Package: a4 Version: 1.36.0 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats License: GPL-3 MD5sum: 80d728f8fe75426db4224f6077b0570c Package: a4Base Version: 1.36.0 Depends: methods, graphics, grid, Biobase, AnnotationDbi, annaffy, mpm, genefilter, limma, multtest, glmnet, a4Preproc, a4Core, gplots Suggests: Cairo, ALL, hgu95av2.db Enhances: gridSVG, JavaGD License: GPL-3 MD5sum: 2ab6de9cd9eb2867858af8e06481ae72 Package: a4Classif Version: 1.36.0 Depends: methods, a4Core, a4Preproc, MLInterfaces, ROCR, pamr, glmnet, varSelRF Imports: a4Core Suggests: ALL, hgu95av2.db License: GPL-3 MD5sum: 8bb5cd8d27bda2b628142e83eab9de79 Package: a4Core Version: 1.36.0 Depends: methods, Biobase, glmnet License: GPL-3 MD5sum: 502ffb3ba79256e7aa0b740dcfdaaf05 Package: a4Preproc Version: 1.36.0 Depends: methods, AnnotationDbi Suggests: ALL, hgu95av2.db License: GPL-3 MD5sum: ddd652c4392d58464d82a3b85691f841 Package: a4Reporting Version: 1.36.0 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(>= 1.9.1), GO.db (>= 1.8.1), graphics, grDevices, KEGG.db (>= 1.8.1), methods, multtest (>= 1.6.0), stats (>= 2.1.0) Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) License: GPL (>= 2) MD5sum: be30ff7d5626bcd715ea0462e4a6b42e Package: AffiXcan Version: 1.6.0 Depends: R (>= 3.6), SummarizedExperiment Imports: MultiAssayExperiment, BiocParallel, crayon Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: d78c62222c998cc79c77ef529cffa286 Package: affxparser Version: 1.60.0 Depends: R (>= 2.14.0) Suggests: R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles License: LGPL (>= 2) MD5sum: 4e5fccd308a81d4f81fa07f91ddda904 Package: affy Version: 1.66.0 Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5) Imports: affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods, preprocessCore, stats, utils, zlibbioc LinkingTo: preprocessCore Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools License: LGPL (>= 2.0) MD5sum: 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shinydashboard, DT, stats, utils, tximport (>= 1.11.5), cowplot, rlang Suggests: knitr, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 9556ab766936f68a988bb3e6e4d78360 Package: AllelicImbalance Version: 1.26.0 Depends: R (>= 4.0.0), grid, GenomicRanges (>= 1.31.8), SummarizedExperiment (>= 0.2.0), GenomicAlignments (>= 1.15.6) Imports: methods, BiocGenerics, AnnotationDbi, BSgenome (>= 1.47.3), VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Rsamtools (>= 1.99.3), GenomicFeatures (>= 1.31.3), Gviz, lattice, latticeExtra, gridExtra, seqinr, GenomeInfoDb, nlme Suggests: testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 9cb5a4369458b5c276d8efb20bbb005e Package: AlphaBeta Version: 1.2.3 Depends: R (>= 3.6.0) Imports: dplyr (>= 0.7), data.table (>= 1.10), stringr (>= 1.3), utils (>= 3.6.0), gtools (>= 3.8.0), optimx (>= 2018-7.10), expm (>= 0.999-4), stats (>= 3.6), BiocParallel (>= 1.18), igraph (>= 1.2.4), graphics (>= 3.6), ggplot2 (>= 3.2), grDevices (>= 3.6), plotly (>= 4.9) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 0d23f8bf7600897ef176cbe301cd39ed Package: alpine Version: 1.14.0 Depends: R (>= 3.3) Imports: Biostrings, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, SummarizedExperiment, GenomicFeatures, speedglm, splines, graph, RBGL, stringr, stats, methods, graphics, GenomeInfoDb, S4Vectors Suggests: knitr, testthat, alpineData, rtracklayer, ensembldb, BSgenome.Hsapiens.NCBI.GRCh38, RColorBrewer License: GPL (>= 2) MD5sum: d6534e1a4c69e2b8035e2681457e38c4 Package: ALPS Version: 1.2.0 Depends: R (>= 3.6) Imports: assertthat, BiocParallel, ChIPseeker, corrplot, data.table, dplyr, GenomicRanges, GGally, genefilter, gghalves, ggplot2, ggseqlogo, Gviz, magrittr, org.Hs.eg.db, plyr, reshape2, rtracklayer, stats, stringr, tibble, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, utils Suggests: knitr, rmarkdown, ComplexHeatmap, circlize, testthat License: MIT + file LICENSE MD5sum: e787f2a83e5dea4566637fd996d9ff89 Package: alsace Version: 1.24.0 Depends: R (>= 2.10), ALS, ptw (>= 1.0.6) Suggests: lattice, knitr License: GPL (>= 2) MD5sum: bc82824d4509309f0ee4d07890fe42ad Package: altcdfenvs Version: 2.50.0 Depends: R (>= 2.7), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.9.25), Biobase (>= 2.15.1), affy, makecdfenv, Biostrings, hypergraph Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer License: GPL (>= 2) MD5sum: 