Package: a4 Version: 1.4.0 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL License: GPL-3 MD5sum: 35cd22093fd51bffa5faf66da960f962 Package: a4Base Version: 1.4.1 Depends: methods, graphics, grid, Biobase, AnnotationDbi, annaffy, mpm, genefilter, limma, multtest, glmnet, a4Preproc, a4Core, gplots Suggests: Cairo, ALL Enhances: gridSVG, JavaGD License: GPL-3 MD5sum: 76f70e652c627abb9761b59523aa4b21 Package: a4Classif Version: 1.4.0 Depends: methods, a4Core, a4Preproc, MLInterfaces, ROCR, pamr, glmnet, varSelRF Imports: a4Core Suggests: ALL License: GPL-3 MD5sum: 8d21f94114a19f4d00cd26e91111d08d Package: a4Core Version: 1.4.0 Depends: methods, Biobase, glmnet License: GPL-3 MD5sum: fd6593e7bac98a63d09d12639ac162be Package: a4Preproc Version: 1.4.0 Depends: methods, AnnotationDbi Suggests: ALL, hgu95av2.db License: GPL-3 MD5sum: b4c615ce42801a307c71404019b3556f Package: a4Reporting Version: 1.4.0 Depends: methods, annaffy Imports: xtable, utils License: GPL-3 MD5sum: 537e5fcea693a5aaebf88e47015a423d Package: ABarray Version: 1.24.0 Imports: Biobase, graphics, grDevices, methods, multtest, stats, tcltk, utils Suggests: limma, LPE License: GPL MD5sum: d75236c4d8ef0aaaa40c82719d8bb936 Package: aCGH Version: 1.34.0 Depends: R (>= 2.10), cluster, survival, multtest Imports: Biobase, cluster, grDevices, graphics, methods, multtest, stats, survival, splines, utils License: GPL-2 MD5sum: b8424335b5f80e83ee0a90b6e5fccc52 Package: ACME Version: 2.12.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), methods Imports: graphics, stats License: GPL (>= 2) MD5sum: b68dd8abdfb4b1463f35f4b95218e730 Package: ADaCGH2 Version: 1.6.0 Depends: R (>= 2.11.0), tilingArray, aCGH, waveslim, cluster, snapCGH, snowfall, ff Suggests: GLAD, DNAcopy, CGHregions, rlecuyer Enhances: Rmpi, multicore License: GPL (>= 3) MD5sum: 4847d314ed4a97d7637c32ff64ff9ce6 Package: adSplit Version: 1.26.0 Depends: R (>= 2.1.0), methods (>= 2.1.0) Imports: AnnotationDbi, Biobase (>= 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affy, graphics, methods, Biobase Suggests: AffymetrixDataTestFiles License: GPL-3 MD5sum: dbb54c5a3b5e23e766ce63ac1bead4bb Package: affyio Version: 1.24.0 Depends: R (>= 2.6.0), methods Imports: zlibbioc License: LGPL (>= 2) MD5sum: 7b2f52916f70871ed2929b2a6f8e53ee Package: affylmGUI Version: 1.30.0 Depends: limma, tcltk, affy, Biobase, affyio Suggests: tkrplot, affyPLM, R2HTML, xtable License: LGPL MD5sum: 8baefdfa8d902109d54b997d118fe68c Package: affyPara Version: 1.16.0 Depends: R (>= 2.5.0), methods, affy (>= 1.20.0), snow (>= 0.2-3), vsn (>= 3.6.0), aplpack (>= 1.1.1) Suggests: affydata Enhances: affy License: GPL-3 MD5sum: bd8d2cb31c2e7be4b0ebb1c4718962dd Package: affypdnn Version: 1.30.0 Depends: R (>= 2.13.0), affy (>= 1.5) Suggests: affydata, hgu95av2probe License: LGPL MD5sum: 1a2f47e07a63be4881d5a002d4548b4f Package: affyPLM Version: 1.32.0 Depends: R (>= 2.6.0), affy (>= 1.11.0), Biobase, gcrma, stats, preprocessCore (>= 1.5.1) Imports: zlibbioc, methods LinkingTo: 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R2HTML, RColorBrewer, Rsamtools, ShortRead, XML, biomaRt, edgeR, grDevices, graphics, methods, rJava, stats, svMisc, utils LinkingTo: Rsamtools License: Artistic License 2.0 MD5sum: 0d22ba3999ae8cf6b150e35744be2529 Package: arrayMvout Version: 1.14.0 Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy, lumi Imports: simpleaffy, mdqc, affyContam, Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf License: Artistic-2.0 MD5sum: 62fed33730cfde4bb8d08bcaff72477b Package: arrayQuality Version: 1.34.