Package: a4 Version: 1.6.1 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL, Cairo License: GPL-3 MD5sum: 07bc5cbc782e672d63d5e6b6c87adf8c Package: a4Base Version: 1.6.0 Depends: methods, graphics, grid, Biobase, AnnotationDbi, annaffy, mpm, genefilter, limma, multtest, glmnet, a4Preproc, a4Core, gplots Suggests: Cairo, ALL Enhances: gridSVG, JavaGD License: GPL-3 MD5sum: 06406dfd887d97c639c179295f6b5b24 Package: a4Classif Version: 1.6.0 Depends: methods, a4Core, a4Preproc, MLInterfaces, ROCR, pamr, glmnet, varSelRF Imports: a4Core Suggests: ALL License: GPL-3 MD5sum: a79af61ae6d5c88e352fab9fbb8fa33a Package: a4Core Version: 1.6.0 Depends: methods, Biobase, glmnet License: GPL-3 MD5sum: 7b6a3c7b7cddb14f5b2bc0b1781e0379 Package: a4Preproc Version: 1.6.0 Depends: methods, AnnotationDbi Suggests: ALL, hgu95av2.db License: GPL-3 MD5sum: d90391402175f298d1fe89f56c2e91bc Package: a4Reporting Version: 1.6.0 Depends: methods, annaffy Imports: xtable, utils 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(>= 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) MD5sum: 0751ef28d4531c8a8c4abc7aeefb49c7 Package: affxparser Version: 1.30.2 Depends: R (>= 2.6.0) Suggests: R.utils (>= 1.19.3), AffymetrixDataTestFiles License: LGPL (>= 2) MD5sum: f0197d2ce532839004ebdcbf0b7fc5de Package: affy Version: 1.36.1 Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5) Imports: BiocGenerics, Biobase, affyio (>= 1.13.3), BiocInstaller, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc LinkingTo: preprocessCore Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools License: LGPL (>= 2.0) MD5sum: ce1da25547feda90c5432b61c2ee9fc9 Package: affycomp Version: 1.34.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.3.3) Suggests: splines, affycompData License: GPL (>= 2) MD5sum: 2dfa3507781f8db9656253aafb3f4cf1 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(>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), IRanges, Biostrings (>= 2.11.32), splines, BiocInstaller Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL MD5sum: 13a24a8182b435d538fc0abb67e47ebd Package: genArise Version: 1.34.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE MD5sum: 8ca70f4c48247ecd1d2cc3bda26c754f Package: gene2pathway Version: 2.12.0 Depends: R (>= 2.10.0), kernlab (>= 0.9), biomaRt (>= 1.12.1), KEGGSOAP (>= 1.12.0), RBGL, AnnotationDbi,org.Dm.eg.db, keggorthology (>= 2.0) Imports: SSOAP, RCurl Enhances: doMC License: GPL (>= 2) MD5sum: 048520597a77d10c57a787b3038013cf Package: GeneAnswers Version: 1.16.0 Depends: R (>= 2.10.0), igraph0, RCurl, annotate, Biobase (>= 1.12.0), methods, XML, RSQLite, MASS, rgl, Heatplus, RColorBrewer Imports: graph, Rgraphviz, RBGL, annotate Suggests: GO.db, KEGG.db, biomaRt, AnnotationDbi, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db License: LGPL (>= 2) MD5sum: a8b1a4bed91ee1a476fe47b1b3f04281 Package: GeneExpressionSignature Version: 1.4.0 Depends: R (>= 2.13), Biobase, PGSEA Suggests: apcluster,GEOquery License: GPL-2 MD5sum: 319d8966b4f6c28aebdbfa4f0b8c2d51 Package: genefilter Version: 1.40.0 Imports: AnnotationDbi, annotate (>= 1.13.7), Biobase (>= 1.99.10), graphics, methods, stats, survival Suggests: Biobase (>= 1.99.10), class, hgu95av2.db, methods, tkWidgets, ALL, ROC License: Artistic-2.0 MD5sum: 3bbb52c4acf1d83d58d45aa4b04397eb Package: genefu Version: 1.8.0 Depends: R (>= 2.10), survcomp, mclust, biomaRt Imports: amap Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable License: Artistic-2.0 MD5sum: d835843e4bce94d514911a91e2b82a57 Package: GeneGA Version: 1.8.0 Depends: seqinr, hash, methods License: GPL-2 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BiocGenerics, IRanges LinkingTo: IRanges Suggests: Biostrings (>= 2.25.3), Rsamtools (>= 1.9.21), BSgenome, rtracklayer, GenomicFeatures, VariantAnnotation, edgeR, DESeq, DEXSeq, EatonEtAlChIPseq (>= 0.0.3), leeBamViews, pasilla, pasillaBamSubset, org.Sc.sgd.