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EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 MD5sum: a9df4412f03ea44ec8605c2fc77ed8b7 NeedsCompilation: no Package: AnnotationFilter Version: 1.10.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db License: Artistic-2.0 MD5sum: f022485a9ad10534d92efb7c02dfdc23 NeedsCompilation: no Package: AnnotationForge Version: 1.28.0 Depends: R (>= 3.5.0), methods, utils, BiocGenerics (>= 0.15.10), Biobase (>= 1.17.0), AnnotationDbi (>= 1.33.14) Imports: DBI, RSQLite, XML, S4Vectors, RCurl Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, hom.Hs.inp.db, GO.db, BiocStyle, knitr, BiocManager License: Artistic-2.0 MD5sum: 1f152e718ef96024db399ced8b7c02f1 NeedsCompilation: no Package: AnnotationFuncs Version: 1.36.0 Depends: R (>= 2.7.0), AnnotationDbi Imports: DBI Suggests: org.Bt.eg.db, GO.db, org.Hs.eg.db, hom.Hs.inp.db License: GPL-2 MD5sum: 71fbf39b6656ad4ef4afbcbcc1aa547a NeedsCompilation: no Package: AnnotationHub Version: 2.18.0 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, interactiveDisplayBase, httr, yaml, dplyr Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 4519881a751b29d40191d8e799b68adf NeedsCompilation: yes Package: AnnotationHubData Version: 1.16.0 Depends: R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges (>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15) Imports: GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocManager, biocViews, AnnotationDbi, Biobase, Biostrings, DBI, GenomeInfoDb (>= 1.15.4), OrganismDbi, RSQLite, rBiopaxParser, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData License: Artistic-2.0 MD5sum: d5ca1fac4a9e3d9672ee447d315ec26e NeedsCompilation: no Package: annotationTools Version: 1.60.0 Imports: Biobase, stats License: GPL MD5sum: 0fd3f1742af81c99be1f0dea73ba3034 NeedsCompilation: no Package: annotatr Version: 1.12.1 Depends: R (>= 3.4.0) Imports: AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures, GenomicRanges, GenomeInfoDb (>= 1.10.3), ggplot2, IRanges, methods, readr, regioneR, reshape2, rtracklayer, S4Vectors (>= 0.23.10), stats, utils Suggests: BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene License: GPL-3 MD5sum: 0655a02357bed2d9f4052c7156d8bcaf NeedsCompilation: no Package: anota Version: 1.34.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: 3e5b4e03de0ad65eca5dd1c375039c4c NeedsCompilation: no Package: anota2seq Version: 1.8.0 Depends: R (>= 3.4.0), methods Imports: multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices, graphics, stats, utils, SummarizedExperiment Suggests: BiocStyle,knitr License: GPL-3 MD5sum: e0d07880d41d3d263e1b2334dd850f65 NeedsCompilation: no Package: antiProfiles Version: 1.26.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: cd396cffde5d306911a1ac2e8ab26165 NeedsCompilation: no Package: APAlyzer Version: 1.0.0 Imports: GenomicRanges, 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rsnps, Biostrings, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.gnomADex.r2.1.hs37d5, COSMIC.67, rentrez, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137, seqinr, openxlsx, Rsamtools, stringr, utils, stats, GenomicRanges, S4Vectors, GenomicFeatures, IRanges, GenomicScores, SummarizedExperiment Suggests: GO.db, org.Hs.eg.db License: LGPL-3 MD5sum: 1833fe8ec6df62cfcc667284cfa946c3 NeedsCompilation: no Package: aroma.light Version: 3.16.0 Depends: R (>= 2.15.2) Imports: stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.22.0), R.utils (>= 2.9.0), matrixStats (>= 0.54.0) Suggests: princurve (>= 2.1.4) License: GPL (>= 2) MD5sum: 9cd884ea8694f15d655f352d48236aec NeedsCompilation: no Package: ArrayExpress Version: 1.46.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: XML, oligo, limma Suggests: affy License: Artistic-2.0 MD5sum: 32b86ec5c3368f60fdf4b886786e7ae0 NeedsCompilation: no Package: ArrayExpressHTS Version: 1.36.0 Depends: sampling, Rsamtools (>= 1.99.0), snow Imports: Biobase, BiocGenerics, Biostrings, DESeq, GenomicRanges, Hmisc, IRanges (>= 2.13.11), R2HTML, RColorBrewer, Rsamtools, ShortRead, XML, biomaRt, edgeR, grDevices, graphics, methods, rJava, stats, svMisc, utils, sendmailR, bitops LinkingTo: Rhtslib (>= 1.15.3) License: Artistic License 2.0 MD5sum: 3c0693690f9e9fc1f4c2211e33c5efb5 NeedsCompilation: yes Package: arrayMvout Version: 1.44.0 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: f3914ec62ee3cc2a805d716b66938ec4 NeedsCompilation: no Package: arrayQuality Version: 1.64.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL MD5sum: fcaece1a0396c894ac944f47243bee56 NeedsCompilation: no Package: 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data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testit, utils LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 2d9e4e7c453eacfe4ca821f6dedf306a NeedsCompilation: yes Package: attract Version: 1.38.0 Depends: R (>= 3.4.0), AnnotationDbi Imports: Biobase, limma, cluster, GOstats, graphics, stats, reactome.db, KEGGREST, org.Hs.eg.db, utils, methods Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) MD5sum: 7ea8ddc5ea6413df5d2036fd3b6d0065 NeedsCompilation: no Package: AUCell Version: 1.8.0 Imports: data.table, graphics, grDevices, GSEABase, methods, mixtools, R.utils, shiny, stats, SummarizedExperiment, BiocGenerics, S4Vectors, utils Suggests: Biobase, BiocStyle, devtools, dynamicTreeCut, DT, GEOquery, knitr, NMF, plotly, R2HTML, rbokeh, rmarkdown, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: 877deddcc88a65ef344d32b9de96ac54 NeedsCompilation: no Package: Autotuner Version: 1.0.1 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glmnet, randomForest, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) License: file LICENSE MD5sum: 8b08f07363a288e99b7e4bc952923f65 NeedsCompilation: no Package: biovizBase Version: 1.34.1 Depends: R (>= 3.5.0), methods Imports: grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors (>= 0.23.19), IRanges (>= 1.99.28), GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21), SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>= 1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4), ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlang Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit License: Artistic-2.0 MD5sum: f65dd3201ecf6517e0b54f1eeb895630 NeedsCompilation: yes Package: BiRewire Version: 3.18.0 Depends: igraph, slam, tsne, Matrix Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 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illuminaHumanv4.db, lumi, knitr License: GPL-3 MD5sum: 782e26e37212d1d87bc91add66a98bb4 NeedsCompilation: yes Package: BLMA Version: 1.10.0 Depends: ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel, Biobase Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 98a53789318812b0320c6f3da98ba090 NeedsCompilation: no Package: bnbc Version: 1.8.0 Depends: R (>= 3.4.0), methods, BiocGenerics, SummarizedExperiment, GenomicRanges Imports: Rcpp (>= 0.12.12), IRanges, GenomeInfoDb, S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: f9deb7c0504c9ea90ef6b3887a0047c7 NeedsCompilation: yes Package: BPRMeth Version: 1.12.0 Depends: R (>= 3.5.0), GenomicRanges Imports: assertthat, methods, MASS, doParallel, parallel, e1071, earth, foreach, randomForest, stats, IRanges, S4Vectors, data.table, graphics, truncnorm, mvtnorm, Rcpp (>= 0.12.14), matrixcalc, magrittr, kernlab, ggplot2, cowplot, BiocStyle LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 272a951d85025b392ff2102cb1d09417 NeedsCompilation: yes Package: BRAIN Version: 1.32.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 MD5sum: 5b3f1aa663c925216cf1d841560b5840 NeedsCompilation: no Package: brainflowprobes Version: 1.0.0 Depends: R (>= 3.6.0) Imports: Biostrings (>= 2.52.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), bumphunter (>= 1.26.0), cowplot (>= 1.0.0), derfinder (>= 1.18.1), derfinderPlot (>= 1.18.1), GenomicRanges (>= 1.36.0), ggplot2 (>= 3.1.1), RColorBrewer (>= 1.1), utils, grDevices, GenomicState (>= 0.99.7) Suggests: BiocStyle, knitcitations, knitr, rmarkdown, sessioninfo, testthat (>= 2.1.0) License: Artistic-2.0 MD5sum: af9495affe5ec1e0e7ce0f269434bb8b NeedsCompilation: no Package: BrainStars Version: 1.30.0 Depends: RCurl, Biobase, methods Imports: RJSONIO, Biobase License: Artistic-2.0 MD5sum: 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methods, Matrix, SummarizedExperiment, SingleCellExperiment, Rtsne, graphics, grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp, Rdpack (>= 0.7) LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 74cdb48734d844e0d2a0ac90ac0c770f NeedsCompilation: yes Package: ccmap Version: 1.12.0 Imports: AnnotationDbi (>= 1.36.2), BiocManager (>= 1.24.0), ccdata (>= 1.1.2), doParallel (>= 1.0.10), data.table (>= 1.10.4), foreach (>= 1.4.3), parallel (>= 3.3.3), xgboost (>= 0.6.4), lsa (>= 0.73.1) Suggests: crossmeta, knitr, rmarkdown, testthat, lydata License: MIT + file LICENSE MD5sum: df700bd09648b2ed38a9f4fcf229f0f5 NeedsCompilation: no Package: CCPROMISE Version: 1.12.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: 43b8aff213c38a2e17e266b5936b8576 NeedsCompilation: no Package: ccrepe Version: 1.22.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat License: MIT + 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limma, multtest, RBGL, graph, BiocManager, stats, regioneR, DBI, ensembldb, Biobase, seqinr, idr, GenomicAlignments, DelayedArray, SummarizedExperiment, rtracklayer, Rsamtools Suggests: reactome.db, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, gplots, BiocStyle, knitr, rmarkdown, testthat, trackViewer, motifStack, OrganismDbi License: GPL (>= 2) MD5sum: 33edc00789df4797fddc70bbfe0de276 NeedsCompilation: no Package: ChIPQC Version: 1.22.0 Depends: R (>= 3.0.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19) Imports: BiocGenerics (>= 0.11.3), S4Vectors (>= 0.1.0), IRanges (>= 1.99.17), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), chipseq (>= 1.12.0), gtools, BiocParallel, methods, reshape2, Nozzle.R1, Biobase, grDevices, stats, utils, GenomicFeatures, 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ggplot2, chromstaRData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, reshape2, Rsamtools, GenomicAlignments, bamsignals, mvtnorm Suggests: knitr, BiocStyle, testthat, biomaRt License: Artistic-2.0 MD5sum: c557372e8c2de6cc2e08479c76ea0e89 NeedsCompilation: yes Package: chromswitch Version: 1.8.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.26.4) Imports: cluster (>= 2.0.6), Biobase (>= 2.36.2), BiocParallel (>= 1.8.2), dplyr (>= 0.5.0), gplots(>= 3.0.1), graphics, grDevices, IRanges (>= 2.4.8), lazyeval (>= 0.2.0), matrixStats (>= 0.52), magrittr (>= 1.5), methods, NMF (>= 0.20.6), rtracklayer (>= 1.36.4), S4Vectors (>= 0.23.19), stats, tidyr (>= 0.6.3) Suggests: BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3), GenomeInfoDb (>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3), testthat License: MIT + file LICENSE MD5sum: 77fca00f1f40f187146efc2af41e4127 NeedsCompilation: no Package: chromVAR Version: 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edgeR, car, Rmixmod, ggplot2 (>= 3.0.0), gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, randomForest, robustbase, glmnet, class License: GPL-3 MD5sum: 3bccbb395529a60e1e6e6ec486eda8c3 NeedsCompilation: no Package: cleanUpdTSeq Version: 1.24.0 Depends: R (>= 2.15), BiocGenerics (>= 0.1.0), methods, stats Imports: BSgenome, GenomicRanges, seqinr, e1071, GenomeInfoDb, IRanges, utils, BSgenome.Drerio.UCSC.danRer7 Suggests: BiocStyle, knitr, RUnit License: GPL-2 MD5sum: 3b0727cb5a1100112d37d21bb667e002 NeedsCompilation: no Package: cleaver Version: 1.24.0 Depends: R (>= 3.0.0), methods, Biostrings (>= 1.29.8) Imports: S4Vectors, IRanges Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.1.4) License: GPL (>= 3) MD5sum: 0ed8d1c82721bd64a54d017f80714b33 NeedsCompilation: no Package: clippda Version: 1.36.