pdf Package: eisa Version: 1.4.1 Depends: methods, isa2, Biobase, AnnotationDbi, Category, genefilter, DBI Suggests: igraph (>= 0.5.2), Matrix, GOstats, GO.db, KEGG.db, biclust, MASS, xtable, ALL, hgu95av2.db License: GPL (>= 2) Title: Expression data analysis via the Iterative Signature Algorithm Description: The Iterative Signature Algorithm (ISA) is a biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data. The ISA is capable of finding overlapping modules and it is resilient to noise. This package provides a convenient interface to the ISA, using standard BioConductor data structures; and also contains various visualization tools that can be used with other biclustering algorithms. biocViews: Classification, Visualization, Microarray, GeneExpression Author: Gabor Csardi Maintainer: Gabor Csardi source.ver: src/contrib/eisa_1.4.1.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/eisa_1.4.1.tgz vignettes: vignettes/eisa/inst/doc/EISA_biclust.pdf, vignettes/eisa/inst/doc/EISA_tutorial.pdf Package: explorase Version: 1.16.2 Depends: R (>= 2.6.2) Imports: limma, rggobi, RGtk2 Suggests: cairoDevice License: GPL-2 Title: GUI for exploratory data analysis of systems biology data Description: explore and analyze *omics data with R and GGobi biocViews: Visualization,Microarray,GUI Author: Michael Lawrence, Eun-kyung Lee, Dianne Cook, Jihong Kim, Hogeun An, and Dongshin Kim Maintainer: Michael Lawrence URL: http://www.metnetdb.org/MetNet_exploRase.htm source.ver: src/contrib/explorase_1.16.2.tar.gz win.binary.ver: bin/windows/contrib/2.13/explorase_1.16.2.zip win64.binary.ver: bin/windows64/contrib/2.13/explorase_1.16.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/explorase_1.16.2.tgz vignettes: vignettes/explorase/inst/doc/explorase.pdf Package: externalVector Version: 1.18.0 Depends: R (>= 1.8.0), methods, stats License: LGPL Archs: i386, x64 Title: Vector objects for R with external storage Description: Basic class definitions and generics for external pointer based vector objects for R. A simple in-memory implementation is also provided. biocViews: Infrastructure Author: Saikat DebRoy Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/externalVector_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/externalVector_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/externalVector_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/externalVector_1.18.0.tgz Package: fabia Version: 1.4.0 Depends: R (>= 2.8.0), methods Imports: methods, graphics Suggests: utils License: LGPL (>= 2.1) Archs: i386, x64 Title: FABIA: Factor Analysis for Bicluster Acquisition Description: Biclustering by "Factor Analysis for Bicluster Acquisition" (FABIA). FABIA is a model-based technique for biclustering, that is clustering rows and columns simultaneously. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. It captures realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. FABIA utilizes well understood model selection techniques like the EM algorithm and variational approaches and is embedded into a Bayesian framework. FABIA ranks biclusters according to their information content and separates spurious biclusters from true biclusters. The code is written in C++ based on Rcpp package. biocViews: Bioinformatics, Statistics, Microarray, DifferentialExpression, MultipleComparisons, Clustering, Visualization Author: Sepp Hochreiter Maintainer: Sepp Hochreiter URL: http://www.bioinf.jku.at/software/fabia/fabia.html source.ver: src/contrib/fabia_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/fabia_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/fabia_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/fabia_1.4.0.tgz vignettes: vignettes/fabia/inst/doc/fabia.pdf Package: factDesign Version: 1.28.0 Depends: Biobase (>= 2.5.5) Imports: stats Suggests: affy, genefilter License: LGPL Title: Factorial designed microarray experiment analysis Description: This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection. biocViews: Bioinformatics, Microarray, DifferentialExpression Author: Denise Scholtens Maintainer: Denise Scholtens source.ver: src/contrib/factDesign_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/factDesign_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.13/factDesign_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/factDesign_1.28.0.tgz vignettes: vignettes/factDesign/inst/doc/factDesign.pdf Package: farms Version: 1.4.0 Depends: R (>= 2.8), affy (>= 1.20.0), MASS, methods Imports: affy, MASS, Biobase (>= 1.13.41), methods, graphics Suggests: affydata, Biobase, utils License: LGPL (>= 2.1) Title: FARMS - Factor Analysis for Robust Microarray Summarization Description: The package provides the summarization algorithm called Factor Analysis for Robust Microarray Summarization (FARMS) and a novel unsupervised feature selection criterion called "I/NI-calls" biocViews: GeneExpression, Microarray, Preprocessing, QualityControl Author: Djork-Arne Clevert Maintainer: Djork-Arne Clevert URL: http://www.bioinf.jku.at/software/farms/farms.html source.ver: src/contrib/farms_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/farms_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/farms_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/farms_1.4.0.tgz vignettes: vignettes/farms/inst/doc/farms.pdf Package: fdrame Version: 1.24.0 Imports: tcltk, graphics, grDevices, stats, utils License: GPL (>= 2) Archs: i386, x64 Title: FDR adjustments of Microarray Experiments (FDR-AME) Description: This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma biocViews: Microarray,DifferentialExpression,MultipleComparisons Author: Yoav Benjamini, Effi Kenigsberg, Anat Reiner, Daniel Yekutieli Maintainer: Effi Kenigsberg source.ver: src/contrib/fdrame_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/fdrame_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/fdrame_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/fdrame_1.24.0.tgz vignettes: vignettes/fdrame/inst/doc/fdrame.pdf Package: flagme Version: 1.8.0 Depends: gcspikelite Imports: gplots, graphics, MASS, methods, SparseM, stats, utils, xcms License: LGPL (>= 2) Archs: i386, x64 Title: Analysis of Metabolomics GC/MS Data Description: Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data biocViews: Bioinformatics, DifferentialExpression, MassSpectrometry Author: Mark Robinson Maintainer: Mark Robinson source.ver: src/contrib/flagme_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/flagme_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/flagme_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/flagme_1.8.0.tgz vignettes: vignettes/flagme/inst/doc/flagme.pdf Package: flowClust Version: 2.10.0 Depends: R(>= 2.5.0), methods, mnormt, ellipse, Biobase, flowCore(>= 1.11.23) Suggests: snowfall Enhances: multicore License: Artistic-2.0 Archs: i386, x64 Title: Clustering for Flow Cytometry Description: Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. biocViews: Clustering, Bioinformatics, Visualization, FlowCytometry Author: Raphael Gottardo , Kenneth Lo Maintainer: Raphael Gottardo source.ver: src/contrib/flowClust_2.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/flowClust_2.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/flowClust_2.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/flowClust_2.10.0.tgz vignettes: vignettes/flowClust/inst/doc/flowClust.pdf Package: flowCore Version: 1.18.0 Depends: R (>= 2.8.1), Biobase, rrcov Imports: Biobase, feature, graph, graphics, grDevices, MASS, methods, rrcov, stats, utils Suggests: Rgraphviz, flowViz, ncdf License: Artistic-2.0 Archs: i386, x64 Title: flowCore: Basic structures for flow cytometry data Description: Provides S4 data structures and basic functions to deal with flow cytometry data. biocViews: Infrastructure, Flowcytometry, CellBasedAssays Author: B. Ellis, P. Haaland, F. Hahne, N. Le Meur, N. Gopalakrishnan Maintainer: F. Hahne source.ver: src/contrib/flowCore_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/flowCore_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/flowCore_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/flowCore_1.18.0.tgz vignettes: vignettes/flowCore/inst/doc/HowTo-flowCore.pdf Package: flowFP Version: 1.8.0 Depends: R(>= 2.5.0), flowCore, flowViz Imports: Biobase, flowCore, flowViz, graphics, grDevices, methods, stats License: Artistic-2.0 Archs: i386, x64 Title: Fingerprinting for Flow Cytometry Description: Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry. biocViews: Bioinformatics, Flowcytometry, CellBasedAssays, Clustering, Visualization Author: Herb Holyst , Wade Rogers Maintainer: Herb Holyst source.ver: src/contrib/flowFP_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/flowFP_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/flowFP_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/flowFP_1.8.0.tgz vignettes: vignettes/flowFP/inst/doc/flowFP_HowTo.pdf Package: flowFlowJo Version: 1.10.0 Depends: R (>= 2.5.0), MASS, Imports: flowCore, XML (>= 1.96), methods, Biobase License: GPL (>=3) Title: Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm. Description: FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the "FlowJo Workspace". This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm. biocViews: FlowCytometry Author: John J. Gosink Maintainer: John J. Gosink source.ver: src/contrib/flowFlowJo_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/flowFlowJo_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/flowFlowJo_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/flowFlowJo_1.10.0.tgz vignettes: vignettes/flowFlowJo/inst/doc/flowFlowJo.pdf Package: flowMeans Version: 1.4.0 Depends: R (>= 2.10.0) Imports: Biobase, graphics, grDevices, methods, rrcov, stats, feature, flowCore License: Artistic-2.0 Title: Non-parametric Flow Cytometry Data Gating Description: Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required. biocViews: Bioinformatics, FlowCytometry, CellBiology, Clustering, Cancer, FlowCytData, StemCells, HIV Author: Nima Aghaeepour Maintainer: Nima Aghaeepour source.ver: src/contrib/flowMeans_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/flowMeans_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/flowMeans_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/flowMeans_1.4.0.tgz vignettes: vignettes/flowMeans/inst/doc/flowMeans.pdf Package: flowMerge Version: 2.0.3 Depends: flowClust, flowCore, methods,snow,foreach,multicore Imports: rrcov, flowClust,flowCore, graphics, methods, rrcov, stats, utils Suggests: doMC License: Artistic-2.0 Title: Cluster Merging for Flow Cytometry Data Description: Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed. biocViews: Bioinformatics, Clustering, FlowCytometry Author: Greg Finak , Raphael Gottardo Maintainer: Greg Finak source.ver: src/contrib/flowMerge_2.0.3.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/flowMerge_2.0.3.tgz vignettes: vignettes/flowMerge/inst/doc/flowMerge.pdf Package: flowPhyto Version: 1.4.0 Depends: R (>= 1.8.0) Imports: caroline, flowClust, flowCore, flowMeans Suggests: RPostgreSQL, zoo, maps, mapdata, plotrix, TTR License: Artistic-2.0 Title: Methods for Continuous Flow Cytometry Description: Automated Analysis of Continuous Flow Cytometry Data. biocViews: FlowCytometry, DataImport, QualityControl, Classification, Bioinformatics, Visualization, Clustering Author: David M. Schruth and Francois Ribalet Maintainer: David M. Schruth URL: http://seaflow.ocean.washington.edu source.ver: src/contrib/flowPhyto_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/flowPhyto_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/flowPhyto_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/flowPhyto_1.4.0.tgz vignettes: vignettes/flowPhyto/inst/doc/flowPhyto.pdf Package: flowPlots Version: 1.0.0 Depends: R (>= 2.13.0), methods Suggests: vcd License: Artistic-2.0 Title: flowPlots: analysis plots and data class for gated flow cytometry data Description: Graphical displays with embedded statistical tests for gated ICS flow cytometry data, and a data class which stores "stacked" data and has methods for computing summary measures on stacked data, such as marginal and polyfunctional degree data. biocViews: FlowCytometry, CellBasedAssays, Visualization, DataRepresentation Author: N. Hawkins, S. Self Maintainer: N. Hawkins source.ver: src/contrib/flowPlots_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/flowPlots_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/flowPlots_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/flowPlots_1.0.0.tgz vignettes: vignettes/flowPlots/inst/doc/flowPlots.pdf Package: flowQ Version: 1.12.0 Depends: R (>= 2.4.0), outliers, lattice, flowViz, methods, mvoutlier, bioDist, parody,RColorBrewer,latticeExtra Imports: geneplotter, flowCore, flowViz License: Artistic-2.0 Title: Quality control for flow cytometry Description: Provides quality control and quality assessment tools for flow cytometry data. biocViews: Infrastructure, Flowcytometry, CellBasedAssays Author: R. Gentleman, F. Hahne, J. Kettman, N. Le Meur, N. Gopalakrishnan Maintainer: F. Hahne SystemRequirements: ImageMagick source.ver: src/contrib/flowQ_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/flowQ_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/flowQ_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/flowQ_1.12.0.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: 1.10.1 Depends: R (>= 2.9.0), flowCore (>= 1.10.0), fda (>= 2.2.6), mvoutlier, cluster Imports: MASS, flowViz, flowCore, fda (>= 2.2.6), Biobase, methods, grDevices, graphics, stats, utils, KernSmooth, lattice Suggests: flowViz, xtable License: Artistic-2.0 Title: Statistical methods for the analysis of flow cytometry data Description: Methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package. biocViews: FlowCytometry, CellBasedAssays, Bioinformatics Author: Florian Hahne, Nishant Gopalakrishnan, Alireza Hadj Khodabakhshi, Chao-Jen Wong, Kyongryun Lee Maintainer: Florian Hahne and Chao-Jen Wong source.ver: src/contrib/flowStats_1.10.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/flowStats_1.10.1.zip win64.binary.ver: bin/windows64/contrib/2.13/flowStats_1.10.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/flowStats_1.10.1.tgz vignettes: vignettes/flowStats/inst/doc/GettingStartedWithFlowStats.pdf Package: flowTrans Version: 1.4.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 Title: Parameter Optimization for Flow Cytometry Data Transformation Description: Profile maximum likelihood estimation of parameters for flow cytometry data transformations. biocViews: Bioinformatics, FlowCytometry Author: Greg Finak , Juan Manuel-Perez , Raphael Gottardo Maintainer: Greg Finak source.ver: src/contrib/flowTrans_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/flowTrans_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/flowTrans_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/flowTrans_1.4.0.tgz vignettes: vignettes/flowTrans/inst/doc/flowTrans.pdf Package: flowUtils Version: 1.12.0 Depends: R (>= 2.2.0), flowCore (>= 1.2.0) Imports: Biobase, flowCore, graph, methods, RUnit, stats, utils, XML, flowViz Suggests: gatingMLData License: Artistic-2.0 Title: Utilities for flow cytometry Description: Provides utilities for flow cytometry data. biocViews: Infrastructure, Flowcytometry, CellBasedAssays Author: Gopalakrishnan N, F. Hahne, B. Ellis, R. Gentleman M. Dalphin,N. Le Meur, B. Purcell. Maintainer: Nishant Gopalakrishnan source.ver: src/contrib/flowUtils_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/flowUtils_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/flowUtils_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/flowUtils_1.12.0.tgz Package: flowViz Version: 1.16.0 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, IDPmisc License: Artistic-2.0 Archs: i386, x64 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 source.ver: src/contrib/flowViz_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/flowViz_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/flowViz_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/flowViz_1.16.0.tgz vignettes: vignettes/flowViz/inst/doc/filters.pdf Package: frmaTools Version: 1.4.0 Depends: R (>= 2.10.0), affy Imports: Biobase, DBI, methods, preprocessCore, stats, utils Suggests: oligo, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData License: GPL (>= 2) Title: Frozen RMA Tools Description: Tools for advanced use of the frma package. biocViews: Software, Microarray, Preprocessing Author: Matthew N. McCall , Rafael A. Irizarry Maintainer: Matthew N. McCall URL: http://bioconductor.org source.ver: src/contrib/frmaTools_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/frmaTools_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/frmaTools_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/frmaTools_1.4.0.tgz vignettes: vignettes/frmaTools/inst/doc/frmaTools.pdf Package: frma Version: 1.4.0 Depends: R (>= 2.10.0), Biobase (>= 2.6.0) Imports: Biobase, MASS, DBI, affy, methods, oligo, oligoClasses, preprocessCore, utils Suggests: hgu133afrmavecs, hgu133abarcodevecs, frmaExampleData License: GPL (>= 2) Title: Frozen RMA and Barcode Description: Preprocessing and analysis for single microarrays and microarray batches. biocViews: Software, Microarray, Preprocessing Author: Matthew N. McCall , Rafael A. Irizarry , with contributions from Terry Therneau Maintainer: Matthew N. McCall URL: http://bioconductor.org source.ver: src/contrib/frma_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/frma_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/frma_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/frma_1.4.0.tgz vignettes: vignettes/frma/inst/doc/frma.pdf Package: gaga Version: 1.12.0 Depends: R (>= 2.5.0), Biobase, coda License: GPL (>= 2) Archs: i386, x64 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 source.ver: src/contrib/gaga_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/gaga_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/gaga_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/gaga_1.12.0.tgz vignettes: vignettes/gaga/inst/doc/gagamanual.pdf Package: gage Version: 2.2.0 Depends: graph, multtest Suggests: gageData, GO.db, GSEABase, KEGG.db, org.Hs.eg.db License: GPL (>=2.0) Title: Generally Applicable Gene-set Enrichment for Pathway Analysis Description: GAGE is a published method for gene set or pathway analysis. GAGE is generally applicable independent of microarray data attributes including sample sizes, experimental designs, microarray platforms, and other types of heterogeneity, and consistently achieves superior performance over other frequently used methods. In gage package, we provide functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies. In addition, we provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods. biocViews: Pathways, GO, DifferentialExpression, Microarray, OneChannel, TwoChannel, RNAseq, DataRepresentation, Genetics, Bioinformatics, MultipleComparisons Author: Weijun Luo Maintainer: Weijun Luo URL: http://www.biomedcentral.com/1471-2105/10/161 source.ver: src/contrib/gage_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/gage_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/gage_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/gage_2.2.0.tgz vignettes: vignettes/gage/inst/doc/gage.pdf Package: gaggle Version: 1.20.