7e419e79aa733cb39ffbc5dc88cef1dd Package: AMARETTO Version: 1.4.0 Depends: R (>= 3.6), impute, doParallel, grDevices, dplyr, methods, ComplexHeatmap Imports: callr (>= 3.0.0.9001), Matrix, Rcpp, BiocFileCache, DT, MultiAssayExperiment, circlize, curatedTCGAData, foreach, glmnet, httr, limma, matrixStats, readr, reshape2, tibble, rmarkdown, graphics, grid, parallel, stats, knitr, ggplot2, gridExtra, utils LinkingTo: Rcpp Suggests: testthat, MASS, knitr License: Apache License (== 2.0) + file LICENSE MD5sum: 552de08db9341f09e5abe1c473b84f41 Package: AMOUNTAIN Version: 1.14.0 Depends: R (>= 3.3.0) Imports: stats Suggests: BiocStyle, qgraph, knitr, rmarkdown License: GPL (>= 2) MD5sum: ef896bca7c3dea6c0e264987aa0fd769 Package: amplican Version: 1.10.1 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.22.0), Biostrings (>= 2.44.2), data.table (>= 1.10.4-3) Imports: Rcpp, utils (>= 3.4.1), S4Vectors (>= 0.14.3), ShortRead (>= 1.34.0), IRanges (>= 2.10.2), GenomicRanges (>= 1.28.4), GenomeInfoDb (>= 1.12.2), BiocParallel (>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 2.2.0), ggthemes (>= 3.4.0), waffle (>= 0.7.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), dplyr (>= 0.7.2), rmarkdown (>= 1.6), knitr (>= 1.16), clusterCrit (>= 1.2.7) LinkingTo: Rcpp Suggests: testthat, BiocStyle, GenomicAlignments License: GPL-3 MD5sum: 3a120d511fbe416f5776feff9a984fed Package: Anaquin Version: 2.12.0 Depends: R (>= 3.3), ggplot2 (>= 2.2.0) Imports: ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils, plyr, DESeq2 Suggests: RUnit, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 89e0a8d071444fc36cc4101f9e75b464 Package: AneuFinder Version: 1.16.0 Depends: R (>= 3.5), GenomicRanges, ggplot2, cowplot, AneuFinderData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, Rsamtools, bamsignals, DNAcopy, ecp, Biostrings, GenomicAlignments, reshape2, ggdendro, ggrepel, ReorderCluster, mclust Suggests: knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: a6ee219220973d6bd0ca58dea9fd6407 Package: ANF Version: 1.10.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 156c27239b3c38c932dae518d29f9fb2 Package: animalcules Version: 1.4.0 Depends: R (>= 3.6.0) Imports: assertthat, shiny, shinyjs, DESeq2, caret, plotly, ggplot2, rentrez, reshape2, covr, ape, vegan, dplyr, magrittr, MultiAssayExperiment, SummarizedExperiment, S4Vectors (>= 0.23.19), XML, forcats, scales, lattice, glmnet, tsne, DMwR, plotROC, DT, reactable, utils, limma, methods, stats, tibble, biomformat, umap, Matrix Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 5e8c92a04acb1eb7019a455daf3dc680 Package: annaffy Version: 1.60.0 Depends: R (>= 2.5.0), methods, Biobase, GO.db, KEGG.db Imports: AnnotationDbi (>= 0.1.15), DBI Suggests: hgu95av2.db, multtest, tcltk License: LGPL MD5sum: fbceaaa28d2c6a066903181ca0b8347b Package: annmap Version: 1.30.0 Depends: R (>= 2.15.0), methods, GenomicRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice, Rsamtools, genefilter, IRanges, BiocGenerics Suggests: RUnit, rjson, Gviz License: GPL-2 MD5sum: 53b3ca5ef3cb858ea57bd2f372d0ba32 Package: annotate Version: 1.66.0 Depends: R (>= 2.10), AnnotationDbi (>= 1.27.5), XML Imports: Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), RCurl Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, License: Artistic-2.0 MD5sum: a553ff7b808885daa79693ddbb661e81 Package: AnnotationDbi Version: 1.50.3 Depends: R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges Imports: DBI, RSQLite, S4Vectors (>= 0.9.25) Suggests: hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 MD5sum: fd268acdefdc7911975e87a57e8985c2 Package: AnnotationFilter Version: 1.12.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db License: Artistic-2.0 MD5sum: e31f2d12318000b3ccb2008a6e9db242 Package: AnnotationForge Version: 1.30.1 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: 79bd821c1fd28f0fac4d37948e0c5720 Package: AnnotationFuncs Version: 1.38.0 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: 3b9dc5627c94d7f001aaf53e1eb0ce62 Package: AnnotationHub Version: 2.20.2 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: 040018e7d9a808eea5b3f3604887b6b0 Package: AnnotationHubData Version: 1.18.1 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: 2eb4d28d1342422ddfb38eb048f84026 Package: annotationTools Version: 1.62.0 Imports: Biobase, stats Suggests: BiocStyle License: GPL MD5sum: 173763a177054afcc1ba34df5fe23ada Package: annotatr Version: 1.14.0 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: b6622d8978d83854067972557495047d Package: anota Version: 1.36.