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, 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testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms License: MIT + file LICENSE MD5sum: 1cd10aab686db9b3b0627e8a5266f9c3 NeedsCompilation: no Package: clustComp Version: 1.14.0 Depends: R (>= 3.3) Imports: sm, stats, graphics, grDevices Suggests: Biobase, colonCA, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 1b2fb64d1c500db97cf3ae7cd0ab203c NeedsCompilation: no Package: clusterExperiment Version: 2.6.1 Depends: R (>= 3.5.0), SingleCellExperiment, SummarizedExperiment, BiocGenerics Imports: methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, howmany, locfdr, matrixStats, graphics, parallel, RSpectra, kernlab, stringr, S4Vectors, grDevices, DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, scRNAseq, MAST, Rtsne, scran, igraph License: Artistic-2.0 MD5sum: 3230217acf4493860045ebe104a8977e NeedsCompilation: yes Package: ClusterJudge 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methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices, simpleCache, fitdistrplus Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 606eae22383b6657f933745d4a7f8ba0 NeedsCompilation: no Package: codelink Version: 1.54.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 MD5sum: d641dd4f8b41d4fa46b9f721d16cfbc8 NeedsCompilation: no Package: CODEX Version: 1.18.0 Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors Suggests: WES.1KG.WUGSC License: GPL-2 MD5sum: 58ebbc73b6497addb33d1568e84508db NeedsCompilation: no Package: coexnet Version: 1.8.0 Depends: R (>= 3.4) Imports: affy, siggenes, GEOquery, vsn, igraph, acde, Biobase, limma, graphics, stats, utils, STRINGdb, SummarizedExperiment, minet, rmarkdown Suggests: RUnit, BiocGenerics, knitr License: LGPL MD5sum: 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S4Vectors, GenomicRanges, stats, corrplot Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: aa23609080690392beba735845319e04 NeedsCompilation: no Package: compartmap Version: 1.4.0 Depends: R (>= 3.5.0), minfi, Homo.sapiens, mixOmics Imports: SummarizedExperiment, GenomicRanges, gtools, parallel Suggests: covr, testthat, knitr License: GPL-3 + file LICENSE MD5sum: b109f4d18841366808899984a846fb82 NeedsCompilation: no Package: COMPASS Version: 1.24.1 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2 License: Artistic-2.0 MD5sum: 51dbfe91c678334785d9a6dd0c14a1a7 NeedsCompilation: yes Package: compcodeR Version: 1.22.0 Depends: R (>= 3.0.2), sm Imports: tcltk, knitr (>= 1.2), 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License: GPL-2 MD5sum: 029213f4cda5de62e79cb93f93003deb NeedsCompilation: no Package: ComplexHeatmap Version: 2.2.0 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.5), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), parallel, png Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, Cairo, jpeg, tiff, fastcluster, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges License: MIT + file LICENSE MD5sum: fbd83bdf32647e4c3d161fd9114b3c02 NeedsCompilation: no Package: CONFESS Version: 1.14.0 Depends: R (>= 3.3),grDevices,utils,stats,graphics Imports: methods,changepoint,cluster,contrast,data.table(>= 1.9.7),ecp,EBImage,flexmix,flowCore,flowClust,flowMeans,flowMerge,flowPeaks,foreach,ggplot2,grid,limma,MASS,moments,outliers,parallel,plotrix,raster,readbitmap,reshape2,SamSPECTRAL,waveslim,wavethresh,zoo Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata License: GPL-2 MD5sum: 6e9600398489df5b3b6bd75a858f2f20 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limma, cluster, dplyr, Biobase, grDevices, stats, graphics, utils Suggests: rmarkdown, testthat, knitr, shiny, shinydashboard, shinyWidgets, shinycssloaders, DT, ggthemes, ggplot2, pheatmap, RColorBrewer, tibble, ggalluvial License: GPL-3 | file LICENSE MD5sum: 7ef9c46d6883f7e051e8ceb8700a1f23 NeedsCompilation: no Package: crossmeta Version: 1.12.0 Depends: R (>= 3.5) Imports: affy (>= 1.52.0), affxparser (>= 1.46.0), AnnotationDbi (>= 1.36.2), Biobase (>= 2.34.0), BiocGenerics (>= 0.20.0), BiocManager (>= 1.30.4), ccmap, DT (>= 0.2), DBI (>= 1.0.0), data.table (>= 1.10.4), doParallel (>= 1.0.10), doRNG (>= 1.6), foreach (>= 1.4.3), fdrtool (>= 1.2.15), ggplot2 (>= 2.2.1), GEOquery (>= 2.40.0), limma (>= 3.30.13), matrixStats (>= 0.51.0), metaMA (>= 3.1.2), metap (>= 0.8), miniUI (>= 0.1.1), oligo (>= 1.38.0), plotly(>= 4.5.6), reshape (>= 0.8.6), reader(>= 1.0.6), RColorBrewer (>= 1.1.2), RCurl (>= 1.95.4.11), RSQLite (>= 2.1.1), rdrop2 (>= 0.7.0), stringr (>= 1.2.0), sva (>= 3.22.0), shiny (>= 1.0.0), stats (>= 3.3.3), XML (>= 3.98.1.17), Suggests: knitr, rmarkdown, lydata, org.Hs.eg.db, testthat, ccdata License: MIT + file LICENSE MD5sum: ca9fff0d56b9bbfe5e213d70be8532a7 NeedsCompilation: no Package: CSAR Version: 1.38.0 Depends: R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 MD5sum: 73ed2b250c451f08f02857b196b18e70 NeedsCompilation: yes Package: csaw Version: 1.20.0 Depends: GenomicRanges, SummarizedExperiment Imports: Rcpp, BiocGenerics, Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, utils LinkingTo: Rhtslib, zlibbioc, Rcpp Suggests: org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager License: GPL-3 MD5sum: 901b971c007be79060e258712d6dab89 NeedsCompilation: yes Package: CSSP Version: 1.24.0 Imports: methods, splines, stats, utils 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Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat License: GPL-2 MD5sum: c93f6f0bba573c02f80c085cc52bdb6d NeedsCompilation: no Package: cummeRbund Version: 2.28.0 Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz Imports: methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson License: Artistic-2.0 MD5sum: 1420d34283af61b3cbc3d8b3aa982f41 NeedsCompilation: no Package: customProDB Version: 1.26.1 Depends: R (>= 3.0.1), IRanges, AnnotationDbi, biomaRt(>= 2.17.1) Imports: S4Vectors (>= 0.9.25), DBI, GenomeInfoDb, GenomicRanges, Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>= 2.26.3), GenomicFeatures (>= 1.32.0), stringr, RCurl, plyr, VariantAnnotation (>= 1.13.44), rtracklayer, RSQLite, AhoCorasickTrie, methods Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 3e0ebccbd884d523a87b005e2953e1f3 NeedsCompilation: no Package: CVE Version: 1.11.2 Depends: R (>= 3.4.0), tidyverse, plyr, ggplot2 Imports: shiny, ConsensusClusterPlus, RColorBrewer, gplots, jsonlite, ape, WGCNA, RTCGAToolbox Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: aaffd085823c868849a496ece8dfb399 NeedsCompilation: no Package: cycle Version: 1.40.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 MD5sum: 92ed47f504ed23ef0264b2b2104039ed NeedsCompilation: no Package: cydar Version: 1.10.0 Depends: BiocParallel, SingleCellExperiment Imports: viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, flowCore, Biobase, Rcpp, BiocNeighbors, SummarizedExperiment LinkingTo: Rcpp Suggests: ncdfFlow, testthat, knitr, edgeR, limma, glmnet, BiocStyle, flowStats License: GPL-3 MD5sum: c088a4650feea2e26ae2fe5e811672ba NeedsCompilation: yes Package: CytoDx Version: 1.6.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr License: GPL-2 MD5sum: e1e7c8c0d12dbad6edd43b4b931fa2d4 NeedsCompilation: no Package: cytofast Version: 1.2.0 Depends: R (>= 3.6.0) Imports: flowCore, ggplot2, ggridges, RColorBrewer, reshape2, stats, grDevices, Rdpack, methods, grid, FlowSOM Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 78d824546a06236d66ee0f134d7b02e3 NeedsCompilation: no Package: cytolib Version: 1.8.0 Depends: R (>= 3.4) Suggests: knitr License: Artistic-2.0 MD5sum: 13205b79dd96542a3a36f9df61622a66 NeedsCompilation: no Package: CytoML Version: 1.12.1 Imports: flowCore (>= 1.43.10), flowWorkspace (>= 3.33.10), openCyto (>= 1.11.3), XML, data.table, jsonlite, RBGL, ncdfFlow, Rgraphviz, Biobase, methods, graph, graphics, utils, base64enc, plyr, dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, lattice, stats, corpcor, RUnit LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.3.7), cytolib(>= 1.3.3), RcppParallel Suggests: testthat, flowWorkspaceData (>= 2.11.1), knitr, parallel License: Artistic-2.0 MD5sum: d3ec97ff9be487ecc8702ed5a8b9990d NeedsCompilation: yes Package: dada2 Version: 1.14.1 Depends: R (>= 3.4.0), Rcpp (>= 0.12.0), methods (>= 3.4.0) Imports: Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), ShortRead (>= 1.32.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0), IRanges (>= 2.6.0), XVector (>= 0.16.0), BiocGenerics (>= 0.22.0) LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, knitr, rmarkdown License: LGPL-3 MD5sum: 11175d8c1d6a3e2c21f39cb398f66ab0 NeedsCompilation: yes Package: dagLogo Version: 1.24.0 Depends: R (>= 3.0.1), methods, biomaRt, grImport2, grid, motifStack Imports: pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils Suggests: XML, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 8899426387a13a9c533691c88a3619f8 NeedsCompilation: no Package: daMA Version: 1.58.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: e543338446d034badfc8b223bac10ef9 NeedsCompilation: no Package: DaMiRseq Version: 1.10.0 Depends: R (>= 3.4), SummarizedExperiment, ggplot2 Imports: DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap, FactoMineR, corrplot, randomForest, e1071, caret, MASS, lubridate, plsVarSel, kknn, FSelector, methods, stats, utils, graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 7bb7ea212d0108b35c8ffc32c4632e1d NeedsCompilation: no Package: DAPAR Version: 1.18.5 Depends: R (>= 3.6.1), foreach, parallel, doParallel, igraph Imports: MSnbase, RColorBrewer,stats,preprocessCore,Cairo,png, lattice,reshape2,gplots,pcaMethods,ggplot2, limma,knitr,tmvtnorm,norm,impute, stringr, grDevices, graphics, openxlsx, utils, cp4p (>= 0.3.5), scales, Matrix, vioplot, imp4p (>= 0.8), highcharter (>= 0.7.0), DAPARdata (>= 1.16.0), siggenes, graph, lme4, readxl, clusterProfiler, dplyr, tidyr,AnnotationDbi, vsn, FactoMineR, factoextra, visNetwork Suggests: BiocGenerics, Biobase, testthat, BiocStyle License: Artistic-2.0 MD5sum: 243bb0f82462dcc1eaba6948f02ca3ab NeedsCompilation: no Package: DART Version: 1.34.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: 93dc85365ab4176d3427fb792ce38407 NeedsCompilation: no Package: DBChIP Version: 1.30.0 Depends: R (>= 2.15.0), edgeR, DESeq Suggests: ShortRead, BiocGenerics License: GPL (>= 2) MD5sum: 75c676926c1b3582ab95b3a0895d15c7 NeedsCompilation: no Package: dcanr Version: 1.2.0 Depends: R (>= 3.6.0) Imports: igraph, foreach, plyr, stringr, reshape2, methods, Matrix, graphics, stats, RColorBrewer, circlize, doRNG Suggests: EBcoexpress, testthat, EBarrays, GeneNet, COSINE, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 MD5sum: 285d1997481828fef7f7cf5448c71d05 NeedsCompilation: no Package: dcGSA Version: 1.14.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: c9e8c209a10fc851f8c4d6dc13069036 NeedsCompilation: no Package: DChIPRep Version: 1.16.0 Depends: R (>= 3.4), DESeq2 Imports: methods, stats, utils, ggplot2, fdrtool, reshape2, GenomicRanges, SummarizedExperiment, smoothmest, plyr, tidyr, assertthat, S4Vectors, purrr, soGGi, ChIPpeakAnno Suggests: mgcv, testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENCE MD5sum: 16c801f06bea6bc489cc6b6ad11abcf0 NeedsCompilation: no Package: ddCt Version: 1.42.