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>= 0.4.17) License: GPL version 2 or newer Title: Broadcast data between R and Gaggle Description: This package contains functions enabling data exchange between R and Gaggle enabled bioinformatics software, including Cytoscape, Firegoose and Gaggle Genome Browser. biocViews: Visualization, Annotation, GraphsAndNetworks, DataImport Author: Paul Shannon Maintainer: Christopher Bare URL: http://gaggle.systemsbiology.net/docs/geese/r/ source.ver: src/contrib/gaggle_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/gaggle_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/gaggle_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/gaggle_1.20.0.tgz vignettes: vignettes/gaggle/inst/doc/gaggle.pdf Package: gaia Version: 1.7.0 Depends: qvalue License: GPL-2 Title: GAIA: An R package for genomic analysis of significant chromosomal aberrations. Description: This package allows to assess the statistical significance of chromosomal aberrations. biocViews: aCGH, DNACopyNumber Author: Sandro Morganella et al. Maintainer: S. Morganella source.ver: src/contrib/gaia_1.7.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/gaia_1.7.0.zip win64.binary.ver: bin/windows64/contrib/2.13/gaia_1.7.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/gaia_1.7.0.tgz vignettes: vignettes/gaia/inst/doc/gaia.pdf Package: gcrma Version: 2.24.1 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), Biostrings (>= 2.11.32), splines Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL Archs: i386, x64 Title: Background Adjustment Using Sequence Information Description: Background adjustment using sequence information biocViews: Microarray, OneChannel, Preprocessing Author: Jean(ZHIJIN) Wu, Rafael Irizarry with contributions from James MacDonald Jeff Gentry Maintainer: Z. Wu source.ver: src/contrib/gcrma_2.24.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/gcrma_2.24.1.zip win64.binary.ver: bin/windows64/contrib/2.13/gcrma_2.24.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/gcrma_2.24.1.tgz vignettes: vignettes/gcrma/inst/doc/gcrma2.0.pdf Package: genArise Version: 1.28.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE Title: Microarray Analysis tool Description: genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer. biocViews: Microarray, TwoChannel, Preprocessing Author: Ana Patricia Gomez Mayen ,\\ Gustavo Corral Guille , \\ Lina Riego Ruiz ,\\ Gerardo Coello Coutino Maintainer: IFC Development Team URL: http://www.ifc.unam.mx/genarise source.ver: src/contrib/genArise_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/genArise_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.13/genArise_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/genArise_1.28.0.tgz vignettes: vignettes/genArise/inst/doc/genArise.pdf Package: gene2pathway Version: 2.2.0 Depends: R (>= 2.10.0), kernlab (>= 0.9), biomaRt (>= 1.12.1), KEGGSOAP (>= 1.12.0), RBGL, AnnotationDbi,org.Dm.eg.db, keggorthology (>= 2.0) Imports: SSOAP, RCurl Enhances: doMC License: GPL (>= 2) Title: Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures Description: The package takes a list of genes and predicts to which KEGG pathway each gene maps to. This is done by looking at the InterPro domains of each gene. Each prediction is assigned a confidence score. The package also allows to predict connected component membership of genes within signaling pathways. Separate models for each organism supported by KEGG can be trained. biocViews: Microarray, Bioinformatics, Classification, GraphsAndNetworks, Pathways Author: Holger Froehlich Maintainer: Holger Froehlich source.ver: src/contrib/gene2pathway_2.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/gene2pathway_2.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/gene2pathway_2.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/gene2pathway_2.2.0.tgz vignettes: vignettes/gene2pathway/inst/doc/gene2pathway.pdf Package: geneRecommender Version: 1.24.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) Title: A gene recommender algorithm to identify genes coexpressed with a query set of genes Description: This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions. biocViews: Microarray, Clustering Author: Gregory J. Hather , with contributions from Art B. Owen and Terence P. Speed Maintainer: Greg Hather source.ver: src/contrib/geneRecommender_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/geneRecommender_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/geneRecommender_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/geneRecommender_1.24.0.tgz vignettes: vignettes/geneRecommender/inst/doc/geneRecommender.pdf Package: genefilter Version: 1.34.0 Imports: AnnotationDbi, annotate (>= 1.13.7), Biobase (>= 1.99.10), graphics, methods, stats, survival Suggests: Biobase (>= 1.99.10), class, hgu95av2.db, methods, tkWidgets, ALL License: Artistic-2.0 Archs: i386, x64 Title: genefilter: methods for filtering genes from microarray experiments Description: Some basic functions for filtering genes biocViews: Bioinformatics, Microarray Author: R. Gentleman, V. Carey, W. Huber, F. Hahne Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/genefilter_1.34.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/genefilter_1.34.0.zip win64.binary.ver: bin/windows64/contrib/2.13/genefilter_1.34.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/genefilter_1.34.0.tgz vignettes: vignettes/genefilter/inst/doc/howtogenefilter.pdf, vignettes/genefilter/inst/doc/howtogenefinder.pdf, vignettes/genefilter/inst/doc/independent_filtering_plots.pdf Package: genefu Version: 1.2.1 Depends: survcomp, mclust Imports: amap, gplots Suggests: GeneMeta License: Artistic-2.0 Title: Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer. Description: This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, survival analysis, ... biocViews: DifferentialExpression, GeneExpression, Visualization, Clustering, Classification Author: Benjamin Haibe-Kains, Markus Schroeder, Aedin Culhane, Gianluca Bontempi, Christos Sotiriou, John Quackenbush Maintainer: Benjamin Haibe-Kains , Markus Schroeder URL: http://compbio.dfci.harvard.edu source.ver: src/contrib/genefu_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/genefu_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.13/genefu_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/genefu_1.2.1.tgz vignettes: vignettes/genefu/inst/doc/genefu.pdf Package: geneplotter Version: 1.30.0 Depends: Biobase (>= 2.5.5), annotate, lattice Imports: annotate, AnnotationDbi, Biobase (>= 2.5.5), graphics, grDevices, grid, methods, RColorBrewer, stats, utils Suggests: Biobase (>= 2.5.5), Rgraphviz, annotate, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db License: Artistic-2.0 Title: Graphics related functions for Bioconductor Description: Some basic functions for plotting genetic data biocViews: Visualization Author: R. Gentleman, Biocore Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/geneplotter_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/geneplotter_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/geneplotter_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/geneplotter_1.30.0.tgz vignettes: vignettes/geneplotter/inst/doc/byChroms.pdf, vignettes/geneplotter/inst/doc/visualize.pdf Package: genoCN Version: 1.4.0 Imports: graphics, stats, utils License: GPL (>=2) Archs: i386, x64 Title: genotyping and copy number study tools Description: Simultaneous identification of copy number states and genotype calls for regions of either copy number variations or copy number aberrations biocViews: Microarray, Genetics Author: Wei Sun and ZhengZheng Tang Maintainer: Wei Sun source.ver: src/contrib/genoCN_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/genoCN_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/genoCN_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/genoCN_1.4.0.tgz vignettes: vignettes/genoCN/inst/doc/genoCN.pdf Package: genomeIntervals Version: 1.8.0 Depends: R (>= 2.8.0), methods, intervals (>= 0.12.2) Imports: methods, Biobase License: Artistic-2.0 Title: Operations on genomic intervals Description: This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package 'girafe'. biocViews: DataImport, Infrastructure, Genetics Author: Julien Gagneur , Joern Toedling, Richard Bourgon Maintainer: Julien Gagneur source.ver: src/contrib/genomeIntervals_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/genomeIntervals_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/genomeIntervals_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/genomeIntervals_1.8.0.tgz vignettes: vignettes/genomeIntervals/inst/doc/genomeIntervals.pdf Package: genomes Version: 1.8.1 Depends: lattice Imports: XML License: Artistic-2.0 Title: Genome sequencing project metadata Description: Collects genome sequencing project metadata from NCBI (http://www.ncbi.nlm.nih.gov) and provides tools to summarize and plot the data. biocViews: Annotation, Genetics Author: Chris Stubben Maintainer: Chris Stubben source.ver: src/contrib/genomes_1.8.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/genomes_1.8.1.zip win64.binary.ver: bin/windows64/contrib/2.13/genomes_1.8.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/genomes_1.8.1.tgz vignettes: vignettes/genomes/inst/doc/genome-tables.pdf Package: genoset Version: 1.0.0 Depends: Biobase, IRanges Imports: Biobase, DNAcopy, graphics, IRanges, methods, stats Suggests: RUnit Enhances: multicore License: Artistic-2.0 Archs: i386, x64 Title: Provides classes similar to ExpressionSet for copy number analysis Description: Load, manipulate, and plot copynumber and BAF data. GenoSet class extends eSet by adding a "locData" slot for a RangedData object from the IRanges package. This object contains feature genome location data and provides for simple subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. biocViews: Infrastructure, DataRepresentation Author: Peter M. Haverty Maintainer: Peter M. Haverty source.ver: src/contrib/genoset_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/genoset_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/genoset_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/genoset_1.0.0.tgz vignettes: vignettes/genoset/inst/doc/genoset.pdf Package: girafe Version: 1.4.0 Depends: R (>= 2.10.0), methods, IRanges (>= 1.3.53), Rsamtools, ShortRead (>= 1.3.21), intervals (>= 0.13.1), genomeIntervals (>= 1.7.3), grid Imports: methods, Biobase, Biostrings, BSgenome, graphics, grDevices, stats, utils, IRanges Suggests: MASS, org.Mm.eg.db, RColorBrewer Enhances: genomeIntervals License: Artistic-2.0 Archs: i386, x64 Title: Genome Intervals and Read Alignments for Functional Exploration Description: The package 'girafe' deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object class for enabling a detailed description of genome intervals with aligned reads and functions for comparing, visualising, exporting and working with such intervals and the aligned reads. As such, the package interacts with and provides a link between the packages ShortRead, IRanges and genomeIntervals. biocViews: Sequencing, HighThroughputSequencing Author: Joern Toedling, with contributions from Constance Ciaudo, Olivier Voinnet, Edith Heard, Emmanuel Barillot, and Wolfgang Huber Maintainer: J. Toedling source.ver: src/contrib/girafe_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/girafe_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/girafe_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/girafe_1.4.0.tgz vignettes: vignettes/girafe/inst/doc/girafe.pdf Package: globaltest Version: 5.6.1 Depends: methods Imports: Biobase (>= 2.5.5), survival, AnnotationDbi, annotate, multtest, graphics Suggests: vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, annotate, Biobase (>= 2.5.5), survival, GSEABase, mboost, penalized License: GPL (>= 2) Title: Testing groups of covariates/features for association with a response variable, with applications to gene set testing Description: The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms. biocViews: Microarray, OneChannel, Bioinformatics, DifferentialExpression, GO, Pathways Author: Jelle Goeman and Jan Oosting Maintainer: Jelle Goeman URL: http://www.msbi.nl/goeman source.ver: src/contrib/globaltest_5.6.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/globaltest_5.6.1.zip win64.binary.ver: bin/windows64/contrib/2.13/globaltest_5.6.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/globaltest_5.6.1.tgz vignettes: vignettes/globaltest/inst/doc/GlobalTest.pdf, vignettes/globaltest/inst/doc/GlobalTest_deprecated.pdf Package: goProfiles Version: 1.14.0 Depends: Biobase, AnnotationDbi, GO.db Suggests: org.Hs.eg.db License: GPL-2 Title: goProfiles: an R package for the statistical analysis of functional profiles Description: The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'. biocViews: Microarray, GO Author: Alex Sanchez, Jordi Ocana and Miquel Salicru Maintainer: Alex Sanchez source.ver: src/contrib/goProfiles_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/goProfiles_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/goProfiles_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/goProfiles_1.14.0.tgz vignettes: vignettes/goProfiles/inst/doc/goProfiles.pdf Package: goTools Version: 1.26.0 Depends: GO.db Suggests: hgu133a.db License: GPL-2 Title: Functions for Gene Ontology database Description: Wraper functions for description/comparison of oligo ID list using Gene Ontology database biocViews: Microarray,GO,Visualization Author: Yee Hwa (Jean) Yang , Agnes Paquet Maintainer: Agnes Paquet source.ver: src/contrib/goTools_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/goTools_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/goTools_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/goTools_1.26.0.tgz vignettes: vignettes/goTools/inst/doc/goTools.pdf Package: goseq Version: 1.4.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase Imports: mgcv, graphics, stats, utils, AnnotationDbi Suggests: GO.db, edgeR, org.Hs.eg.db License: LGPL (>= 2) Title: Gene Ontology analyser for RNA-seq and other length biased data Description: Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data biocViews: HighThroughputSequencingData, GO, GeneExpression, Transcription, RNAseq Author: Matthew Young Maintainer: Matthew Young source.ver: src/contrib/goseq_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/goseq_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/goseq_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/goseq_1.4.0.tgz vignettes: vignettes/goseq/inst/doc/goseq.pdf Package: gpls Version: 1.24.0 Imports: stats License: Artistic-2.0 Title: Classification using generalized partial least squares Description: Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification. biocViews: Bioinformatics, Classification, Microarray Author: Beiying Ding Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/gpls_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/gpls_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/gpls_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/gpls_1.24.0.tgz vignettes: vignettes/gpls/inst/doc/gpls.pdf Package: graph Version: 1.30.0 Depends: R (>= 2.6.0), methods Imports: methods, stats, tools, utils Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster Enhances: Rgraphviz License: Artistic-2.0 Archs: i386, x64 Title: graph: A package to handle graph data structures Description: A package that implements some simple graph handling capabilities. biocViews: GraphsAndNetworks Author: R. Gentleman, Elizabeth Whalen, W. Huber, S. Falcon Maintainer: Seth Falcon source.ver: src/contrib/graph_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/graph_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/graph_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/graph_1.30.0.tgz vignettes: vignettes/graph/inst/doc/GraphClass.pdf, vignettes/graph/inst/doc/MultiGraphClass.pdf, vignettes/graph/inst/doc/clusterGraph.pdf, vignettes/graph/inst/doc/graph.pdf, vignettes/graph/inst/doc/graphAttributes.pdf Package: hexbin Version: 1.26.0 Depends: R (>= 2.0.1), methods, grid, lattice Imports: methods, grid, lattice, graphics, grDevices, stats, utils Suggests: marray, affy, Biobase License: GPL-2 Archs: i386, x64 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: Software Author: Dan Carr , ported by Nicholas Lewin-Koh and Martin Maechler Maintainer: Nicholas Lewin-Koh source.ver: src/contrib/hexbin_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/hexbin_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/hexbin_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/hexbin_1.26.0.tgz vignettes: vignettes/hexbin/inst/doc/hexagon_binning.pdf Package: hopach Version: 2.12.0 Depends: R (>= 2.11.0), cluster, Biobase, methods Imports: Biobase, cluster, graphics, grDevices, methods, stats, utils License: GPL (>= 2) Archs: i386, x64 Title: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) Description: The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering). biocViews: Clustering Author: Katherine S. Pollard, with Mark J. van der Laan and Greg Wall Maintainer: Katherine S. Pollard URL: http://www.stat.berkeley.edu/~laan/, http://docpollard.com/ source.ver: src/contrib/hopach_2.