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Dmelanogaster.UCSC.dm3, RUnit, digest License: Artistic-2.0 MD5sum: c0cea669b165acc0e6498e0345e916c4 Package: Genominator Version: 1.12.0 Depends: R (>= 2.10), methods, RSQLite, DBI (>= 0.2-5), BiocGenerics (>= 0.1.0), IRanges, GenomeGraphs Imports: graphics, stats, utils Suggests: biomaRt, ShortRead, yeastRNASeq License: Artistic-2.0 MD5sum: e53345554364e32d5cd8705b40485c8b Package: genoset Version: 1.10.1 Depends: R (>= 2.10), BiocGenerics (>= 0.1.6), Biobase (>= 2.15.1), IRanges (>= 1.13.5), GenomicRanges Imports: methods, graphics, GenomicRanges Suggests: RUnit, DNAcopy, stats Enhances: parallel License: Artistic-2.0 MD5sum: 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gridExtra, scales, plyr, VariantAnnotation, Hmisc, rtracklayer Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, affyPLM, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr License: Artistic-2.0 MD5sum: 89b73a756bf8379858aa7d14ef9bb02a Package: GGtools Version: 4.6.2 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.20111119 Enhances: MatrixEQTL License: Artistic-2.0 MD5sum: bc707b416bad4184abdbfd7082cfaf10 Package: girafe Version: 1.10.1 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 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VariantAnnotation, tools, Biobase Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, VariantAnnotation, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines License: Artistic-2.0 MD5sum: 0a8cd0a1ff17ec52c5665ceae6228a90 Package: GOFunction Version: 1.4.0 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) MD5sum: 312ae67efb12ffe8b727f53478b44273 Package: goProfiles Version: 1.20.0 Depends: Biobase, AnnotationDbi, GO.db Suggests: org.Hs.eg.db License: GPL-2 MD5sum: 6b04464d9c10553a880adce884ca7e32 Package: GOSemSim Version: 1.16.1 Depends: R (>= 2.10), Rcpp Imports: methods, AnnotationDbi, GO.db, org.Hs.eg.db LinkingTo: Rcpp Suggests: DOSE, clusterProfiler License: GPL-2 MD5sum: bf4823b5f8d58a24aaf2d4f62e995edb Package: goseq Version: 1.10.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase Imports: mgcv, graphics, stats, utils, AnnotationDbi Suggests: GO.db, edgeR, org.Hs.eg.db License: LGPL (>= 2) MD5sum: 4568343d70df2b15964fbc3316d7676b Package: GOstats Version: 2.24.0 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 MD5sum: 7530e5a062aa69555de8aaa00ac200a5 Package: goTools Version: 1.32.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 MD5sum: bf402f36354117cee1b0cc136a8464d8 Package: gpls Version: 1.30.0 Imports: stats 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AGPL-3 MD5sum: b843bdd5db84a6a719336fd719bc3f0f Package: GRENITS Version: 1.10.0 Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) Imports: graphics, grDevices, reshape2, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: network License: GPL (>= 2) MD5sum: f608423bca1f467bd1572422125fcab4 Package: GSEABase Version: 1.20.2 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), annotate, methods, graph Imports: BiocGenerics, annotate, AnnotationDbi, Biobase, graph, methods, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz License: Artistic-2.0 MD5sum: 6eb22d9195f1d742afd9cb087031d179 Package: GSEAlm Version: 1.18.