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: RUnit License: LGPL-3 MD5sum: 901a0b2157bbd0b9c6bb98f340b82af0 NeedsCompilation: no Package: ddPCRclust Version: 1.6.0 Depends: R (>= 3.5) Imports: plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore, flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks Suggests: BiocStyle License: Artistic-2.0 MD5sum: bad57a519fafe6dd639ab66f14566da6 NeedsCompilation: no Package: debCAM Version: 1.4.0 Depends: R (>= 3.5) Imports: methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 MD5sum: 1021b7d8a0f8026db2e6f7d010cdfd93 NeedsCompilation: no Package: debrowser Version: 1.14.2 Depends: R (>= 3.5.0), Imports: shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT, ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE, igraph, grDevices, graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, d3heatmap, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker, plotly, heatmaply, Harman, pathview Suggests: testthat, rmarkdown, knitr, R.rsp License: GPL-3 + file LICENSE MD5sum: 60e4916b4986994566a159b26d712e17 NeedsCompilation: no Package: DECIPHER Version: 2.14.0 Depends: R (>= 3.3.0), Biostrings (>= 2.35.12), RSQLite (>= 1.1), stats, parallel Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector License: GPL-3 MD5sum: 647cef126b0a6cf38aeab5ae366c0851 NeedsCompilation: yes Package: deco Version: 1.2.0 Depends: R (>= 3.5.0), AnnotationDbi, BiocParallel, SummarizedExperiment, limma Imports: stats, methods, ggplot2, foreign, graphics, BiocStyle, Biobase, cluster, gplots, RColorBrewer, locfit, made4, ade4, sfsmisc, scatterplot3d, gdata, grDevices, utils, reshape2, gridExtra Suggests: knitr, curatedTCGAData, MultiAssayExperiment, Homo.sapiens License: GPL (>= 3) MD5sum: 901e7b70f92ac1dcaa63970ce8ad7c1c NeedsCompilation: no Package: DEComplexDisease Version: 1.6.0 Depends: R (>= 3.3.3) Imports: Rcpp (>= 0.12.7), DESeq2, edgeR, SummarizedExperiment, ComplexHeatmap, grid, parallel, BiocParallel, grDevices, graphics, stats, methods, utils LinkingTo: Rcpp Suggests: knitr License: GPL-3 MD5sum: 0b2c6295a415351351c64a3588dccad8 NeedsCompilation: yes Package: decompTumor2Sig Version: 2.2.0 Depends: R(>= 3.6), ggplot2 Imports: methods, Matrix, quadprog(>= 1.5-5), vcfR, GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 43da910c3b77e6d61bbf5a625d7d8637 NeedsCompilation: no Package: DeconRNASeq Version: 1.28.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 MD5sum: 9ccaab63d80443c96b92b06d0d296732 NeedsCompilation: no Package: decontam Version: 1.6.0 Depends: R (>= 3.4.1), methods (>= 3.4.1) Imports: ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats Suggests: BiocStyle, knitr, rmarkdown, phyloseq License: Artistic-2.0 MD5sum: 55db2a9c9c7fdf8e889596b759ee14c0 NeedsCompilation: no Package: DEDS Version: 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SummarizedExperiment Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat License: GPL-3 MD5sum: ff0865faaf368f2a261fcaaade075e22 NeedsCompilation: no Package: DEGraph Version: 1.38.0 Depends: R (>= 2.10.0), R.utils Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph License: GPL-3 MD5sum: 3275104ce2c5f2882bade0664258e4e5 NeedsCompilation: no Package: DEGreport Version: 1.22.0 Depends: R (>= 3.5.0) Imports: utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, lasso2, magrittr, Nozzle.R1, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE MD5sum: 9d356a3f768532bcd04867b0708a52c5 NeedsCompilation: no Package: DEGseq Version: 1.40.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: f61f9ad7fc7b0b65401e726e2f4648c4 NeedsCompilation: yes Package: DelayedArray Version: 0.12.3 Depends: R (>= 3.4), methods, stats4, matrixStats, BiocGenerics (>= 0.31.5), S4Vectors (>= 0.24.4), IRanges (>= 2.17.3), BiocParallel Imports: stats, Matrix LinkingTo: S4Vectors Suggests: HDF5Array, genefilter, SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit License: Artistic-2.0 MD5sum: e32a42555bcff7780ae635d2e1e38f88 NeedsCompilation: yes Package: DelayedDataFrame Version: 1.2.0 Depends: R (>= 3.6), S4Vectors (>= 0.23.19), DelayedArray (>= 0.7.5) Imports: methods, stats, BiocGenerics Suggests: testthat, knitr, rmarkdown, SeqArray, GDSArray License: GPL-3 MD5sum: 7c946cb48021a7733d64e807d6fd9d64 NeedsCompilation: no Package: DelayedMatrixStats Version: 1.8.0 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S4Vectors (>= 0.9.38), scales, utils Suggests: biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData (>= 0.99.0), sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, RefManageR, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 97b07710130a47acf0262633377d5b85 NeedsCompilation: no Package: DEScan2 Version: 1.6.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocParallel, BiocGenerics, ChIPpeakAnno, data.table, DelayedArray, GenomeInfoDb, GenomicAlignments, glue, IRanges, plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors (>= 0.23.19), SummarizedExperiment, tools, utils LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod License: Artistic-2.0 MD5sum: c808381ccdc5f2571c5fd4f64834b79d NeedsCompilation: yes Package: DESeq Version: 1.38.0 Depends: BiocGenerics (>= 0.7.5), Biobase (>= 2.21.7), locfit, lattice Imports: 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openCyto License: Artistic-2.0 MD5sum: b8247d1703049c39f334684ad672ce7a NeedsCompilation: yes Package: fmcsR Version: 1.28.0 Depends: R (>= 2.10.0), ChemmineR, methods Imports: RUnit, methods, ChemmineR, BiocGenerics, parallel Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap License: Artistic-2.0 MD5sum: ea6e8e9c1504eeac2bfbf1092a237d83 NeedsCompilation: yes Package: focalCall Version: 1.20.0 Depends: R(>= 2.10.0), CGHcall Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: faf4416577a8c95f47d103a01e852665 NeedsCompilation: no Package: FoldGO Version: 1.4.0 Depends: R (>= 3.5) Imports: topGO (>= 2.30.1), ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), stats, methods Suggests: knitr, rmarkdown, devtools, kableExtra License: GPL-3 MD5sum: cd47367dac62b2d047c5cb986e73be96 NeedsCompilation: no Package: FourCSeq Version: 1.20.0 Depends: R (>= 3.0), GenomicRanges, ggplot2, DESeq2 (>= 1.9.11), splines, methods, LSD Imports: DESeq2, Biobase, Biostrings, GenomicRanges, SummarizedExperiment, Rsamtools, ggbio, reshape2, rtracklayer, fda, GenomicAlignments, gtools, Matrix Suggests: BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene License: GPL (>= 3) MD5sum: 7df8f716ae68d253c8424ad468ffe540 NeedsCompilation: no Package: FRGEpistasis Version: 1.22.0 Depends: R (>= 2.15), MASS, fda, methods, stats Imports: utils License: GPL-2 MD5sum: f7f3df112470b7f1daf02600c438bb43 NeedsCompilation: no Package: frma Version: 1.38.0 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: c8a769a86f5e804451962edc5d5dea1b NeedsCompilation: no Package: frmaTools Version: 1.38.0 Depends: R (>= 2.10.0), affy Imports: Biobase, DBI, methods, preprocessCore, stats, utils Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: 1fcc298352734490125e2f55ead27ad5 NeedsCompilation: no Package: FunChIP Version: 1.12.0 Depends: R (>= 3.2), GenomicRanges Imports: shiny, fda, doParallel, GenomicAlignments, Rcpp, methods, foreach, parallel, GenomeInfoDb, Rsamtools, grDevices, graphics, stats, RColorBrewer LinkingTo: Rcpp License: Artistic-2.0 MD5sum: 3b1472707675d917ac5df030706ea0c9 NeedsCompilation: yes Package: FunciSNP Version: 1.30.0 Depends: R (>= 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene, FunciSNP.data Imports: methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools (>= 1.6.1), rtracklayer (>= 1.14.1), ChIPpeakAnno (>= 2.2.0), VariantAnnotation, plyr, snpStats, ggplot2 (>= 0.9.0), reshape (>= 0.8.4), scales Suggests: org.Hs.eg.db Enhances: parallel License: GPL-3 MD5sum: 630eebac20ca5bb99931083cd3c61734 NeedsCompilation: no Package: funtooNorm Version: 1.10.0 Depends: R(>= 3.4) Imports: pls, matrixStats, minfi, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb, grDevices, graphics, stats Suggests: prettydoc, minfiData, knitr, rmarkdown License: GPL-3 MD5sum: 3197c1dd33d4736f5fa37b955fbd42c9 NeedsCompilation: no Package: GA4GHclient Version: 1.10.0 Depends: S4Vectors Imports: BiocGenerics, Biostrings, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, methods, VariantAnnotation Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 33a15f83d7b3c7728cc7cec7c0e19805 NeedsCompilation: no Package: GA4GHshiny Version: 1.8.0 Depends: GA4GHclient Imports: AnnotationDbi, BiocGenerics, dplyr, DT, GenomeInfoDb, openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny, shinyjs, tidyr, shinythemes Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 07797b0eb6302428914df94887ed62f3 NeedsCompilation: no Package: gaga Version: 2.32.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: parallel License: GPL (>= 2) MD5sum: 7fe14f50aca1d741dc7a7aced43403e9 NeedsCompilation: yes Package: gage Version: 2.36.0 Depends: R (>= 2.10) Imports: graph, KEGGREST, AnnotationDbi Suggests: pathview, gageData, GO.db, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq, DESeq2, edgeR, limma License: GPL (>= 2.0) MD5sum: 5e81b50bc80e002eb0070c620d5299d6 NeedsCompilation: no Package: gaggle Version: 1.54.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>= 0.4.17) License: GPL (>= 2) MD5sum: 56418fb53779bbfdd1685f2540446181 NeedsCompilation: no Package: gaia Version: 2.30.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: 0a4a037fe542ff91ca4b884ceca707ca NeedsCompilation: no Package: GAPGOM Version: 1.2.0 Depends: R (>= 3.6.0) Imports: stats, utils, methods, Matrix, fastmatch, plyr, dplyr, magrittr, data.table, igraph, graph, RBGL, GO.db, org.Hs.eg.db, org.Mm.eg.db, GOSemSim, GEOquery, AnnotationDbi, Biobase, BiocFileCache, matrixStats Suggests: org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Dr.eg.db, org.Ce.eg.db, org.At.tair.db, org.EcK12.eg.db, org.Bt.eg.db, org.Cf.eg.db, org.Ag.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Pt.eg.db, org.Pf.plasmo.db, org.Mmu.eg.db, org.Ss.eg.db, org.Xl.eg.db, testthat, pryr, knitr, rmarkdown, prettydoc, ggplot2, kableExtra, profvis, reshape2 License: MIT + file LICENSE MD5sum: 80c85b252f189d38fc87dfd90b5a28f6 NeedsCompilation: no Package: GAprediction Version: 1.12.0 Depends: R (>= 3.3) Imports: glmnet, stats, utils, Matrix Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: e787e47d7e66b27eaf0120ce279b28ac NeedsCompilation: no Package: garfield Version: 1.14.0 Suggests: knitr License: GPL-3 MD5sum: 5bea2098a03e413b9814cfbabe75e360 NeedsCompilation: yes Package: GARS Version: 1.6.0 Depends: R (>= 3.5), ggplot2, cluster Imports: DaMiRseq, MLSeq, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 3ab0ba2bb49e2503a266da0cd7b89d03 NeedsCompilation: no Package: GateFinder Version: 1.6.0 Imports: splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: ba0c5250f2b86b940509038029017fdd NeedsCompilation: no Package: gcapc Version: 1.10.0 Depends: R (>= 3.4) Imports: BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings, BSgenome, GenomicRanges, Rsamtools, GenomicAlignments, matrixStats, MASS, splines, grDevices, graphics, stats, methods Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: GPL-3 MD5sum: 0db687d4176302902d1e0a63a77a8dab NeedsCompilation: no Package: gcatest Version: 1.16.0 Depends: R (>= 3.2) Imports: lfa Suggests: knitr, ggplot2 License: GPL-3 MD5sum: 3a185d45ed564ef8b63e7a060311ebfa NeedsCompilation: yes Package: gCMAP Version: 1.30.0 Depends: GSEABase, limma (>= 3.20.0) Imports: Biobase, methods, GSEAlm, Category, Matrix (>= 1.0.9), parallel, annotate, genefilter, AnnotationDbi, DESeq, grDevices, graphics, stats, utils, bigmemory, bigmemoryExtras (>= 1.1.2) Suggests: BiocGenerics, KEGG.db, reactome.db, RUnit, GO.db, mgsa License: Artistic-2.0 OS_type: unix MD5sum: 3611402da38904edbb197c8f6e4ea08c NeedsCompilation: no Package: gCMAPWeb Version: 1.26.0 Depends: Biobase, gCMAP (>= 1.3.0), methods, R (>= 3.4), Rook Imports: brew, BiocGenerics, annotate, AnnotationDbi, graphics, grDevices, GSEABase, hwriter, parallel, stats, utils, yaml Suggests: affy, ArrayExpress, hgfocus.db, hgu133a.db, mgug4104a.db, org.Hs.eg.db, org.Mm.eg.db, RUnit Enhances: bigmemory, bigmemoryExtras License: Artistic-2.0 OS_type: unix MD5sum: 5595d509d6189389a5667e7b340b0965 NeedsCompilation: no Package: gCrisprTools Version: 1.14.0 Depends: R (>= 3.3) Imports: Biobase, limma, RobustRankAggreg, ggplot2, PANTHER.db, rmarkdown, grDevices, graphics, stats, utils, parallel Suggests: edgeR, knitr, grid, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 9975ef9ec0c42cf8cebc5f9b4eba532f NeedsCompilation: no Package: gcrma Version: 2.58.