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/hopach_2.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/hopach_2.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/hopach_2.12.0.tgz vignettes: vignettes/hopach/inst/doc/MSS.pdf, vignettes/hopach/inst/doc/bootplot.pdf, vignettes/hopach/inst/doc/dplot.pdf, vignettes/hopach/inst/doc/hopach.pdf, vignettes/hopach/inst/doc/hopachManuscript.pdf Package: hyperdraw Version: 1.4.0 Depends: R (>= 2.9.0), methods, grid, graph, hypergraph, Rgraphviz License: GPL (>= 2) Title: Visualizing Hypergaphs Description: Functions for visualizing hypergraphs. biocViews: GraphsAndNetworks Author: Paul Murrell Maintainer: Paul Murrell SystemRequirements: graphviz source.ver: src/contrib/hyperdraw_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/hyperdraw_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/hyperdraw_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/hyperdraw_1.4.0.tgz vignettes: vignettes/hyperdraw/inst/doc/hyperdraw.pdf Package: hypergraph Version: 1.24.0 Depends: R (>= 2.1.0), methods, graph License: Artistic-2.0 Title: A package providing hypergraph data structures Description: A package that implements some simple capabilities for representing and manipulating hypergraphs. biocViews: Infrastructure, GraphsAndNetworks Author: Seth Falcon, Robert Gentleman Maintainer: Biocore Team c/o BioC user list source.ver: src/contrib/hypergraph_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/hypergraph_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/hypergraph_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/hypergraph_1.24.0.tgz Package: iChip Version: 1.6.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) Archs: i386, x64 Title: Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models Description: This package uses hidden Ising models to identify enriched genomic regions in ChIP-chip data. It can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates. biocViews: ChIP-chip, NimbleGen, Microarray, Bioinformatics Author: Qianxing Mo Maintainer: Qianxing Mo source.ver: src/contrib/iChip_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/iChip_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/iChip_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/iChip_1.6.0.tgz vignettes: vignettes/iChip/inst/doc/iChip.pdf Package: iFlow Version: 2.4.0 Depends: R (>= 2.13.0), flowCore, flowViz, flowStats (>= 1.3.20) Imports: Biobase, RGtk2, cairoDevice, flowCore, flowStats, flowViz, grDevices, graphics, methods, utils License: Artistic-2.0 Title: GUI based visualization for flow cytometry Description: Tool to explore and visualize flow cytometry biocViews: FlowCytometry, Bioinformatics, GUI Author: Kyongryun Lee, Florian Hahne, Deepayan Sarkar Maintainer: Kyongryun Lee URL: http://www.hindawi.com/journals/abi/2009/103839.html source.ver: src/contrib/iFlow_2.4.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/iFlow_2.4.0.tgz vignettes: vignettes/iFlow/inst/doc/iflow.pdf Package: iSeq Version: 1.4.0 Depends: R (>= 2.10.0) License: GPL (>= 2) Archs: i386, x64 Title: Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models Description: This package uses Bayesian hidden Ising models to identify IP-enriched genomic regions from ChIP-seq data. It can be used to analyze ChIP-seq data with or without controls. biocViews: ChIP-seq, next generation sequencing, massively parallel sequencing, bioinformatics Author: Qianxing Mo Maintainer: Qianxing Mo source.ver: src/contrib/iSeq_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/iSeq_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/iSeq_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/iSeq_1.4.0.tgz vignettes: vignettes/iSeq/inst/doc/iSeq.pdf Package: ibh Version: 1.0.0 Depends: simpIntLists Suggests: yeastCC, stats License: GPL (>= 2) Title: Interaction Based Homogeneity for Evaluating Gene Lists Description: This package contains methods for calculating Interaction Based Homogeneity to evaluate fitness of gene lists to an interaction network which is useful for evaluation of clustering results and gene list analysis. BioGRID interactions are used in the calculation. The user can also provide their own interactions. biocViews: QualityControl, DataImport, GraphsAndNetworks, Bioinformatics Author: Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin Atalay. Maintainer: Kircicegi Korkmaz source.ver: src/contrib/ibh_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ibh_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ibh_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ibh_1.0.0.tgz vignettes: vignettes/ibh/inst/doc/ibh.pdf Package: idiogram Version: 1.28.0 Depends: R (>= 2.0.0), methods, Biobase, annotate, plotrix Suggests: hu6800.db, golubEsets License: GPL-2 Title: idiogram Description: A package for plotting genomic data by chromosomal location biocViews: Visualization Author: Karl J. Dykema Maintainer: Karl J. Dykema source.ver: src/contrib/idiogram_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/idiogram_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.13/idiogram_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/idiogram_1.28.0.tgz vignettes: vignettes/idiogram/inst/doc/idiogram.pdf Package: imageHTS Version: 1.2.0 Depends: R (>= 2.9.0), EBImage (>= 3.7.1), cellHTS2 (>= 2.10.0) Imports: tools, Biobase, hwriter, methods, vsn, stats, utils, e1071 License: LGPL-2.1 Title: Analysis of high-throughput microscopy-based screens Description: imageHTS is an R package dedicated to the analysis of high-throughput microscopy-based screens. The package provides a modular and extensible framework to segment cells, extract quantitative cell features, predict cell types and browse screen data through web interfaces. Designed to operate in distributed environments, imageHTS provides a standardized access to remote screen data, facilitating the dissemination of high-throughput microscopy-based screens. biocViews: CellBasedAssays, Visualization, Preprocessing Author: Gregoire Pau, Xian Zhang, Michael Boutros, Wolfgang Huber Maintainer: Gregoire Pau source.ver: src/contrib/imageHTS_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/imageHTS_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/imageHTS_1.2.0.zip vignettes: vignettes/imageHTS/inst/doc/imageHTS-introduction.pdf Package: impute Version: 1.26.0 Depends: R (>= 1.7.0) License: GPL-2 Archs: i386, x64 Title: impute: Imputation for microarray data Description: Imputation for microarray data (currently KNN only) biocViews: Bioinformatics, Microarray Author: Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, Gilbert Chu Maintainer: Balasubramanian Narasimhan source.ver: src/contrib/impute_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/impute_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/impute_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/impute_1.26.0.tgz Package: inveRsion Version: 1.0.0 Depends: methods, haplo.stats Imports: graphics, methods, utils License: GPL (>= 2) Archs: i386, x64 Title: Inversions in genotype data Description: Package to find genetic inversions in genotype (SNP array) data. biocViews: Microarray, SNPsAndGeneticVariability Author: Alejandro Caceres Maintainer: Alejandro Caceres source.ver: src/contrib/inveRsion_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/inveRsion_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/inveRsion_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/inveRsion_1.0.0.tgz vignettes: vignettes/inveRsion/inst/doc/Manual.pdf, vignettes/inveRsion/inst/doc/inveRsion.pdf Package: iterativeBMA Version: 1.10.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) Title: The Iterative Bayesian Model Averaging (BMA) algorithm Description: The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402). biocViews: Microarray, Bioinformatics, Classification Author: Ka Yee Yeung, University of Washington, Seattle, WA, with contributions from Adrian Raftery and Ian Painter Maintainer: Ka Yee Yeung URL: http://faculty.washington.edu/kayee/research.html source.ver: src/contrib/iterativeBMA_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/iterativeBMA_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/iterativeBMA_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/iterativeBMA_1.10.0.tgz vignettes: vignettes/iterativeBMA/inst/doc/iterativeBMA.pdf Package: iterativeBMAsurv Version: 1.10.0 Depends: BMA, leaps, survival, splines Imports: graphics, grDevices, stats, survival, utils License: GPL (>= 2) Title: The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis Description: The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data. biocViews: Microarray, Bioinformatics Author: Amalia Annest, University of Washington, Tacoma, WA Ka Yee Yeung, University of Washington, Seattle, WA Maintainer: Ka Yee Yeung URL: http://expression.washington.edu/ibmasurv/protected source.ver: src/contrib/iterativeBMAsurv_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/iterativeBMAsurv_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/iterativeBMAsurv_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/iterativeBMAsurv_1.10.0.tgz vignettes: vignettes/iterativeBMAsurv/inst/doc/iterativeBMAsurv.pdf Package: joda Version: 1.0.0 Depends: R (>= 2.0), bgmm, RBGL License: GPL (>= 2) Title: JODA algorithm for quantifying gene deregulation using knowledge Description: Package 'joda' implements three steps of an algorithm called JODA. The algorithm computes gene deregulation scores. For each gene, its deregulation score reflects how strongly an effect of a certain regulator's perturbation on this gene differs between two different cell populations. The algorithm utilizes regulator knockdown expression data as well as knowledge about signaling pathways in which the regulators are involved (formalized in a simple matrix model). biocViews: Microarray, Bioinformatics, Pathways, GraphsAnNetworks, Statistics Author: Ewa Szczurek Maintainer: Ewa Szczurek URL: http://www.bioconductor.org source.ver: src/contrib/joda_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/joda_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/joda_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/joda_1.0.0.tgz vignettes: vignettes/joda/inst/doc/JodaVignette.pdf Package: keggorthology Version: 2.4.0 Depends: R (>= 2.5.0),stats,graph,hgu95av2.db Imports: AnnotationDbi,graph,DBI, graph, grDevices, methods, stats, tools, utils Suggests: RBGL,ALL License: Artistic-2.0 Title: graph support for KO, KEGG Orthology Description: graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs. biocViews: Pathways,GraphsAndNetworks Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/keggorthology_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/keggorthology_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/keggorthology_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/keggorthology_2.4.0.tgz vignettes: vignettes/keggorthology/inst/doc/keggorth.pdf Package: lapmix Version: 1.18.0 Depends: R (>= 2.6.0),stats Imports: Biobase, graphics, grDevices, methods, stats, tools, utils License: GPL (>= 2) Title: Laplace Mixture Model in Microarray Experiments Description: Laplace mixture modelling of microarray experiments. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. The main purpose is to identify differentially expressed genes. biocViews: Bioinformatics, Microarray, OneChannel, DifferentialExpression Author: Yann Ruffieux, contributions from Debjani Bhowmick, Anthony C. Davison, and Darlene R. Goldstein Maintainer: Yann Ruffieux URL: http://www.r-project.org, http://www.bioconductor.org, http://stat.epfl.ch source.ver: src/contrib/lapmix_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/lapmix_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/lapmix_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/lapmix_1.18.0.tgz vignettes: vignettes/lapmix/inst/doc/lapmix-example.pdf Package: les Version: 1.2.0 Depends: R (>= 2.12.1), methods, graphics, fdrtool Imports: boot, gplots, RColorBrewer Suggests: Biobase, limma Enhances: multicore License: GPL-3 Title: Identifying Differential Effects in Tiling Microarray Data Description: The 'les' package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes. biocViews: Microarray, Bioinformatics, DifferentialExpression, ChIPchip, DNAMethylation, Transcription Author: Julian Gehring, Clemens Kreutz, Jens Timmer Maintainer: Julian Gehring URL: http://www.fdmold.uni-freiburg.de/~jgehring/ source.ver: src/contrib/les_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/les_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/les_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/les_1.2.0.tgz vignettes: vignettes/les/inst/doc/les.pdf Package: limmaGUI Version: 1.28.0 Depends: limma, tcltk Suggests: statmod, R2HTML, xtable, tkrplot License: LGPL Title: GUI for limma package Description: A Graphical User Interface for the limma Microarray package biocViews: Microarray, TwoChannel, DataImport, QualityControl, Preprocessing, Bioinformatics, DifferentialExpression, MultipleComparisons, GUI Author: James Wettenhall Division of Genetics and Bioinformatics, WEHI Maintainer: Keith Satterley URL: http://bioinf.wehi.edu.au/limmaGUI/ source.ver: src/contrib/limmaGUI_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/limmaGUI_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.13/limmaGUI_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/limmaGUI_1.28.0.tgz vignettes: vignettes/limmaGUI/inst/doc/LinModIntro.pdf, vignettes/limmaGUI/inst/doc/extract.pdf, vignettes/limmaGUI/inst/doc/limmaGUI.pdf Package: limma Version: 3.8.3 Depends: R (>= 2.3.0), methods Suggests: affy, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn License: LGPL Archs: i386, x64 Title: Linear Models for Microarray Data Description: Data analysis, linear models and differential expression for microarray data. biocViews: Microarray, OneChannel, TwoChannel, DataImport, QualityControl, Preprocessing, Bioinformatics, DifferentialExpression, MultipleComparisons, TimeCourse Author: Gordon Smyth with contributions from Matthew Ritchie, Jeremy Silver, James Wettenhall, Natalie Thorne, Mette Langaas, Egil Ferkingstad, Marcus Davy, Francois Pepin, Dongseok Choi, Davis McCarthy, Di Wu, Alicia Oshlack, Carolyn de Graaf, Yifang Hu, Wei Shi and Belinda Phipson. Maintainer: Gordon Smyth URL: http://bioinf.wehi.edu.au/limma source.ver: src/contrib/limma_3.8.3.tar.gz win.binary.ver: bin/windows/contrib/2.13/limma_3.8.3.zip win64.binary.ver: bin/windows64/contrib/2.13/limma_3.8.3.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/limma_3.8.3.tgz vignettes: vignettes/limma/inst/doc/limma.pdf, vignettes/limma/inst/doc/usersguide.pdf Package: logicFS Version: 1.22.0 Depends: LogicReg Suggests: genefilter, siggenes License: LGPL (>= 2) Title: Identification of SNP Interactions Description: Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification. biocViews: SNP, Classification, Genetics Author: Holger Schwender Maintainer: Holger Schwender source.ver: src/contrib/logicFS_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/logicFS_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.13/logicFS_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/logicFS_1.22.0.tgz vignettes: vignettes/logicFS/inst/doc/logicFS.pdf Package: logitT Version: 1.10.0 Depends: affy Suggests: SpikeInSubset License: GPL (>= 2) Archs: i386, x64 Title: logit-t Package Description: The logitT library implements the Logit-t algorithm introduced in --A high performance test of differential gene expression for oligonucleotide arrays-- by William J Lemon, Sandya Liyanarachchi and Ming You for use with Affymetrix data stored in an AffyBatch object in R. biocViews: Microarray, DifferentialExpression Author: Tobias Guennel Maintainer: Tobias Guennel URL: http://www.bioconductor.org source.ver: src/contrib/logitT_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/logitT_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/logitT_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/logitT_1.10.0.tgz vignettes: vignettes/logitT/inst/doc/logitT.pdf Package: lol Version: 1.0.1 Depends: penalized, Matrix Imports: Matrix, penalized, graphics, grDevices, stats License: GPL-2 Title: Lots Of Lasso Description: Various optimization methods for Lasso inference with matrix warpper biocViews: Software Author: Yinyin Yuan Maintainer: Yinyin Yuan source.ver: src/contrib/lol_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/lol_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.13/lol_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/lol_1.0.1.tgz vignettes: vignettes/lol/inst/doc/lol.pdf Package: lumi Version: 2.4.0 Depends: R (>= 2.4.0), Biobase (>= 2.5.5), nleqslv Imports: affy (>= 1.23.4), methylumi, annotate, Biobase (>= 2.5.5), mgcv (>= 1.4-0), hdrcde, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, methods Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer License: LGPL (>= 2) Title: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays Description: The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays. biocViews: Microarray, OneChannel, Preprocessing, DNAMethylation, QualityControl, TwoChannel Author: Pan Du, Gang Feng, Warren Kibbe, Simon Lin Maintainer: Pan Du source.ver: src/contrib/lumi_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/lumi_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/lumi_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/lumi_2.4.0.tgz vignettes: vignettes/lumi/inst/doc/Bioc2007_lumi_presentation.pdf, vignettes/lumi/inst/doc/IlluminaAnnotation.pdf, vignettes/lumi/inst/doc/lumi.pdf, vignettes/lumi/inst/doc/lumi_VST_evaluation.pdf, vignettes/lumi/inst/doc/methylationAnalysis.pdf Package: mBPCR Version: 1.6.0 Depends: oligoClasses, SNPchip Imports: Biobase Suggests: xtable License: GPL (>= 2) Title: Bayesian Piecewise Constant Regression for DNA copy number estimation Description: Estimates the DNA copy number profile using mBPCR to detect regions with copy number changes biocViews: aCGH, SNP, Microarray, CopyNumberVariants, Bioinformatics Author: P.M.V. Rancoita , with contributions from M. Hutter Maintainer: P.M.V. Rancoita URL: http://www.idsia.ch/~paola/mBPCR source.ver: src/contrib/mBPCR_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/mBPCR_1.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/mBPCR_1.