Package: a4 Version: 1.10.0 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL, Cairo License: GPL-3 Package: a4Base Version: 1.10.0 Depends: methods, graphics, grid, Biobase, AnnotationDbi, annaffy, mpm, genefilter, limma, multtest, glmnet, a4Preproc, a4Core, gplots Suggests: Cairo, ALL Enhances: gridSVG, JavaGD License: GPL-3 Package: a4Classif Version: 1.10.0 Depends: methods, a4Core, a4Preproc, MLInterfaces, ROCR, pamr, glmnet, varSelRF Imports: a4Core Suggests: ALL License: GPL-3 Package: a4Core Version: 1.10.0 Depends: methods, Biobase, glmnet License: GPL-3 Package: a4Preproc Version: 1.10.0 Depends: methods, AnnotationDbi Suggests: ALL, hgu95av2.db License: GPL-3 Package: a4Reporting Version: 1.10.0 Depends: methods, annaffy Imports: xtable, utils License: GPL-3 Package: ABarray Version: 1.30.0 Imports: Biobase, graphics, grDevices, methods, multtest, stats, tcltk, utils Suggests: limma, LPE License: GPL Package: aCGH Version: 1.40.0 Depends: R (>= 2.10), cluster, survival, multtest Imports: Biobase, cluster, grDevices, graphics, methods, multtest, stats, survival, splines, utils License: GPL-2 Archs: i386, x64 Package: ACME Version: 2.18.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), methods Imports: graphics, stats License: GPL (>= 2) Archs: i386, x64 Package: ADaCGH2 Version: 2.2.0 Depends: R (>= 2.15.0), parallel, ff Imports: bit, ffbase, DNAcopy, snapCGH, tilingArray, aCGH, GLAD, waveslim, cluster Suggests: CGHregions, Cairo, limma Enhances: Rmpi License: GPL (>= 3) Archs: i386, x64 Package: adSplit Version: 1.32.0 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 Package: affxparser Version: 1.34.2 Depends: R (>= 2.6.0) Suggests: R.utils (>= 1.29.8), 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gplots, R2HTML, oligoClasses, ReportingTools, hwriter Suggests: affydata, hgfocuscdf, rgl License: Artistic-2.0 Package: AffyExpress Version: 1.28.0 Depends: R (>= 2.10), affy (>= 1.23.4), limma Suggests: simpleaffy, R2HTML, affyPLM, hgu95av2cdf, hgu95av2, test3cdf, genefilter, estrogen, annaffy, gcrma License: LGPL Package: affyILM Version: 1.14.0 Depends: R (>= 2.10.0), methods, gcrma Imports: affxparser (>= 1.16.0), affy, graphics, methods, Biobase Suggests: AffymetrixDataTestFiles License: GPL-3 Package: affyio Version: 1.30.0 Depends: R (>= 2.6.0) Imports: zlibbioc License: LGPL (>= 2) Archs: i386, x64 Package: affylmGUI Version: 1.36.0 Depends: limma, tcltk, affy, BiocInstaller, affyio, affy, tkrplot, affyPLM, R2HTML, xtable, gcrma, affyPLM, AnnotationDbi License: LGPL Package: affyPara Version: 1.22.0 Depends: R (>= 2.5.0), methods, affy (>= 1.20.0), snow (>= 0.2-3), vsn (>= 3.6.0), aplpack (>= 1.1.1), affyio Suggests: affydata Enhances: affy License: GPL-3 Package: affypdnn 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Depends: R (>= 2.7.0), methods, utils, BiocGenerics (>= 0.5.4), Biobase (>= 1.17.0) Imports: methods, utils, DBI, RSQLite, BiocGenerics, Biobase, IRanges Suggests: DBI (>= 0.2-4), RSQLite (>= 0.6-4), hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db, seqnames.db, reactome.db, AnnotationForge, graph, org.TguttataTestingSubset.eg.db License: Artistic-2.0 Package: AnnotationForge Version: 1.4.4 Depends: R (>= 2.7.0), methods, utils, BiocGenerics (>= 0.1.13), Biobase (>= 1.17.0), AnnotationDbi (>= 1.19.15), org.Hs.eg.db Imports: methods, utils, DBI, RSQLite, BiocGenerics, Biobase Suggests: DBI (>= 0.2-4), RSQLite (>= 0.6-4), XML, RCurl, hgu95av2.db, human.db0, affy, Homo.sapiens, hom.Hs.inp.db, GO.db, BiocStyle, knitr License: Artistic-2.0 Package: AnnotationFuncs Version: 1.12.0 Depends: R (>= 2.7.0), AnnotationDbi Suggests: org.Bt.eg.db, GO.db, org.Hs.eg.db, hom.Hs.inp.db License: GPL-2 Package: AnnotationHub Version: 1.2.0 Depends: IRanges Imports: methods, stats, utils, rjson, BiocGenerics, BiocInstaller (>= 1.11.0), AnnotationDbi, GenomicRanges Suggests: RUnit, RCurl, Rsamtools License: Artistic-2.0 Package: annotationTools Version: 1.36.0 Imports: Biobase, stats License: GPL Package: anota Version: 1.10.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 Package: antiProfiles Version: 1.2.0 Depends: R (>= 3.0), matrixStats (>= 0.5), methods (>= 2.14), Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 Package: apComplex Version: 2.28.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL Package: aroma.light Version: 1.32.0 Depends: R (>= 2.14.0), matrixStats (>= 0.8.12) Imports: R.methodsS3 (>= 1.5.2), R.oo (>= 1.15.1) Suggests: R.utils (>= 1.27.1), princurve (>= 1.1-12) License: GPL (>= 2) Package: ArrayExpress Version: 1.22.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: XML, affy, limma License: Artistic-2.0 Package: arrayMvout Version: 1.20.0 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 Package: arrayQuality Version: 1.40.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL Package: arrayQualityMetrics Version: 3.18.0 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, Cairo (>= 1.4-6), genefilter, graphics, grDevices, grid, Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, simpleaffy, stats, SVGAnnotation (>= 0.9-0), utils, vsn (>= 3.23.3), XML Suggests: ALLMLL, CCl4 License: LGPL (>= 2) Package: ArrayTools Version: 1.22.0 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) Package: ArrayTV Version: 1.0.0 Depends: R (>= 2.14) Imports: foreach, DNAcopy, methods, oligoClasses (>= 1.21.3) Suggests: RColorBrewer, crlmm, ff, BSgenome.Hsapiens.UCSC.hg18,BSgenome.Hsapiens.UCSC.hg19, lattice, latticeExtra, RUnit, BiocGenerics Enhances: doMC, doSNOW, doParallel License: GPL (>= 2) Package: ARRmNormalization Version: 1.2.0 Depends: R (>= 2.15.1), ARRmData License: Artistic-2.0 Package: ASEB Version: 1.6.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) Archs: i386, x64 Package: ASSET Version: 1.0.0 Depends: MASS, msm, rmeta Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE Package: attract Version: 1.14.0 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) Package: BAC Version: 1.22.0 Depends: R (>= 2.10) License: Artistic-2.0 Archs: i386, x64 Package: BADER Version: 1.0.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 Archs: i386, x64 Package: BAGS Version: 2.2.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 Archs: i386, x64 Package: BaseSpaceR Version: 1.2.0 Depends: R (>= 2.15.0), RCurl, RJSONIO Imports: methods Suggests: RUnit License: Apache License 2.0 Package: BayesPeak Version: 1.14.0 Depends: R (>= 2.14), IRanges Imports: IRanges, graphics License: GPL (>= 2) Archs: i386, x64 Package: baySeq Version: 1.16.0 Depends: R (>= 2.3.0), methods, GenomicRanges Suggests: snow, edgeR License: GPL-3 Package: BCRANK Version: 1.24.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 Archs: i386, x64 Package: beadarray Version: 2.12.0 Depends: R (>= 2.13.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), methods, ggplot2 Imports: BeadDataPackR, 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geneplotter, hgu95av2.db License: Artistic-2.0 Package: BiocInstaller Version: 1.12.1 Depends: R (>= 3.0.0) Suggests: RUnit, BiocGenerics License: Artistic-2.0 Package: BiocParallel Version: 0.4.1 Imports: methods, parallel, foreach, tools, BatchJobs, BBmisc Suggests: BiocGenerics, doParallel, RUnit License: GPL-2 | GPL-3 Package: BiocStyle Version: 1.0.0 License: Artistic-2.0 Package: biocViews Version: 1.30.1 Depends: R (>= 2.4.0) Imports: Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools, utils, XML, RCurl, RUnit, knitr Suggests: Biobase License: Artistic-2.0 Package: bioDist Version: 1.34.0 Depends: R (>= 2.0), methods, Biobase,KernSmooth Suggests: locfit License: Artistic-2.0 Package: biomaRt Version: 2.18.0 Depends: methods Imports: utils, XML, RCurl Suggests: annotate License: Artistic-2.0 Package: BioMVCClass Version: 1.30.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz License: LGPL Package: biomvRCNS Version: 1.2.0 Depends: IRanges, GenomicRanges, Gviz Imports: methods, mvtnorm Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) Archs: i386, x64 Package: BioNet Version: 1.23.2 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) Package: BioSeqClass Version: 1.20.0 Depends: R (>= 2.10), scatterplot3d Imports: Biostrings, ipred, e1071, klaR, randomForest, class, tree, nnet, rpart, party, foreign, Biobase, utils, stats, grDevices Suggests: scatterplot3d License: LGPL (>= 2.0) Package: Biostrings Version: 2.30.1 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.5.4), IRanges (>= 1.19.34), XVector (>= 0.1.3) Imports: graphics, methods, stats, utils, BiocGenerics, IRanges, XVector LinkingTo: IRanges, XVector Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), 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parallel, betareg, lokern, Formula, globaltest License: LGPL-3 Package: BitSeq Version: 1.6.1 Depends: Rsamtools, zlibbioc Imports: IRanges LinkingTo: Rsamtools, zlibbioc Suggests: edgeR, DESeq License: Artistic-2.0 + file LICENSE Archs: i386, x64 Package: BRAIN Version: 1.8.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 Package: BrainStars Version: 1.6.0 Depends: RCurl, Biobase, methods Imports: RJSONIO, Biobase License: Artistic-2.0 Package: bridge Version: 1.26.0 Depends: R (>= 1.9.0), rama License: GPL (>= 2) Archs: i386, x64 Package: BSgenome Version: 1.30.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.1.2), IRanges (>= 1.13.6), GenomicRanges (>= 1.11.46), Biostrings (>= 2.23.3) Suggests: RUnit, BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.11), SNPlocs.Hsapiens.dbSNP.20100427, hgu95av2probe, Biobase License: Artistic-2.0 Package: bsseq Version: 0.10.0 Depends: R (>= 2.15), methods, BiocGenerics, IRanges, GenomicRanges, parallel, matrixStats Imports: scales, stats, graphics, Biobase, locfit Suggests: RUnit, bsseqData License: Artistic-2.0 Package: BufferedMatrix Version: 1.26.