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector, Biostrings (>= 2.11.32), splines, BiocManager Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL MD5sum: eebdd0da64c4b0d92b22af22168f03fd NeedsCompilation: yes Package: GCSscore Version: 1.0.0 Depends: R (>= 3.6) Imports: BiocManager, Biobase, utils, methods, RSQLite, AnnotationForge, devtools, dplR, stringr, graphics, stats, affxparser, data.table License: GPL (>= 3) MD5sum: 18c6008719935e67feff81853d4125c9 NeedsCompilation: no Package: GDCRNATools Version: 1.6.0 Depends: R (>= 3.5.0) Imports: shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel Suggests: knitr, testthat License: Artistic-2.0 MD5sum: bf32fbeb6874845e8397f932f41e9aff NeedsCompilation: no Package: GDSArray Version: 1.6.0 Depends: R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>= 0.5.32) Imports: tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray Suggests: testthat, knitr, BiocStyle, BiocManager License: GPL-3 MD5sum: f3a5ebb545320529c94adc320cd79afd NeedsCompilation: no Package: gdsfmt Version: 1.22.0 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, crayon, RUnit, knitr, BiocGenerics License: LGPL-3 MD5sum: e57f542e1fd0dc7b6be4cf3d610e324d NeedsCompilation: yes Package: geecc Version: 1.20.0 Depends: R (>= 3.3.0), methods Imports: MASS, hypergea (>= 1.3.0), gplots, Rcpp (>= 0.11.3), graphics, stats, utils LinkingTo: Rcpp Suggests: hgu133plus2.db, GO.db, AnnotationDbi License: GPL (>= 2) MD5sum: c53dd77ed87ff9458ef6a9b75558df5b NeedsCompilation: yes Package: GEM Version: 1.12.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics License: Artistic-2.0 MD5sum: 610d496c0d3a5262756fdf2a03dc2c80 NeedsCompilation: no Package: gemini Version: 1.0.0 Depends: R (>= 3.6.0) Imports: dplyr, grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 8ac72cd8ca83e11d225e5a40e302ad5a NeedsCompilation: no Package: genArise Version: 1.62.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: cec96e4b7460a6cf185faae83971eafa NeedsCompilation: no Package: genbankr Version: 1.14.0 Depends: methods Imports: BiocGenerics, IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), GenomicFeatures (>= 1.31.5), Biostrings, VariantAnnotation, rtracklayer, S4Vectors (>= 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org.Hs.eg.db, BiocGenerics, GenomeInfoDb, GenomicFeatures, IRanges, rtracklayer Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: e81d6f83fce4728c87d0a5d343aa41e2 NeedsCompilation: no Package: GeneBreak Version: 1.16.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: 33bd1ffc50de66e3152d86f26a4f2093 NeedsCompilation: no Package: geneClassifiers Version: 1.10.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: 245cd31e22585b33eab5e5ec6de96aae NeedsCompilation: no Package: GeneExpressionSignature Version: 1.32.0 Depends: R (>= 2.13), Biobase, PGSEA Suggests: apcluster,GEOquery License: GPL-2 MD5sum: 7bcd17aad804b94684e8d35659efcacf NeedsCompilation: no Package: genefilter Version: 1.68.0 Imports: BiocGenerics (>= 0.31.2), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 MD5sum: 7230c58b5b6d7ea99296a1a5e1da96c9 NeedsCompilation: yes Package: genefu Version: 2.18.1 Depends: survcomp, mclust, limma, biomaRt, iC10, AIMS, R (>= 2.10) Imports: amap, impute Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival License: Artistic-2.0 MD5sum: d9fdd36bd1a91aed72df6ec23701f23c NeedsCompilation: no Package: GeneGA Version: 1.36.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: 5a0862300f31b66f65b80d87b7c9e544 NeedsCompilation: no Package: GeneGeneInteR Version: 1.12.0 Depends: R (>= 3.5) Imports: snpStats, mvtnorm, GGtools, Rsamtools, igraph, kernlab, FactoMineR, plspm, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods License: GPL (>= 2) MD5sum: 3062693e1333045c529a55dfefdec343 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BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: 7bb06e9cbedc1412c956bc0d7e77fa9d NeedsCompilation: no Package: geneplotter Version: 1.64.0 Depends: R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate Imports: AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db License: Artistic-2.0 MD5sum: 44ee8c53a3daa6e0564b7cf13988a488 NeedsCompilation: no Package: geneRecommender Version: 1.58.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: ed64747892fbd596f6415f7ce4c3754d NeedsCompilation: no Package: GeneRegionScan Version: 1.42.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) MD5sum: 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Imports: Biostrings,GenomicRanges,IRanges,data.table,plyr,stringdist,stringr,S4Vectors,BSgenome.Mmusculus.UCSC.mm10,stats,utils,Gviz,rtracklayer,methods Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 7573793df01224cf512a313eea14e5e9 NeedsCompilation: no Package: geNetClassifier Version: 1.26.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) MD5sum: 4c8f609e9c8292aa8d1c3155c0413e5c NeedsCompilation: no Package: GeneticsDesign Version: 1.54.0 Imports: gmodels, graphics, gtools (>= 2.4.0), mvtnorm, stats License: GPL-2 MD5sum: 544e1731be7163ac7106ea6af379759c NeedsCompilation: no Package: GeneticsPed Version: 1.48.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: 0eed7a10dc5820cd22d0dbad1dfdf0c7 NeedsCompilation: yes Package: geneXtendeR Version: 1.12.0 Depends: rtracklayer, GO.db, R (>= 3.5.0) Imports: data.table, dplyr, graphics, networkD3, RColorBrewer, SnowballC, tm, utils, wordcloud, AnnotationDbi, BiocStyle, org.Rn.eg.db Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer License: GPL (>= 3) MD5sum: ff35d4bc4dbfa17698de0b02493b42de NeedsCompilation: yes Package: GENIE3 Version: 1.8.0 Imports: stats, reshape2 Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods License: GPL (>= 2) MD5sum: 229e576a21ba8c55d9f43a4955afbe85 NeedsCompilation: yes Package: genoCN Version: 1.38.0 Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: 3da29c5c79318ecec77567b3d05b1612 NeedsCompilation: yes Package: GenoGAM Version: 2.4.0 Depends: R (>= 3.5), SummarizedExperiment (>= 1.1.19), HDF5Array (>= 1.8.0), rhdf5 (>= 2.21.6), S4Vectors (>= 0.23.18), Matrix (>= 1.2-8), data.table (>= 1.9.4) Imports: Rcpp (>= 0.12.14), sparseinv (>= 0.1.1), Rsamtools (>= 1.18.2), GenomicRanges (>= 1.23.16), BiocParallel (>= 1.5.17), DESeq2 (>= 1.11.23), futile.logger (>= 1.4.1), GenomeInfoDb (>= 1.7.6), GenomicAlignments (>= 1.7.17), IRanges (>= 2.5.30), Biostrings (>= 2.39.14), DelayedArray (>= 0.3.19), methods, stats LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, chipseq (>= 1.21.2), LSD (>= 3.0.0), genefilter (>= 1.54.2), ggplot2 (>= 2.1.0), testthat, knitr, rmarkdown License: GPL-2 MD5sum: 3ef3d724ec8e9f92de3a781a01343a69 NeedsCompilation: yes Package: genomation Version: 1.18.0 Depends: R (>= 3.0.0),grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), RUnit, Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown License: Artistic-2.0 MD5sum: 67f92320f24a839fc870940775330607 NeedsCompilation: yes Package: GenomeGraphs Version: 1.46.0 Depends: R (>= 2.10), methods, biomaRt, grid License: Artistic-2.0 MD5sum: 431337c4b88464c4ad8d2753db69e546 NeedsCompilation: no Package: GenomeInfoDb Version: 1.22.1 Depends: R (>= 3.1), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12) Imports: stats, stats4, utils, RCurl, GenomeInfoDbData Suggests: GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 3fdc0c86b77fd0ac96f17ff37d974f03 NeedsCompilation: no Package: genomeIntervals Version: 1.42.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 1.5.8), GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: 01f41a46768b8c4f72557eeb3634c984 NeedsCompilation: no Package: genomes Version: 3.16.0 Depends: readr, curl License: GPL-3 MD5sum: 8dfe7fa325bf5d234643ad8136c1e131 NeedsCompilation: no Package: GenomicAlignments Version: 1.22.1 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.23.19), IRanges (>= 2.15.12), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.37.2), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 6fb92061c3ffbeb89423f731f662f9d1 NeedsCompilation: yes Package: GenomicDataCommons Version: 1.10.0 Depends: R (>= 3.4.0), magrittr Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, SummarizedExperiment, S4Vectors, tibble Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools License: Artistic-2.0 MD5sum: 46239b3fc502a1f5464f7bdad0cdb1b9 NeedsCompilation: no Package: GenomicFeatures Version: 1.38.2 Depends: BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29), IRanges (>= 2.13.23), GenomeInfoDb (>= 1.15.4), GenomicRanges (>= 1.31.17), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl, XVector (>= 0.19.7), Biostrings (>= 2.47.6), rtracklayer (>= 1.39.7), biomaRt (>= 2.17.1), Biobase (>= 2.15.1) Suggests: RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: b4afee3b93fd793d848f03c494411462 NeedsCompilation: no Package: GenomicFiles Version: 1.22.0 Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), GenomicRanges (>= 1.31.16), SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3) Imports: GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25), VariantAnnotation (>= 1.27.9), GenomeInfoDb Suggests: BiocStyle, RUnit, genefilter, deepSNV, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens License: Artistic-2.0 MD5sum: d3e841e39f7505dfc9c8aa2711b09802 NeedsCompilation: no Package: GenomicInteractions Version: 1.20.3 Depends: R (>= 3.5), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices Suggests: knitr, BiocStyle, testthat License: GPL-3 MD5sum: 642e819a0d7df5c5da8b2f2bac3c4851 NeedsCompilation: no Package: GenomicOZone Version: 1.0.0 Depends: R (>= 3.6), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2 Imports: grDevices, stats, utils, plyr, gridExtra, sjstats, parallel, ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack Suggests: readxl, GEOquery, knitr, rmarkdown License: LGPL (>= 3) MD5sum: 00f14e9476303d3dfd60e98674038ec4 NeedsCompilation: no Package: GenomicRanges Version: 1.38.0 Depends: R (>= 2.10), methods, stats4, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.23.19), IRanges (>= 2.19.9), GenomeInfoDb (>= 1.15.2) Imports: utils, stats, XVector (>= 0.19.8) LinkingTo: S4Vectors, IRanges Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, BiocStyle License: Artistic-2.0 MD5sum: 1cee38e912a367f89297097a1cdbfdb2 NeedsCompilation: yes Package: GenomicScores Version: 1.10.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: utils, XML, Biobase, IRanges (>= 2.3.23), Biostrings, BSgenome, GenomeInfoDb, AnnotationHub Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5, SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer License: Artistic-2.0 MD5sum: c21fbb5652aa5017f81352ff4e20e914 NeedsCompilation: no Package: GenomicTuples Version: 1.20.0 Depends: R (>= 3.3.0), GenomicRanges (>= 1.37.4), GenomeInfoDb (>= 1.15.2), S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4 LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: e3b932960895f76747ee54d5cbcd1751 NeedsCompilation: yes Package: Genominator Version: 1.40.0 Depends: R (>= 2.10), methods, RSQLite, DBI (>= 0.2-5), BiocGenerics (>= 0.1.0), IRanges (>= 2.5.27), GenomeGraphs Imports: graphics, stats, utils Suggests: biomaRt, ShortRead, yeastRNASeq License: Artistic-2.0 MD5sum: 6a2344af8d7d6d8e5d8306ecb12260d7 NeedsCompilation: no Package: genoset Version: 1.42.0 Depends: R (>= 2.10), BiocGenerics (>= 0.11.3), GenomicRanges (>= 1.17.19), SummarizedExperiment (>= 1.1.6) Imports: S4Vectors (>= 0.23.18), GenomeInfoDb (>= 1.1.3), IRanges (>= 2.5.12), methods, graphics Suggests: testthat, knitr, BiocStyle, rmarkdown, DNAcopy, stats, BSgenome, Biostrings Enhances: parallel License: Artistic-2.0 MD5sum: 0b156cf6d3a2794a02fd4a6ae9ef60de NeedsCompilation: yes Package: genotypeeval Version: 1.18.0 Depends: R (>= 3.4.0), VariantAnnotation Imports: ggplot2, rtracklayer, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, methods, BiocParallel, graphics, stats Suggests: rmarkdown, testthat, SNPlocs.Hsapiens.dbSNP141.