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/mBPCR_1.6.0.tgz vignettes: vignettes/mBPCR/inst/doc/mBPCR.pdf Package: maCorrPlot Version: 1.22.0 Depends: lattice Imports: graphics, grDevices, lattice, stats License: GPL (>= 2) Title: Visualize artificial correlation in microarray data Description: Graphically displays correlation in microarray data that is due to insufficient normalization biocViews: Microarray, Preprocessing, Visualization Author: Alexander Ploner Maintainer: Alexander Ploner URL: http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15799785 source.ver: src/contrib/maCorrPlot_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/maCorrPlot_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.13/maCorrPlot_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/maCorrPlot_1.22.0.tgz vignettes: vignettes/maCorrPlot/inst/doc/maCorrPlot.pdf Package: maDB Version: 1.24.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), affy (>= 1.23.4), pgUtils (>= 1.23.2), limma (>= 1.8.0), methods Suggests: annaffy (>= 1.6.2), biomaRt (>= 1.8.2), geneplotter License: LGPL (>= 2) Title: Microarray database and utility functions for microarray data analysis. Description: maDB allows to create a simple microarray database to store microarray experiments and annotation data into it. Affymetrix GeneChip expression values as well as values from two color microarrays can be stored into the database. Whole experiments or subsets from a experiment (or also values for a subset of genes in a subset of microarrays) can be fetched back to R. Additionally maDB provides different utility functions for the microarray data analysis like functions to draw MA plots or volcano plots with the data points color coded according to the local point density or functions that allow a replicate handling of miroarrays. biocViews: Microarray,TwoChannel,OneChannel,Visualization Author: Johannes Rainer Maintainer: Johannes Rainer source.ver: src/contrib/maDB_1.24.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/maDB_1.24.0.tgz vignettes: vignettes/maDB/inst/doc/maDB-015.pdf, vignettes/maDB/inst/doc/maDB-016.pdf, vignettes/maDB/inst/doc/maDB.pdf Package: maSigPro Version: 1.24.1 Depends: R (>= 2.3.1), stats, Biobase Imports: Biobase, graphics, grDevices, limma, Mfuzz, stats, utils License: GPL (>= 2) Title: Significant Gene Expression Profile Differences in Time Course Microarray Data Description: maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments. biocViews: Microarray, DifferentialExpression, TimeCourse Author: Ana Conesa , Maria Jose Nueda Maintainer: Maria Jose Nueda URL: http://bioinfo.cipf.es/ source.ver: src/contrib/maSigPro_1.24.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/maSigPro_1.24.1.zip win64.binary.ver: bin/windows64/contrib/2.13/maSigPro_1.24.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/maSigPro_1.24.1.tgz vignettes: vignettes/maSigPro/inst/doc/PLOTGROUPS.pdf, vignettes/maSigPro/inst/doc/PLOTPROFILES.pdf, vignettes/maSigPro/inst/doc/maSigPro-tutorial.pdf Package: maanova Version: 1.22.0 Depends: R (>= 2.7.0) Imports: Biobase, graphics, grDevices, methods, stats, utils Suggests: qvalue, snow Enhances: Rmpi License: GPL (>= 2) Archs: i386, x64 Title: Tools for analyzing Micro Array experiments Description: Analysis of N-dye Micro Array experiment using mixed model effect. Containing analysis of variance, permutation and bootstrap, cluster and consensus tree. biocViews: Microarray, DifferentialExpression, Clustering Author: Hao Wu, modified by Hyuna Yang and Keith Sheppard with ideas from Gary Churchill, Katie Kerr and Xiangqin Cui. Maintainer: Keith Sheppard URL: http://research.jax.org/faculty/churchill source.ver: src/contrib/maanova_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/maanova_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.13/maanova_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/maanova_1.22.0.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: 1.26.0 Depends: Biobase, annotate Suggests: hgu95av2.db, stjudem License: Artistic-2.0 Title: MicroArray Chromosome Analysis Tool Description: This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. MACAT is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library 'stjudem'. biocViews: Microarray, DifferentialExpression, Visualization Author: Benjamin Georgi, Matthias Heinig, Stefan Roepcke, Sebastian Schmeier, Joern Toedling Maintainer: Joern Toedling source.ver: src/contrib/macat_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/macat_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/macat_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/macat_1.26.0.tgz vignettes: vignettes/macat/inst/doc/Slidingchrom6s3.pdf, vignettes/macat/inst/doc/chrom6T.pdf, vignettes/macat/inst/doc/chrom6TkNN.pdf, vignettes/macat/inst/doc/evalkNN6.pdf Package: made4 Version: 1.26.0 Depends: ade4, RColorBrewer,gplots,scatterplot3d Suggests: affy License: Artistic-2.0 Title: Multivariate analysis of microarray data using ADE4 Description: Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4. biocViews: Bioinformatics, Clustering, Classification, MultipleComparisons Author: Aedin Culhane Maintainer: Aedin Culhane URL: http://www.hsph.harvard.edu/researchers/aculhane.html source.ver: src/contrib/made4_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/made4_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/made4_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/made4_1.26.0.tgz vignettes: vignettes/made4/inst/doc/html3D.pdf, vignettes/made4/inst/doc/introduction.pdf Package: maigesPack Version: 1.16.0 Depends: R (>= 2.0.0), convert, graph, limma, marray, methods Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML, rgl, som License: GPL (>= 2) Archs: i386, x64 Title: Functions to handle cDNA microarray data, including several methods of data analysis Description: This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data biocViews: Microarray, TwoChannel, Preprocessing, Bioinformatics, DifferentialExpression, Clustering, Classification, GraphsAndNetworks Author: Gustavo H. Esteves , with contributions from Roberto Hirata Jr , E. Jordao Neves , Elier B. Cristo , Ana C. Simoes and Lucas Fahham Maintainer: Gustavo H. Esteves URL: http://www.maiges.org/en/software/ source.ver: src/contrib/maigesPack_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/maigesPack_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/maigesPack_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/maigesPack_1.16.0.tgz vignettes: vignettes/maigesPack/inst/doc/maigesPack_tutorial.pdf Package: makePlatformDesign Version: 1.16.0 Depends: R (>= 2.6.0) Imports: Biobase, affyio, methods, stats, utils, oligo License: LGPL (>= 2) Archs: i386, x64 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 source.ver: src/contrib/makePlatformDesign_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/makePlatformDesign_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/makePlatformDesign_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/makePlatformDesign_1.16.0.tgz Package: makecdfenv Version: 1.30.0 Depends: R (>= 2.6.0), methods Imports: Biobase, affy, methods, stats, utils License: GPL (>= 2) Archs: i386, x64 Title: CDF Environment Maker Description: This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment. biocViews: OneChannel, DataImport, Preprocessing Author: Rafael A. Irizarry , Laurent Gautier , Wolfgang Huber , Ben Bolstad Maintainer: James W. MacDonald source.ver: src/contrib/makecdfenv_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/makecdfenv_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/makecdfenv_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/makecdfenv_1.30.0.tgz vignettes: vignettes/makecdfenv/inst/doc/makecdfenv.pdf Package: marray Version: 1.30.0 Depends: R (>= 1.9.0), limma, methods Suggests: tkWidgets License: LGPL Title: Exploratory analysis for two-color spotted microarray data Description: Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking. biocViews: Microarray, TwoChannel, Preprocessing Author: Yee Hwa (Jean) Yang with contributions from Agnes Paquet and Sandrine Dudoit. Maintainer: Yee Hwa (Jean) Yang URL: http://www.maths.usyd.edu.au/u/jeany/ source.ver: src/contrib/marray_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/marray_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/marray_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/marray_1.30.0.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: mcaGUI Version: 1.0.0 Depends: lattice, MASS, proto, foreign, gWidgets(>= 0.0-36), gWidgetsRGtk2(>= 0.0-53), OTUbase, vegan, bpca Enhances: iplots, reshape, ggplot2, cairoDevice, OTUbase License: GPL (>= 2) Title: Microbial Community Analysis GUI Description: Microbial community analysis GUI for R using gWidgets. biocViews: GUI, Visualization, Bioinformatics, Clustering, Sequencing Author: Wade K. Copeland, Vandhana Krishnan, Daniel Beck, Matt Settles, James Foster, Kyu-Chul Cho, Mitch Day, Roxana Hickey, Ursel M.E. Schutte, Xia Zhou, Chris Williams, Larry J. Forney, Zaid Abdo, Poor Man's GUI (PMG) base code by John Verzani with contributions by Yvonnick Noel Maintainer: Wade K. Copeland URL: http://www.ibest.uidaho.edu/ibest/index.php source.ver: src/contrib/mcaGUI_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/mcaGUI_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/mcaGUI_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/mcaGUI_1.0.0.tgz vignettes: vignettes/mcaGUI/inst/doc/An_Introduction_and_User_Guide_for_mcaGUI.pdf Package: mdqc Version: 1.14.0 Depends: R (>= 2.2.1), cluster, MASS License: LGPL (>= 2) Title: Mahalanobis Distance Quality Control for microarrays Description: MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality. biocViews: Microarray, QualityControl Author: Justin Harrington Maintainer: Gabriela Cohen-Freue source.ver: src/contrib/mdqc_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/mdqc_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/mdqc_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/mdqc_1.14.0.tgz vignettes: vignettes/mdqc/inst/doc/mdqcvignette.pdf Package: metaArray Version: 1.28.0 Imports: Biobase, MergeMaid, graphics, stats License: LGPL-2 Archs: i386, x64 Title: Integration of Microarray Data for Meta-analysis Description: 1) Data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) 2) Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform biocViews: Microarray, Bioinformatics, DifferentialExpression Author: Debashis Ghosh Hyungwon Choi Maintainer: Hyungwon Choi source.ver: src/contrib/metaArray_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/metaArray_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.13/metaArray_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/metaArray_1.28.0.tgz vignettes: vignettes/metaArray/inst/doc/metaArray.pdf Package: metahdep Version: 1.10.0 Depends: methods Suggests: affyPLM License: GPL-3 Archs: i386, x64 Title: Hierarchical Dependence in Meta-Analysis Description: Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies biocViews: Microarray, Bioinformatics, DifferentialExpression Author: John R. Stevens, Gabriel Nicholas Maintainer: John R. Stevens source.ver: src/contrib/metahdep_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/metahdep_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/metahdep_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/metahdep_1.10.0.tgz vignettes: vignettes/metahdep/inst/doc/metahdep.pdf Package: methVisual Version: 1.4.0 Depends: R (>= 2.11.0), Biostrings(>= 2.4.8), plotrix,gsubfn, grid,sqldf Imports: Biostrings, ca, graphics, grDevices, grid, gridBase, IRanges, stats, utils License: GPL (>= 2) Title: Methods for visualization and statistics on DNA methylation data Description: The package 'methVisual' allows the visualization of DNA methylation data after bisulfite sequencing. biocViews: Bioinformatics, DNAMethylation, Clustering, Classification Author: A. Zackay, C. Steinhoff Maintainer: Arie Zackay source.ver: src/contrib/methVisual_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/methVisual_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/methVisual_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/methVisual_1.4.0.tgz vignettes: vignettes/methVisual/inst/doc/methVisual.pdf Package: methylumi Version: 1.8.0 Depends: R (>= 2.9), Biobase, methods Imports: Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi Suggests: lumi, lattice, limma, xtable, GGHumanMethCancerPanelv1.db License: GPL-2 Title: Handle Illumina methylation data Description: This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. Normalization and quality control features for GoldenGate arrays are also included. biocViews: DNAMethylation, TwoChannel, Preprocessing, QualityControl, CpGIsland Author: Sean Davis, Pan Du, Sven Bilke Maintainer: Sean Davis source.ver: src/contrib/methylumi_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/methylumi_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/methylumi_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/methylumi_1.8.0.tgz vignettes: vignettes/methylumi/inst/doc/methylumi.pdf Package: mgsa Version: 1.0.0 Depends: R (>= 2.9.0), methods, gplots Imports: gplots, graphics, stats, utils Suggests: DBI, RSQLite, GO.db License: Artistic-2.0 Archs: i386, x64 Title: Model-based gene set analysis Description: Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology. biocViews: Pathways, GO Author: Sebastian Bauer , Julien Gagneur Maintainer: Sebastian Bauer source.ver: src/contrib/mgsa_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/mgsa_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/mgsa_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/mgsa_1.0.0.tgz vignettes: vignettes/mgsa/inst/doc/mgsa.pdf Package: miRNApath Version: 1.12.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 Title: miRNApath: Pathway Enrichment for miRNA Expression Data Description: This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes. biocViews: Annotation, Pathways, Bioinformatics, DifferentialExpression Author: James M. Ward with contributions from Yunling Shi, Cindy Richards, John P. Cogswell Maintainer: James M. Ward source.ver: src/contrib/miRNApath_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/miRNApath_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/miRNApath_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/miRNApath_1.12.0.tgz vignettes: vignettes/miRNApath/inst/doc/miRNApath.pdf Package: microRNA Version: 1.10.0 Imports: Biostrings (>= 2.11.32) Suggests: Biostrings (>= 2.11.32) Enhances: Rlibstree License: Artistic-2.0 Title: Data and functions for dealing with microRNAs Description: Different data resources for microRNAs and some functions for manipulating them. biocViews: Infrastructure, SequenceAnnotation, SequenceMatching Author: R. Gentleman, S. Falcon Maintainer: Chao-Jen Wong source.ver: src/contrib/microRNA_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/microRNA_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/microRNA_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/microRNA_1.10.0.tgz Package: minet Version: 3.6.0 Depends: infotheo License: file LICENSE Archs: i386, x64 Title: Mutual Information NETworks Description: This package implements various algorithms for inferring mutual information networks from data. biocViews: Microarray, GraphsAndNetworks Author: Patrick E. Meyer, Frederic Lafitte, Gianluca Bontempi Maintainer: Patrick E. Meyer URL: http://minet.meyerp.com source.ver: src/contrib/minet_3.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/minet_3.6.0.zip win64.binary.ver: bin/windows64/contrib/2.13/minet_3.6.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/minet_3.6.0.tgz Package: mosaics Version: 1.0.1 Depends: R (>= 2.11.1), methods, graphics Imports: MASS, splines, lattice, IRanges Suggests: mosaicsExample, rtracklayer, cosmo License: GPL (>= 2) Title: MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq) Description: This package provides functions for fitting MOSAiCS, a statistical framework to analyze one-sample or two-sample ChIP-seq data. biocViews: ChIPseq, Sequencing, Transcription, Genetics, Bioinformatics Author: Dongjun Chung, Pei Fen Kuan, Sunduz Keles Maintainer: Dongjun Chung URL: http://groups.google.com/group/mosaics_user_group source.ver: src/contrib/mosaics_1.0.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/mosaics_1.0.1.zip win64.binary.ver: bin/windows64/contrib/2.13/mosaics_1.0.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/mosaics_1.0.1.tgz vignettes: vignettes/mosaics/inst/doc/mosaics-example.pdf Package: multiscan Version: 1.12.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) Archs: i386, x64 Title: R package for combining multiple scans Description: Estimates gene expressions from several laser scans of the same microarray biocViews: Microarray, Preprocessing Author: Mizanur Khondoker , Chris Glasbey, Bruce Worton. Maintainer: Mizanur Khondoker source.ver: src/contrib/multiscan_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/multiscan_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/multiscan_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/multiscan_1.12.0.tgz vignettes: vignettes/multiscan/inst/doc/multiscan.pdf Package: multtest Version: 2.8.0 Depends: R (>= 2.9.0), methods, Biobase Imports: survival, MASS Suggests: snow License: LGPL Archs: i386, x64 Title: Resampling-based multiple hypothesis testing Description: Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments. biocViews: Microarray, DifferentialExpression, MultipleComparisons Author: Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra Taylor, Sandrine Dudoit Maintainer: Katherine S. Pollard source.ver: src/contrib/multtest_2.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/multtest_2.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/multtest_2.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/multtest_2.8.0.tgz vignettes: vignettes/multtest/inst/doc/MTP.pdf, vignettes/multtest/inst/doc/MTPALL.pdf, vignettes/multtest/inst/doc/multtest.pdf Package: nem Version: 2.16.1 Depends: R (>= 2.0), e1071 (>= 1.5), graph (>= 1.24), Rgraphviz (>= 1.22), plotrix, limma, time (>= 1.0), cluster (>= 1.11), statmod Imports: boot, e1071, graph, graphics, grDevices, methods, RBGL (>= 1.8.1), RColorBrewer, Rgraphviz, stats, utils Suggests: Biobase (>= 1.10) Enhances: doMC License: GPL (>= 2) 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: Holger Froehlich URL: http://www.bioconductor.org source.ver: src/contrib/nem_2.16.