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) Archs: i386, x64 Package: BufferedMatrixMethods Version: 1.26.0 Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods LinkingTo: BufferedMatrix Suggests: affyio, affy License: GPL (>= 2) Archs: i386, x64 Package: bumphunter Version: 1.2.0 Depends: R (>= 2.10), IRanges, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, itertools, doRNG Suggests: RUnit, BiocGenerics, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 Package: BUS Version: 1.18.0 Depends: R (>= 2.3.0), minet Imports: stats License: GPL-3 Archs: i386, x64 Package: CAGEr Version: 1.4.1 Depends: methods, R (>= 2.15.0), BSgenome, BSgenome.Mmusculus.UCSC.mm9 Imports: Rsamtools, GenomicRanges, IRanges, data.table, beanplot, rtracklayer, som, VGAM Suggests: BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18, FANTOM3and4CAGE Enhances: parallel License: GPL-3 Package: CALIB Version: 1.28.0 Depends: R (>= 2.10), limma, methods Imports: limma, methods, graphics, stats, utils License: LGPL Archs: i386, x64 Package: CAMERA Version: 1.18.0 Depends: R (>= 2.1.0), methods, Biobase, xcms (>= 1.13.5), igraph Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph Suggests: faahKO, RUnit, BiocGenerics Enhances: Rmpi, snow License: GPL (>= 2) Archs: i386, x64 Package: cancerclass Version: 1.6.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats License: GPL-3 Archs: i386, x64 Package: CancerMutationAnalysis Version: 1.6.0 Depends: R (>= 2.10.0), qvalue Imports: AnnotationDbi, limma, methods, stats Suggests: KEGG.db License: GPL (>= 2) + file LICENSE Archs: i386, x64 Package: casper Version: 1.4.0 Depends: R (>= 2.14.1), Biobase, IRanges, methods, gtools, GenomicRanges, Rsamtools, plyr, gaga Imports: VGAM, mgcv, GenomicFeatures, survival, sqldf Enhances: parallel License: GPL (>= 2) Archs: i386, x64 Package: Category Version: 2.28.0 Depends: BiocGenerics, AnnotationDbi, Biobase, Matrix, GO.db, methods Imports: BiocGenerics, graph, methods, Biobase, AnnotationDbi, RBGL, GSEABase (>= 1.19.3), genefilter, annotate (>= 1.15.6), stats, utils Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGG.db, SNPchip, geneplotter, limma, lattice, graph, Biobase, genefilter, methods, RUnit, org.Sc.sgd.db, GOstats License: Artistic-2.0 Package: categoryCompare Version: 1.6.0 Depends: R (>= 2.10), Biobase, BiocGenerics Imports: AnnotationDbi, hwriter, GSEABase, Category, GOstats, annotate, colorspace, graph, RCytoscape (>= 1.5.11) Suggests: methods, GO.db, KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter License: GPL-2 Package: cellGrowth Version: 1.6.0 Depends: R (>= 2.12.0), locfit (>= 1.5-4) Imports: lattice License: Artistic-2.0 Package: cellHTS Version: 1.32.0 Depends: R (>= 2.10), prada (>= 1.9.4), RColorBrewer, Biobase (>= 1.11.12), genefilter (>= 1.11.2) Suggests: Category, GO.db, vsn (>= 2.0.35) License: Artistic-2.0 Package: cellHTS2 Version: 2.26.0 Depends: R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid Imports: prada, GSEABase, Category, stats4 License: Artistic-2.0 Package: CellNOptR Version: 1.8.0 Depends: R (>= 2.15.0), RBGL, graph, methods, hash, ggplot2, RCurl, Rgraphviz, XML Suggests: RUnit, BiocGenerics, igraph License: GPL-3 Archs: i386, x64 Package: CexoR Version: 1.0.0 Depends: R (>= 2.10.0), IRanges Imports: Rsamtools, GenomicRanges, rtracklayer, idr Suggests: RUnit, BiocGenerics License: Artistic-2.0 | GPL-2 + file LICENSE Package: CGEN Version: 2.4.0 Depends: R (>= 2.10.1), survival Suggests: cluster License: GPL-2 + file LICENSE Archs: i386, x64 Package: CGHbase Version: 1.22.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL Package: CGHcall Version: 2.22.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall License: GPL Package: cghMCR Version: 1.20.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL Package: CGHnormaliter Version: 1.16.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) Package: CGHregions Version: 1.20.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase License: GPL Package: ChAMP Version: 1.0.7 Depends: R (>= 3.0.1), minfi, ChAMPdata, Illumina450ProbeVariants.db Imports: sva, IlluminaHumanMethylation450kmanifest, limma, RPMM, DNAcopy, preprocessCore, impute, marray, wateRmelon License: GPL-3 Package: charm Version: 2.8.0 Depends: R (>= 2.14.0), Biobase, SQN, fields, RColorBrewer, genefilter Imports: BSgenome, Biobase, oligo (>= 1.11.31), oligoClasses(>= 1.17.39), ff, preprocessCore, methods, stats, Biostrings, IRanges, siggenes, nor1mix, gtools, grDevices, graphics, utils, limma, parallel, sva(>= 3.1.2) Suggests: charmData, BSgenome.Hsapiens.UCSC.hg18, corpcor License: LGPL (>= 2) Package: ChemmineOB Version: 1.0.1 Depends: R (>= 2.15.1) Imports: BiocGenerics, zlibbioc Suggests: ChemmineR, BiocStyle Enhances: ChemmineR (>= 2.13.0) License: file LICENSE Archs: i386, x64 Package: ChemmineR Version: 2.14.3 Depends: R (>= 2.10.0), methods Imports: graphics, methods, stats, RCurl, DBI, digest, BiocGenerics Suggests: RSQLite, scatterplot3d, gplots, fmcsR,snow, RPostgreSQL, BiocStyle Enhances: ChemmineOB License: Artistic-2.0 Archs: i386, x64 Package: chimera Version: 1.4.6 Depends: Biobase, GenomicRanges (>= 1.13.3), Rsamtools (>= 1.13.1), methods, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, BiocParallel Enhances: Rsubread License: Artistic-2.0 Package: chipenrich Version: 1.0.0 Depends: R (>= 2.15.1) Imports: chipenrich.data, methods, GenomicRanges (>= 1.10.0), IRanges (>= 1.16.0), mgcv, plyr (>= 1.7.0), lattice, latticeExtra, grid, stringr (>= 0.6), reshape License: GPL-3 Package: ChIPpeakAnno Version: 2.10.0 Depends: R (>= 2.10), grid,VennDiagram, BiocGenerics (>= 0.1.0), biomaRt, multtest, IRanges, Biostrings, BSgenome, BSgenome.Ecoli.NCBI.20080805, GO.db, org.Hs.eg.db, limma, GenomicFeatures Imports: gplots, BiocGenerics, biomaRt, multtest, IRanges, Biostrings, BSgenome, GO.db, limma, AnnotationDbi, GenomicFeatures Suggests: reactome.db, RUnit, BiocGenerics License: GPL (>= 2) Package: chipseq Version: 1.12.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.4), GenomicRanges (>= 1.7.7), BSgenome, ShortRead Imports: methods, BiocGenerics, IRanges, BSgenome, GenomicRanges, lattice, ShortRead, stats Suggests: GenomicFeatures, BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene License: Artistic-2.0 Archs: i386, x64 Package: ChIPseqR Version: 1.16.0 Depends: R (>= 2.10.0), methods, BiocGenerics, ShortRead Imports: Biostrings, fBasics, GenomicRanges, graphics, grDevices, HilbertVis, IRanges, methods, ShortRead, stats, timsac, utils License: GPL (>= 2) Archs: i386, x64 Package: ChIPsim Version: 1.16.0 Depends: Biostrings (>= 2.29.2) Imports: IRanges, XVector, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) Package: chopsticks Version: 1.26.1 Depends: R(>= 2.10.0), survival, methods Suggests: hexbin License: GPL-3 Archs: i386, x64 Package: chroGPS Version: 1.6.1 Depends: R (>= 2.13.0), IRanges, methods, Biobase, MASS, graphics, stats, rgl, changepoint Imports: graphics, cluster, DPpackage, ICSNP Enhances: parallel, XML License: GPL (>= 2) Package: ChromHeatMap Version: 1.16.0 Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0), hgu95av2.db Imports: BiocGenerics, annotate, AnnotationDbi, Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer Suggests: ALL License: Artistic-2.0 Package: cisPath Version: 1.2.7 Depends: R (>= 2.10.0) Imports: methods, utils License: GPL (>= 3) Archs: i386, x64 Package: cleanUpdTSeq Version: 1.0.2 Depends: R (>= 2.15), BiocGenerics (>= 0.1.0), BSgenome, BSgenome.Drerio.UCSC.danRer7, GenomicRanges, seqinr, e1071 License: GPL-2 Package: cleaver Version: 1.0.0 Depends: R (>= 3.0.0), methods, Biostrings (>= 1.29.8) Imports: IRanges Suggests: testthat, knitr, BiocStyle (>= 0.0.14), BRAIN, UniProt.ws (>= 2.1.4) License: GPL (>= 3) Package: clippda Version: 1.12.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>= 2) Package: clipper Version: 1.2.3 Depends: R (>= 2.15.0), Matrix, graph Imports: methods, Biobase, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor, RBGL, Rcpp Suggests: RUnit, BiocGenerics, 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dyebiasexamples, methods License: GPL-3 Package: DynDoc Version: 1.40.0 Depends: methods, utils Imports: methods License: Artistic-2.0 Package: EasyqpcR Version: 1.5.0 Imports: plyr, matrixStats, plotrix, gWidgetsRGtk2 Suggests: SLqPCR, qpcrNorm, qpcR, knitr License: GPL (>= 2) Package: easyRNASeq Version: 1.8.8 Depends: genomeIntervals (>= 1.18.0), Biobase (>= 2.22.0), biomaRt (>= 2.18.0), edgeR (>= 3.4.0), Biostrings (>= 2.30.0), DESeq (>= 1.14.0), GenomicRanges (>= 1.14.3), IRanges (>= 1.20.5), Rsamtools (>= 1.14.1), ShortRead (>= 1.20.0) Imports: graphics, methods, parallel, utils, BiocGenerics (>= 0.8.0), LSD (>= 2.5) Suggests: BSgenome (>= 1.30.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.19), GenomicFeatures (>= 1.14.0), RnaSeqTutorial (>= 0.0.13), BiocStyle (>= 1.0.0) License: Artistic-2.0 Package: EBarrays Version: 2.26.0 Depends: R (>= 1.8.0), Biobase, lattice, methods Imports: Biobase, cluster, graphics, grDevices, lattice, methods, stats License: GPL (>= 2) Archs: i386, x64 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(>= 2) Archs: i386, x64 Package: eisa Version: 1.14.0 Depends: isa2, Biobase (>= 2.17.8), AnnotationDbi, methods Imports: BiocGenerics, Category, genefilter, DBI Suggests: igraph (>= 0.6), Matrix, GOstats, GO.db, KEGG.db, biclust, MASS, xtable, ALL, hgu95av2.db, targetscan.Hs.eg.db, org.Hs.eg.db License: GPL (>= 2) Package: ensemblVEP Version: 1.2.2 Depends: methods, BiocGenerics, GenomicRanges, VariantAnnotation Imports: Biostrings, IRanges Suggests: RUnit, BiocGenerics License: Artistic-2.0 Package: ENVISIONQuery Version: 1.10.0 Depends: rJava, XML, utils License: GPL-2 Package: epigenomix Version: 1.2.0 Depends: R (>= 2.12.0), methods, Biobase, IRanges, GenomicRanges Imports: methods, BiocGenerics, Biobase, IRanges, GenomicRanges, beadarray License: LGPL-3 Package: epivizr Version: 1.0.0 Depends: R (>= 3.0.1), methods, Biobase, GenomicRanges (>= 1.13.47), Imports: httpuv, rjson LinkingTo: GenomicRanges, httpuv Suggests: testthat, roxygen2, knitr, antiProfilesData, hgu133plus2.db 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flowCore, methods,snow,foreach,graph,feature Imports: rrcov, flowClust,flowCore, graphics, methods, rrcov, stats, utils, BiocGenerics (>= 0.1.6) Suggests: Rgraphviz Enhances: doMC, multicore License: Artistic-2.0 Package: flowPeaks Version: 1.4.0 Depends: R (>= 2.12.0) Enhances: flowCore License: Artistic-1.0 Archs: i386, x64 Package: flowPhyto Version: 1.14.0 Depends: R (>= 1.8.0) Imports: flowClust, flowCore, flowMeans, TTR, caroline(>= 0.6.6) Suggests: RPostgreSQL, zoo, maps, mapdata, plotrix License: Artistic-2.0 Package: flowPlots Version: 1.10.0 Depends: R (>= 2.13.0), methods Suggests: vcd License: Artistic-2.0 Package: flowQB Version: 1.4.0 Imports: Biobase, graphics,methods, flowCore,stats,MASS Suggests: MASS, flowCore, xtable License: Artistic-2.0 Package: flowStats Version: 3.20.3 Depends: R (>= 2.10), flowCore (>= 1.10.0), fda (>= 2.2.6), mvoutlier, cluster, flowWorkspace (>= 3.8.29) Imports: BiocGenerics, MASS, flowViz, flowCore, fda (>= 2.2.6), Biobase, methods, 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License: Artistic-2.0 Archs: i386, x64 Package: GEOmetadb Version: 1.22.0 Depends: GEOquery,RSQLite License: Artistic-2.0 Package: GEOquery Version: 2.28.0 Depends: methods, Biobase Imports: XML, RCurl Suggests: limma, RUnit License: GPL-2 Package: GEOsubmission Version: 1.14.0 Imports: affy, Biobase, utils License: GPL (>= 2) Package: GEWIST Version: 1.6.0 Depends: R (>= 2.10), car License: GPL-2 Package: GGBase Version: 3.24.0 Depends: R (>= 2.14), methods, snpStats Imports: limma, genefilter, Biobase, BiocGenerics, Matrix, AnnotationDbi License: Artistic-2.0 Package: ggbio Version: 1.10.16 Depends: methods, ggplot2 (>= 0.9.3) Imports: methods, biovizBase(>= 1.10.5), reshape2, gtable, ggplot2(>= 0.9.2), lattice, BiocGenerics, Biobase, IRanges, GenomicRanges (>= 1.13.3), GenomicFeatures, Rsamtools (>= 1.13.1), BSgenome, gridExtra, scales, plyr, VariantAnnotation, Hmisc, rtracklayer Suggests: vsn, RUnit, testthat, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, affyPLM, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr License: Artistic-2.0 Package: GGtools Version: 4.10.0 Depends: R (>= 2.14), stats4, GGBase (>= 3.19.7), IRanges, GenomicRanges, Rsamtools Imports: methods, utils, stats, BiocGenerics, snpStats, ff, AnnotationDbi, Biobase, bit, VariantAnnotation Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP.20120608 Enhances: MatrixEQTL License: Artistic-2.0 Package: girafe Version: 1.14.0 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 Package: GLAD Version: 2.26.0 Depends: R (>= 2.10) Suggests: aws, tcltk License: GPL-2 Archs: i386, x64 Package: GlobalAncova Version: 3.30.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi Suggests: Biobase, annotate, GO.db, KEGG.db, golubEsets, hu6800.db, vsn, GSEABase, Rgraphviz License: GPL (>= 2) Archs: i386, x64 Package: globaltest Version: 5.16.0 Depends: methods Imports: Biobase, survival, AnnotationDbi, annotate, multtest, graphics Suggests: vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, annotate, Biobase, survival, GSEABase, penalized, gss, MASS, boot, rpart License: GPL (>= 2) Package: GOFunction Version: 1.10.0 Depends: R (>= 2.11.0), methods, Biobase (>= 2.8.0), graph (>= 1.26.0), Rgraphviz (>= 1.26.0), GO.db (>= 2.4.1), AnnotationDbi (>= 1.10.2), SparseM (>= 0.85) Imports: methods, Biobase, graph, Rgraphviz, GO.db, AnnotationDbi, SparseM License: GPL (>= 2) Package: goProfiles Version: 1.24.0 Depends: Biobase, AnnotationDbi, GO.db Suggests: org.Hs.eg.db License: GPL-2 Package: GOSemSim Version: 1.20.3 Depends: R (>= 2.10), Rcpp Imports: methods, AnnotationDbi, GO.db, org.Hs.eg.db, Rcpp LinkingTo: Rcpp Suggests: DOSE, clusterProfiler, BiocInstaller, knitr License: GPL-2 Archs: i386, x64 Package: goseq Version: 1.14.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase Imports: mgcv, graphics, stats, utils, AnnotationDbi Suggests: GO.db, edgeR, org.Hs.eg.db, rtracklayer License: LGPL (>= 2) Package: GOSim Version: 1.4.2 Depends: GO.db, annotate, igraph Imports: org.Hs.eg.db, AnnotationDbi, topGO, cluster, flexmix, RBGL, graph, Matrix, corpcor, Rcpp, utils LinkingTo: Rcpp License: GPL (>= 2) Archs: i386, x64 Package: GOstats Version: 2.28.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.3.26), graph Imports: AnnotationDbi (>= 0.0.89), Biobase (>= 1.15.29), Category (>= 2.3.26), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), graph (>= 1.15.15), methods, stats , AnnotationForge Suggests: hgu95av2.db (>= 1.13.0), ALL, GO.db (>= 1.13.0), annotate, multtest, genefilter, RColorBrewer, Rgraphviz, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics License: Artistic-2.0 Package: goTools Version: 1.36.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 Package: gpls Version: 1.34.0 Imports: stats Suggests: MASS License: Artistic-2.0 Package: gprege Version: 1.6.0 Depends: R (>= 2.8.0), gptk Suggests: spam License: AGPL-3 Package: graph Version: 1.40.1 Depends: R (>= 2.10), methods Imports: methods, stats, stats4, tools, utils, BiocGenerics (>= 0.1.11) Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster Enhances: Rgraphviz License: Artistic-2.0 Archs: i386, x64 Package: GraphAlignment Version: 1.26.0 License: file LICENSE License_restricts_use: yes Archs: i386, x64 Package: GraphAT Version: 1.34.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL Package: graphite Version: 1.8.1 Depends: R (>= 2.10) Imports: AnnotationDbi, graph, graphics, methods, org.Hs.eg.db, stats, utils Suggests: DEGraph (>= 1.4), hgu133plus2.db, RCytoscape (>= 1.6), SPIA (>= 2.2), topologyGSA (>= 1.0), clipper, ALL License: AGPL-3 Package: GraphPAC Version: 1.4.0 Depends: R(>= 2.15),iPAC, igraph, TSP, RMallow Suggests: RUnit, BiocGenerics License: GPL-2 Package: GRENITS Version: 1.14.1 Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) Imports: graphics, grDevices, reshape2, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: network License: GPL (>= 2) Archs: i386, x64 Package: GSEABase Version: 1.24.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), annotate, methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools License: Artistic-2.0 Package: GSEAlm Version: 1.22.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 Package: GSRI Version: 2.10.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 Package: GSVA Version: 1.10.3 Depends: R (>= 2.13.0), methods, GSEABase (>= 1.17.4) Imports: methods, BiocGenerics, Biobase, GSEABase Suggests: limma, RColorBrewer, genefilter, mclust, edgeR, GSVAdata Enhances: snow, parallel License: GPL (>= 2) Archs: i386, x64 Package: Gviz Version: 1.6.0 Depends: R (>= 2.10.0), methods, grid Imports: IRanges (>= 1.19.5), XVector, rtracklayer (>= 1.15.5), lattice, RColorBrewer, biomaRt (>= 2.11.0), GenomicRanges (>= 1.7.14), AnnotationDbi (>= 1.17.11), Biobase (>= 2.15.3), BiocGenerics (>= 0.1.4), GenomicFeatures (>= 1.9.7), BSgenome (>= 1.25.1), Biostrings (>= 2.25.1), biovizBase (>= 1.5.7), Rsamtools(>= 1.11.1), latticeExtra(>= 0.6-26) Suggests: xtable, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, biomaRt, rtracklayer License: Artistic-2.0 Package: gwascat Version: 1.6.0 Depends: R (>= 2.14.0), methods, IRanges, GenomicRanges, snpStats, graph, BiocGenerics Imports: Biostrings Suggests: DO.db, Gviz, ggbio, rtracklayer Enhances: SNPlocs.Hsapiens.dbSNP.20111119, pd.genomewidesnp.6 License: Artistic-2.0 Package: GWASTools Version: 1.8.1 Depends: Biobase, ncdf, gdsfmt, sandwich Imports: methods, DBI, RSQLite, GWASExactHW, DNAcopy, survival, lmtest, quantsmooth Suggests: GWASdata, BiocGenerics, RUnit, SNPRelate, snpStats, VariantAnnotation License: Artistic-2.0 Package: h5vc Version: 1.0.6 Imports: rhdf5, ggplot2, reshape, bit64, IRanges, GenomicRanges, Biostrings Suggests: knitr, locfit, deepSNV, BSgenome.Hsapiens.UCSC.hg19, h5vcData License: GPL (>= 3) Package: hapFabia Version: 1.4.2 Depends: R (>= 2.12.0), Biobase, fabia (>= 2.3.1) Imports: methods, graphics, grDevices, stats, utils, KernSmooth License: LGPL (>= 2.1) Archs: i386, x64 Package: Harshlight Version: 1.34.0 Depends: R (>= 2.10) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) Archs: i386, x64 Package: HCsnip Version: 1.2.0 Depends: R(>= 2.10.0), survival, coin, fpc, clusterRepro, impute, randomForestSRC, sm, sigaR, Biobase License: GPL (>= 2) Package: Heatplus Version: 2.8.0 Imports: graphics, grDevices, stats Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) Package: HELP Version: 1.20.0 Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods License: GPL (>= 2) Package: HEM Version: 1.34.0 Depends: R (>= 2.1.0) Imports: Biobase, grDevices, stats, utils License: GPL (>= 2) Archs: i386, x64 Package: HilbertVis Version: 1.20.0 Depends: R (>= 2.6.0), grid, lattice Suggests: IRanges, EBImage License: GPL (>= 3) Archs: i386, x64 Package: HilbertVisGUI Version: 1.20.0 Depends: R (>= 2.6.0), HilbertVis (>= 1.1.6) Suggests: lattice, IRanges License: GPL (>= 3) Archs: i386, x64 Package: HiTC Version: 1.6.0 Depends: R (>= 2.15.0), methods, GenomicRanges, IRanges, Matrix, RColorBrewer Imports: methods, Biobase, Biostrings, graphics, grDevices, rtracklayer Suggests: rtracklayer,BiocStyle License: Artistic-2.0 Package: HMMcopy Version: 1.4.0 Depends: R (>= 2.10.0), IRanges (>= 1.4.16), geneplotter (>= 1.24.0) License: GPL-3 Archs: i386, x64 Package: hopach Version: 2.22.0 Depends: R (>= 2.11.0), cluster, Biobase, methods Imports: Biobase, cluster, graphics, grDevices, methods, stats, utils, BiocGenerics License: GPL (>= 2) Archs: i386, x64 Package: hpar Version: 1.4.0 Depends: R (>= 2.15) Suggests: org.Hs.eg.db, GO.db, knitr License: Artistic-2.0 Package: HTqPCR Version: 1.16.0 Depends: Biobase, RColorBrewer, limma Imports: affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils Suggests: statmod License: Artistic-2.0 Package: HTSanalyzeR Version: 2.14.0 Depends: R (>= 2.15), igraph, methods Imports: graph, igraph, GSEABase, BioNet, cellHTS2, AnnotationDbi, biomaRt, RankProd Suggests: KEGG.db, GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow License: Artistic-2.0 Package: htSeqTools Version: 1.8.0 Depends: R (>= 2.12.2), methods, BiocGenerics (>= 0.1.0), Biobase, IRanges, methods, MASS, BSgenome, GenomicRanges Enhances: multicore License: GPL (>= 2) Package: HTSFilter Version: 1.2.1 Depends: methods, Biobase (>= 2.16.0), R (>= 2.10.0) Imports: DESeq (>= 1.8.3), edgeR (>= 2.6.12), DESeq2 (>= 1.2.8), GenomicRanges, IRanges Suggests: EDASeq (>= 1.2.0) License: Artistic-2.0 Package: HybridMTest Version: 1.6.0 Depends: R (>= 2.9.0), Biobase, fdrtool, MASS, survival Imports: stats License: GPL (>= 2) Package: hyperdraw Version: 1.14.0 Depends: R (>= 2.9.0), methods, grid, graph, hypergraph, Rgraphviz Imports: stats4 License: GPL (>= 2) Package: hypergraph Version: 1.34.0 Depends: R (>= 2.1.0), methods, graph License: Artistic-2.0 Package: iASeq Version: 1.6.0 Depends: R (>= 2.14.1) Imports: graphics, grDevices License: GPL-2 Package: iBBiG Version: 1.6.0 Depends: biclust Imports: stats4,xtable,ade4 Suggests: methods License: Artistic-2.0 Archs: i386, x64 Package: ibh Version: 1.10.0 Depends: simpIntLists Suggests: yeastCC, stats License: GPL (>= 2) Package: iBMQ Version: 1.2.0 Depends: R(>= 2.15.0),Biobase (>= 2.16.0), ggplot2 (>= 0.9.2) License: Artistic-2.0 Archs: i386, x64 Package: Icens Version: 1.34.0 Depends: survival Imports: graphics License: Artistic-2.0 Package: iChip Version: 1.16.