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: b196ca7302a91ddfbf5af12223313a2b NeedsCompilation: no Package: genphen Version: 1.14.0 Depends: R (>= 3.5.0), Rcpp (>= 0.12.17), methods, stats, graphics Imports: rstan (>= 2.17.3), ranger, parallel, foreach, doParallel, e1071, Biostrings, rPref Suggests: testthat, ggplot2, gridExtra, ape, ggrepel, knitr, reshape, xtable License: GPL (>= 2) MD5sum: 11dfb801e7622369d7783a23938dd7dd NeedsCompilation: no Package: GenRank Version: 1.14.0 Depends: R (>= 3.2.3) Imports: matrixStats, reshape2, survcomp Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 6ef2edd846f9e051960741bed3c71f29 NeedsCompilation: no Package: GenVisR Version: 1.18.1 Depends: R (>= 3.3.0), methods Imports: AnnotationDbi, biomaRt, BiocGenerics, Biostrings, DBI, FField, GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), grid, gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, stats, utils, viridis, data.table, BSgenome, grDevices, GenomeInfoDb, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 + file LICENSE MD5sum: 10d6170755acfdfe634ebf409a036aad NeedsCompilation: no Package: GEOmetadb Version: 1.48.0 Depends: GEOquery,RSQLite Suggests: knitr, rmarkdown, dplyr, tm, wordcloud License: Artistic-2.0 MD5sum: 81fa87021bf28ed54504952d4d5d2805 NeedsCompilation: no Package: GEOquery Version: 2.54.1 Depends: methods, Biobase Imports: httr, readr (>= 1.3.1), xml2, dplyr, tidyr, magrittr, limma Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr License: GPL-2 MD5sum: 83b7e177214cc471e8a9265317aa4dde NeedsCompilation: no Package: GEOsubmission Version: 1.38.0 Imports: affy, Biobase, utils License: GPL (>= 2) MD5sum: 0cc56604a506fe5d12f80d742d4ff3c2 NeedsCompilation: no Package: gep2pep Version: 1.6.0 Imports: repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators Suggests: WriteXLS, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 2773a95f5bbe50a1e81bc46d7b2dc634 NeedsCompilation: no Package: gespeR Version: 1.18.0 Depends: methods, graphics, ggplot2, R(>= 2.10) Imports: Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel, parallel, foreach, reshape2, dplyr Suggests: knitr License: GPL-3 MD5sum: dc27a63afa1adefb273115109519bbf8 NeedsCompilation: no Package: GEWIST Version: 1.30.0 Depends: R (>= 2.10), car License: GPL-2 MD5sum: 08eb40e85cb57f0051230c9520427b35 NeedsCompilation: no Package: GGBase Version: 3.48.0 Depends: R (>= 2.14), methods, snpStats Imports: limma, genefilter, Biobase, BiocGenerics, S4Vectors, IRanges, Matrix, AnnotationDbi, digest, GenomicRanges, SummarizedExperiment Suggests: GGtools, illuminaHumanv1.db, knitr License: Artistic-2.0 MD5sum: 951b3a2da50ad58ff26011e29ce0c797 NeedsCompilation: no Package: ggbio Version: 1.34.0 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.29.14), SummarizedExperiment, Biostrings, Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer (>= 1.25.16), GenomicFeatures (>= 1.29.11), OrganismDbi, GGally, ensembldb (>= 1.99.13), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: c14b3c14020fb81a529d6c5c1d213368 NeedsCompilation: no Package: ggcyto Version: 1.14.1 Depends: methods, ggplot2(>= 3.3.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 3.33.1) Imports: plyr, scales, data.table, RColorBrewer, gridExtra, rlang Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr License: Artistic-2.0 MD5sum: 6dc7dcfb30f3337a4c31b45a96574c74 NeedsCompilation: no Package: GGtools Version: 5.22.0 Depends: R (>= 2.14), GGBase (>= 3.19.7), data.table, parallel, Homo.sapiens Imports: methods, utils, stats, BiocGenerics (>= 0.25.1), snpStats, ff, Rsamtools, AnnotationDbi, Biobase, bit, VariantAnnotation, hexbin, rtracklayer, Gviz, stats4, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges (>= 1.29.6), iterators, Biostrings, ROCR, biglm, ggplot2, reshape2 Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37, multtest, aod, rmeta Enhances: MatrixEQTL, foreach, doParallel, gwascat License: Artistic-2.0 MD5sum: 82eeed4df6faa345e8f9e350d57f74ca NeedsCompilation: no Package: ggtree Version: 2.0.4 Depends: R (>= 3.4.0) Imports: ape, dplyr, ggplot2 (>= 3.0.0), grid, magrittr, methods, purrr, rlang, rvcheck, tidyr, tidytree (>= 0.2.6), treeio (>= 1.8.0), utils Suggests: emojifont, ggimage, ggplotify, grDevices, knitr, prettydoc, rmarkdown, scales, stats, testthat, tibble License: Artistic-2.0 MD5sum: e41db4ee9a7bab9012e97bffe294d40f NeedsCompilation: no Package: GIGSEA Version: 1.4.0 Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils Suggests: knitr, rmarkdown License: LGPL-3 MD5sum: 202dc84a2e54b9e073dfcf1cc426ff8a NeedsCompilation: no Package: girafe Version: 1.38.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), Rsamtools (>= 1.31.2), intervals (>= 0.13.1), ShortRead (>= 1.37.1), genomeIntervals (>= 1.25.1), grid Imports: methods, Biobase, Biostrings (>= 2.47.6), graphics, grDevices, stats, utils, IRanges (>= 2.13.12) Suggests: MASS, org.Mm.eg.db, RColorBrewer Enhances: genomeIntervals License: Artistic-2.0 MD5sum: f7a140bbe1ce6a52b090d5196df00129 NeedsCompilation: yes Package: GISPA Version: 1.10.0 Depends: R (>= 3.3.2) Imports: Biobase, changepoint, data.table, genefilter, graphics, GSEABase, HH, lattice, latticeExtra, plyr, scatterplot3d, stats Suggests: knitr License: GPL-2 MD5sum: 542aa47b58946e5ee40262d610cac904 NeedsCompilation: no Package: GLAD Version: 2.50.0 Depends: R (>= 2.10) Imports: aws License: GPL-2 MD5sum: 20f690eaa7a178117b04ad58f63a862d NeedsCompilation: yes Package: GladiaTOX Version: 1.2.0 Depends: R (>= 3.6.0), data.table (>= 1.9.4) Imports: DBI, RMySQL, RSQLite, numDeriv, RColorBrewer, parallel, stats, methods, graphics, grDevices, xtable, tools, brew, stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: d50fc47c7603f926b7835bb81b6b8095 NeedsCompilation: no Package: Glimma Version: 1.14.0 Depends: R (>= 3.4.0) Imports: edgeR, grDevices, jsonlite, methods, stats, S4Vectors, utils Suggests: BiocStyle, IRanges, GenomicRanges, SummarizedExperiment, DESeq2, limma, testthat, knitr, rmarkdown, pryr License: GPL-3 | file LICENSE MD5sum: cbaccdb212bd00b5fc62ff41e9426145 NeedsCompilation: no Package: glmSparseNet Version: 1.4.0 Depends: R (>= 3.5), Matrix, MultiAssayExperiment, glmnet Imports: SummarizedExperiment, STRINGdb, biomaRt, futile.logger, sparsebn, sparsebnUtils, forcats, dplyr, readr, ggplot2, survminer, reshape2, stats, stringr, rlang, parallel, methods, loose.rock (>= 1.0.12) Suggests: testthat, knitr, rmarkdown, survival, survcomp, pROC, VennDiagram, BiocStyle, curatedTCGAData, TCGAutils License: GPL (>= 3) MD5sum: aaef0f9d13d40b540c61b3c96c0eae4f NeedsCompilation: no Package: GlobalAncova Version: 4.4.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, KEGG.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: 756487a87919a0a913b6003560fc57f4 NeedsCompilation: yes Package: globalSeq Version: 1.14.0 Depends: R (>= 3.5.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 MD5sum: aad82a1fb2429ee03092cf81b3074de8 NeedsCompilation: no Package: globaltest Version: 5.40.0 Depends: methods, survival Imports: Biobase, AnnotationDbi, annotate, graphics Suggests: vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart, mstate License: GPL (>= 2) MD5sum: 07a7f70811bb9210ebac185a8be0e040 NeedsCompilation: no Package: gmapR Version: 1.28.0 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2) Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome, GenomicAlignments (>= 1.15.6), BiocParallel Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines License: Artistic-2.0 MD5sum: 9c4474292a223a706376374d03a2b429 NeedsCompilation: yes Package: GmicR Version: 1.0.6 Imports: AnnotationDbi, ape, bnlearn, Category, DT, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db, org.Mm.eg.db, reshape2, shiny, WGCNA, data.table, grDevices, graphics, stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 + file LICENSE MD5sum: 995b96feaaef0a2c30092e3490bf1fab NeedsCompilation: no Package: GMRP Version: 1.14.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: b894f4d088c05901860ddee4e950374c NeedsCompilation: no Package: GNET2 Version: 1.2.0 Depends: R (>= 3.6) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 MD5sum: c00561da14adbb304f9c989638a86776 NeedsCompilation: yes Package: GOexpress Version: 1.20.0 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 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dendextend, doParallel, foreach, parallel, org.Hs.eg.db, GO.db, Rcpp, stats, graphics, MultiAssayExperiment, IRanges, S4Vectors LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat License: GPL-3 MD5sum: 4e7052da47f62339372573f78994be75 NeedsCompilation: yes Package: goProfiles Version: 1.48.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: 365fbbdce68290c7a75bf19789f69eb4 NeedsCompilation: no Package: GOSemSim Version: 2.12.1 Depends: R (>= 3.4.0) Imports: AnnotationDbi, GO.db, methods, utils LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, testthat License: Artistic-2.0 MD5sum: 9f8945c8578a7c3d22a8c1d4b0a4c7d6 NeedsCompilation: yes Package: goseq Version: 1.38.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2) Imports: mgcv, graphics, stats, utils, AnnotationDbi, GO.db,BiocGenerics Suggests: edgeR, org.Hs.eg.db, 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TxDb.Hsapiens.UCSC.hg38.knownGene, Imports: igraph, biomaRt, Rcpp, data.table, OrganismDbi, AnnotationDbi, grDevices, stats, utils, GenomicRanges, IRanges LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 31ed1a5c8b4b1300d42ef17cb5415ac2 NeedsCompilation: yes Package: gpls Version: 1.58.0 Imports: stats Suggests: MASS License: Artistic-2.0 MD5sum: d06b2d565bae224541a87685a85b4149 NeedsCompilation: no Package: gprege Version: 1.30.0 Depends: R (>= 2.10), gptk Suggests: spam License: AGPL-3 MD5sum: 7e09902bcd183fa9475752a8e90b5b5d NeedsCompilation: no Package: gQTLBase Version: 1.18.0 Imports: GenomicRanges, methods, BatchJobs, BBmisc, S4Vectors, BiocGenerics, foreach, doParallel, bit, ff, rtracklayer, ffbase, GenomicFiles, SummarizedExperiment Suggests: geuvStore2, knitr, rmarkdown, BiocStyle, RUnit, GGtools, Homo.sapiens, IRanges, erma, GenomeInfoDb, gwascat, geuvPack License: Artistic-2.0 MD5sum: 191261e2ca486bc541118536afaf5337 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checkmate, graph, httr, rappdirs, stats, utils Suggests: a4Preproc, ALL, BiocStyle, clipper, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) License: AGPL-3 MD5sum: 828080683364be145dde282bb78aeaa1 NeedsCompilation: no Package: GraphPAC Version: 1.28.0 Depends: R(>= 2.15),iPAC, igraph, TSP, RMallow Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 521b3fe0ef2c631e65aba2364553e735 NeedsCompilation: no Package: GRENITS Version: 1.38.0 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: e836c11b62b1f5bfed1128eb75465125 NeedsCompilation: yes Package: GreyListChIP Version: 1.18.0 Depends: R (>= 3.5), methods, GenomicRanges Imports: GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, 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NeedsCompilation: no Package: Guitar Version: 2.2.