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/nem_2.16.1.zip win64.binary.ver: bin/windows64/contrib/2.13/nem_2.16.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/nem_2.16.1.tgz vignettes: vignettes/nem/inst/doc/markowetz-thesis-2006.pdf, vignettes/nem/inst/doc/nem.pdf Package: netresponse Version: 1.4.0 Depends: methods, igraph, graph, minet License: GPL (>=2) Archs: i386, x64 Title: NetResponse: functional network analysis Description: Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling. biocViews: CellBiology, Clustering, GeneExpression, Genetics, GraphsAndNetworks, DifferentialExpression, Microarray, Transcription Author: Leo Lahti, Olli-Pekka Huovilainen, Antonio Gusmao and Juuso Parkkinen Maintainer: Leo Lahti URL: http://netpro.r-forge.r-project.org/ source.ver: src/contrib/netresponse_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/netresponse_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/netresponse_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/netresponse_1.4.0.tgz vignettes: vignettes/netresponse/inst/doc/netresponse.pdf Package: nnNorm Version: 2.16.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL Title: Spatial and intensity based normalization of cDNA microarray data based on robust neural nets Description: This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting. biocViews: Microarray, TwoChannel, Preprocessing Author: Adi Laurentiu Tarca Maintainer: Adi Laurentiu Tarca URL: http://bioinformaticsprb.med.wayne.edu/tarca/ source.ver: src/contrib/nnNorm_2.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/nnNorm_2.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/nnNorm_2.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/nnNorm_2.16.0.tgz vignettes: vignettes/nnNorm/inst/doc/nnNorm.pdf, vignettes/nnNorm/inst/doc/nnNormGuide.pdf Package: nudge Version: 1.18.0 Imports: stats License: GPL-2 Title: Normal Uniform Differential Gene Expression detection Description: Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample) biocViews: Microarray, TwoChannel, DifferentialExpression Author: N. Dean and A. E. Raftery Maintainer: N. Dean source.ver: src/contrib/nudge_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/nudge_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/nudge_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/nudge_1.18.0.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: 1.12.0 Depends: R (>= 2.0.0) License: GPL (>= 2) Title: Functions for Multinomial Occupancy Distribution Description: Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries. biocViews: Bioinformatics,Annotation,Pathways Author: Oliver Will Maintainer: Oliver Will source.ver: src/contrib/occugene_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/occugene_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/occugene_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/occugene_1.12.0.tgz vignettes: vignettes/occugene/inst/doc/occugene.pdf Package: oligoClasses Version: 1.14.0 Depends: Biobase (>= 2.11.6), methods Imports: graphics, Biostrings (>= 2.19.0), affyio (>= 1.19.2) Suggests: pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm, genomewidesnp5Crlmm Enhances: ff, snow License: GPL (>= 2) Title: Classes for high-throughput arrays supported by oligo and crlmm Description: This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages. biocViews: Infrastructure Author: Benilton Carvalho and Robert Scharpf Maintainer: Benilton Carvalho and Robert Scharpf source.ver: src/contrib/oligoClasses_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/oligoClasses_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/oligoClasses_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/oligoClasses_1.14.0.tgz Package: oligo Version: 1.16.2 Depends: R (>= 2.13.0), oligoClasses (>= 1.13.9), preprocessCore (>= 1.13.5) Imports: affyio (>= 1.19.4), affxparser (>= 1.23.1), Biobase (>= 2.11.8), Biostrings, DBI (>= 0.2-5), ff, graphics, methods, splines, stats, utils LinkingTo: preprocessCore Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData Enhances: ff, snow License: LGPL (>= 2) Archs: i386, x64 Title: Preprocessing tools for oligonucleotide arrays. Description: A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, DNAMethylation, ExonArray, GeneExpression, Bioinformatics, DataImport, Transcription, ChIPchip, CopyNumberVariants, CpGIsland Author: Benilton Carvalho , Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber Maintainer: Benilton Carvalho source.ver: src/contrib/oligo_1.16.2.tar.gz win.binary.ver: bin/windows/contrib/2.13/oligo_1.16.2.zip win64.binary.ver: bin/windows64/contrib/2.13/oligo_1.16.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/oligo_1.16.2.tgz vignettes: vignettes/oligo/inst/doc/V1Overview.pdf, vignettes/oligo/inst/doc/V2NExpression.pdf, vignettes/oligo/inst/doc/V3AffySnpGenotype.pdf, vignettes/oligo/inst/doc/V4Experimental.pdf, vignettes/oligo/inst/doc/V5ExonGene.pdf Package: oneChannelGUI Version: 1.18.7 Depends: Biobase, limma, affylmGUI, tkWidgets, GOstats, AnnotationDbi, preprocessCore, IRanges, edgeR, baySeq, girafe Suggests: annotate, genefilter, maSigPro, pamr, pdmclass, ChIPpeakAnno, chipseq, BSgenome, 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, Genominator, hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db, ragene10sttranscriptcluster.db, HuExExonProbesetLocation, MoExExonProbesetLocation, RaExExonProbesetLocation, snow, RmiR, RmiR.Hs.miRNA License: The Artistic License, Version 2.0 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. Next Generation Sequencing secondary analysis for ncRNA quantification is also available. Description: This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface for microarray gene and exon level analysis as well as basic secondary analysis of NGS data for ncRNA quantification. biocViews: HighThroughputSequencing, RNAseq, Microarray, OneChannel, DataImport, QualityControl, Preprocessing, Statistics, DifferentialExpression, GUI, 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/ source.ver: src/contrib/oneChannelGUI_1.18.7.tar.gz win.binary.ver: bin/windows/contrib/2.13/oneChannelGUI_1.18.7.zip win64.binary.ver: bin/windows64/contrib/2.13/oneChannelGUI_1.18.7.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/oneChannelGUI_1.18.7.tgz vignettes: vignettes/oneChannelGUI/inst/doc/NGS.pdf, vignettes/oneChannelGUI/inst/doc/fignew42.pdf, vignettes/oneChannelGUI/inst/doc/install.pdf, vignettes/oneChannelGUI/inst/doc/oneChannelGUI.pdf, vignettes/oneChannelGUI/inst/doc/standAloneFunctions.pdf, vignettes/oneChannelGUI/inst/doc/whatIsNew.pdf Package: ontoCAT Version: 1.4.2 Depends: rJava, methods License: Apache License 2.0 Title: Ontology traversal and search Description: The ontoCAT R package provides a simple interface to ontologies described in widely used standard formats, stored locally in the filesystem or accessible online. The full version of ontoCAT R package also supports searching for ontology terms across multiple ontologies and in major ontology repositories, as well as a number of advanced ontology navigation functions: www.ontocat.org/wiki/r biocViews: Classification, DataRepresentation Author: Natalja Kurbatova, Tomasz Adamusiak, Pavel Kurnosov, Morris Swertz, Misha Kapushevsky Maintainer: Natalja Kurbatova source.ver: src/contrib/ontoCAT_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.13/ontoCAT_1.4.2.zip win64.binary.ver: bin/windows64/contrib/2.13/ontoCAT_1.4.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ontoCAT_1.4.2.tgz vignettes: vignettes/ontoCAT/inst/doc/ontoCAT.pdf Package: ontoTools Version: 1.30.0 Depends: R (>= 2.4.0), methods, graph, Biobase (>= 2.5.5), AnnotationDbi, SparseM, GO.db, annotate Suggests: combinat, Iyer517, org.Hs.eg.db, KEGG.db License: GPL-2 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 source.ver: src/contrib/ontoTools_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ontoTools_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ontoTools_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ontoTools_1.30.0.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: pamr Version: 1.50.0 Depends: cluster, survival License: GPL-2 Archs: i386, x64 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 source.ver: src/contrib/pamr_1.50.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/pamr_1.50.0.zip win64.binary.ver: bin/windows64/contrib/2.13/pamr_1.50.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/pamr_1.50.0.tgz Package: panp Version: 1.22.0 Depends: R (>= 2.5.0), affy (>= 1.23.4), Biobase (>= 2.5.5) Imports: Biobase, methods, stats, utils License: GPL (>= 2) Title: Presence-Absence Calls from Negative Strand Matching Probesets Description: A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date. biocViews: Infrastructure Author: Peter Warren Maintainer: Peter Warren source.ver: src/contrib/panp_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/panp_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.13/panp_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/panp_1.22.0.tgz vignettes: vignettes/panp/inst/doc/panp.pdf Package: parody Version: 1.10.0 Depends: R (>= 2.5.0), methods, tools, utils License: Artistic-2.0 Title: Parametric And Resistant Outlier DYtection Description: routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics biocViews: Bioinformatics, MultipleComparisons Author: VJ Carey Maintainer: VJ Carey source.ver: src/contrib/parody_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/parody_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/parody_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/parody_1.10.0.tgz vignettes: vignettes/parody/inst/doc/parody.pdf Package: pathRender Version: 1.20.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods Suggests: ALL, hgu95av2.db License: LGPL Title: Render molecular pathways Description: build graphs from pathway databases, render them by Rgraphviz biocViews: GraphsAndNetworks Author: Li Long Maintainer: Li Long URL: http://www.bioconductor.org source.ver: src/contrib/pathRender_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/pathRender_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/pathRender_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/pathRender_1.20.0.tgz vignettes: vignettes/pathRender/inst/doc/pathRender.pdf, vignettes/pathRender/inst/doc/plotExG.pdf Package: pcaMethods Version: 1.36.0 Depends: Biobase, MASS, pls, methods, Rcpp (>= 0.8.7) LinkingTo: Rcpp Suggests: aroma.light License: GPL (>= 3) Archs: i386, x64 Title: A collection of PCA methods. Description: Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a unique interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany. Now developed at CAS-MPG Partner Institute for Computational Biology (PICB) Shanghai, P.R. China and RIKEN Plant Science Center, Yokohama Japan. biocViews: Bioinformatics Author: Wolfram Stacklies, Henning Redestig, Kevin Wright Maintainer: Wolfram Stacklies SystemRequirements: Rcpp source.ver: src/contrib/pcaMethods_1.36.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/pcaMethods_1.36.0.zip win64.binary.ver: bin/windows64/contrib/2.13/pcaMethods_1.36.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/pcaMethods_1.36.0.tgz vignettes: vignettes/pcaMethods/inst/doc/missingValues.pdf, vignettes/pcaMethods/inst/doc/outliers.pdf, vignettes/pcaMethods/inst/doc/pcaMethods.pdf Package: pcot2 Version: 1.20.0 Depends: R (>= 2.0.0), grDevices, Biobase, amap Suggests: multtest, hu6800.db, KEGG.db, mvtnorm License: GPL (>= 2) Title: Principal Coordinates and Hotelling's T-Square method Description: PCOT2 is a permutation-based method for investigating changes in the activity of multi-gene networks. It utilizes inter-gene correlation information to detect significant alterations in gene network activities. Currently it can be applied to two-sample comparisons. biocViews: Microarray, DifferentialExpression Author: Sarah Song, Mik Black Maintainer: Sarah Song source.ver: src/contrib/pcot2_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/pcot2_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/pcot2_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/pcot2_1.20.0.tgz vignettes: vignettes/pcot2/inst/doc/HowToUseGeneLocator.pdf, vignettes/pcot2/inst/doc/pcot2.pdf Package: pdInfoBuilder Version: 1.16.0 Depends: R (>= 2.11.0), methods, Biobase (>= 2.5.5), RSQLite (>= 0.7-1), affxparser (>= 1.7.3), oligo (>= 1.9.19) Imports: Biostrings (>= 2.13.50), IRanges (>= 1.3.89) License: Artistic-2.0 Archs: i386, x64 Title: Platform Design Information Package Builder Description: Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg. biocViews: Annotation, Infrastructure Author: Seth Falcon, Benilton Carvalho with contributions by Vince Carey and Matt Settles Maintainer: Benilton Carvalho source.ver: src/contrib/pdInfoBuilder_1.16.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/pdInfoBuilder_1.16.0.zip win64.binary.ver: bin/windows64/contrib/2.13/pdInfoBuilder_1.16.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/pdInfoBuilder_1.16.0.tgz vignettes: vignettes/pdInfoBuilder/inst/doc/BuildingPDInfoPkgs.pdf Package: pdmclass Version: 1.24.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), fibroEset, mda License: Artistic-2.0 Title: Classification of Microarray Samples using Penalized Discriminant Methods Description: This package can be used to classify microarray data using one of three penalized regression methods; partial least squares, principal components regression, or ridge regression. biocViews: Classification Author: James W. MacDonald, Debashis Ghosh, based in part on pls code of Mike Denham Maintainer: James W. MacDonald source.ver: src/contrib/pdmclass_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/pdmclass_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/pdmclass_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/pdmclass_1.24.0.tgz vignettes: vignettes/pdmclass/inst/doc/pdmclass.pdf Package: pgUtils Version: 1.24.0 Depends: R (>= 1.8.0), methods, RPostgreSQL (>= 0.1) Imports: methods, RPostgreSQL (>= 0.1) License: LGPL (>= 2) Title: Utility functions for PostgreSQL databases Description: Functions for creating PostgreSQL database tables, with auto incrementing primary keys, selection of foreign keys to allow referential integrity and a logging mechanism. biocViews: Infrastructure Author: Johannes Rainer Maintainer: Johannes Rainer source.ver: src/contrib/pgUtils_1.24.0.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/pgUtils_1.24.0.tgz vignettes: vignettes/pgUtils/inst/doc/pgUtils.pdf Package: phenoDist Version: 1.0.0 Depends: R (>= 2.9.0), imageHTS, e1071 Suggests: GOstats, MASS License: LGPL-2.1 Title: Phenotypic distance measures Description: PhenoDist is designed for measuring phenotypic distance in image-based high-throughput screening, in order to identify strong phenotypes and to group treatments into functional clusters. biocViews: CellBasedAssays, Bioinformatics Author: Xian Zhang, Gregoire Pau, Wolfgang Huber, Michael Boutros Maintainer: Xian Zhang URL: http://www.dkfz.de/signaling, http://www.embl.de/research/units/genome_biology/huber/ source.ver: src/contrib/phenoDist_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/phenoDist_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/phenoDist_1.0.0.zip vignettes: vignettes/phenoDist/inst/doc/phenoDist.pdf Package: phenoTest Version: 1.0.0 Depends: R (>= 2.9.0), Biobase, methods, annotate, Heatplus Imports: survival, limma, Hmisc, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate Suggests: GSEABase Enhances: multicore License: GPL (>=2) Archs: i386, x64 Title: Tools to test correlation between gene expression and phenotype. Description: Tools to test correlation between gene expression and phenotype. biocViews: Microarray, Bioinformatics, DifferentialExpression, MultipleComparisons, Clustering, Classification Author: Evarist Planet Maintainer: Evarist Planet source.ver: src/contrib/phenoTest_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/phenoTest_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/phenoTest_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/phenoTest_1.0.0.tgz vignettes: vignettes/phenoTest/inst/doc/phenoTest.pdf Package: pickgene Version: 1.24.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) Title: Adaptive Gene Picking for Microarray Expression Data Analysis Description: Functions to Analyze Microarray (Gene Expression) Data. biocViews: Microarray, DifferentialExpression Author: Brian S. Yandell Maintainer: Brian S. Yandell URL: http://www.stat.wisc.edu/~yandell/statgen source.ver: src/contrib/pickgene_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/pickgene_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/pickgene_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/pickgene_1.24.0.tgz vignettes: vignettes/pickgene/inst/doc/pickgene.pdf Package: pint Version: 1.4.04 Depends: mvtnorm, methods, graphics, Matrix, dmt License: FreeBSD Title: Pairwise INTegration of functional genomics data Description: Pairwise data integration for functional genomics. In particular, tools to screen functionally active chromosomal aberrations from paired copy number, gene expression and miRNA measurements from the same patients. biocViews: aCGH, GeneExpression, Genetics, DifferentialExpression, Microarray Author: Olli-Pekka Huovilainen and Leo Lahti Maintainer: Olli-Pekka Huovilainen source.ver: src/contrib/pint_1.4.04.tar.gz win.binary.ver: bin/windows/contrib/2.13/pint_1.4.04.zip win64.binary.ver: bin/windows64/contrib/2.13/pint_1.4.04.