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) Archs: i386, x64 Package: idiogram Version: 1.38.0 Depends: R (>= 2.10), methods, Biobase, annotate, plotrix Suggests: hu6800.db, hgu95av2.db, golubEsets License: GPL-2 Package: IdMappingAnalysis Version: 1.6.0 Depends: R (>= 2.14), R.oo (>= 1.13.0), rChoiceDialogs Imports: boot, mclust, RColorBrewer, Biobase License: GPL-2 Package: IdMappingRetrieval Version: 1.8.0 Depends: R.oo, XML, RCurl, rChoiceDialogs, ENVISIONQuery Imports: biomaRt, ENVISIONQuery, DAVIDQuery, AffyCompatible, R.methodsS3, R.oo, utils License: GPL-2 Package: illuminaio Version: 0.4.0 Imports: base64 Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles, BiocStyle License: GPL-2 Archs: i386, x64 Package: imageHTS Version: 1.12.0 Depends: R (>= 2.9.0), EBImage (>= 4.3.12), cellHTS2 (>= 2.10.0) Imports: tools, Biobase, hwriter, methods, vsn, stats, utils, e1071 Suggests: BiocStyle, MASS License: LGPL-2.1 Package: impute Version: 1.36.0 Depends: R (>= 2.10) License: GPL-2 Archs: i386, x64 Package: inSilicoDb Version: 1.10.1 Depends: R (>= 2.11.0), rjson, Biobase Imports: RCurl Suggests: limma License: GPL-2 Package: inSilicoMerging Version: 1.6.0 Depends: R (>= 2.11.1), Biobase, DWD Suggests: BiocGenerics, inSilicoDb License: GPL-2 Package: intansv Version: 1.2.0 Depends: R (>= 2.14.0), plyr, ggbio, GenomicRanges Imports: BiocGenerics, IRanges License: Artistic-2.0 Package: interactiveDisplay Version: 1.0.9 Depends: R (>= 2.10), methods, BiocGenerics, grid Imports: shiny, GenomicRanges, Gviz, RColorBrewer, ggplot2, reshape2, rtracklayer, GO.db, plyr, gridSVG, XML Suggests: RUnit, hgu95av2.db, knitr License: Artistic-2.0 Package: inveRsion Version: 1.10.0 Depends: methods, haplo.stats Imports: graphics, methods, utils License: GPL (>= 2) Archs: i386, x64 Package: iontree Version: 1.8.0 Depends: methods, rJava, RSQLite, XML Suggests: iontreeData License: GPL-2 Package: iPAC Version: 1.6.0 Depends: R(>= 2.15),gdata, scatterplot3d, Biostrings, multtest License: GPL-2 Package: IPPD Version: 1.10.0 Depends: R (>= 2.12.0), MASS, Matrix, XML, digest, bitops Imports: methods, stats, graphics License: GPL (>= 2) Archs: i386, x64 Package: IRanges Version: 1.20.7 Depends: R (>= 2.8.0), methods, utils, stats, BiocGenerics (>= 0.7.7) Imports: methods, utils, stats, BiocGenerics, stats4 Suggests: XVector, GenomicRanges, BSgenome.Celegans.UCSC.ce2, RUnit License: Artistic-2.0 Archs: i386, x64 Package: iSeq Version: 1.14.0 Depends: R (>= 2.10.0) License: GPL (>= 2) Archs: i386, x64 Package: isobar Version: 1.8.1 Depends: R (>= 2.10.0), Biobase, stats, methods, plyr Imports: distr Suggests: MSnbase, OrgMassSpecR, XML, biomaRt, ggplot2, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, distr License: LGPL-2 Package: IsoGeneGUI Version: 1.18.0 Depends: tcltk, tkrplot, IsoGene Imports: multtest, relimp, WriteXLS,gdata, RColorBrewer, geneplotter Suggests: RUnit License: GPL-2 Package: ITALICS Version: 2.22.0 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 Package: iterativeBMA Version: 1.20.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) Package: iterativeBMAsurv Version: 1.20.0 Depends: BMA, leaps, survival, splines Imports: graphics, grDevices, stats, survival, utils License: GPL (>= 2) Package: jmosaics Version: 1.2.0 Depends: R (>= 2.15.2), mosaics License: GPL (>= 2) Package: joda Version: 1.10.0 Depends: R (>= 2.0), bgmm, RBGL License: GPL (>= 2) Package: KCsmart Version: 2.20.0 Depends: siggenes, multtest, KernSmooth Imports: methods, BiocGenerics Enhances: Biobase, CGHbase License: GPL-3 Package: KEGGgraph Version: 1.20.0 Depends: R (>= 2.10), methods, XML (>= 2.3-0), graph Imports: methods, XML, graph Suggests: Rgraphviz, RBGL, RUnit, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) Package: keggorthology Version: 2.14.0 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 Package: KEGGprofile Version: 1.4.0 Depends: XML, png, TeachingDemos, KEGG.db Imports: AnnotationDbi License: GPL (>= 2) Package: KEGGREST Version: 1.2.2 Imports: methods, httr, png, Biostrings Suggests: RUnit, BiocGenerics, knitr License: Artistic-2.0 Package: lapmix Version: 1.28.0 Depends: R (>= 2.6.0),stats Imports: Biobase, graphics, grDevices, methods, stats, tools, utils License: GPL (>= 2) Package: LBE Version: 1.30.0 Depends: stats Imports: graphics, grDevices, methods, stats, utils Suggests: 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LogicReg, mcbiopi Suggests: genefilter, siggenes License: LGPL (>= 2) Package: logitT Version: 1.20.0 Depends: affy Suggests: SpikeInSubset License: GPL (>= 2) Archs: i386, x64 Package: lol Version: 1.10.0 Depends: penalized, Matrix Imports: Matrix, penalized, graphics, grDevices, stats License: GPL-2 Package: LPE Version: 1.36.0 Depends: R (>= 2.10) Imports: stats License: LGPL Package: LPEadj Version: 1.22.0 Depends: LPE Imports: LPE, stats License: LGPL Package: lpNet Version: 1.2.0 Depends: lpSolve, nem License: Artistic License 2.0 Package: lumi Version: 2.14.2 Depends: R (>= 2.10), Biobase (>= 2.5.5) Imports: affy (>= 1.23.4), methylumi (>= 2.3.2), GenomicFeatures, GenomicRanges, annotate, Biobase (>= 2.5.5), lattice, mgcv (>= 1.4-0), nleqslv, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, stats4, methods Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer License: LGPL (>= 2) Package: LVSmiRNA Version: 1.12.0 Depends: R (>= 2.10), Biobase,quantreg,splines,MASS,limma,affy,methods, SparseM, vsn Imports: BiocGenerics, stats4 Enhances: parallel,snow, Rmpi License: GPL-2 Archs: i386, x64 Package: maanova Version: 1.33.2 Depends: R (>= 2.10) Imports: Biobase, graphics, grDevices, methods, stats, utils Suggests: qvalue, snow Enhances: Rmpi License: GPL (>= 2) Archs: i386, x64 Package: macat Version: 1.36.0 Depends: Biobase, annotate Suggests: hgu95av2.db, stjudem License: Artistic-2.0 Package: maCorrPlot Version: 1.32.0 Depends: lattice Imports: graphics, grDevices, lattice, stats License: GPL (>= 2) Package: made4 Version: 1.36.1 Depends: ade4, RColorBrewer,gplots,scatterplot3d Suggests: affy License: Artistic-2.0 Package: maigesPack Version: 1.26.0 Depends: R (>= 2.10), convert, graph, limma, marray, methods Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML, rgl, som License: GPL (>= 2) Archs: i386, x64 Package: makecdfenv Version: 1.38.0 Depends: R (>= 2.6.0), methods, affyio Imports: Biobase, affy, methods, stats, utils, zlibbioc License: GPL (>= 2) Archs: i386, x64 Package: MANOR Version: 1.34.0 Depends: R (>= 2.10), GLAD Imports: GLAD, graphics, grDevices, stats, utils License: GPL-2 Archs: i386, x64 Package: manta Version: 1.8.0 Depends: R (>= 1.8.0), methods, edgeR (>= 2.5.13) Imports: Hmisc, caroline(>= 0.6.6) Suggests: RSQLite, plotrix License: Artistic-2.0 Package: MantelCorr Version: 1.32.0 Depends: R (>= 2.10) Imports: stats License: GPL (>= 2) Package: maPredictDSC Version: 1.0.0 Depends: R (>= 2.15.0), MASS,affy,limma,gcrma,ROC,class,e1071,caret,hgu133plus2.db,ROCR,AnnotationDbi,LungCancerACvsSCCGEO Suggests: parallel License: GPL-2 Package: marray Version: 1.40.0 Depends: R (>= 2.10.0), limma, methods Suggests: tkWidgets License: LGPL Package: maSigPro Version: 1.34.1 Depends: R (>= 2.3.1), stats, Biobase, MASS Imports: Biobase, graphics, grDevices, limma, Mfuzz, stats, utils, MASS License: GPL (>= 2) Package: maskBAD Version: 1.6.0 Depends: R (>= 2.10), gcrma (>= 2.27.1), affy Suggests: hgu95av2probe License: GPL (>= 2) Package: MassArray Version: 1.14.0 Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, methods, stats, utils License: GPL (>= 2) Package: MassSpecWavelet Version: 1.28.0 Depends: waveslim Suggests: xcms, caTools License: LGPL (>= 2) Archs: i386, x64 Package: matchBox Version: 1.4.0 Depends: R (>= 2.8.0) License: Artistic-2.0 Package: MBCB Version: 1.16.0 Depends: R (>= 2.9.0), tcltk, tcltk2 Imports: preprocessCore, stats, utils License: GPL (>= 2) Package: mBPCR Version: 1.16.0 Depends: oligoClasses, SNPchip Imports: Biobase Suggests: xtable License: GPL (>= 2) Package: mcaGUI Version: 1.10.0 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) Package: MCRestimate Version: 2.18.0 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) Package: mdqc Version: 1.24.0 Depends: R (>= 2.2.1), cluster, MASS License: LGPL (>= 2) Package: MeasurementError.cor Version: 1.34.0 License: LGPL Package: MEDIPS Version: 1.12.0 Depends: R (>= 3.0), BSgenome, DNAcopy Imports: Biostrings, BSgenome, Rsamtools, graphics, gtools, IRanges, methods, stats, utils, GenomicRanges, edgeR, GenomicFeatures, DNAcopy, biomaRt, rtracklayer Suggests: BSgenome, BSgenome.Hsapiens.UCSC.hg19, MEDIPSData License: GPL (>= 2) Package: MEDME Version: 1.22.0 Depends: R (>= 2.15), grDevices, graphics, methods, stats, utils Imports: Biostrings, MASS, drc Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 License: GPL (>= 2) Archs: i386, x64 Package: MergeMaid Version: 2.34.0 Depends: R (>= 2.10.0), survival, Biobase, MASS, methods License: GPL (>= 2) Package: metaArray Version: 1.40.0 Imports: Biobase, MergeMaid, graphics, stats License: LGPL-2 Archs: i386, x64 Package: metagenomeSeq Version: 1.4.2 Depends: R(>= 3.0), Biobase, limma, matrixStats, methods, RColorBrewer, gplots Suggests: annotate, knitr License: Artistic-2.0 Package: metahdep Version: 1.20.