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges, magrittr, ggplot2, methods, stats,utils ,knitr,dplyr License: GPL-2 MD5sum: 97a0c98414ea86dd5a0a60699418dc61 NeedsCompilation: no Package: Gviz Version: 1.30.3 Depends: R (>= 2.10.0), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.17.20), grid Imports: XVector (>= 0.5.7), rtracklayer (>= 1.25.13), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.17.22), BSgenome (>= 1.33.1), Biostrings (>= 2.33.11), biovizBase (>= 1.13.8), Rsamtools (>= 1.17.28), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>= 1.1.16), GenomeInfoDb (>= 1.1.3), BiocGenerics (>= 0.11.3), digest(>= 0.6.8) Suggests: BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: c657fab644afbac73fbde590ffcd685f NeedsCompilation: no Package: gwascat Version: 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BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva License: GPL-3 + file LICENCE MD5sum: 143dbee8ffaa73680e5df1288775be49 NeedsCompilation: yes Package: Harshlight Version: 1.58.0 Depends: R (>= 2.10) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) MD5sum: 6ffd19901e6bfc2dba65647adcdf1d7b NeedsCompilation: yes Package: HCABrowser Version: 1.2.0 Depends: R (>= 3.6.0), dplyr Imports: BiocFileCache, S4Vectors, curl, googleAuthR, httr, jsonlite, methods, plyr, readr, rlang, stringr, tibble, tidygraph, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 9b388c068b5952c3bf74231b10325e22 NeedsCompilation: no Package: HCAExplorer Version: 1.0.0 Depends: R (>= 3.6.0), dplyr Imports: S4Vectors, vctrs, curl, httr, jsonlite, methods, plyr, rlang, tibble, tidygraph, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0) License: Artistic-2.0 MD5sum: 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BiocParallel, grDevices, base64enc, methods Suggests: testthat, BiocStyle, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR License: MIT + file LICENSE MD5sum: bd8708b147fbde697c93fbf7be302faf NeedsCompilation: no Package: IdeoViz Version: 1.22.0 Depends: Biobase, IRanges, GenomicRanges, RColorBrewer, rtracklayer,graphics,GenomeInfoDb License: GPL-2 MD5sum: 9fa2e4e8864e11572efd3a9f4378f8db NeedsCompilation: no Package: idiogram Version: 1.62.0 Depends: R (>= 2.10), methods, Biobase, annotate, plotrix Suggests: hu6800.db, hgu95av2.db, golubEsets License: GPL-2 MD5sum: fbc280c9b6aedada6a339e29edb7166e NeedsCompilation: no Package: IdMappingAnalysis Version: 1.30.0 Depends: R (>= 2.14), R.oo (>= 1.13.0), rChoiceDialogs Imports: boot, mclust, RColorBrewer, Biobase License: GPL-2 MD5sum: afaa1ce733d68fd9a5ca194ad775da85 NeedsCompilation: no Package: IdMappingRetrieval Version: 1.34.0 Depends: R.oo, XML, RCurl, rChoiceDialogs Imports: biomaRt, ENVISIONQuery, 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GenomicRanges, SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer, metagenomeSeq, gplots, vegan, Biobase Enhances: rstudio License: Artistic-2.0 MD5sum: b3c93dbb117b1488a2456dca84edbdf7 NeedsCompilation: no Package: interactiveDisplayBase Version: 1.24.0 Depends: R (>= 2.10), methods, BiocGenerics Imports: shiny Suggests: knitr Enhances: rstudioapi License: Artistic-2.0 MD5sum: c0c12ee30f198c1db5a24955efda2f5d NeedsCompilation: no Package: IntEREst Version: 1.10.2 Depends: R (>= 3.4), GenomicRanges, Rsamtools, SummarizedExperiment, edgeR, S4Vectors Imports: seqLogo, Biostrings, GenomicFeatures, IRanges, seqinr, graphics, grDevices, stats, utils, grid, methods, DBI, RMySQL, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2 Suggests: clinfun, knitr, BSgenome.Hsapiens.UCSC.hg19 License: GPL-2 MD5sum: 32a3edb92fc61047f3013fd959144322 NeedsCompilation: no Package: InterMineR Version: 1.8.1 Depends: R (>= 3.4.1) Imports: Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, 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License: GPL (>= 2) MD5sum: 53fcecdc49a39209cbc26517ba833d8f NeedsCompilation: no Package: methyAnalysis Version: 1.28.0 Depends: R (>= 2.10), grid, BiocGenerics, IRanges, GenomeInfoDb, GenomicRanges, Biobase (>= 2.34.0), org.Hs.eg.db Imports: grDevices, stats, utils, lumi, methylumi, Gviz, genoset, SummarizedExperiment, IRanges, GenomicRanges, VariantAnnotation, rtracklayer, GenomicFeatures, annotate, Biobase (>= 2.5.5), AnnotationDbi, genefilter, biomaRt, methods, parallel Suggests: FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: d828e1a53c9b284cdea7b5879c27a744 NeedsCompilation: no Package: MethylAid Version: 1.20.0 Depends: R (>= 3.4) Imports: Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: 1f0409f92a419006303b518efb0ce7ee NeedsCompilation: no Package: methylCC Version: 1.0.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: CC BY 4.0 MD5sum: 379b27d0b20f977bd53838bd4e216c86 NeedsCompilation: no Package: methylGSA Version: 1.4.9 Depends: R (>= 3.5) Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, shiny, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr, rmarkdown, testthat, enrichplot License: GPL-2 MD5sum: ab5f82ad569dea88da61e915e8a02626 NeedsCompilation: no Package: methylInheritance Version: 1.10.0 Depends: R (>= 3.5) Imports: methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors, methods, parallel, ggplot2, gridExtra, rebus Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim License: Artistic-2.0 MD5sum: 4c0e6f0f005ed4e8cf365c38268b6fb9 NeedsCompilation: no Package: methylKit Version: 1.12.0 Depends: R (>= 3.3.0), GenomicRanges (>= 1.18.1), methods Imports: IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>= 0.13.13), GenomeInfoDb, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat,knitr, rmarkdown, genomation, BiocManager License: Artistic-2.0 MD5sum: 5c85fe9214f8269edfce8137944eb52f NeedsCompilation: yes Package: MethylMix Version: 2.16.0 Depends: R (>= 3.2.0) Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown License: GPL-2 MD5sum: 546ce7cae0655dfa35fbfbd2f63489ba NeedsCompilation: no Package: methylMnM Version: 1.24.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: 90eb32c9e1f3c0b2443466468a0aa7e5 NeedsCompilation: yes Package: methylPipe Version: 1.20.0 Depends: R (>= 3.2.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) MD5sum: eddecfb8e8c22cfbab97f720d49dbb96 NeedsCompilation: yes Package: MethylSeekR Version: 1.26.0 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) MD5sum: 08594097ebb798c3c5e2e7daf2fd7556 NeedsCompilation: no Package: methylumi Version: 2.32.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, methyAnalysis, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 MD5sum: 57d9b0e72e0145434c3f90c4dd2fd680 NeedsCompilation: no Package: methyvim Version: 1.8.0 Depends: R (>= 3.4.0) Imports: stats, cluster, methods, ggplot2, ggsci, gridExtra, superheat, dplyr, gtools, tmle (>= 1.4.0.1), future, doFuture, S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, GenomeInfoDb, bumphunter, IRanges, limma, minfi Suggests: testthat, knitr, rmarkdown, BiocStyle, SuperLearner, earth, nnet, gam, arm, snow, parallel, BatchJobs, minfiData, methyvimData License: file LICENSE MD5sum: 49592ffc7e7ec763810aa02bd5c0b57d NeedsCompilation: no Package: MetID Version: 1.4.0 Depends: R (>= 3.5) Imports: utils (>= 3.3.1), stats (>= 3.4.2), devtools (>= 1.13.0), stringr (>= 1.3.0), Matrix (>= 1.2-12), igraph (>= 1.2.1), ChemmineR (>= 2.30.2) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) License: Artistic-2.0 MD5sum: f8016e43fcfa54e21919e2217db34dc2 NeedsCompilation: no Package: MetNet Version: 1.4.2 Depends: R (>= 3.5) Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), GENIE3 (>= 1.7.0), methods (>= 3.5), mpmi (>= 0.42), parmigene (>= 1.0.2), ppcor (>= 1.1), sna (>= 2.4), stabs (>= 0.6), stats (>= 3.6) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 2.0-18), igraph (>= 1.1.2), knitr 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methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: 5a8415a83d63b6689df8f88545716501 NeedsCompilation: yes Package: MiChip Version: 1.40.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: e876b00dedff1e52ef1f74aa53754f18 NeedsCompilation: no Package: microbiome Version: 1.8.0 Depends: R (>= 3.3.0), phyloseq, ggplot2 Imports: dplyr, reshape2, Rtsne, scales, stats, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitcitations, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE MD5sum: bad34f19360b750f8ac6643ce2a6c5c8 NeedsCompilation: no Package: microbiomeDASim Version: 1.0.0 Depends: R (>= 3.6.0) Imports: graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats Suggests: testthat (>= 2.1.0), knitr, devtools License: MIT + file LICENSE MD5sum: a946db90bbc40630bbd5d0a044088717 NeedsCompilation: no Package: microRNA Version: 1.44.0 Depends: R (>= 2.10) Imports: 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LICENSE MD5sum: cadc6fde8b95303022ad589b74fcdfa3 NeedsCompilation: no Package: MIMOSA Version: 1.24.0 Depends: R (>= 3.0.2), MASS, plyr, reshape, Biobase, ggplot2 Imports: methods, Formula, data.table, pracma, MCMCpack, coda, modeest, testthat, Rcpp, scales, LinkingTo: Rcpp, RcppArmadillo Suggests: parallel, knitr License: Artistic-2.0 MD5sum: 11a68963e17d75bd8dc8c40d98ccee4c NeedsCompilation: yes Package: MineICA Version: 1.26.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX Enhances: doMC License: GPL-2 MD5sum: 64b9d80b136635afa6cddf868239414d NeedsCompilation: no Package: minet Version: 3.44.1 Imports: 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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 MD5sum: 07a485d8598c65452fc1af6f5a45d103 NeedsCompilation: no Package: MLSeq Version: 2.4.0 Depends: caret, ggplot2 Imports: methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, testthat, BiocStyle, VennDiagram, pamr License: GPL (>= 2) MD5sum: 2cb943dc4a7d5ccbf86ef83c94fda2ac NeedsCompilation: no Package: MMAPPR2 Version: 1.0.0 Depends: R (>= 3.6.0) Imports: ensemblVEP (>= 1.20.0), gmapR, Rsamtools, VariantAnnotation, BiocParallel, Biobase, BiocGenerics, dplyr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, tidyr, VariantTools, magrittr, methods, grDevices, graphics, stats, utils, stringr, data.table Suggests: testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle, MMAPPR2data License: GPL-3 OS_type: unix MD5sum: af68b0f8af62f38d4929de39986a6a5e NeedsCompilation: no Package: MMDiff2 Version: 1.14.0 Depends: R (>= 3.3), Rsamtools, Biobase, Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 MD5sum: 653169209bfcf633f42238a3225a5f64 NeedsCompilation: no Package: MmPalateMiRNA Version: 1.36.0 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 MD5sum: 2e66a9518fd38ced3f145b22cfd62e79 NeedsCompilation: no Package: MMUPHin Version: 1.0.0 Depends: R (>= 3.6) Imports: Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr, cowplot, utils, stats, grDevices Suggests: testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter License: MIT + file LICENSE MD5sum: 2f3b3816c123bfceabf431d639ef790f NeedsCompilation: no Package: mnem Version: 1.2.0 Depends: R (>= 3.6) Imports: cluster, nem, epiNEM, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit License: GPL-3 MD5sum: 74fdf3785b1bcdd07f94b68494ea6547 NeedsCompilation: yes Package: MODA Version: 1.12.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 51d05f3feca6bde4f0e0f4f38d62036d NeedsCompilation: no Package: Modstrings Version: 1.2.1 Depends: R (>= 3.6), Biostrings (>= 2.51.5) Imports: methods, assertive, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr 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BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP142.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle License: GPL-2 MD5sum: 235326b824fe9163b6d7a997bae37cac NeedsCompilation: no Package: motifcounter Version: 1.10.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: baec624f1247d7c85982b1fd30a2959a NeedsCompilation: yes Package: MotifDb Version: 1.28.