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/pint_1.4.04.tgz vignettes: vignettes/pint/inst/doc/depsearch.pdf Package: pkgDepTools Version: 1.18.0 Depends: methods, graph, RBGL Imports: graph, RBGL Suggests: Biobase, Rgraphviz, RCurl License: GPL-2 Title: Package Dependency Tools Description: This package provides tools for computing and analyzing dependency relationships among R packages. It provides tools for building a graph-based representation of the dependencies among all packages in a list of CRAN-style package repositories. There are also utilities for computing installation order of a given package. If the RCurl package is available, an estimate of the download size required to install a given package and its dependencies can be obtained. biocViews: Infrastructure, GraphsAndNetworks Author: Seth Falcon Maintainer: Seth Falcon source.ver: src/contrib/pkgDepTools_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/pkgDepTools_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/pkgDepTools_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/pkgDepTools_1.18.0.tgz vignettes: vignettes/pkgDepTools/inst/doc/pkgDepTools.pdf Package: plateCore Version: 1.10.0 Depends: R (>= 2.8.0), flowCore, flowViz, lattice, latticeExtra Imports: Biobase, flowCore, graphics, grDevices, lattice, MASS, methods, robustbase, stats, utils Suggests: gplots License: Artistic-2.0 Title: Statistical tools and data structures for plate-based flow cytometry Description: Provides basic S4 data structures and routines for analyzing plate based flow cytometry data. biocViews: Flowcytometry, Infrastructure, CellBasedAssays Author: Errol Strain, Florian Hahne, and Perry Haaland Maintainer: Errol Strain URL: http://www.bioconductor.org source.ver: src/contrib/plateCore_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/plateCore_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/plateCore_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/plateCore_1.10.0.tgz vignettes: vignettes/plateCore/inst/doc/expDens.pdf, vignettes/plateCore/inst/doc/plateCoreVig.pdf Package: plgem Version: 1.24.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), MASS Imports: utils License: GPL-2 Title: Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM) Description: The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use of PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets. biocViews: Microarray, DifferentialExpression, Proteomics Author: Mattia Pelizzola and Norman Pavelka Maintainer: Norman Pavelka URL: http://www.genopolis.it source.ver: src/contrib/plgem_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/plgem_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/plgem_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/plgem_1.24.0.tgz vignettes: vignettes/plgem/inst/doc/plgem.pdf Package: plier Version: 1.22.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) Archs: i386, x64 Title: Implements the Affymetrix PLIER algorithm Description: The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values. biocViews: Software Author: Affymetrix Inc., Crispin J Miller, PICR Maintainer: Crispin Miller source.ver: src/contrib/plier_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/plier_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.13/plier_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/plier_1.22.0.tgz Package: plw Version: 1.12.0 Depends: affy (>= 1.23.4) Imports: MASS, affy, graphics, splines, stats Suggests: limma License: GPL-2 Archs: i386, x64 Title: Probe level Locally moderated Weighted t-tests. Description: Probe level Locally moderated Weighted median-t (PLW) and Locally Moderated Weighted-t (LMW). biocViews: Microarray, OneChannel, TwoChannel, Bioinformatics, DifferentialExpression Author: Magnus Astrand Maintainer: Magnus Astrand source.ver: src/contrib/plw_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/plw_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/plw_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/plw_1.12.0.tgz vignettes: vignettes/plw/inst/doc/HowToPLW.pdf Package: ppiStats Version: 1.18.0 Depends: ScISI (>= 1.13.2), lattice, ppiData (>= 0.1.6) Imports: Biobase, Category, graph, graphics, grDevices, lattice, methods, RColorBrewer, stats Suggests: yeastExpData, xtable License: Artistic-2.0 Title: Protein-Protein Interaction Statistical Package Description: Tools for the analysis of protein interaction data. biocViews: Proteomics, GraphsAndNetworks Author: T. Chiang and D. Scholtens with contributions from W. Huber and L. Wang Maintainer: Tony Chiang source.ver: src/contrib/ppiStats_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ppiStats_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ppiStats_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ppiStats_1.18.0.tgz vignettes: vignettes/ppiStats/inst/doc/ppiStats.pdf Package: prada Version: 1.28.0 Depends: R (>= 2.1.0), Biobase, RColorBrewer, grid, methods, rrcov Imports: Biobase, graphics, grDevices, grid, MASS, methods, RColorBrewer, rrcov, utils Suggests: cellHTS, rflowcyt, tcltk License: LGPL Archs: i386, x64 Title: Data analysis for cell-based functional assays Description: Tools for analysing and navigating data from high-throughput phenotyping experiments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy). biocViews: CellBasedAssays, Visualization Author: Florian Hahne , Wolfgang Huber , Markus Ruschhaupt, Joern Toedling Maintainer: Florian Hahne URL: http://www.dkfz.de/mga/whuber, http://www.dkfz.de/LIFEdb source.ver: src/contrib/prada_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/prada_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.13/prada_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/prada_1.28.0.tgz vignettes: vignettes/prada/inst/doc/norm2.pdf, vignettes/prada/inst/doc/prada2cellHTS.pdf Package: preprocessCore Version: 1.14.0 Depends: methods Imports: stats License: LGPL (>= 2) Archs: i386, x64 Title: A collection of pre-processing functions Description: A library of core preprocessing routines biocViews: Infrastructure Author: Benjamin Milo Bolstad Maintainer: Benjamin Milo Bolstad source.ver: src/contrib/preprocessCore_1.14.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/preprocessCore_1.14.0.zip win64.binary.ver: bin/windows64/contrib/2.13/preprocessCore_1.14.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/preprocessCore_1.14.0.tgz Package: procoil Version: 1.2.0 Depends: R (>= 2.10.1), methods Imports: methods, stats, graphics, utils Suggests: Biostrings License: GPL (>= 2) Title: Prediction of Oligomerization of Coiled Coil Proteins Description: The procoil package allows to predict whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer. The predict function not only computes the prediction itself, but also a profile which allows to determine the strengths to which the individual residues are indicative for either class. Profiles can also be plotted and exported to files. biocViews: Proteomics, Classification Author: Ulrich Bodenhofer Maintainer: Ulrich Bodenhofer URL: http://www.bioinf.jku.at/software/procoil/ source.ver: src/contrib/procoil_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/procoil_1.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/procoil_1.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/procoil_1.2.0.tgz vignettes: vignettes/procoil/inst/doc/procoil.pdf Package: puma Version: 2.4.0 Depends: R (>= 2.6.0), Biobase (>= 2.5.5), affy (>= 1.23.4), graphics, grDevices, methods, stats, utils, mclust Imports: Biobase (>= 2.5.5), affy (>= 1.23.4) Suggests: pumadata, affydata, snow, limma, annotate, ROCR License: LGPL Archs: i386, x64 Title: Propagating Uncertainty in Microarray Analysis Description: Most analyses of Affymetrix GeneChip data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting and data manipulation functions. biocViews: Microarray, OneChannel, Preprocessing, Bioinformatics, DifferentialExpression, Clustering Author: Richard D. Pearson, Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence, Guido Sanguinetti, Li Zhang Maintainer: Richard Pearson , Li Zhang URL: http://umber.sbs.man.ac.uk/resources/puma source.ver: src/contrib/puma_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/puma_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/puma_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/puma_2.4.0.tgz vignettes: vignettes/puma/inst/doc/puma-014.pdf, vignettes/puma/inst/doc/puma-015.pdf, vignettes/puma/inst/doc/puma-016.pdf, vignettes/puma/inst/doc/puma-022.pdf, vignettes/puma/inst/doc/puma-023.pdf, vignettes/puma/inst/doc/puma-024.pdf, vignettes/puma/inst/doc/puma.pdf Package: pvac Version: 1.0.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) Title: PCA-based gene filtering for Affymetrix arrays Description: The package contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC). biocViews: Bioinformatics, Microarray, OneChannel, QualityControl Author: Jun Lu and Pierre R. Bushel Maintainer: Jun Lu , Pierre R. Bushel source.ver: src/contrib/pvac_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/pvac_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/pvac_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/pvac_1.0.0.tgz vignettes: vignettes/pvac/inst/doc/density.pdf, vignettes/pvac/inst/doc/pvac.pdf Package: qpcrNorm Version: 1.10.0 Depends: methods, Biobase, limma, affy License: LGPL (>= 2) Title: Data-driven normalization strategies for high-throughput qPCR data. Description: The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available. biocViews: Preprocessing, GeneExpression Author: Jessica Mar Maintainer: Jessica Mar source.ver: src/contrib/qpcrNorm_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/qpcrNorm_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/qpcrNorm_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/qpcrNorm_1.10.0.tgz vignettes: vignettes/qpcrNorm/inst/doc/qpcrNorm.pdf Package: qpgraph Version: 1.8.2 Depends: methods Imports: methods, annotate, Matrix, graph, Biobase, AnnotationDbi Suggests: Matrix, mvtnorm, graph, genefilter, Category, org.EcK12.eg.db, GOstats Enhances: rlecuyer, snow, Rgraphviz License: GPL (>= 2) Archs: i386, x64 Title: Reverse engineering of molecular regulatory networks with qp-graphs Description: q-order partial correlation graphs, or qp-graphs for short, are undirected Gaussian graphical Markov models built from q-order partial correlations. They are useful for learning undirected graphical Gaussian Markov models from data sets where the number of random variables p exceeds the available sample size n as, for instance, in the case of microarray data where they can be employed to reverse engineer a molecular regulatory network. biocViews: Microarray, GeneExpression, Transcription, Pathways, Bioinformatics, GraphsAndNetworks Author: R. Castelo and A. Roverato Maintainer: Robert Castelo URL: http://functionalgenomics.upf.edu/qpgraph source.ver: src/contrib/qpgraph_1.8.2.tar.gz win.binary.ver: bin/windows/contrib/2.13/qpgraph_1.8.2.zip win64.binary.ver: bin/windows64/contrib/2.13/qpgraph_1.8.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/qpgraph_1.8.2.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: qrqc Version: 1.0.0 Depends: Rsamtools (>= 1.3.28), methods, tools, utils Imports: reshape, brew, xtable, testthat LinkingTo: Rsamtools License: GPL (>=2) Archs: i386, x64 Title: Quick Read Quality Control Description: Quickly scans reads and gathers statistics on base and quality frequencies, read length, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected. biocViews: Sequencing, QualityControl, DataImport, Preprocessing, Visualization, HighThroughputSequencing Author: Vince Buffalo Maintainer: Vince Buffalo URL: http://bioinformatics.ucdavis.edu source.ver: src/contrib/qrqc_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/qrqc_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/qrqc_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/qrqc_1.0.0.tgz vignettes: vignettes/qrqc/inst/doc/qrqc.pdf Package: quantsmooth Version: 1.18.0 Depends: quantreg, lodplot, grid License: GPL-2 Title: Quantile smoothing and genomic visualization of array data Description: Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53. biocViews: Visualization, CopyNumberVariants Author: Jan Oosting, Paul Eilers, Renee Menezes Maintainer: Jan Oosting source.ver: src/contrib/quantsmooth_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/quantsmooth_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/quantsmooth_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/quantsmooth_1.18.0.tgz vignettes: vignettes/quantsmooth/inst/doc/quantsmooth.pdf Package: qvalue Version: 1.26.0 Imports: graphics, grDevices, stats, tcltk License: LGPL Title: Q-value estimation for false discovery rate control Description: This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining. biocViews: MultipleComparisons Author: Alan Dabney and John D. Storey , with assistance from Gregory R. Warnes Maintainer: John D. Storey source.ver: src/contrib/qvalue_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/qvalue_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/qvalue_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/qvalue_1.26.0.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: rGADEM Version: 1.4.0 Depends: R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo Imports: Biostrings, IRanges, methods, graphics, seqLogo Suggests: BSgenome.Hsapiens.UCSC.hg18 License: Artistic-2.0 Archs: i386, x64 Title: de novo motif discovery Description: rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software. biocViews: Microarray, ChIPchip, Sequencing, ChIPSeq, GenomicSequence Author: Arnaud Droit, Raphael Gottardo, Gordon Robertson and Leiping Li Maintainer: Arnaud Droit source.ver: src/contrib/rGADEM_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/rGADEM_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/rGADEM_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/rGADEM_1.4.0.tgz vignettes: vignettes/rGADEM/inst/doc/rGADEM.pdf Package: rHVDM Version: 1.18.0 Depends: R (>= 2.3), R2HTML (>= 1.5), affy (>= 1.23.4), minpack.lm (>= 1.0-5), Biobase (>= 2.5.5) License: GPL-2 Title: Hidden Variable Dynamic Modeling Description: A R implementation of HVDM (Genome Biol 2006, V7(3) R25) biocViews: Microarray, GraphsAndNetworks, Transcription, Classification Author: Martino Barenco Maintainer: Martino Barenco source.ver: src/contrib/rHVDM_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/rHVDM_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/rHVDM_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/rHVDM_1.18.0.tgz vignettes: vignettes/rHVDM/inst/doc/rHVDM.pdf Package: rMAT Version: 3.2.0 Depends: R(>= 2.9.0), IRanges, Biobase, affxparser Imports: Biobase (>= 2.5.5), methods, IRanges Suggests: GenomeGraphs, rtracklayer License: Artistic-2.0 Archs: i386 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'. Snow Leopard users can take advantage of increase speed with Grand Central Dispatch! biocViews: Microarray, Preprocessing Author: Charles Cheung and Arnaud Droit and Raphael Gottardo Maintainer: Arnaud Droit and Raphael Gottardo URL: http://www.rglab.org source.ver: src/contrib/rMAT_3.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/rMAT_3.2.0.zip win64.binary.ver: bin/windows64/contrib/2.13/rMAT_3.2.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/rMAT_3.2.0.tgz vignettes: vignettes/rMAT/inst/doc/rMAT.pdf Package: rama Version: 1.26.0 Depends: R(>= 2.5.0) License: GPL (>= 2) Archs: i386, x64 Title: Robust Analysis of MicroArrays Description: Robust estimation of cDNA microarray intensities with replicates. The package uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution, and the model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance. biocViews: Microarray, TwoChannel, QualityControl, Preprocessing Author: Raphael Gottardo Maintainer: Raphael Gottardo source.ver: src/contrib/rama_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/rama_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/rama_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/rama_1.26.0.tgz vignettes: vignettes/rama/inst/doc/rama.pdf Package: rbsurv Version: 2.10.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), survival License: GPL (>= 2) Title: Robust likelihood-based survival modeling with microarray data Description: This package selects genes associated with survival. biocViews: Microarray, Bioinformatics Author: HyungJun Cho , Sukwoo Kim , Soo-heang Eo , Jaewoo Kang Maintainer: Soo-heang Eo URL: http://www.korea.ac.kr/~stat2242/ source.ver: src/contrib/rbsurv_2.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/rbsurv_2.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/rbsurv_2.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/rbsurv_2.10.0.tgz vignettes: vignettes/rbsurv/inst/doc/rbsurv.pdf Package: reb Version: 1.28.0 Depends: R (>= 2.0), Biobase, idiogram (>= 1.5.3) License: GPL-2 Archs: i386, x64 Title: Regional Expression Biases Description: A set of functions to dentify regional expression biases biocViews: Microarray, CopyNumberVariants, Visualization Author: Kyle A. Furge and Karl Dykema Maintainer: Karl J. Dykema source.ver: src/contrib/reb_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/reb_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.13/reb_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/reb_1.28.0.tgz vignettes: vignettes/reb/inst/doc/reb.pdf Package: rflowcyt Version: 1.24.0 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 License: GPL-2 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 source.ver: src/contrib/rflowcyt_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/rflowcyt_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/rflowcyt_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/rflowcyt_1.24.0.tgz vignettes: vignettes/rflowcyt/inst/doc/rflowcyt.pdf Package: rnaSeqMap Version: 2.7.12 Depends: R (>= 2.11.0), methods, xmapcore, Biobase, Rsamtools Imports: GenomicRanges, IRanges, edgeR, DESeq, DBI, RMySQL (>= 0.6-0) License: GPL-2 Archs: i386, x64 Title: rnaSeq analyses using xmapcore database Description: Provides means of analysis for RNAseq data, used together with genomic annotation from Ensembl. Requires a set of BAM files on the input or alternatively, an xmapcore database in MySQL as a back-end, which is also a storage for sequencing reads. Front-end analyses include transformations of the coverage function, splicing analysis, finding irreducible regions with the two-sliding-windows algorithm and genomic region visualizations. biocViews: Annotation, Bioinformatics, ReportWriting, Transcription, GeneExpression, DifferentialExpression, HighThroughputSequencing, RNAseq, SAGE, Visualization Author: Anna Lesniewska ; Michal Okoniewski Maintainer: Michal Okoniewski source.ver: src/contrib/rnaSeqMap_2.7.12.tar.gz win.binary.ver: bin/windows/contrib/2.13/rnaSeqMap_2.7.12.zip win64.binary.ver: bin/windows64/contrib/2.13/rnaSeqMap_2.7.12.