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL MD5sum: eb7ab08e1b040eb2b1a3aca30946785f Package: arrayQualityMetrics Version: 3.12.0 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, Cairo (>= 1.4-6), genefilter, graphics, grDevices, grid, Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, 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genomeIntervals, DESeq, ShortRead License: Artistic-2.0 MD5sum: d86aa7f517cc25f0ebb79f1d0b7148a3 Package: EBarrays Version: 2.20.0 Depends: R (>= 1.8.0), Biobase, lattice, methods Imports: Biobase, cluster, graphics, grDevices, lattice, methods, stats License: GPL (>= 2) MD5sum: 3c9b3ba8a5c1cffe9b3c44cdf568c618 Package: EBcoexpress Version: 1.0.0 Depends: EBarrays, mclust, minqa Suggests: graph, igraph, colorspace License: GPL (>= 2) MD5sum: f94186b42a44c3d37baf870cc5aceab1 Package: EBImage Version: 3.12.0 Depends: R (>= 2.8.0), methods, graphics, stats, utils, abind License: Artistic-2.0 MD5sum: 70b87e7db3814d98dfc0cfd97883c480 Package: ecolitk Version: 1.28.0 Depends: R (>= 2.10) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest License: GPL (>= 2) MD5sum: d6e49e5a06433e60cd91f1828ff8a680 Package: EDASeq Version: 1.2.0 Depends: BiocGenerics (>= 0.1.3), Biobase (>= 2.15.1), ShortRead (>= 1.11.42), Rsamtools (>= 1.5.75), aroma.light Imports: methods, graphics, BiocGenerics, IRanges (>= 1.13.9), DESeq Suggests: yeastRNASeq, leeBamViews, edgeR, DESeq License: Artistic-2.0 MD5sum: 7fdb9952bb083069027b693883ed2010 Package: edgeR Version: 2.6.12 Depends: R (>= 2.3.0), methods, limma Suggests: MASS, statmod, splines License: LGPL (>= 2) MD5sum: f402845accfd3517fdf1b6860f95f695 Package: eisa Version: 1.8.2 Depends: methods, isa2, Biobase, AnnotationDbi, Category, genefilter, DBI Suggests: igraph0 (>= 0.5.5), Matrix, GOstats, GO.db, KEGG.db, biclust, MASS, xtable, ALL, hgu95av2.db, targetscan.Hs.eg.db, org.Hs.eg.db License: GPL (>= 2) MD5sum: b3415dbb471739eb89ce09221a0d9f77 Package: ENVISIONQuery Version: 1.4.0 Depends: rJava, XML, utils License: GPL-2 MD5sum: 9622d7da92f2790b788059dd532cec9d Package: ExiMiR Version: 1.4.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.26.1) Imports: affyio(>= 1.13.3), Biobase(>= 2.5.5), preprocessCore(>= 1.10.0) License: GPL-2 MD5sum: 9fa57c3130cca955d6562e556a6fc44b Package: exomeCopy Version: 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methods, BiocGenerics (>= 0.1.3), outliers, lattice, flowViz, mvoutlier, bioDist, parody, RColorBrewer, latticeExtra Imports: methods, BiocGenerics, geneplotter, flowCore, flowViz, IRanges Suggests: flowStats License: Artistic-2.0 MD5sum: f738d153ac3107522f266095752232b7 Package: flowStats Version: 1.14.0 Depends: R (>= 2.10), flowCore (>= 1.10.0), fda (>= 2.2.6), mvoutlier, cluster, flowWorkspace Imports: BiocGenerics, MASS, flowViz, flowCore, fda (>= 2.2.6), Biobase, methods, grDevices, graphics, stats, utils, KernSmooth, lattice,compositions Suggests: flowViz, xtable Enhances: RBGL,ncdfFlow,graph License: Artistic-2.0 MD5sum: 9f3cf6875450b23ebdd186772c84f46a Package: flowTrans Version: 1.8.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 MD5sum: 07f4ee10f4b50c1ecbde8508a326dc95 Package: flowType Version: 1.2.0 Depends: R (>= 2.10) Imports: Biobase, graphics, grDevices, methods, flowCore, flowMeans, sfsmisc, rrcov, flowClust, flowMerge, stats Suggests: xtable License: Artistic-2.0 MD5sum: 27a798afa1c4b831a6554cd4476bde24 Package: flowUtils Version: 1.16.0 Depends: R (>= 2.2.0), flowCore (>= 1.2.0) Imports: Biobase, flowCore, graph, methods, RUnit, stats, utils, XML, flowViz Suggests: gatingMLData License: Artistic-2.0 MD5sum: f664cf076e39b6b04c2997b248f5d5bc Package: flowViz Version: 1.20.0 Depends: R (>= 2.7.0), flowCore (>= 1.5.17), lattice Imports: stats4, Biobase, flowCore, graphics, grDevices, grid, KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer, stats, utils Suggests: RColorBrewer, IDPmisc,colorspace License: Artistic-2.0 MD5sum: 56fe868b10c69c79f8bab0b7d922f61e Package: flowWorkspace Version: 1.2.0 Depends: Cairo, BiocGenerics, methods, RBGL, graph, XML, flowCore, flowViz, Biobase, IDPmisc, tools,hexbin Imports: Biobase, XML, flowCore, graph, graphics, lattice, methods, stats, stats4, utils Suggests: testthat, flowWorkspaceData, Rgraphviz Enhances: multicore,Rmpi,ncdfFlow License: Artistic-2.0 MD5sum: d10f55c8a2e49c0b6cd7596b30e9bc83 Package: frma Version: 1.8.0 Depends: R (>= 2.10.0), Biobase (>= 2.6.0) Imports: Biobase, MASS, DBI, affy, methods, oligo, oligoClasses, preprocessCore, utils, BiocGenerics Suggests: hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: 021027de53fb724a1639a4882d14a091 Package: frmaTools Version: 1.8.0 Depends: R (>= 2.10.0), affy Imports: Biobase, DBI, methods, preprocessCore, stats, utils Suggests: oligo, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: ca11d043dd6540759c8d0e9cb5c86ae2 Package: gaga Version: 2.2.