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 Archs: i386, x64 Package: metaSeq Version: 1.2.2 Depends: R (>= 2.13.0), NOISeq, snow License: Artistic-2.0 Package: methVisual Version: 1.14.0 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) Package: methyAnalysis Version: 1.4.2 Depends: R (>= 2.10), grid, IRanges, GenomicRanges, Biobase (>= 2.5.5), org.Hs.eg.db Imports: lumi, methylumi, Gviz, genoset, GenomicRanges, IRanges, rtracklayer, GenomicFeatures, annotate, Biobase (>= 2.5.5), AnnotationDbi, genefilter, biomaRt, methods Suggests: FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 Package: methylMnM Version: 1.0.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 Archs: i386, x64 Package: MethylSeekR Version: 1.2.2 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), graphics (>= 2.15.2), grDevices (>= 2.15.2), parallel (>= 2.15.2), stats (>= 2.15.2), utils (>= 2.15.2) Suggests: BSgenome.Hsapiens.UCSC.hg18 License: GPL (>= 2) Package: methylumi Version: 2.8.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats Imports: Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, BiocGenerics Suggests: lumi, lattice, limma, xtable, IlluminaHumanMethylation27k.db (>= 1.4.4), IlluminaHumanMethylation450k.db, SQN, GenomicRanges, MASS, matrixStats, parallel, rtracklayer, Biostrings, methyAnalysis, FDb.InfiniumMethylation.hg19 License: GPL-2 Package: Mfuzz Version: 2.20.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 Package: mgsa Version: 1.10.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db License: Artistic-2.0 Archs: i386, x64 Package: MiChip Version: 1.16.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) Package: microRNA Version: 1.20.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) Suggests: Biostrings (>= 2.11.32) Enhances: Rlibstree License: Artistic-2.0 Package: MineICA Version: 1.2.2 Depends: R (>= 2.10), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE, methods Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX Enhances: doMC License: GPL-2 Package: minet Version: 3.16.0 Depends: infotheo License: CC BY-NC-SA 3.0 Archs: i386, x64 Package: minfi Version: 1.8.9 Depends: methods, BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), lattice, reshape, GenomicRanges, Biostrings, utils, bumphunter (>= 1.1.9) Imports: IRanges, beanplot, RColorBrewer, nor1mix, siggenes, limma, preprocessCore, illuminaio, matrixStats, mclust, genefilter, nlme Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, minfiData (>= 0.4.1), quadprog, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest License: Artistic-2.0 Package: MinimumDistance Version: 1.6.0 Depends: R (>= 2.14), BiocGenerics (>= 0.3.2), IRanges (>= 1.13.30) Imports: methods, DNAcopy, utils, msm, lattice, BiocGenerics, VanillaICE (>= 1.21.24), ff, Biobase (>= 2.17.8), foreach, oligoClasses (>= 1.21.12), GenomicRanges, matrixStats Suggests: human610quadv1bCrlmm (>= 1.0.3), SNPchip, RUnit Enhances: snow, doSNOW License: Artistic-2.0 Package: MiPP Version: 1.34.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) Package: MiRaGE Version: 1.4.0 Depends: R (>= 2.12.1), Biobase(>= 2.16.0) Imports: AnnotationDbi, BiocGenerics Suggests: seqinr (>= 3.0.3), biomaRt (>= 2.6.0), GenomicFeatures (>= 1.8.1), Biostrings (>= 2.24.1), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, miRNATarget, humanStemCell, IRanges , GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL Package: miRNApath Version: 1.22.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 Package: mitoODE Version: 1.0.0 Depends: R (>= 2.14.0), minpack.lm, MASS, parallel, mitoODEdata, KernSmooth License: LGPL Archs: i386, x64 Package: MLInterfaces Version: 1.42.0 Depends: R (>= 2.9), Biobase, MASS, methods, genefilter, rpart, rda, annotate, cluster, sfsmisc Imports: mboost, gdata, pls Suggests: class, e1071, ipred, randomForest, gpls, pamr, rpart, MASS, nnet, ALL, gbm, mlbench, hgu95av2.db, som, RColorBrewer, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, gbm, mboost, sfsmisc, party Enhances: parallel License: LGPL Package: MLP Version: 1.10.0 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 Package: MMDiff Version: 1.2.1 Depends: R (>= 2.14.0),GenomicRanges,parallel,DiffBind,GMD,Rsamtools Imports: GenomicRanges,IRanges,Biobase Suggests: MMDiffBamSubset License: Artistic-2.0 Package: MmPalateMiRNA Version: 1.12.0 Depends: R (>= 2.13.0), methods, Biobase, xtable, limma, statmod, lattice, vsn Imports: limma, lattice, Biobase Suggests: GOstats, graph, Category, org.Mm.eg.db, microRNA, targetscan.Mm.eg.db, RSQLite, DBI, AnnotationDbi, clValid, class, cluster, multtest, RColorBrewer, latticeExtra License: GPL-3 Package: mosaics Version: 1.10.1 Depends: R (>= 2.11.1), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) Archs: i386, x64 Package: MotifDb Version: 1.4.1 Depends: R (>= 2.15.0), methods, IRanges, Biostrings Imports: BiocGenerics, rtracklayer Suggests: RUnit, MotIV, seqLogo License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes Package: motifRG Version: 1.6.0 Depends: R (>= 2.15), Biostrings (>= 2.26), IRanges, seqLogo, parallel, methods, grid, graphics, BSgenome, XVector, BSgenome.Hsapiens.UCSC.hg19 Imports: Biostrings,IRanges,seqLogo,parallel,methods,grid,graphics,XVector License: Artistic-2.0 Package: motifStack Version: 1.6.5 Depends: R (>= 2.15.1), methods, grImport, grid, MotIV, ade4 Imports: XML Suggests: RUnit, BiocGenerics, MotifDb, RColorBrewer, BiocStyle License: GPL (>= 2) Package: MotIV Version: 1.18.0 Depends: R (>= 2.10), BiocGenerics (>= 0.1.0) Imports: graphics, grid, methods, BiocGenerics, IRanges (>= 1.13.5), Biostrings (>= 1.24.0), lattice, rGADEM, stats, utils Suggests: rtracklayer License: GPL-2 Archs: i386, x64 Package: msmsEDA Version: 1.0.0 Depends: R (>= 3.0.1), MSnbase Imports: MASS, gplots, RColorBrewer License: GPL-2 Package: msmsTests Version: 1.0.0 Depends: R (>= 3.0.1), MSnbase, msmsEDA Imports: edgeR, qvalue License: GPL-2 Package: MSnbase Version: 1.10.4 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.7.1), Biobase (>= 2.15.2), ggplot2, mzR Imports: plyr, IRanges, preprocessCore, vsn, grid, reshape2, stats4, affy, impute Suggests: testthat, zoo, knitr (>= 1.1.0), rols, Rdisop, pRolocdata, msdata Enhances: foreach, doMC, parallel License: Artistic-2.0 Package: MSstats Version: 2.0.1 Depends: R (>= 3.0), Rcpp, MSnbase Imports: lme4,marray,limma,gplots,ggplot2 License: Artistic-2.0 Package: Mulcom Version: 1.12.0 Depends: R (>= 2.10), fields, Biobase Imports: graphics, grDevices, stats, methods License: GPL-2 Archs: i386, x64 Package: multiscan Version: 1.22.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) Archs: i386, x64 Package: multtest Version: 2.18.0 Depends: R (>= 2.10), methods, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL Archs: i386, x64 Package: MVCClass Version: 1.36.0 Depends: R (>= 2.1.0), methods License: LGPL Package: mzID Version: 1.0.0 Depends: methods, XML Imports: plyr License: GPL (>= 2) Package: mzR Version: 1.8.1 Depends: Rcpp (>= 0.10.1), methods, utils Imports: Biobase LinkingTo: Rcpp Suggests: msdata (>= 0.1.9), RUnit, faahKO License: Artistic-2.0 Archs: i386, x64 Package: NarrowPeaks Version: 1.6.0 Depends: R (>= 2.10.0), splines Imports: GenomicRanges, IRanges, fda, CSAR Suggests: rtracklayer, GenomicRanges, CSAR License: Artistic-2.0 Archs: i386, x64 Package: ncdfFlow Version: 2.8.22 Depends: R (>= 2.14.0), flowCore, flowViz Imports: Biobase,flowCore,flowViz,methods,zlibbioc License: Artistic-2.0 Archs: i386, x64 Package: NCIgraph Version: 1.10.0 Depends: graph, R (>= 2.10.0) Imports: graph, KEGGgraph, methods, RBGL, RCytoscape, R.methodsS3 Suggests: Rgraphviz Enhances: DEGraph License: GPL-3 Package: neaGUI Version: 1.0.0 Depends: tcltk Imports: hwriter Suggests: AnnotationDbi, org.Hs.eg.db, KEGG.db, GO.db, reactome.db, RUnit, GOstats,hwriter License: GPL-2 Package: nem Version: 2.36.0 Depends: R (>= 2.0), e1071 (>= 1.5), graph (>= 1.24), plotrix, limma, cluster (>= 1.11), statmod, Hmisc, Rgraphviz Imports: boot, e1071, graph, graphics, grDevices, methods, RBGL (>= 1.8.1), RColorBrewer, stats, utils, Rgraphviz Suggests: Biobase (>= 1.10) Enhances: doMC, Rglpk License: GPL (>= 2) Archs: i386, x64 Package: netresponse Version: 1.14.0 Depends: R (>= 2.15.1), dmt, igraph, infotheo, ggplot2, graph, mclust, methods, minet, parallel, qvalue, RColorBrewer, reshape, Rgraphviz License: GPL (>= 2) Archs: i386, x64 Package: NetSAM Version: 1.2.1 Depends: R (>= 2.15.1), methods, igraph (>= 0.6-1), seriation (>= 1.0-6), graph (>= 1.34.0) Imports: methods Suggests: RUnit, BiocGenerics License: LGPL Package: networkBMA Version: 1.4.0 Depends: R (>= 2.15.0), stats, utils, BMA License: GPL (>= 2) Package: nnNorm Version: 2.26.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL Package: NOISeq Version: 2.6.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1) License: Artistic-2.0 Package: NormqPCR Version: 1.8.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR Imports: ReadqPCR License: LGPL-3 Package: NTW Version: 1.12.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 Package: nucleR Version: 1.10.