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/rnaSeqMap_2.7.12.tgz vignettes: vignettes/rnaSeqMap/inst/doc/rnaSeqMap.pdf Package: rsbml Version: 2.10.0 Depends: R (>= 2.6.0), methods, utils Imports: graph, utils License: Artistic-2.0 Archs: i386 Title: R support for SBML, using libsbml Description: Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models. biocViews: GraphsAndNetworks Author: Michael Lawrence Maintainer: Michael Lawrence URL: http://www.sbml.org SystemRequirements: libsbml (>=3.0.3) source.ver: src/contrib/rsbml_2.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/rsbml_2.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/rsbml_2.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/rsbml_2.10.0.tgz vignettes: vignettes/rsbml/inst/doc/quick-start.pdf Package: rtracklayer Version: 1.12.5 Depends: R (>= 2.7.0), methods, RCurl (>= 1.4-2) Imports: XML (>= 1.98-0), IRanges (>= 1.9.26), GenomicRanges (>= 1.1.34), Biostrings (>= 2.15.22), BSgenome (>= 1.15.17) LinkingTo: IRanges Suggests: humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 Archs: i386, x64 Title: R interface to genome browsers and their annotation tracks Description: Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, 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, Vince Carey, Robert Gentleman Maintainer: Michael Lawrence source.ver: src/contrib/rtracklayer_1.12.5.tar.gz win.binary.ver: bin/windows/contrib/2.13/rtracklayer_1.12.5.zip win64.binary.ver: bin/windows64/contrib/2.13/rtracklayer_1.12.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/rtracklayer_1.12.5.tgz vignettes: vignettes/rtracklayer/inst/doc/rtracklayer.pdf Package: safe Version: 2.12.0 Depends: R (>= 2.4.0), Biobase, annotate, methods Imports: SparseM, GO.db, annotate, AnnotationDbi, survival, Biobase Suggests: GO.db, GOstats, Rgraphviz, multtest, hu6800.db, survival License: GPL (>= 2) Title: Significance Analysis of Function and Expression Description: SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions. biocViews: GeneExpression, FunctionalAnnotation Author: William T. Barry Maintainer: William T. Barry URL: http://www.duke.edu/~dinbarry/SAFE/ source.ver: src/contrib/safe_2.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/safe_2.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/safe_2.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/safe_2.12.0.tgz vignettes: vignettes/safe/inst/doc/SAFEmanual2.pdf Package: sagenhaft Version: 1.22.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, methods, SparseM, stats, utils License: GPL (>= 2) Title: Collection of functions for reading and comparing SAGE libraries Description: This package implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison. Sequencing error correction is implementing using an Expectation Maximization Algorithm based on a Mixture Model of tag counts. biocViews: SAGE Author: Tim Beissbarth , with contributions from Gordon Smyth and Lavinia Hyde . Maintainer: Tim Beissbarth URL: http://tagcalling.mbgproject.org source.ver: src/contrib/sagenhaft_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/sagenhaft_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.13/sagenhaft_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/sagenhaft_1.22.0.tgz vignettes: vignettes/sagenhaft/inst/doc/SAGEnhaft.pdf Package: segmentSeq Version: 1.4.0 Depends: R (>= 2.3.0), methods, baySeq (>= 1.1.23), ShortRead Imports: baySeq, graphics, grDevices, IRanges, methods, utils Suggests: snow License: GPL-3 Title: Methods for identifying small RNA loci from high-throughput sequencing data Description: High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery. biocViews: Bioinformatics, HighThroughputSequencing, MultipleComparisons Author: Thomas J. Hardcastle Maintainer: Thomas J. Hardcastle source.ver: src/contrib/segmentSeq_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/segmentSeq_1.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/segmentSeq_1.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/segmentSeq_1.4.0.tgz vignettes: vignettes/segmentSeq/inst/doc/segmentSeq.pdf Package: seqLogo Version: 1.18.0 Depends: methods, grid License: LGPL (>= 2) Title: Sequence logos for DNA sequence alignments Description: seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990). biocViews: SequenceMatching Author: Oliver Bembom Maintainer: Oliver Bembom source.ver: src/contrib/seqLogo_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/seqLogo_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/seqLogo_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/seqLogo_1.18.0.tgz vignettes: vignettes/seqLogo/inst/doc/seqLogo.pdf Package: seqbias Version: 1.0.0 Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0), Biostrings (>= 2.15.0), methods LinkingTo: Rsamtools License: LGPL-3 Archs: i386, x64 Title: Estimation of per-position bias in high-throughput sequencing data Description: This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence. biocViews: Sequencing, HighThroughputSequencing Author: Daniel Jones Maintainer: Daniel Jones source.ver: src/contrib/seqbias_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/seqbias_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/seqbias_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/seqbias_1.0.0.tgz vignettes: vignettes/seqbias/inst/doc/overview.pdf Package: sigPathway Version: 1.20.0 Depends: R (>= 2.0.0) Suggests: hgu133a.db (>= 1.10.0), XML (>= 1.6-3), AnnotationDbi (>= 1.3.12) License: GPL-2 Archs: i386, x64 Title: Pathway Analysis Description: Conducts pathway analysis by calculating the NT_k and NE_k statistics as described in Tian et al. (2005) biocViews: Bioinformatics, DifferentialExpression, MultipleComparisons Author: Weil Lai (optimized R and C code), Lu Tian and Peter Park (algorithm development and initial R code) Maintainer: Weil Lai URL: http://www.pnas.org/cgi/doi/10.1073/pnas.0506577102, http://www.chip.org/~ppark/Supplements/PNAS05.html source.ver: src/contrib/sigPathway_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/sigPathway_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/sigPathway_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/sigPathway_1.20.0.tgz vignettes: vignettes/sigPathway/inst/doc/sigPathway-vignette.pdf Package: siggenes Version: 1.26.0 Depends: methods, multtest, Biobase, splines Suggests: affy, annotate, genefilter, KernSmooth, scrime (>= 1.2.5) License: LGPL (>= 2) Title: Multiple testing using SAM and Efron's empirical Bayes approaches Description: Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM). biocViews: MultipleComparisons, Microarray, GeneExpression, SNP, ExonArray, DifferentialExpression Author: Holger Schwender Maintainer: Holger Schwender source.ver: src/contrib/siggenes_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/siggenes_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/siggenes_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/siggenes_1.26.0.tgz vignettes: vignettes/siggenes/inst/doc/siggenes.pdf, vignettes/siggenes/inst/doc/siggenesRnews.pdf Package: simpleaffy Version: 2.28.0 Depends: R (>= 2.0.0), affy, genefilter, Biobase, methods, utils, gcrma Imports: affy, Biobase, gcrma, genefilter, graphics, grDevices, methods, stats, utils License: GPL (>= 2) Archs: i386, x64 Title: Very simple high level analysis of Affymetrix data Description: Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures... biocViews: Microarray, OneChannel, QualityControl, Preprocessing, Transcription, DataImport, Bioinformatics, DifferentialExpression, Annotation, ReportWriting, Visualization Author: Crispin J Miller Maintainer: Crispin Miller URL: http://www.bioconductor.org, http://bioinformatics.picr.man.ac.uk/simpleaffy/ source.ver: src/contrib/simpleaffy_2.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/simpleaffy_2.28.0.zip win64.binary.ver: bin/windows64/contrib/2.13/simpleaffy_2.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/simpleaffy_2.28.0.tgz vignettes: vignettes/simpleaffy/inst/doc/QCandSimpleaffy.pdf, vignettes/simpleaffy/inst/doc/simpleAffy.pdf Package: simulatorAPMS Version: 1.24.0 Depends: ScISI, apComplex Imports: ScISI License: LGPL 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 source.ver: src/contrib/simulatorAPMS_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/simulatorAPMS_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/simulatorAPMS_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/simulatorAPMS_1.24.0.tgz vignettes: vignettes/simulatorAPMS/inst/doc/simulatorAPMS.pdf Package: sizepower Version: 1.22.0 Depends: stats License: LGPL Title: Sample Size and Power Calculation in Micorarray Studies Description: This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. These five types can be adapted in various ways to encompass many of the standard designs encountered in practice. biocViews: Microarray, Bioinformatics Author: Weiliang Qiu and Mei-Ling Ting Lee and George Alex Whitmore Maintainer: Weiliang Qiu source.ver: src/contrib/sizepower_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/sizepower_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.13/sizepower_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/sizepower_1.22.0.tgz vignettes: vignettes/sizepower/inst/doc/sizepower.pdf Package: snapCGH Version: 1.22.0 Depends: limma, DNAcopy, methods Imports: aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma, methods, stats, tilingArray, utils License: GPL Archs: i386, x64 Title: Segmentation, normalisation and processing of aCGH data. Description: Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays. biocViews: Microarray, CopyNumberVariants, TwoChannel, Preprocessing Author: Mike L. Smith, John C. Marioni, Steven McKinney, Thomas Hardcastle, Natalie P. Thorne Maintainer: John Marioni source.ver: src/contrib/snapCGH_1.22.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/snapCGH_1.22.0.zip win64.binary.ver: bin/windows64/contrib/2.13/snapCGH_1.22.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/snapCGH_1.22.0.tgz vignettes: vignettes/snapCGH/inst/doc/snapCGHguide.pdf Package: snm Version: 1.0.0 Depends: R(>= 2.12.0), lme4, splines, corpcor License: LGPL Title: Supervised Normalization of Microarrays Description: SNM is a modeling strategy especially designed for normalizing high-throughput genomic data. The underlying premise of our approach is that your data is a function of what we refer to as study-specific variables. These variables are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest. biocViews: Microarray, OneChannel, TwoChannel, MultiChannel, DifferentialExpression, ExonArray, GeneExpression, Transcription, MultipleComparisons, Preprocessing, QualityControl Author: Brig Mecham and John D. Storey Maintainer: Brig Mecham source.ver: src/contrib/snm_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/snm_1.0.0.zip win64.binary.ver: bin/windows64/contrib/2.13/snm_1.0.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/snm_1.0.0.tgz vignettes: vignettes/snm/inst/doc/snm.pdf Package: snpMatrix Version: 1.16.5 Depends: R(>= 2.3.0), survival, methods Imports: graphics, grDevices, methods, stats, survival, utils Suggests: hexbin License: GPL-3 Archs: i386, x64 Title: The snp.matrix and X.snp.matrix classes Description: Implements classes and methods for large-scale SNP association studies biocViews: Microarray, SNP, GeneticVariability Author: David Clayton and Hin-Tak Leung Maintainer: David Clayton URL: http://www-gene.cimr.cam.ac.uk/clayton/software/ source.ver: src/contrib/snpMatrix_1.16.5.tar.gz win.binary.ver: bin/windows/contrib/2.13/snpMatrix_1.16.5.zip win64.binary.ver: bin/windows64/contrib/2.13/snpMatrix_1.16.5.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/snpMatrix_1.16.5.tgz vignettes: vignettes/snpMatrix/inst/doc/clustering-comparison-vignette.pdf, 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/snpStatsBug-vignette.pdf, vignettes/snpMatrix/inst/doc/tdt-vignette.pdf Package: snpStats Version: 1.2.1 Depends: R(>= 2.3.0), survival, methods, Matrix Imports: graphics, grDevices, methods, stats, survival, utils, Matrix Suggests: hexbin License: GPL-3 Archs: i386, x64 Title: SnpMatrix and XSnpMatrix classes and methods Description: Classes and statistical methods for large SNP association studies, extending the snpMatrix package biocViews: Microarray, SNP, GeneticVariability Author: David Clayton Maintainer: David Clayton URL: http://www-gene.cimr.cam.ac.uk/clayton source.ver: src/contrib/snpStats_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/snpStats_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.13/snpStats_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/snpStats_1.2.1.tgz vignettes: vignettes/snpStats/inst/doc/data-input-vignette.pdf, vignettes/snpStats/inst/doc/differences.pdf, vignettes/snpStats/inst/doc/imputation-vignette.pdf, vignettes/snpStats/inst/doc/ld-vignette.pdf, vignettes/snpStats/inst/doc/pca-vignette.pdf, vignettes/snpStats/inst/doc/snpStats-vignette.pdf, vignettes/snpStats/inst/doc/tdt-vignette.pdf Package: spikeLI Version: 2.12.0 Imports: graphics, grDevices, stats, utils License: GPL-2 Title: Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool Description: SpikeLI is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006). biocViews: Microarray, QualityControl Author: Delphine Baillon, Paul Leclercq , Sarah Ternisien, Thomas Heim, Enrico Carlon Maintainer: Enrico Carlon source.ver: src/contrib/spikeLI_2.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/spikeLI_2.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/spikeLI_2.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/spikeLI_2.12.0.tgz vignettes: vignettes/spikeLI/inst/doc/IvsDG_TagE.pdf, vignettes/spikeLI/inst/doc/Ivsc.pdf, vignettes/spikeLI/inst/doc/collapse_A14.pdf, vignettes/spikeLI/inst/doc/langmuir2.pdf, vignettes/spikeLI/inst/doc/spikeLI.pdf Package: spkTools Version: 1.8.0 Depends: R (>= 2.7.0), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), graphics, grDevices, gtools, methods, RColorBrewer, stats, utils Suggests: xtable License: GPL (>= 2) Title: Methods for Spike-in Arrays Description: The package contains functions that can be used to compare expression measures on different array platforms. biocViews: Software, AssayTechnologies, Microarray Author: Matthew N McCall , Rafael A Irizarry Maintainer: Matthew N McCall URL: http://bioconductor.org source.ver: src/contrib/spkTools_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/spkTools_1.8.0.zip win64.binary.ver: bin/windows64/contrib/2.13/spkTools_1.8.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/spkTools_1.8.0.tgz vignettes: vignettes/spkTools/inst/doc/spkDoc.pdf Package: splicegear Version: 1.24.0 Depends: R (>= 2.6.0), methods, Biobase(>= 2.5.5) Imports: annotate, Biobase, graphics, grDevices, grid, methods, utils, XML License: LGPL Title: splicegear Description: A set of tools to work with alternative splicing biocViews: Infrastructure, Transcription Author: Laurent Gautier Maintainer: Laurent Gautier source.ver: src/contrib/splicegear_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/splicegear_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/splicegear_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/splicegear_1.24.0.tgz vignettes: vignettes/splicegear/inst/doc/splicegear.pdf Package: splots Version: 1.18.0 Imports: grid, RColorBrewer License: LGPL Title: Visualization of high-throughput assays in microtitre plate or slide format Description: The splots package provides the plotScreen function for visualising data in microtitre plate or slide format. biocViews: Visualization, HighThroughputSequencing, MicrotitrePlateAssay Author: Wolfgang Huber, Oleg Sklyar Maintainer: Wolfgang Huber source.ver: src/contrib/splots_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/splots_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/splots_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/splots_1.18.0.tgz vignettes: vignettes/splots/inst/doc/splotsHOWTO.pdf Package: spotSegmentation Version: 1.26.0 Depends: R (>= 1.7.0), mclust License: GPL (>= 2) Title: Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots Description: Spot segmentation via model-based clustering and gridding for blocks within microarray slides, as described in Li et al, Robust Model-Based Segmentation of Microarray Images, Technical Report no. 473, Department of Statistics, University of Washington. biocViews: Microarray, TwoChannel, QualityControl, Preprocessing Author: Qunhua Li, Chris Fraley, Adrian Raftery Department of Statistics, University of Washington Maintainer: Chris Fraley URL: http://www.stat.washington.edu/fraley source.ver: src/contrib/spotSegmentation_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/spotSegmentation_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/spotSegmentation_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/spotSegmentation_1.26.0.tgz vignettes: vignettes/spotSegmentation/inst/doc/spotsegdoc.pdf Package: sscore Version: 1.24.0 Depends: R (>= 1.8.0), affy, affyio Suggests: affydata License: GPL (>= 2) Title: S-Score Algorithm for Affymetrix Oligonucleotide Microarrays Description: This package contains an implementation of the S-Score algorithm as described by Zhang et al (2002). biocViews: Bioinformatics, DifferentialExpression Author: Richard Kennedy , based on C++ code from Li Zhang and Borland Delphi code from Robnet Kerns . Maintainer: Richard Kennedy URL: http://home.att.net/~richard-kennedy/professional.html source.ver: src/contrib/sscore_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/sscore_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/sscore_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/sscore_1.24.0.tgz vignettes: vignettes/sscore/inst/doc/sscore.pdf Package: ssize Version: 1.26.0 Depends: gdata, xtable License: LGPL Title: Estimate Microarray Sample Size Description: Functions for computing and displaying sample size information for gene expression arrays. biocViews: Bioinformatics, Microarray, DifferentialExpression Author: Gregory R. Warnes, Peng Liu, and Fasheng Li Maintainer: Gregory R. Warnes source.ver: src/contrib/ssize_1.26.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/ssize_1.26.0.zip win64.binary.ver: bin/windows64/contrib/2.13/ssize_1.26.