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes MD5sum: 995a35861aeb026c36a00c1f65efe977 NeedsCompilation: no Package: motifmatchr Version: 1.8.0 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, 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grDevices, graphics, stats, doSNOW, snow, foreach, data.table, MASS, dplyr, tidyr, broom, purrr, stringr Suggests: BiocStyle, knitr, rmarkdown, MSstatsBioData License: Artistic-2.0 MD5sum: 00d09ee969adab7c63f2f988cf430545 NeedsCompilation: no Package: MSstatsQC Version: 2.4.0 Imports: dplyr,plotly,RecordLinkage,ggplot2,ggExtra, stats,grid, MSnbase, qcmetrics Suggests: knitr,rmarkdown, testthat, RforProteomics License: Artistic License 2.0 MD5sum: 91f53b4e18dc8cb7c9f057e957a46098 NeedsCompilation: no Package: MSstatsQCgui Version: 1.6.0 Imports: shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, RecordLinkage, grid Suggests: knitr License: Artistic License 2.0 MD5sum: b7c7451034c037e2019890e9028277c4 NeedsCompilation: no Package: MSstatsSampleSize Version: 1.0.1 Depends: R (>= 3.6) Imports: ggplot2, BiocParallel, caret, gridExtra, reshape2, stats, utils, grDevices, graphics, MSstats Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: cddfd197ec5fc66f327928b4389fe4ca NeedsCompilation: no Package: MSstatsTMT Version: 1.4.6 Depends: R (>= 3.6) Imports: limma, lme4, lmerTest, dplyr, tidyr, statmod, methods, reshape2, data.table, matrixStats, stats, utils, ggplot2, grDevices, graphics, MSstats Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: b4f9b7fd22b07db215abcd1ae12b74c0 NeedsCompilation: no Package: MTseeker Version: 1.3.0 Depends: viridis, S4Vectors, GenomeInfoDb, GenomicAlignments, VariantAnnotation Imports: xml2, utils, gmapR, methods, IRanges, Biobase, circlize, jsonlite, graphics, Rsamtools, grDevices, Biostrings, rtracklayer, VariantTools, Homo.sapiens, BiocGenerics, GenomicRanges, GenomicFeatures, SummarizedExperiment Suggests: MTseekerData, BiocStyle, rmarkdown, ggthemes, ggplot2, pkgdown, knitr, rsvg License: GPL-3 MD5sum: 65f9efdacb7aa51bbfa1593643b2b0d3 NeedsCompilation: no Package: Mulcom Version: 1.36.0 Depends: R (>= 2.10), Biobase Imports: graphics, grDevices, stats, 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brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment License: file LICENSE MD5sum: ba9b0dd6133035c6a16bbae989e060f3 NeedsCompilation: no Package: multiHiCcompare Version: 1.4.0 Depends: R (>= 3.5.0) Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, metap, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, BLMA, GenomeInfoDb Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: fcd3c85e612e7f9768f1c9e71079b2d5 NeedsCompilation: no Package: MultiMed Version: 2.8.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE MD5sum: 766c6cbb686bafe486cd61fce4a8a072 NeedsCompilation: no Package: multiMiR Version: 1.8.0 Depends: R (>= 3.4) Imports: stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 1.2), methods, BiocGenerics, AnnotationDbi, dplyr, Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat 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matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 2) MD5sum: f6fdab706cfa58b3f99e2ec9feda8864 NeedsCompilation: no Package: OmnipathR Version: 1.0.1 Depends: igraph, graphics, methods, utils Imports: dplyr, rlang Suggests: tidyr, dnet, gprofiler2, BiocStyle, testthat License: MIT + file LICENSE MD5sum: daf1c5869b3d0ab48df8acae3e7de826 NeedsCompilation: no Package: Onassis Version: 1.8.2 Depends: R (>= 3.4), rJava, OnassisJavaLibs Imports: GEOmetadb, RSQLite, data.table, methods, tools, utils, AnnotationDbi, RCurl, stats, DT, data.table, knitr, Rtsne, dendextend, clusteval, ggplot2, ggfortify Suggests: BiocStyle, rmarkdown, htmltools, org.Hs.eg.db, gplots, GenomicRanges, kableExtra License: GPL-2 MD5sum: 4bfacb1fde686a8a369935419bfa3bc4 NeedsCompilation: no Package: oncomix 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MIT + file LICENSE MD5sum: c48f5b9e664a5328795d5cc1db249dc5 NeedsCompilation: no Package: REMP Version: 1.10.1 Depends: R (>= 3.6), SummarizedExperiment(>= 1.1.6), minfi (>= 1.22.0) Imports: readr, rtracklayer, graphics, stats, utils, methods, settings, BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel, doParallel, parallel, foreach, caret, kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db, impute, iterators Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC License: GPL-3 MD5sum: 6aad6412097ad5ab0810a03dd55c13cc NeedsCompilation: no Package: Repitools Version: 1.32.0 Depends: R (>= 3.0.0), methods, BiocGenerics (>= 0.8.0) Imports: parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, BSgenome (>= 1.47.3), gplots, grid, 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Depends: R (>= 3.3.2) Imports: glmnet, pROC, ggplot2, graphics, stats, Biobase, methods, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools License: GPL (>= 2) MD5sum: 04c9abc7f3573851f692316b006598a0 NeedsCompilation: no Package: RJMCMCNucleosomes Version: 1.10.0 Depends: R (>= 3.4), IRanges, GenomicRanges Imports: Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb, S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit License: Artistic-2.0 MD5sum: c59ed9a04a450ca85a2cd94a96d39bcf NeedsCompilation: yes Package: RLMM Version: 1.48.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) MD5sum: be36a5d8018d389f078fdb3076cece86 NeedsCompilation: no Package: Rmagpie Version: 1.42.0 Depends: R (>= 2.6.1), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab, methods, pamr, stats, utils Suggests: xtable 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TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle License: Artistic-2.0 | file LICENSE MD5sum: 6a6dac898ab4664214d346be0c755ec5 NeedsCompilation: yes Package: rsbml Version: 2.44.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils Imports: BiocGenerics, graph, utils License: Artistic-2.0 MD5sum: 92a38a0be748f0ed7dfb6342301dcff2 NeedsCompilation: yes Package: rScudo Version: 1.2.0 Depends: R (>= 3.6) Imports: methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, SummarizedExperiment, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel License: GPL-3 MD5sum: ddf6c0573187b986219a36a0c8892955 NeedsCompilation: no Package: RSeqAn Version: 1.6.0 Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 6e26c43d876e39b42f38fb53244b449d NeedsCompilation: yes 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SummarizedExperiment, SingleCellExperiment, scran, scater, data.table, dplyr, ggplot2, randomForest, graphics, methods, stats, DelayedArray Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 6f54baa8050bc68ccadc029cd1f4380f NeedsCompilation: no Package: scDD Version: 1.10.0 Depends: R (>= 3.4) Imports: fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm, SingleCellExperiment, SummarizedExperiment, grDevices, graphics, stats, S4Vectors, scran Suggests: BiocStyle, knitr, gridExtra License: GPL-2 MD5sum: fcf1093e7703d0a4842500b66aea74b6 NeedsCompilation: yes Package: scde Version: 2.14.0 Depends: R (>= 3.0.0), flexmix Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown License: GPL-2 MD5sum: d130468976480caaa535ef867db4b055 NeedsCompilation: yes Package: scds Version: 1.2.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot License: MIT + file LICENSE MD5sum: e787a1ebbc90803c9f80e4b958aa3c51 NeedsCompilation: no Package: scFeatureFilter Version: 1.6.0 Depends: R (>= 3.5) Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods Suggests: testthat, knitr, rmarkdown, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE MD5sum: 67c85a195034dcd56443d96f888af2ba NeedsCompilation: no Package: scfind Version: 1.8.0 Depends: R(>= 3.4) Imports: SingleCellExperiment, SummarizedExperiment, methods, stats, bit, dplyr, hash, reshape2, Rcpp(>= 0.12.12) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: a49088473985b6fbfb107cc84434a4f9 NeedsCompilation: yes Package: scGPS Version: 1.0.0 Depends: R (>= 3.6), SummarizedExperiment, dynamicTreeCut, SingleCellExperiment Imports: glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1), fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel, grDevices, graphics, stats, utils, DESeq, locfit LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE License: GPL-3 MD5sum: 538cbf78562b1ac4f907d5d8f9c57497 NeedsCompilation: yes Package: schex Version: 1.0.55 Depends: SingleCellExperiment (>= 1.7.4), Seurat, ggplot2 Imports: hexbin, stats, methods, cluster, dplyr, entropy Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran License: GPL-3 MD5sum: 679058276bfa869e835a93572fc46687 NeedsCompilation: no Package: ScISI Version: 1.58.0 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 MD5sum: 217860d1a650a492fc16747f009f7aef NeedsCompilation: no Package: scmap Version: 1.8.0 Depends: R(>= 3.4) Imports: Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown License: GPL-3 MD5sum: c70dbe7c517c3130bbb196fb5108d86e NeedsCompilation: yes Package: scMerge Version: 1.2.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), parallel, pdist, proxy, Rcpp (>= 0.12.18), RcppEigen (>= 0.3.3.4.0), ruv, S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3), SummarizedExperiment LinkingTo: Rcpp (>= 0.12.18), RcppEigen, testthat Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, scater, testthat, badger License: GPL-3 MD5sum: 71667dbd5c459a7db1c812ae8a7d13c1 NeedsCompilation: yes Package: scmeth Version: 1.6.0 Depends: R (>= 3.5.0) Imports: knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes License: GPL-2 MD5sum: fa96b1ceaf9c03d23a16dc1d263a8dda NeedsCompilation: no Package: SCnorm Version: 1.8.2 Depends: R (>= 3.4.0), Imports: SingleCellExperiment, SummarizedExperiment, stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, S4Vectors, ggplot2, forcats, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) MD5sum: df71bb49708a0c1175474175f4b2f279 NeedsCompilation: no Package: scone Version: 1.10.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, BatchJobs License: Artistic-2.0 MD5sum: aef6aaf5cb6c0bd44186071262c1e6f4 NeedsCompilation: no Package: Sconify Version: 1.6.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: a45a53bc271fe9c4de1477631a3e315c NeedsCompilation: no Package: scoreInvHap Version: 1.8.0 Depends: R (>= 3.4.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: b3c2da04eaa4af3c8865a3fa5cb9224f NeedsCompilation: no Package: scPCA Version: 1.0.0 Depends: R (>= 3.6) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, BiocParallel, elasticnet, cluster, kernlab, origami Suggests: testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, Matrix, ggplot2, ggpubr, splatter, SingleCellExperiment License: MIT + file LICENSE MD5sum: da5ad612b6b0ee32ca77b1fd3200f1dd NeedsCompilation: no Package: scPipe Version: 1.8.0 Depends: R (>= 3.4), ggplot2, methods, SingleCellExperiment Imports: Rhtslib, biomaRt, GGally, MASS, mclust, Rcpp (>= 0.11.3), reshape, BiocGenerics, robustbase, scales, utils, stats, S4Vectors, SummarizedExperiment, AnnotationDbi, org.Hs.eg.db, org.Mm.eg.db, stringr, rtracklayer, hashmap, dplyr, GenomicRanges, magrittr, glue LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat Suggests: Rsubread, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 218f9b23a6d5ea6310bd98990a9c6efb NeedsCompilation: yes Package: scran Version: 1.14.6 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, scater, edgeR, limma, BiocNeighbors, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, dqrng LinkingTo: Rcpp, beachmat, BH, dqrng Suggests: testthat, BiocStyle, knitr, beachmat, HDF5Array, scRNAseq, dynamicTreeCut, DESeq2, monocle, Biobase, aroma.light, pheatmap License: GPL-3 MD5sum: 04c9ccec2e065cc94cf183b6ac836032 NeedsCompilation: yes Package: scRecover Version: 1.2.0 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), Rmagic (>= 1.3.0), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL MD5sum: 605f7faf7dfef3fbfbe392499310cd5c NeedsCompilation: no Package: scruff Version: 1.4.2 Depends: R (>= 3.5.0) Imports: data.table, GenomicAlignments, GenomicFeatures, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, Rsubread, testthat License: MIT + file LICENSE MD5sum: 0501d543e1f1c2b3280d0c66235cb1aa NeedsCompilation: no Package: scsR Version: 1.22.0 Depends: R (>= 2.14.0), STRINGdb, methods, BiocGenerics, Biostrings, IRanges, plyr, tcltk Imports: sqldf, hash, ggplot2, graphics,grDevices, RColorBrewer Suggests: RUnit License: GPL-2 MD5sum: 9a4ddb0ac265666e64bc51950d437333 NeedsCompilation: no Package: scTensor Version: 1.2.1 Depends: R (>= 3.5.