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Biobase (>= 2.15.1), ShortRead, parallel Imports: methods, BiocGenerics, IRanges, Biobase, ShortRead, GenomicRanges, stats Enhances: htSeqTools License: LGPL (>= 3) Package: nudge Version: 1.28.0 Imports: stats License: GPL-2 Package: NuPoP Version: 1.12.0 Depends: R (>= 2.10) License: GPL-2 Archs: i386, x64 Package: occugene Version: 1.22.0 Depends: R (>= 2.0.0) License: GPL (>= 2) Package: OCplus Version: 1.36.0 Depends: R (>= 2.1.0), akima Imports: multtest (>= 1.7.3), graphics, grDevices, stats License: LGPL Package: oligo Version: 1.26.6 Depends: R (>= 2.15.0), BiocGenerics (>= 0.3.2), oligoClasses (>= 1.19.43), Biobase (>= 2.17.8), Biostrings (>= 2.25.12) Imports: affyio (>= 1.25.0), affxparser (>= 1.29.11), BiocGenerics (>= 0.3.2), DBI (>= 0.2-5), ff, graphics, methods, preprocessCore (>= 1.19.0), splines, stats, stats4, utils, zlibbioc LinkingTo: preprocessCore Suggests: hapmap100kxba, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, RUnit Enhances: ff, doMC, doMPI License: LGPL (>= 2) Archs: i386, x64 Package: oligoClasses Version: 1.24.0 Depends: R (>= 2.14), BiocGenerics (>= 0.3.2) Imports: BiocGenerics, Biobase (>= 2.17.8), methods, graphics, IRanges (>= 1.13.30), GenomicRanges, Biostrings (>= 2.23.6), affyio (>= 1.23.2), ff, foreach, BiocInstaller, utils Suggests: RSQLite, hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), crlmm, SNPchip, VanillaICE, RUnit, human370v1cCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) Package: OLIN Version: 1.40.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 Package: OLINgui Version: 1.36.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 Package: omicade4 Version: 1.2.2 Depends: R (>= 3.0.0), ade4 Imports: made4 Suggests: BiocStyle License: GPL-2 Package: OmicCircos Version: 1.0.0 Depends: R (>= 2.14.0),methods,GenomicRanges Suggests: knitr License: GPL-2 Package: oneChannelGUI Version: 1.28.6 Depends: Biobase, affylmGUI, tkWidgets, IRanges, Rsamtools (>= 1.13.1), Biostrings, siggenes, chimera Suggests: annotate, genefilter, maSigPro, pamr, pdmclass, ChIPpeakAnno, chipseq, BSgenome, Rgraphviz, affy ,annaffy, affyPLM, multtest, ssize, sizepower, RankProd, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, edgeR, metaArray, MergeMaid, biomaRt, GenomeGraphs,AffyCompatible, rtracklayer, Genominator, EDASeq, limma, DESeq, DEXSeq, goseq, hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db, ragene10sttranscriptcluster.db, GOstats, AnnotationDbi, preprocessCore, baySeq, HuExExonProbesetLocation, MoExExonProbesetLocation, RaExExonProbesetLocation, snow, RmiR, RmiR.Hs.miRNA, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn4, R.utils, cummeRbund License: Artistic-2.0 Package: ontoCAT Version: 1.14.0 Depends: rJava, methods License: Apache License 2.0 Package: openCyto Version: 1.0.14 Depends: methods,flowWorkspace Imports: Biobase,gtools,flowCore,flowStats,flowClust,MASS,clue,plyr,RBGL,Rgraphviz,graph,data.table,ks,RColorBrewer,lattice,rrcov,R.utils Suggests: flowWorkspaceData, knitr, testthat, utils, tools Enhances: flowDensity License: Artistic-2.0 Archs: i386, x64 Package: OrderedList Version: 1.34.0 Depends: R (>= 2.1.0), Biobase (>= 1.5.12), twilight (>= 1.9.2), methods Imports: Biobase, graphics, methods, stats, twilight License: GPL (>= 2) Package: OrganismDbi Version: 1.4.0 Depends: R (>= 2.14.0), methods, AnnotationDbi (>= 1.16.10), GenomicFeatures Imports: BiocGenerics, graph, RBGL, AnnotationDbi Suggests: Homo.sapiens, Rattus.norvegicus, RUnit License: Artistic-2.0 Package: OSAT Version: 1.10.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 Package: OTUbase Version: 1.12.0 Depends: R (>= 2.9.0), methods, ShortRead (>= 1.4.0), Biobase, vegan Imports: Biostrings, ShortRead, IRanges License: Artistic-2.0 Package: OutlierD Version: 1.26.0 Depends: R (>= 2.3.0), Biobase, quantreg License: GPL (>= 2) Package: PADOG Version: 1.4.0 Depends: R (>= 2.14.0), KEGGdzPathwaysGEO, graphics, limma, AnnotationDbi, Biobase, methods, nlme, GSA,KEGG.db Imports: graphics, limma, hgu133plus2.db, hgu133a.db, KEGG.db, AnnotationDbi, Biobase, methods, nlme Suggests: parallel License: GPL (>= 2) Package: paircompviz Version: 1.0.0 Depends: R (>= 2.10), Rgraphviz Imports: Rgraphviz Suggests: multcomp, reshape, rpart, plyr, xtable License: GPL (>= 3.0) Package: PAnnBuilder Version: 1.26.0 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) Package: panp Version: 1.32.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) Imports: Biobase, methods, stats, utils Suggests: gcrma License: GPL (>= 2) Package: PANR Version: 1.8.0 Depends: R (>= 2.14), igraph Imports: graphics, grDevices, MASS, methods, pvclust, stats, utils Suggests: snow, RedeR License: Artistic-2.0 Package: PAPi Version: 1.2.0 Depends: R (>= 2.15.2), svDialogs, KEGGREST License: GPL (>= 2) Package: parody Version: 1.20.0 Depends: R (>= 2.5.0), methods, tools, utils License: Artistic-2.0 Package: pathifier Version: 1.0.0 Imports: R.oo, princurve License: Artistic-1.0 Package: PathNet Version: 1.2.0 Depends: R (>= 1.14.0) Suggests: PathNetData, RUnit, BiocGenerics License: GPL-3 Package: pathRender Version: 1.30.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods Suggests: ALL, hgu95av2.db License: LGPL Package: pathview Version: 1.2.4 Depends: R (>= 2.10), KEGGgraph, org.Hs.eg.db Imports: Rgraphviz, graph, png, AnnotationDbi, KEGGREST, methods, utils Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) Package: pcaGoPromoter Version: 1.6.0 Depends: R (>= 2.14.0) , ellipse Imports: Biobase (>= 2.10.0) , AnnotationDbi Suggests: Rgraphviz, GO.db, hgu133plus2.db, mouse4302.db, rat2302.db, hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db, Biostrings, pcaGoPromoter.Hs.hg19, pcaGoPromoter.Mm.mm9, pcaGoPromoter.Rn.rn4, serumStimulation, parallel License: GPL (>= 2) Package: pcaMethods Version: 1.52.1 Depends: Biobase, methods, Rcpp (>= 0.8.7) Imports: BiocGenerics, MASS LinkingTo: Rcpp Suggests: matrixStats, lattice License: GPL (>= 3) Archs: i386, x64 Package: pcot2 Version: 1.30.0 Depends: R (>= 2.0.0), grDevices, Biobase, amap Suggests: multtest, hu6800.db, KEGG.db, mvtnorm License: GPL (>= 2) Package: PCpheno Version: 1.24.0 Depends: R (>= 2.10), Category, ScISI (>= 1.3.0), SLGI, ppiStats, ppiData, annotate (>= 1.17.4) Imports: AnnotationDbi, Biobase, Category, GO.db, graph, graphics, GSEABase, KEGG.db, methods, ScISI, stats, stats4 Suggests: KEGG.db, GO.db, org.Sc.sgd.db License: Artistic-2.0 Package: pdInfoBuilder Version: 1.26.0 Depends: R (>= 2.15.0), methods, Biobase (>= 2.17.7), RSQLite (>= 0.11.1), affxparser (>= 1.29.12), oligo (>= 1.21.5) Imports: Biostrings (>= 2.25.12), IRanges (>= 1.15.44) License: Artistic-2.0 Archs: i386, x64 Package: pdmclass Version: 1.34.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), fibroEset, mda License: Artistic-2.0 Package: PGSEA Version: 1.36.0 Depends: R (>= 2.10), GO.db, KEGG.db, AnnotationDbi, annaffy, methods, Biobase (>= 2.5.5) Suggests: GSEABase, GEOquery, org.Hs.eg.db, hgu95av2.db, limma License: GPL-2 Package: phenoDist Version: 1.10.0 Depends: R (>= 2.9.0), imageHTS, e1071 Suggests: GOstats, MASS License: LGPL-2.1 Package: phenoTest Version: 1.10.0 Depends: R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2, gridExtra Imports: survival, limma, Hmisc, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, SNPchip, hgu133a.db, HTSanalyzeR, ellipse Suggests: GSEABase, KEGG.db, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) Package: phyloseq Version: 1.6.1 Depends: R (>= 3.0.0), methods, ade4 (>= 1.5.2), picante (>= 1.5.2) Imports: ape (>= 3.0.8), biom (>= 0.3.9), Biostrings (>= 2.28.0), cluster (>= 1.14.4), foreach (>= 1.4), ggplot2 (>= 0.9.3.1), igraph (>= 0.6.5.2), multtest (>= 2.16.0), plyr (>= 1.8), reshape2 (>= 1.2.2), scales (>= 0.2.3), vegan (>= 2.0.7) Suggests: genefilter (>= 1.42.0), testthat (>= 0.7.1) Enhances: doParallel (>= 1.0.1) License: AGPL-3 Package: piano Version: 1.2.12 Depends: R (>= 2.14.0) Imports: Biobase, gplots, igraph, relations, marray Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall License: GPL (>= 2) Package: pickgene Version: 1.34.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) Package: PICS Version: 2.6.0 Depends: R (>= 2.14.0), BiocGenerics (>= 0.1.3) Imports: methods, stats4, IRanges, GenomicRanges, graphics, grDevices, stats, Rsamtools Suggests: ShortRead, rtracklayer, parallel License: Artistic-2.0 Archs: i386, x64 Package: PING Version: 2.6.0 Depends: R(>= 2.15.0), chipseq, IRanges, GenomicRanges Imports: methods, PICS, graphics, grDevices, stats, Gviz, fda, BSgenome, stats4, BiocGenerics Suggests: parallel, ShortRead, rtracklayer License: Artistic-2.0 Archs: i386, x64 Package: pint Version: 1.14.0 Depends: mvtnorm, methods, graphics, Matrix, dmt License: FreeBSD Package: pkgDepTools Version: 1.28.0 Depends: methods, graph, RBGL Imports: graph, RBGL Suggests: Biobase, Rgraphviz, RCurl, BiocInstaller License: GPL-2 Package: plateCore Version: 1.20.0 Depends: R (>= 2.10), flowCore, flowViz, lattice, latticeExtra Imports: Biobase, flowCore, graphics, grDevices, lattice, MASS, methods, robustbase, stats, utils Suggests: gplots License: Artistic-2.0 Package: plethy Version: 1.0.0 Depends: R (>= 3.0.0) Imports: Streamer, DBI, RSQLite, methods, IRanges, reshape2, batch Suggests: RUnit, BiocGenerics License: GPL-3 Package: plgem Version: 1.34.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), MASS Imports: utils License: GPL-2 Package: plier Version: 1.32.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) Archs: i386, x64 Package: PLPE Version: 1.22.