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/ssize_1.26.0.tgz vignettes: vignettes/ssize/inst/doc/ssize.pdf Package: stepNorm Version: 1.24.0 Depends: R (>= 1.8.0), marray, methods Imports: marray, MASS, methods, stats License: LGPL Title: Stepwise normalization functions for cDNA microarrays Description: Stepwise normalization functions for cDNA microarray data. biocViews: Microarray, TwoChannel, Preprocessing Author: Yuanyuan Xiao , Yee Hwa (Jean) Yang Maintainer: Yuanyuan Xiao URL: http://www.biostat.ucsf.edu/jean/ source.ver: src/contrib/stepNorm_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/stepNorm_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/stepNorm_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/stepNorm_1.24.0.tgz Package: survcomp Version: 1.2.1 Depends: survival, ipred, prodlim, survivalROC, SuppDists, grid, rmeta, bootstrap Suggests: Hmisc, CPE, clinfun, survJamda, Biobase License: Artistic-2.0 Archs: i386, x64 Title: Performance Assessment and Comparison for Survival Analysis Description: R package providing functions to assess and to compare the performance of risk prediction (survival) models. biocViews: GeneExpression, DifferentialExpression, Visualization Author: Benjamin Haibe-Kains, Markus Schroeder, Christos Sotiriou, Gianluca Bontempi, John Quackenbush Maintainer: Benjamin Haibe-Kains , Markus Schroeder URL: http://compbio.dfci.harvard.edu source.ver: src/contrib/survcomp_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/survcomp_1.2.1.zip win64.binary.ver: bin/windows64/contrib/2.13/survcomp_1.2.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/survcomp_1.2.1.tgz vignettes: vignettes/survcomp/inst/doc/survcomp.pdf Package: tigre Version: 1.6.2 Depends: R (>= 2.11.0), Biobase Imports: Biobase, methods, AnnotationDbi, gplots, graphics, puma, stats, utils, annotate, DBI, RSQLite Suggests: puma, drosgenome1.db, annotate License: AGPL-3 Archs: i386, x64 Title: Transcription factor Inference through Gaussian process Reconstruction of Expression Description: The tigre package implements our methodology of Gaussian process differential equation models for analysis of gene expression time series from single input motif networks. The package can be used for inferring unobserved transcription factor (TF) protein concentrations from expression measurements of known target genes, or for ranking candidate targets of a TF. biocViews: Microarray, Bioinformatics, TimeCourse, GeneExpression, Transcription Author: Antti Honkela, Pei Gao, Jonatan Ropponen, Miika-Petteri Matikainen, Magnus Rattray, Neil D. Lawrence Maintainer: Antti Honkela URL: http://www.bioinf.manchester.ac.uk/resources/tiger/ source.ver: src/contrib/tigre_1.6.2.tar.gz win.binary.ver: bin/windows/contrib/2.13/tigre_1.6.2.zip win64.binary.ver: bin/windows64/contrib/2.13/tigre_1.6.2.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/tigre_1.6.2.tgz vignettes: vignettes/tigre/inst/doc/tigre-009.pdf, vignettes/tigre/inst/doc/tigre-010.pdf, vignettes/tigre/inst/doc/tigre-011.pdf, vignettes/tigre/inst/doc/tigre.pdf, vignettes/tigre/inst/doc/tigre_quick.pdf Package: tilingArray Version: 1.30.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid License: Artistic-2.0 Archs: i386, x64 Title: Transcript mapping with high-density oligonucleotide tiling arrays Description: The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class 'segmentation' for representing partitionings of a linear series of data; 2. the function 'segment' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function 'confint' for calculating confidence intervals using the strucchange package; 4. the function 'plotAlongChrom' for generating pretty plots; 5. the function 'normalizeByReference' for probe-sequence dependent response adjustment from a (set of) reference hybridizations. biocViews: Microarray, OneChannel, Preprocessing, Visualization Author: Wolfgang Huber, Zhenyu Xu, Joern Toedling with contributions from Matt Ritchie Maintainer: Zhenyu Xu source.ver: src/contrib/tilingArray_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/tilingArray_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/tilingArray_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/tilingArray_1.30.0.tgz vignettes: vignettes/tilingArray/inst/doc/assessNorm.pdf, vignettes/tilingArray/inst/doc/costMatrix.pdf, vignettes/tilingArray/inst/doc/findsegments.pdf, vignettes/tilingArray/inst/doc/plotAlongChrom.pdf, vignettes/tilingArray/inst/doc/segmentation.pdf Package: timecourse Version: 1.24.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL Title: Statistical Analysis for Developmental Microarray Time Course Data Description: Functions for data analysis and graphical displays for developmental microarray time course data. biocViews: Microarray, TimeCourse, DifferentialExpression Author: Yu Chuan Tai Maintainer: Yu Chuan Tai URL: http://www.bioconductor.org source.ver: src/contrib/timecourse_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/timecourse_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/timecourse_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/timecourse_1.24.0.tgz vignettes: vignettes/timecourse/inst/doc/timecourse.pdf Package: tkWidgets Version: 1.30.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase License: Artistic-2.0 Title: R based tk widgets Description: Widgets to provide user interfaces. tcltk should have been installed for the widgets to run. biocViews: Infrastructure Author: J. Zhang Maintainer: J. Zhang source.ver: src/contrib/tkWidgets_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/tkWidgets_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/tkWidgets_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/tkWidgets_1.30.0.tgz vignettes: vignettes/tkWidgets/inst/doc/importWizard.pdf, vignettes/tkWidgets/inst/doc/tkWidgets.pdf Package: topGO Version: 2.4.0 Depends: R (>= 2.10.0), methods, graph (>= 1.14.0), Biobase (>= 2.0.0), GO.db (>= 2.3.0), AnnotationDbi (>= 1.7.19), SparseM (>= 0.73) Imports: methods, graph, Biobase, SparseM, AnnotationDbi, lattice Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest License: LGPL Title: topGO: Enrichment analysis for Gene Ontology Description: topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. biocViews: Microarray,Bioinformatics,Visualization Author: Adrian Alexa, Jorg Rahnenfuhrer Maintainer: Adrian Alexa source.ver: src/contrib/topGO_2.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/topGO_2.4.0.zip win64.binary.ver: bin/windows64/contrib/2.13/topGO_2.4.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/topGO_2.4.0.tgz vignettes: vignettes/topGO/inst/doc/topGO.pdf, vignettes/topGO/inst/doc/topGO_classes_v3.pdf Package: tspair Version: 1.10.0 Depends: R (>= 2.2.1), Biobase (>= 2.4.0), time License: GPL-2 Archs: i386, x64 Title: Top Scoring Pairs for Microarray Classification Description: These functions calculate the pair of genes that show the maximum difference in ranking between two user specified groups. This "top scoring pair" maximizes the average of sensitivity and specificity over all rank based classifiers using a pair of genes in the data set. The advantage of classifying samples based on only the relative rank of a pair of genes is (a) the classifiers are much simpler and often more interpretable than more complicated classification schemes and (b) if arrays can be classified using only a pair of genes, PCR based tests could be used for classification of samples. See the references for the tspcalc() function for references regarding TSP classifiers. biocViews: Microarray, Bioinformatics Author: Jeffrey T. Leek Maintainer: Jeffrey T. Leek source.ver: src/contrib/tspair_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/tspair_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/tspair_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/tspair_1.10.0.tgz vignettes: vignettes/tspair/inst/doc/tsp.pdf, vignettes/tspair/inst/doc/tsp1.pdf Package: twilight Version: 1.28.0 Depends: R (>= 2.1.0), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, grDevices, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) Archs: i386, x64 Title: Estimation of local false discovery rate Description: In a typical microarray setting with gene expression data observed under two conditions, the local false discovery rate describes the probability that a gene is not differentially expressed between the two conditions given its corrresponding observed score or p-value level. The resulting curve of p-values versus local false discovery rate offers an insight into the twilight zone between clear differential and clear non-differential gene expression. Package 'twilight' contains two main functions: Function twilight.pval performs a two-condition test on differences in means for a given input matrix or expression set and computes permutation based p-values. Function twilight performs a stochastic downhill search to estimate local false discovery rates and effect size distributions. The package further provides means to filter for permutations that describe the null distribution correctly. Using filtered permutations, the influence of hidden confounders could be diminished. biocViews: Microarray, Bioinformatics, DifferentialExpression, MultipleComparisons Author: Stefanie Scheid Maintainer: Stefanie Scheid URL: http://compdiag.molgen.mpg.de/software/twilight.shtml source.ver: src/contrib/twilight_1.28.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/twilight_1.28.0.zip win64.binary.ver: bin/windows64/contrib/2.13/twilight_1.28.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/twilight_1.28.0.tgz vignettes: vignettes/twilight/inst/doc/bcb_logo.pdf, vignettes/twilight/inst/doc/tr_2004_01.pdf Package: vbmp Version: 1.20.0 Depends: R (>= 2.5) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) Title: Variational Bayesian Multinomial Probit Regression Description: Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination. biocViews: Bioinformatics,Classification Author: Nicola Lama , Mark Girolami Maintainer: Nicola Lama URL: http://bioinformatics.oxfordjournals.org/cgi/content/short/btm535v1 source.ver: src/contrib/vbmp_1.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/vbmp_1.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/vbmp_1.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/vbmp_1.20.0.tgz vignettes: vignettes/vbmp/inst/doc/vbmp.pdf Package: vsn Version: 3.20.0 Depends: Biobase (>= 2.5.5) Imports: methods, affy (>= 1.23.4), limma, lattice Suggests: affydata, hgu95av2cdf License: Artistic-2.0 Archs: i386, x64 Title: Variance stabilization and calibration for microarray data Description: The package implements a method for normalising microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references (see vignette). The model incorporates data calibration (a.k.a. normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription. biocViews: Microarray, OneChannel, TwoChannel, Preprocessing Author: Wolfgang Huber, with contributions from Anja von Heydebreck. Many comments and suggestions by users are acknowledged, among them Dennis Kostka, David Kreil, Hans-Ulrich Klein, Robert Gentleman, Deepayan Sarkar and Gordon Smyth. Maintainer: Wolfgang Huber URL: http://www.r-project.org, http://www.ebi.ac.uk/huber source.ver: src/contrib/vsn_3.20.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/vsn_3.20.0.zip win64.binary.ver: bin/windows64/contrib/2.13/vsn_3.20.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/vsn_3.20.0.tgz vignettes: vignettes/vsn/inst/doc/convergence2.pdf, vignettes/vsn/inst/doc/likelihoodcomputations.pdf, vignettes/vsn/inst/doc/vsn.pdf Package: weaver Version: 1.18.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 Title: Tools and extensions for processing Sweave documents Description: This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included. biocViews: Infrastructure Author: Seth Falcon Maintainer: Seth Falcon source.ver: src/contrib/weaver_1.18.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/weaver_1.18.0.zip win64.binary.ver: bin/windows64/contrib/2.13/weaver_1.18.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/weaver_1.18.0.tgz vignettes: vignettes/weaver/inst/doc/weaver_howTo.pdf Package: webbioc Version: 1.24.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: Biobase, multtest, qvalue, stats, utils License: GPL (>= 2) Title: Bioconductor Web Interface Description: An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. (Currently only Affymetrix oligonucleotide analysis is supported.) biocViews: Infrastructure, Microarray, OneChannel, DifferentialExpression Author: Colin A. Smith Maintainer: Colin A. Smith URL: http://www.bioconductor.org/ SystemRequirements: Unix, Perl (>= 5.6.0), Netpbm source.ver: src/contrib/webbioc_1.24.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/webbioc_1.24.0.zip win64.binary.ver: bin/windows64/contrib/2.13/webbioc_1.24.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/webbioc_1.24.0.tgz vignettes: vignettes/webbioc/inst/doc/demoscript.pdf, vignettes/webbioc/inst/doc/webbioc.pdf Package: widgetTools Version: 1.30.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL Title: Creates an interactive tcltk widget Description: This packages contains tools to support the construction of tcltk widgets biocViews: Infrastructure Author: Jianhua Zhang Maintainer: Jianhua Zhang source.ver: src/contrib/widgetTools_1.30.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/widgetTools_1.30.0.zip win64.binary.ver: bin/windows64/contrib/2.13/widgetTools_1.30.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/widgetTools_1.30.0.tgz vignettes: vignettes/widgetTools/inst/doc/widget.pdf, vignettes/widgetTools/inst/doc/widgetTools.pdf Package: xcms Version: 1.26.1 Depends: R (>= 1.9.0), methods Suggests: faahKO, msdata, multtest, ncdf, rgl, MassSpecWavelet (>= 1.5.2), RANN, snow Enhances: Rgraphviz, XML, KEGGSOAP License: GPL (>= 2) Archs: i386, x64 Title: LC/MS and GC/MS Data Analysis Description: Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling. biocViews: MassSpectrometry Author: Colin A. Smith , Ralf Tautenhahn , Steffen Neumann , Paul Benton Maintainer: Ralf Tautenhahn URL: http://metlin.scripps.edu/download/ SystemRequirements: NetCDF, zlib source.ver: src/contrib/xcms_1.26.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/xcms_1.26.1.zip win64.binary.ver: bin/windows64/contrib/2.13/xcms_1.26.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/xcms_1.26.1.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: xmapbridge Version: 1.10.0 Depends: R (>= 2.0), methods License: LGPL-3 Title: Export plotting files to the xmapBridge for visualisation in X:Map Description: xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format. biocViews: Annotation, ReportWriting, Visualization Author: Tim Yates and Crispin J Miller Maintainer: Tim Yates URL: http://xmap.picr.man.ac.uk, http://www.bioconductor.org source.ver: src/contrib/xmapbridge_1.10.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/xmapbridge_1.10.0.zip win64.binary.ver: bin/windows64/contrib/2.13/xmapbridge_1.10.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/xmapbridge_1.10.0.tgz vignettes: vignettes/xmapbridge/inst/doc/xmapbridge.pdf Package: xmapcore Version: 1.6.2 Depends: R (>= 2.8.0), methods, IRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase Suggests: RUnit License: GPL-2 Title: Core access to the xmap database (installed separately) Description: xmapcore allows mapping between genetic features and any available Affymetrix Exon arrays for Homo Sapiens, Mus Musculus, Rattus Norvegicus and Schizosaccharomyces Pombe. biocViews: Annotation, Bioinformatics, Microarray, OneChannel, ReportWriting, Transcription, Visualization Author: Tim Yates Maintainer: Tim Yates URL: http://xmap.picr.man.ac.uk, http://www.bioconductor.org source.ver: src/contrib/xmapcore_1.6.2.tar.gz mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/xmapcore_1.6.2.tgz vignettes: vignettes/xmapcore/inst/doc/INSTALL.pdf, vignettes/xmapcore/inst/doc/SplicingIndexExample.pdf, vignettes/xmapcore/inst/doc/cookbook.pdf, vignettes/xmapcore/inst/doc/xmapcore.pdf Package: xps Version: 1.12.1 Depends: R (>= 2.6.0), methods License: GPL (>= 2.0) Archs: i386 Title: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays Description: The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays, including exon arrays (Exon 1.0 ST: core, extended, full probesets), gene arrays (Gene 1.0 ST) and plate arrays on computers with 1 GB RAM only. It imports Affymetrix .CDF, .CLF, .PGF and .CEL as well as annotation files, and computes e.g. RMA, MAS5, FARMS, DFW, FIRMA, tRMA, MAS5-calls, DABG-calls, I/NI-calls. It is an R wrapper to XPS (eXpression Profiling System), which is based on ROOT, an object-oriented framework developed at CERN. Thus, the prior installation of ROOT is a prerequisite for the usage of this package, however, no knowledge of ROOT is required. ROOT is licensed under LGPL and can be downloaded from http://root.cern.ch. biocViews: ExonArray, GeneExpression, Microarray, OneChannel, DataImport, Preprocessing, Transcription, DifferentialExpression Author: Christian Stratowa, Vienna, Austria Maintainer: Christian Stratowa SystemRequirements: root_v5.27.04 - See README file for installation instructions. source.ver: src/contrib/xps_1.12.1.tar.gz win.binary.ver: bin/windows/contrib/2.13/xps_1.12.1.zip win64.binary.ver: bin/windows64/contrib/2.13/xps_1.12.1.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/xps_1.12.1.tgz vignettes: vignettes/xps/inst/doc/APTvsXPS.pdf, vignettes/xps/inst/doc/xps.pdf, vignettes/xps/inst/doc/xpsClasses.pdf, vignettes/xps/inst/doc/xpsPreprocess.pdf Package: yaqcaffy Version: 1.12.0 Depends: simpleaffy (>= 2.19.3), methods Suggests: MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk License: Artistic-2.0 Title: Affymetrix expression data quality control and reproducibility analysis Description: Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets. biocViews: Microarray,OneChannel,QualityControl,ReportWriting Author: Laurent Gatto Maintainer: Laurent Gatto URL: http://sites.google.com/site/laurentgatto/r-bioconductor/yaqcaffy source.ver: src/contrib/yaqcaffy_1.12.0.tar.gz win.binary.ver: bin/windows/contrib/2.13/yaqcaffy_1.12.0.zip win64.binary.ver: bin/windows64/contrib/2.13/yaqcaffy_1.12.0.zip mac.binary.leopard.ver: bin/macosx/leopard/contrib/2.13/yaqcaffy_1.12.0.tgz vignettes: vignettes/yaqcaffy/inst/doc/yaqcaffy.pdf