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: multicore License: GPL (>= 2) MD5sum: 63a521a705395c5bfd1220068a6173a1 Package: gage Version: 2.6.0 Depends: R (>= 2.10), graph, multtest Suggests: gageData, GO.db, GSEABase, KEGG.db, org.Hs.eg.db 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methods, RColorBrewer, stats, utils Suggests: Biobase (>= 2.5.5), Rgraphviz, annotate, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db License: Artistic-2.0 MD5sum: 59a917e6968ee0f5c8e853d020b03a07 Package: geneRecommender Version: 1.28.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: a92ce8d36f259c7a7b69c2d495d7ad93 Package: GeneRegionScan Version: 1.12.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) MD5sum: ce2a729a4c20ae7be0addcca3a247d4d Package: GeneSelectMMD Version: 1.12.0 Depends: R (>= 2.13.2), Biobase Imports: Biobase, MASS, graphics, stats, survival, limma Suggests: ALL License: GPL (>= 2) MD5sum: 8bd5a0f24c3d3993c79a168672cdd021 Package: GeneSelector Version: 2.6.0 Depends: R (>= 2.5.1), methods, stats, Biobase Imports: multtest, siggenes, samr, limma Suggests: multtest, siggenes, 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2.23.4), zlibbioc, BSgenome, GenomicFeatures, snpStats, DBI LinkingTo: IRanges, Biostrings, Rsamtools Suggests: RUnit, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20110815, SIFT.Hsapiens.dbSNP132, PolyPhen.Hsapiens.dbSNP131 License: Artistic-2.0 MD5sum: e79b631bb8bcc79a7f9e95fdcfe55d63 Package: vbmp Version: 1.24.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: 2492570243913ac1e17b5427ef52a982 Package: Vega Version: 1.4.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: 9bd2f633d47f5b5b6a2a4fa0c3024624 Package: VegaMC Version: 2.0.0 Depends: R (>= 2.10.0), biomaRt, Biobase, genoset Imports: methods License: GPL-2 MD5sum: ee682456b512b787dbc11a1733c13ac9 Package: virtualArray Version: 1.0.0 Depends: R (>= 2.3.0), methods, plyr, preprocessCore Imports: affy, affyPLM, AnnotationDbi, Biobase, gcrma, GEOquery, graphics, methods, reshape2, stats, utils Suggests: affydata, plier, limma, lumi, org.Hs.eg.db Enhances: 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Rgraphviz, XML, KEGGSOAP License: GPL (>= 2) MD5sum: cd9c2cb991bd62121d132d888f8364ed Package: XDE Version: 2.2.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5), methods, graphics Imports: Biobase, BiocGenerics, genefilter, graphics, grDevices, gtools, MergeMaid, methods, stats, utils, mvtnorm Suggests: siggenes, genefilter, MASS, RColorBrewer, GeneMeta Enhances: coda License: LGPL-2 MD5sum: 7e3b4a8e1d1b17e53828a7a8e8094f1a Package: xmapbridge Version: 1.14.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 MD5sum: eac88e58499b1c1ec2d71dda98486b01 Package: xmapcore Version: 1.10.0 Depends: R (>= 2.8.0), methods, IRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase Suggests: RUnit License: GPL-2 MD5sum: c85a17fd3ec25eb45b1ca3650c994455 Package: xps Version: 1.16.0 Depends: R (>= 2.6.0), methods Suggests: tools License: GPL (>= 2.0) MD5sum: a0add6886bd4927523f6382462c58e0f Package: yaqcaffy Version: 1.16.1 Depends: simpleaffy (>= 2.19.3), methods Imports: stats4 Suggests: MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk License: Artistic-2.0 MD5sum: cc21902783e00e7ff9a8e99f3fcb2ea8 Package: zlibbioc Version: 1.2.0 License: Artistic-2.0 + file LICENSE MD5sum: a74eaf384f87a81900882695361b401a