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) Package: plrs Version: 1.2.0 Depends: R (>= 2.10), Biobase Imports: BiocGenerics, CGHbase, graphics, grDevices, ic.infer, marray, methods, quadprog, Rcsdp, stats, stats4, utils Suggests: mvtnorm, methods License: GPL (>= 2.0) Package: plw Version: 1.22.0 Depends: R (>= 2.10), affy (>= 1.23.4) Imports: MASS, affy, graphics, splines, stats Suggests: limma License: GPL-2 Archs: i386, x64 Package: ppiStats Version: 1.28.0 Depends: ScISI (>= 1.13.2), lattice, ppiData (>= 0.1.19) Imports: Biobase, Category, graph, graphics, grDevices, lattice, methods, RColorBrewer, stats Suggests: yeastExpData, xtable License: Artistic-2.0 Package: prada Version: 1.38.0 Depends: R (>= 2.10), Biobase, RColorBrewer, grid, methods, rrcov Imports: Biobase, BiocGenerics, graphics, grDevices, grid, MASS, methods, RColorBrewer, rrcov, stats4, utils Suggests: cellHTS, tcltk License: LGPL Archs: i386, x64 Package: prebs Version: 1.2.1 Depends: R (>= 2.14.0), Rsamtools (>= 1.13.1), affy Imports: parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe License: Artistic-2.0 Package: PREDA Version: 1.8.0 Depends: R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats, methods, annotate Suggests: quantsmooth, qvalue, samr, limma, caTools, affy, PREDAsampledata Enhances: Rmpi, rsprng License: GPL-2 Package: preprocessCore Version: 1.24.0 Depends: methods Imports: stats License: LGPL (>= 2) Archs: i386, x64 Package: PROcess Version: 1.38.0 Depends: Icens Imports: graphics, grDevices, Icens, stats, utils License: Artistic-2.0 Package: 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Version: 1.2.0 Depends: R (>= 2.15.2) Imports: graphics, stats Suggests: testthat License: GPL-3 Package: PSICQUIC Version: 1.0.1 Depends: R (>= 2.15.0), methods, IRanges, biomaRt, BiocGenerics Imports: RCurl License: Apache License 2.0 Package: puma Version: 3.4.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.23.4), graphics, grDevices, methods, stats, utils, mclust Imports: Biobase (>= 2.5.5), affy (>= 1.23.4),affyio Suggests: pumadata, affydata, snow, limma, annotate, ROCR License: LGPL Archs: i386, x64 Package: pvac Version: 1.10.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) Package: pvca Version: 1.2.0 Depends: R (>= 2.15.1) Imports: Matrix, Biobase, vsn, lme4 Suggests: golubEsets License: LGPL (>= 2.0) Package: PWMEnrich Version: 2.6.2 Depends: methods, grid, BiocGenerics, Biostrings, Imports: seqLogo, gdata, evd Suggests: MotifDb, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel License: GPL-3 Package: qcmetrics Version: 1.0.0 Depends: R (>= 2.10) Imports: Biobase, methods, knitr, tools, Nozzle.R1, xtable, pander Suggests: affy, MSnbase, ggplot2, lattice, yaqcaffy, MAQCsubsetAFX, RforProteomics, AnnotationDbi, mzR, hgu133plus2cdf License: GPL-2 Package: qpcrNorm Version: 1.20.0 Depends: methods, Biobase, limma, affy License: LGPL (>= 2) Package: qpgraph Version: 1.18.9 Depends: R (>= 3.0.0) Imports: methods, parallel, Matrix (>= 1.0), annotate, graph (>= 1.40.1), Biobase, GGBase, AnnotationDbi, mvtnorm, qtl, Rgraphviz Suggests: BiocStyle, genefilter, org.EcK12.eg.db Enhances: rlecuyer, snow, Category, GOstats License: GPL (>= 2) Archs: i386, x64 Package: qrqc Version: 1.16.0 Depends: reshape, ggplot2, Biostrings, biovizBase, brew, xtable, Rsamtools (>= 1.3.28), testthat Imports: reshape, ggplot2, Biostrings, biovizBase, graphics, methods, plyr, stats LinkingTo: Rsamtools License: GPL (>= 2) Archs: i386, x64 Package: QUALIFIER Version: 1.6.21 Depends: R (>= 2.14.0),flowCore,flowViz,ncdfFlow,flowWorkspace (>= 3.8.37), data.table,reshape Imports: MASS,hwriter,RSVGTipsDevice,lattice,stats4,flowCore,flowViz,methods,flowWorkspace,latticeExtra,grDevices,tools, Biobase,XML License: Artistic-2.0 Package: quantsmooth Version: 1.28.0 Depends: R(>= 2.10.0), quantreg, grid License: GPL-2 Package: QuasR Version: 1.2.2 Depends: R (>= 2.15.0), parallel, GenomicRanges (>= 1.13.3), Rbowtie Imports: methods, zlibbioc, BiocGenerics, IRanges, BiocInstaller, Biobase, Biostrings, GenomicRanges, BSgenome, Rsamtools (>= 1.13.1), GenomicFeatures, ShortRead (>= 1.19.1) LinkingTo: Rsamtools Suggests: Rsamtools, rtracklayer, Gviz, RUnit, BiocStyle License: GPL-2 Archs: i386, x64 Package: qusage Version: 1.2.0 Depends: R (>= 2.10), limma (>= 3.14), methods Imports: utils, Biobase License: GPL (>= 2) Package: qvalue Version: 1.36.0 Imports: graphics, grDevices, stats, tcltk License: LGPL Package: r3Cseq Version: 1.8.0 Depends: GenomicRanges,Rsamtools,data.table,rtracklayer,VGAM,qvalue,RColorBrewer,sqldf,methods Suggests: BSgenome.Mmusculus.UCSC.mm9,BSgenome.Hsapiens.UCSC.hg18,BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 Package: R453Plus1Toolbox Version: 1.12.0 Depends: R (>= 2.12.0), BiocGenerics, Biobase, Biostrings (>= 2.29.2), BSgenome.Scerevisiae.UCSC.sacCer2,TeachingDemos Imports: BiocGenerics (>= 0.1.3), Biobase (>= 2.15.1), biomaRt, Biostrings, BSgenome, IRanges (>= 1.19.5), XVector, methods, R2HTML, Rsamtools, ShortRead, VariantAnnotation, xtable, tools Suggests: rtracklayer, ShortRead, Rsamtools, BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 Archs: i386, x64 Package: rama Version: 1.36.0 Depends: R(>= 2.5.0) License: GPL (>= 2) Archs: i386, x64 Package: RamiGO Version: 1.8.1 Depends: gsubfn,methods Imports: igraph,RCurl,png,RCytoscape,graph License: Artistic-2.0 Package: randPack Version: 1.8.0 Depends: methods Imports: Biobase License: Artistic-2.0 Package: RankProd Version: 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golubEsets License: GPL (>= 2) Package: ReactomePA Version: 1.6.1 Imports: methods, AnnotationDbi, reactome.db, org.Hs.eg.db, DOSE, stats4, plyr, igraph, qvalue, graphics, graphite Suggests: clusterProfiler, GOSemSim, knitr License: GPL-2 Package: ReadqPCR Version: 1.8.0 Depends: R(>= 2.14.0), Biobase, methods, affy Imports: Biobase Suggests: qpcR License: LGPL-3 Package: reb Version: 1.40.0 Depends: R (>= 2.0), Biobase, idiogram (>= 1.5.3) License: GPL-2 Archs: i386, x64 Package: RedeR Version: 1.10.1 Depends: R (>= 2.15), methods, igraph Imports: RCurl, XML, XMLRPC, rJava Suggests: PANR, pvclust License: GPL (>= 2) Package: REDseq Version: 1.8.0 Depends: R (>= 2.15.0), BiocGenerics (>= 0.1.0), BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno Imports: BiocGenerics, AnnotationDbi, Biostrings, ChIPpeakAnno, graphics, IRanges (>= 1.13.5), multtest, stats, utils License: GPL (>= 2) Package: RefPlus Version: 1.32.0 Depends: R (>= 2.8.0), Biobase (>= 2.1.0), affy (>= 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bit64,BiocStyle License: Artistic-2.0 Archs: i386, x64 Package: rHVDM Version: 1.28.0 Depends: R (>= 2.10), R2HTML (>= 1.5), affy (>= 1.23.4), minpack.lm (>= 1.0-5), Biobase (>= 2.5.5) License: GPL-2 Package: Ringo Version: 1.26.1 Depends: methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix, grid, lattice Imports: BiocGenerics (>= 0.1.11), genefilter, limma, vsn, stats4 Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0) License: Artistic-2.0 Archs: i386, x64 Package: RIPSeeker Version: 1.2.0 Depends: R (>= 2.15), methods, IRanges, GenomicRanges, rtracklayer, Rsamtools Suggests: biomaRt, ChIPpeakAnno, parallel, GenomicFeatures License: GPL-2 Package: Risa Version: 1.4.1 Depends: R (>= 2.0.9), Biobase (>= 2.4.0), methods, Rcpp (>= 0.9.13), biocViews, affy Imports: xcms Suggests: faahKO (>= 1.2.11) License: LGPL Package: RLMM Version: 1.24.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) Package: Rmagpie Version: 1.18.0 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) Package: RMAPPER Version: 1.12.0 Depends: methods Suggests: RCurl License: Artistic-2.0 Package: RMassBank Version: 1.4.0 Depends: mzR,rcdk,yaml,methods Imports: XML,RCurl,rjson Suggests: gplots,RMassBankData, xcms (>= 1.37.1), CAMERA, ontoCAT, RUnit License: Artistic-2.0 Package: RmiR Version: 1.18.0 Depends: R (>= 2.7.0), RmiR.Hs.miRNA, RSVGTipsDevice Imports: DBI, methods, stats Suggests: hgug4112a.db,org.Hs.eg.db License: Artistic-2.0 Package: RNAinteract Version: 1.10.0 Depends: R (>= 2.12.0), abind, locfit, Biobase Imports: RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid, hwriter, lattice, latticeExtra, limma, methods, splots (>= 1.13.12) License: Artistic-2.0 Package: RNAither Version: 2.10.0 Depends: R (>= 2.10), topGO, RankProd, prada Imports: geneplotter, limma, biomaRt, car, splots, methods License: Artistic-2.0 Package: rnaSeqMap Version: 2.18.0 Depends: R (>= 2.11.0), methods, Biobase, Rsamtools Imports: GenomicRanges , IRanges, edgeR, DESeq, DBI License: GPL-2 Archs: i386, x64 Package: RNASeqPower Version: 1.2.0 License: LGPL (>= 2) Package: ROC Version: 1.38.0 Depends: R (>= 1.9.0), utils, methods Suggests: Biobase License: Artistic-2.0 Archs: i386, x64 Package: Roleswitch Version: 1.0.0 Depends: R (>= 2.10), pracma, reshape, plotrix, microRNA, biomaRt, Biostrings, Biobase, DBI Suggests: ggplot2 License: GPL-2 Package: Rolexa Version: 1.18.0 Depends: R (>= 2.9.0), graphics, grDevices, methods, ShortRead Imports: mclust, Biostrings, graphics, grDevices, IRanges, methods, ShortRead, stats Enhances: fork License: GPL-2 Package: rols Version: 1.4.0 Depends: methods Imports: XML, XMLSchema (>= 0.6.0), SSOAP (>= 0.8.0), Biobase Suggests: xtable, GO.db, knitr (>= 1.1.0) License: GPL-2 Package: ROntoTools Version: 1.2.0 Depends: methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz 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1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, RUnit, BiocStyle License: Artistic-2.0 | file LICENSE Archs: i386, x64 Package: rsbml Version: 2.20.1 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils Imports: BiocGenerics, graph, utils License: Artistic-2.0 Archs: i386, x64 Package: RSVSim Version: 1.2.1 Depends: R (>= 3.0.0), Biostrings, GenomicRanges Imports: methods, IRanges, ShortRead Suggests: BSgenome.Hsapiens.UCSC.hg19, MASS, rtracklayer License: LGPL-3 Package: rTANDEM Version: 1.2.1 Depends: XML, Rcpp, data.table (>= 1.8.8) Imports: methods LinkingTo: Rcpp Suggests: biomaRt License: Artistic-1.0 | file LICENSE Archs: i386, x64 Package: RTCA Version: 1.14.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 Package: RTN Version: 1.0.0 Depends: R (>= 2.15), methods, igraph Imports: minet, snow, limma, RedeR (>= 1.8.1) Suggests: HTSanalyzeR, RUnit, BiocGenerics License: Artistic-2.0 Package: RTopper Version: 1.8.0 Depends: R (>= 2.11.0), Biobase Imports: limma, multtest Suggests: limma, org.Hs.eg.db, KEGG.db, GO.db License: GPL (>= 3) Package: rtracklayer Version: 1.22.7 Depends: R (>= 2.10), methods, GenomicRanges (>= 1.13.3) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.7.7), IRanges (>= 1.19.34), XVector (>= 0.1.3), GenomicRanges (>= 1.13.43), Biostrings (>= 2.29.18), BSgenome (>= 1.23.1), zlibbioc, RCurl (>= 1.4-2), Rsamtools (>= 1.13.1) LinkingTo: IRanges, XVector Suggests: humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, hgu133plus2.db License: Artistic-2.0 Archs: i386, x64 Package: Rtreemix Version: 1.24.0 Depends: R (>= 2.5.0), methods, graph, Biobase Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz License: LGPL Archs: i386, x64 Package: rTRM Version: 1.0.5 Depends: R (>= 2.10), igraph, RSQLite, annotate Imports: AnnotationDbi Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8, org.Mm.eg.db License: GPL-3 Package: rTRMui Version: 1.0.4 Depends: shiny (>= 0.5), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 Package: safe Version: 3.2.0 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, KEGG.