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor, rTensor, abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi, grDevices, graphics, stats, utils, outliers, Category, meshr, GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork Suggests: testthat, LRBase.Hsa.eg.db, MeSH.Hsa.eg.db, LRBase.Mmu.eg.db, MeSH.Mmu.eg.db, LRBaseDbi, Seurat, Homo.sapiens License: Artistic-2.0 MD5sum: f02d0af02b63e3368dbfa7425197cc7e NeedsCompilation: no Package: scTGIF Version: 1.0.0 Depends: R (>= 3.6.0) Imports: GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly, tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr, S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor, methods, scales, msigdbr Suggests: testthat License: Artistic-2.0 MD5sum: 704f14f0be35d49505d366c939ed4c2e NeedsCompilation: no Package: SDAMS Version: 1.6.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: e7b2bfc31bc7214a74610e325bbf7546 NeedsCompilation: no Package: segmentSeq Version: 2.20.0 Depends: R (>= 3.0.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: 0224dcb2fb78bae6c6329f49de097409 NeedsCompilation: no Package: SELEX Version: 1.18.0 Depends: R (>= 2.7.0), rJava (>= 0.5-0), Biostrings (>= 2.26.0) License: GPL (>= 2) MD5sum: ffe0fd9a6d854508b3147396438dedd7 NeedsCompilation: no Package: SemDist Version: 1.20.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) MD5sum: 6ccbdbba997ffdf59e3d091ffc085eba NeedsCompilation: no Package: semisup Version: 1.10.0 Depends: R (>= 3.5.0) Imports: VGAM Suggests: knitr, testthat, SummarizedExperiment License: GPL-3 MD5sum: 39b963548fa0c661fd230e6b150928a4 NeedsCompilation: no Package: SEPIRA Version: 1.6.0 Depends: R (>= 3.5.0) Imports: limma (>= 3.32.5), corpcor (>= 1.6.9), parallel (>= 3.3.1), stats Suggests: knitr, rmarkdown, testthat, igraph License: GPL-3 MD5sum: 6ec7f5617147b0d80c82caaf690451b3 NeedsCompilation: no Package: seq2pathway Version: 1.18.0 Depends: R (>= 2.10.0) Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data License: GPL-2 MD5sum: 6963117e7c00b3237d17f6ebfcf28ea9 NeedsCompilation: no Package: SeqArray Version: 1.26.2 Depends: R (>= 3.5.0), gdsfmt (>= 1.18.0) Imports: methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors LinkingTo: gdsfmt Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, Rsamtools, VariantAnnotation License: GPL-3 MD5sum: a2dfba8da2942bd0559b7d29f29c7d9e NeedsCompilation: yes Package: seqbias Version: 1.34.0 Depends: R (>= 3.0.2), GenomicRanges (>= 0.1.0), Biostrings (>= 2.15.0), methods LinkingTo: Rhtslib (>= 1.15.3) Suggests: Rsamtools, ggplot2 License: LGPL-3 MD5sum: 143a9b594c7e162ef08c5ca6b152ebaa NeedsCompilation: yes Package: seqCAT Version: 1.8.1 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE MD5sum: 50586b82f734a2239e1371e0a757c2be NeedsCompilation: no Package: seqCNA Version: 1.32.0 Depends: R (>= 3.0), GLAD (>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot (>= 0.99), methods License: GPL-3 MD5sum: e12dc93565001d38fad1f5399135ba2e NeedsCompilation: yes Package: seqcombo Version: 1.8.0 Depends: R (>= 3.4.0) Imports: Biostrings, cowplot, dplyr, ggplot2, grid, igraph, magrittr, methods, rvcheck, utils Suggests: emojifont, knitr, prettydoc, tibble License: Artistic-2.0 MD5sum: 31282e6d977d13d2abf2674f0bfa3841 NeedsCompilation: no Package: SeqGSEA Version: 1.26.0 Depends: Biobase, doParallel, DESeq Imports: methods, biomaRt Suggests: easyRNASeq, GenomicRanges License: GPL (>= 3) MD5sum: 91a4442561d3495bd69c6e673685a6bb NeedsCompilation: no Package: seqLogo Version: 1.52.0 Depends: methods, grid Imports: stats4 License: LGPL (>= 2) MD5sum: 4df973b10b87c62034a92a3d721baa4b NeedsCompilation: no Package: seqPattern Version: 1.18.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 MD5sum: 2f1ba0555af7ef9264f89f5097058c12 NeedsCompilation: no Package: seqplots Version: 1.24.0 Depends: R (>= 3.2.0) Imports: methods, IRanges, BSgenome, digest, rtracklayer, GenomicRanges, Biostrings, shiny (>= 0.13.0), DBI, RSQLite, plotrix, fields, grid, kohonen, parallel, GenomeInfoDb, class, S4Vectors, ggplot2, reshape2, gridExtra, jsonlite, DT (>= 0.1.0), RColorBrewer, Rsamtools, GenomicAlignments, BiocManager Suggests: testthat, BiocStyle, knitr, rmarkdown, covr License: GPL-3 MD5sum: a66ed641c8a0d65bfd98628b6cbda004 NeedsCompilation: no Package: seqsetvis Version: 1.6.0 Depends: R (>= 3.5), ggplot2 Imports: data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, IRanges, limma, methods, parallel, pbapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, stats Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, cowplot, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 10da95c3807e4b08e81a20dc404e894a NeedsCompilation: no Package: SeqSQC Version: 1.8.1 Depends: R (>= 3.4), ExperimentHub (>= 1.3.7), SNPRelate (>= 1.10.2) Imports: e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, rbokeh, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: 47e9ef506d9e7c67c4a6d6531e0704b2 NeedsCompilation: no Package: seqTools Version: 1.20.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: a95db5dd95072e4d568b89ef2fa103f2 NeedsCompilation: yes Package: SeqVarTools Version: 1.24.1 Depends: SeqArray Imports: grDevices, graphics, stats, methods, Biobase, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, dplyr, rlang, tidyr Suggests: BiocGenerics, BiocStyle, RUnit, stringr License: GPL-3 MD5sum: 848bdbd13d0dc40c515ed5a75f8250a2 NeedsCompilation: no Package: sesame Version: 1.4.0 Depends: R (>= 3.6), sesameData, methods Imports: BiocParallel, R6, grDevices, utils, illuminaio, MASS, GenomicRanges, IRanges, grid, preprocessCore, stats, S4Vectors, randomForest, wheatmap, ggplot2, parallel, matrixStats, DNAcopy Suggests: scales, knitr, rmarkdown, testthat, minfi, SummarizedExperiment, FlowSorted.CordBloodNorway.450k, FlowSorted.Blood.450k, dplyr, tidyr, BiocStyle License: MIT + file LICENSE MD5sum: 35d0b2495a491568137ec0ee7aea4117 NeedsCompilation: no Package: SEtools Version: 1.0.0 Depends: R (>= 3.6) Imports: SummarizedExperiment, data.table, pheatmap, seriation, ComplexHeatmap, circlize, methods Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL MD5sum: 824c673a36aa31cfd9bc24ae8dca2177 NeedsCompilation: no Package: sevenbridges Version: 1.16.1 Depends: methods, utils, stats Imports: httr, jsonlite, yaml, objectProperties, stringr, S4Vectors, docopt, curl, uuid, dplyr Suggests: knitr, rmarkdown, testthat, readr License: Apache License 2.0 | file LICENSE MD5sum: 53c9f8090fc354f0fc2ee459dda97093 NeedsCompilation: no Package: sevenC Version: 1.6.0 Depends: R (>= 3.5), InteractionSet (>= 1.2.0) Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), GenomeInfoDb (>= 1.12.2), GenomicRanges (>= 1.28.5), IRanges (>= 2.10.3), S4Vectors (>= 0.14.4), readr (>= 1.1.0), purrr (>= 0.2.2), data.table (>= 1.10.4), boot (>= 1.3-20), 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Suggests: Biobase, BiocFileCache (>= 1.5.8), circlize, ComplexHeatmap, GO.db, grDevices, grid, knitr, org.Mm.eg.db, org.Hs.eg.db, MASS, RColorBrewer, rmarkdown, UpSetR, License: LGPL (>= 3) MD5sum: ebd9d5357fbd2a67a7c543573c958ee0 NeedsCompilation: no Package: TIN Version: 1.18.0 Depends: R (>= 2.12.0), data.table, impute, aroma.affymetrix Imports: WGCNA, squash, stringr Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 55167eb639b889f0521a8124e7803f10 NeedsCompilation: no Package: TissueEnrich Version: 1.6.0 Depends: R (>= 3.5), ensurer (>= 1.1.0), ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), SummarizedExperiment (>= 1.6.5), GSEABase (>= 1.38.2) Imports: dplyr (>= 0.7.3), stats Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 113159e6e0525fdbe63f6f06f7ad0f5f NeedsCompilation: no Package: TitanCNA Version: 1.24.0 Depends: R (>= 3.5.1) Imports: BiocGenerics (>= 0.31.6), IRanges (>= 2.6.1), GenomicRanges (>= 1.24.3), 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DT, S4Vectors, SummarizedExperiment, methods, shiny, shinyFiles Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL-3 MD5sum: 3ebcbb295169e8547999d597ed55eadb NeedsCompilation: no Package: triform Version: 1.28.0 Depends: R (>= 2.11.0), IRanges, yaml Imports: BiocGenerics, IRanges (>= 2.5.27), yaml Suggests: RUnit License: GPL-2 MD5sum: 8744d13213a0edf1b370b6c7c7254ace NeedsCompilation: no Package: trigger Version: 1.32.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 MD5sum: 14d7492e2fdc134559dd17f1e16dfeaf NeedsCompilation: yes Package: trio Version: 3.24.3 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1) Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 MD5sum: 5dd922e5476791e7a33f8330495e3a47 NeedsCompilation: no Package: triplex Version: 1.26.0 Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 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AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments, Organism.dplyr, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, Sushi, yaml Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: cb25fefc9225afa7448b89b09eca0512 NeedsCompilation: no Package: UNDO Version: 1.28.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: e235ce98eb89d1a22ef4740c39e315ec NeedsCompilation: no Package: unifiedWMWqPCR Version: 1.22.0 Depends: methods Imports: BiocGenerics, stats, graphics, HTqPCR License: GPL (>= 2) MD5sum: 218d3e4cbaa64742ad3e6c8273e82dcd NeedsCompilation: no Package: UniProt.ws Version: 2.26.0 Depends: methods, utils, RSQLite, RCurl, BiocGenerics (>= 0.13.8) Imports: 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pbkrtest (>= 0.4-4), lmerTest, iterators, splines, colorRamps, BiocParallel, gplots, progress, reshape2, lme4 (>= 1.1-10), doParallel, grDevices, graphics, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr License: GPL (>= 2) MD5sum: 9e6367c118c385935215a22df0915d96 NeedsCompilation: no Package: VariantAnnotation Version: 1.32.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.15.3), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.37.4), SummarizedExperiment (>= 1.9.9), Rsamtools (>= 1.99.0) Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.17.24), IRanges (>= 2.13.13), XVector (>= 0.19.7), Biostrings (>= 2.47.6), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome (>= 1.47.3), GenomicFeatures (>= 1.31.3) LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle License: Artistic-2.0 MD5sum: 51e434870b0e3fbf4cbbd9133f3ba962 NeedsCompilation: yes Package: VariantExperiment Version: 1.0.0 Depends: R (>= 3.6.0), S4Vectors (>= 0.21.24), SummarizedExperiment (>= 1.13.0), GenomicRanges, GDSArray (>= 1.3.0), DelayedDataFrame (>= 1.0.0) Imports: tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray, SeqVarTools, DelayedArray, Biostrings, IRanges Suggests: testthat, knitr License: GPL-3 MD5sum: c7875a1dde482a6ac2bd4e5cfbd2229f NeedsCompilation: no Package: VariantFiltering Version: 1.22.0 Depends: R (>= 3.0.0), methods, BiocGenerics (>= 0.25.1), VariantAnnotation (>= 1.13.29) Imports: utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Biostrings (>= 2.33.11), GenomeInfoDb (>= 1.3.6), GenomicRanges (>= 1.19.13), SummarizedExperiment, GenomicFeatures, 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htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager License: GPL-3 MD5sum: c63ffef44194ebea20b599edfdce8c87 NeedsCompilation: no Package: vsn Version: 3.54.0 Depends: R (>= 3.4.0), Biobase Imports: methods, affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat License: Artistic-2.0 MD5sum: 4aa21023b404468ae5246826f49c40ce NeedsCompilation: yes Package: vtpnet Version: 0.26.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: 92c57191cf5e303cd78f566e1e064a04 NeedsCompilation: no Package: vulcan Version: 1.8.0 Depends: R (>= 3.4), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene, zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit Imports: wordcloud, csaw, gplots, stats, utils, caTools, graphics, DESeq, Biobase Suggests: vulcandata License: LGPL-3 MD5sum: 131c6c0c801f38dec885f212b5536126 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