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: 5918af9b11bc6ad26c64398bd760a746 Package: GSRI Version: 2.6.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: multicore License: GPL-3 MD5sum: 833026887975f2a7e7bc834bb4a4b121 Package: GSVA Version: 1.6.6 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) MD5sum: cafb387a55ff0ea7929c4c5278f093ce Package: Gviz Version: 1.2.1 Depends: R (>= 2.10.0), methods, grid Imports: IRanges (>= 1.13.19), rtracklayer (>= 1.15.5), lattice, RColorBrewer, biomaRt (>= 2.11.0), GenomicRanges (>= 1.7.14), AnnotationDbi (>= 1.17.11), Biobase (>= 2.15.3), BiocGenerics (>= 0.1.4), GenomicFeatures (>= 1.9.7), BSgenome (>= 1.25.1), Biostrings (>= 2.25.1), biovizBase (>= 1.5.7) Suggests: xtable, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 24bb5af31cbc4195c274e8bd671c3751 Package: gwascat Version: 1.2.1 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 MD5sum: dbf9b89bf9f80086ba7c48fd6be0388b Package: GWASTools Version: 1.4.2 Depends: Biobase, ncdf, GWASExactHW, sandwich, gdsfmt Imports: methods, DBI, RSQLite, DNAcopy, survival, lmtest, quantsmooth Suggests: GWASdata, RUnit, SNPRelate, snpStats, VariantAnnotation License: Artistic-2.0 MD5sum: 1f9a54055d2fae2992905f8fdb8d32ea Package: hapFabia Version: 1.0.6 Depends: R (>= 2.12.0), Biobase, fabia (>= 2.3.1) Imports: methods, graphics, grDevices, stats, utils, KernSmooth License: LGPL (>= 2.1) MD5sum: 8a078f2aa5f82b2f2bde86c338289f82 Package: Harshlight Version: 1.30.0 Depends: R (>= 2.10) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) MD5sum: 880e4c22d5297bc3782535c320c20838 Package: Heatplus Version: 2.4.0 Imports: graphics, grDevices, stats Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) MD5sum: c71428fe38f6fa181635704c305935b6 Package: HELP Version: 1.16.1 Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods License: GPL (>= 2) MD5sum: 2bc77c138616f52637bd08719b33462d Package: HEM Version: 1.30.0 Depends: R (>= 2.1.0) Imports: Biobase, grDevices, stats, utils License: GPL (>= 2) MD5sum: 8724bedcde18ebcda3ddd94dd05fe7e1 Package: HilbertVis Version: 1.16.0 Depends: R (>= 2.6.0), grid, lattice Suggests: IRanges, EBImage License: GPL (>= 3) MD5sum: c01bec820963ab1678bea22d1e85c41b Package: HilbertVisGUI Version: 1.16.0 Depends: R (>= 2.6.0), HilbertVis (>= 1.1.6) Suggests: lattice, IRanges License: GPL (>= 3) MD5sum: 39eef101ff3b3bd1551087004b7d453e Package: HiTC Version: 1.2.0 Depends: R (>= 2.10.0), methods, girafe (>= 1.3.1), genomeIntervals (>= 1.7.1), RColorBrewer Imports: methods, Biobase, Biostrings, graphics, grDevices, ShortRead License: Artistic-2.0 MD5sum: 62fd8b518c55cf7d6f9236745f0efd25 Package: HMMcopy Version: 1.0.0 Depends: R (>= 2.10.0), 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RUnit, LungCancerLines (>= 0.0.6) License: Artistic-2.0 MD5sum: 1b9e5f0c9fac87d43ad315a833c742ea Package: vbmp Version: 1.26.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: 66df78e52188b52adf10129032b510ce Package: Vega Version: 1.6.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: 7d76d43137b98eb9353227e2a4e24110 Package: VegaMC Version: 2.2.0 Depends: R (>= 2.10.0), biomaRt, Biobase, genoset Imports: methods License: GPL-2 MD5sum: 8609d4bc81efde0a6a418e28e508fb60 Package: virtualArray Version: 1.2.1 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: parallel License: GPL-3 MD5sum: 80d81ba648d88ca00c03d765c2273b96 Package: vsn Version: 3.26.0 Depends: R (>= 2.10), Biobase (>= 2.5.5) Imports: methods, affy (>= 1.23.4), limma, lattice Suggests: affydata, hgu95av2cdf License: 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