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: GPL (>= 2) Package: sagenhaft Version: 1.32.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, methods, SparseM, stats, utils License: GPL (>= 2) Package: SAGx Version: 1.36.0 Depends: R (>= 2.5.0), stats, multtest, methods Imports: Biobase, stats4 Suggests: KEGG.db, hu6800.db, MASS License: GPL-3 Archs: i386, x64 Package: SamSPECTRAL Version: 1.16.0 Depends: R (>= 2.10) Imports: methods License: GPL (>= 2) Archs: i386, x64 Package: SANTA Version: 1.2.0 Depends: R (>= 2.14), igraph Imports: msm, snow Suggests: RUnit, BiocGenerics, org.Sc.sgd.db License: Artistic-2.0 Archs: i386, x64 Package: SBMLR Version: 1.58.0 Depends: XML, deSolve Suggests: rsbml License: GPL-2 Package: SCAN.UPC Version: 2.4.2 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach Imports: utils, methods, MASS, tools Suggests: pd.hg.u95a License: MIT Package: ScISI Version: 1.34.0 Depends: R (>= 2.10), GO.db, RpsiXML, annotate, apComplex Imports: AnnotationDbi, GO.db, RpsiXML, annotate, methods, org.Sc.sgd.db, utils Suggests: ppiData, xtable License: LGPL Package: segmentSeq Version: 1.14.0 Depends: R (>= 2.3.0), methods, baySeq (>= 1.15.4), ShortRead, GenomicRanges, IRanges Imports: baySeq, graphics, grDevices, IRanges, methods, utils, GenomicRanges Suggests: snow License: GPL-3 Package: SeqArray Version: 1.2.1 Depends: gdsfmt (>= 1.0.0) Imports: methods, Biostrings, GenomicRanges, IRanges, VariantAnnotation Suggests: parallel, snow, BiocGenerics, RUnit, Rcpp License: GPL-3 Archs: i386, x64 Package: seqbias Version: 1.10.0 Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0), Biostrings (>= 2.15.0), methods Imports: zlibbioc LinkingTo: Rsamtools Suggests: Rsamtools, ggplot2 License: LGPL-3 Archs: i386, x64 Package: seqCNA Version: 1.2.0 Depends: R (>= 2.10), GLAD (>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot (>= 0.99), methods License: GPL-3 Archs: i386, x64 Package: SeqGSEA Version: 1.2.1 Depends: Biobase, BiocGenerics, DESeq, biomaRt, foreach Imports: methods, doParallel License: GPL (>= 3) Package: seqLogo Version: 1.28.0 Depends: methods, grid License: LGPL (>= 2) Package: SeqVarTools Version: 1.0.0 Depends: SeqArray (>= 1.1.1) Imports: methods, GenomicRanges, IRanges, GWASExactHW Suggests: BiocGenerics, RUnit License: GPL-3 Package: shinyTANDEM Version: 1.0.0 Depends: rTANDEM, shiny, biomaRt License: GPL-3 Package: ShortRead Version: 1.20.0 Depends: 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(>= 2) Archs: i386, x64 Package: TFBSTools Version: 1.0.0 Depends: R (>= 3.0.1), methods, IRanges(>= 1.19.38) Imports: Biostrings(>= 2.29.19), RSQLite(>= 0.11.4), seqLogo License: GPL-2 Package: tigre Version: 1.16.1 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, BiocGenerics, Biobase, AnnotationDbi, gplots, graphics, puma, stats, utils, annotate, DBI, RSQLite Suggests: puma, drosgenome1.db, annotate, lumi License: AGPL-3 Archs: i386, x64 Package: tilingArray Version: 1.40.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 Archs: i386, x64 Package: timecourse Version: 1.34.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL Package: tkWidgets Version: 1.40.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 Package: topGO Version: 2.14.0 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 Package: tRanslatome Version: 1.0.0 Depends: R (>= 2.15.0), methods, limma, sigPathway, samr, anota, DESeq, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix License: LGPL Package: TransView Version: 1.6.1 Depends: methods,GenomicRanges Imports: Rsamtools,zlibbioc,gplots,IRanges LinkingTo: Rsamtools Suggests: RUnit,pasillaBamSubset License: GPL-3 Archs: i386, x64 Package: triform Version: 1.4.0 Depends: R (>= 2.11.0), IRanges, yaml Imports: IRanges, yaml, BiocGenerics Suggests: RUnit License: GPL-2 Package: trigger Version: 1.8.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 Archs: i386, x64 Package: trio Version: 3.0.0 Depends: R (>= 3.0.1) Suggests: survival, haplo.stats, mcbiopi, siggenes, splines, LogicReg (>= 1.5.3), logicFS (>= 1.28.1), KernSmooth License: LGPL-2 Package: triplex Version: 1.2.2 Depends: R (>= 2.15.0), IRanges (>= 1.19.5), XVector, Biostrings (>= 2.29.2) Imports: methods, grid, GenomicRanges LinkingTo: IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer, GenomeGraphs License: BSD_2_clause + file LICENSE Archs: i386, x64 Package: tspair Version: 1.20.0 Depends: R (>= 2.10), Biobase (>= 2.4.0) License: GPL-2 Archs: i386, x64 Package: TSSi Version: 1.8.0 Depends: R (>= 2.13.2), BiocGenerics (>= 0.3.2) Imports: BiocGenerics, methods, Hmisc, minqa, stats, Biobase (>= 0.3.2), plyr, IRanges Suggests: rtracklayer Enhances: parallel License: GPL-3 Archs: i386, x64 Package: TurboNorm Version: 1.10.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: affydata, affy, lattice License: LGPL Archs: i386, x64 Package: tweeDEseq Version: 1.8.0 Depends: R (>= 2.12.0) Imports: MASS, limma, edgeR, parallel, cqn Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) Archs: i386, x64 Package: twilight Version: 1.38.0 Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, grDevices, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) Archs: i386, x64 Package: TypeInfo Version: 1.28.0 Depends: methods Suggests: Biobase License: BSD Package: UniProt.ws Version: 2.2.1 Depends: RSQLite, RCurl, methods, utils Imports: BiocGenerics, AnnotationDbi Suggests: RUnit License: Artistic License 2.0 Package: VanillaICE Version: 1.24.0 Depends: R (>= 2.14.0) Imports: stats, utils, methods, Biobase, oligoClasses (>= 1.21.12),lattice, IRanges (>= 1.13.22), grid, msm, iterators, foreach, GenomicRanges, matrixStats Suggests: genomewidesnp6Crlmm (>= 1.0.7), hapmapsnp6, RColorBrewer, genefilter, RSQLite, foreach, RUnit, pd.mapping50k.hind240, SNPchip (>= 2.5.7), doSNOW Enhances: DNAcopy, crlmm (>= 1.17.14) License: LGPL-2 Archs: i386, x64 Package: VariantAnnotation Version: 1.8.13 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.7.7), GenomicRanges (>= 1.13.51), Rsamtools (>= 1.13.47), IRanges (>= 1.19.36), XVector Imports: methods, BiocGenerics, IRanges, XVector, Biostrings (>= 2.29.2), Biobase, Rsamtools, AnnotationDbi (>= 1.17.11), zlibbioc, BSgenome, GenomicFeatures (>= 1.13.11), DBI, utils, rtracklayer LinkingTo: IRanges, XVector, Biostrings, Rsamtools Suggests: RUnit, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle License: Artistic-2.0 Archs: i386, x64 Package: vbmp Version: 1.30.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) Package: Vega Version: 1.10.0 Depends: R (>= 2.10) License: GPL-2 Archs: i386, x64 Package: VegaMC Version: 2.8.0 Depends: R (>= 2.10.0), biomaRt, Biobase, genoset Imports: methods License: GPL-2 Archs: i386, x64 Package: virtualArray Version: 1.6.0 Depends: R (>= 2.15.0), BiocGenerics, methods, plyr, preprocessCore Imports: affy, affyPLM, AnnotationDbi, Biobase, gcrma, GEOquery, graphics, methods, reshape2, stats, utils, tseries, outliers Suggests: affydata, plier, limma, lumi, org.Hs.eg.db Enhances: multicore,BiocParallel License: GPL-3 Package: vsn Version: 3.30.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Imports: methods, affy (>= 1.23.4), limma, lattice Suggests: affydata, hgu95av2cdf License: Artistic-2.0 Archs: i386, x64 Package: vtpnet Version: 0.2.0 Depends: R (>= 3.0.0), graph, GenomicRanges Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 Package: wateRmelon Version: 1.2.2 Depends: R (>= 2.10), limma, methods, matrixStats, methylumi, lumi, IlluminaHumanMethylation450k.db, ROC Suggests: RPMM Enhances: minfi, methylumi, IMA License: GPL-3 Package: waveTiling Version: 1.4.0 Depends: oligo, oligoClasses, Biobase, Biostrings, GenomeGraphs Imports: methods, affy, preprocessCore, GenomicRanges, waveslim, IRanges Suggests: BSgenome, BSgenome.Athaliana.TAIR.TAIR9, waveTilingData, pd.atdschip.tiling, TxDb.Athaliana.BioMart.plantsmart12 License: GPL (>= 2) Archs: i386, x64 Package: weaver Version: 1.28.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 Package: webbioc Version: 1.34.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocInstaller License: GPL (>= 2) Package: widgetTools Version: 1.40.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL Package: xcms Version: 1.38.0 Depends: R (>= 2.14.0), methods, mzR (>= 1.1.6), BiocGenerics, Biobase Suggests: faahKO, msdata, ncdf, multtest, rgl, MassSpecWavelet (>= 1.5.2), RANN, RUnit Enhances: Rgraphviz, KEGGSOAP, Rmpi, XML License: GPL (>= 2) Archs: i386, x64 Package: XDE Version: 2.8.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5), methods, graphics Imports: Biobase, BiocGenerics, genefilter, graphics, grDevices, gtools, MergeMaid, methods, stats, utils, mvtnorm Suggests: siggenes, genefilter, MASS, RColorBrewer, GeneMeta, RUnit Enhances: coda License: LGPL-2 Archs: i386, x64 Package: xmapbridge Version: 1.20.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 Package: xps Version: 1.22.2 Depends: R (>= 2.6.0), methods, utils Suggests: tools License: GPL (>= 2.0) Archs: i386 Package: XVector Version: 0.2.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.7.2), IRanges (>= 1.19.36) Imports: methods, BiocGenerics, IRanges LinkingTo: IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 Archs: i386, x64 Package: yaqcaffy Version: 1.22.0 Depends: simpleaffy (>= 2.19.3), methods Imports: stats4 Suggests: MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk License: Artistic-2.0 Package: zlibbioc Version: 1.8.0 License: Artistic-2.0 + file LICENSE Archs: i386, x64