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: 77b91081e0f65ab8577be56a6cad48b9 Package: anota2seq Version: 1.10.0 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: f5ed291cf53a3c6f0404a26915f58077 Package: antiProfiles Version: 1.28.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: 427173dc537183b4beb39c0c015487d6 Package: AnVIL Version: 1.0.3 Depends: R (>= 4.0), dplyr Imports: stats, utils, methods, futile.logger, jsonlite, httr, curl, rapiclient (>= 0.1.3), tibble, BiocManager Suggests: knitr, testthat, withr, readr License: Artistic-2.0 MD5sum: 480b1ce4ae8cc7b7ebe2c623fcadf805 Package: APAlyzer Version: 1.2.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, ensembldb, VariantAnnotation, dplyr, tidyr, repmis Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, Rsamtools, testthat License: LGPL-3 MD5sum: 668dbefdffe89f7d2043f45c8dc5e35f Package: apComplex Version: 2.54.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: 5bf4a392b4f0b57de40122cedfffd166 Package: apeglm Version: 1.10.0 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 MD5sum: d3caf55f092da77627a10efc68514250 Package: appreci8R Version: 1.6.0 Imports: shiny, shinyjs, DT, VariantAnnotation, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, rsnps, Biostrings, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.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: e3a0b5cf8aef5b3e78c78b2ba8f0c3c3 Package: aroma.light Version: 3.18.0 Depends: R (>= 2.15.2) Imports: stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.23.0), R.utils (>= 2.9.0), matrixStats (>= 0.55.0) Suggests: princurve (>= 2.1.4) License: GPL (>= 2) MD5sum: b7ef2e98adcfc7ae447ce1c67d1d0194 Package: ArrayExpress Version: 1.48.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: XML, oligo, limma Suggests: affy License: Artistic-2.0 MD5sum: d4657e2a368c448be6115a318409cd59 Package: ArrayExpressHTS Version: 1.38.0 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: 842a502a95df1966efe9a6959df060df Package: arrayMvout Version: 1.46.0 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: 3509afefcff75b51bc02c39b19acb40b Package: arrayQuality Version: 1.66.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL MD5sum: 0244c6a911e2e9e8847ba78a7e8ed3ff Package: arrayQualityMetrics Version: 3.44.0 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, genefilter, graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, stats, utils, vsn (>= 3.23.3), XML, svglite Suggests: ALLMLL, CCl4, BiocStyle, knitr License: LGPL (>= 2) MD5sum: 46f6229b008f3089140b4d4d11af145a Package: ArrayTools Version: 1.48.0 Depends: R (>= 2.7.0), affy (>= 1.23.4), Biobase (>= 2.5.5), methods Imports: affy, Biobase, graphics, grDevices, limma, methods, stats, utils, xtable Suggests: simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy, gcrma, hugene10sttranscriptcluster.db License: LGPL (>= 2.0) MD5sum: fe1f1375b1d6125fe93f9039c6ff4b0d Package: ARRmNormalization Version: 1.28.0 Depends: R (>= 2.15.1), ARRmData License: Artistic-2.0 MD5sum: 46c0b7f8a8058fffc9b107b78e574237 Package: artMS Version: 1.6.5 Depends: R (>= 3.6.0) Imports: AnnotationDbi, biomaRt, bit64, circlize, cluster, ComplexHeatmap, corrplot, data.table, dplyr, factoextra, FactoMineR, getopt, ggdendro, ggplot2, gplots, ggrepel, gProfileR, graphics, grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db, org.Mm.eg.db, PerformanceAnalytics, pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 3) + file LICENSE MD5sum: d1168147b63f2b420cde333f24179404 Package: ASAFE Version: 1.14.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 11802c51d3067ee07bb7da481d1a3228 Package: ASEB Version: 1.32.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) MD5sum: 4f09a3dc7e38554911bbce769139f78b Package: ASGSCA Version: 1.22.0 Imports: Matrix, MASS Suggests: BiocStyle License: GPL-3 MD5sum: 93678bb5924d4c267c316f1af16a0198 Package: ASICS Version: 2.4.3 Depends: R (>= 3.5) Imports: BiocParallel, ggplot2, grDevices, gridExtra, methods, mvtnorm, PepsNMR, plyr, quadprog, ropls, stats, SummarizedExperiment, utils, Matrix, zoo Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata License: GPL (>= 2) MD5sum: 1a74d5898dc1491f34182d14dc7a7aea Package: ASpediaFI Version: 1.2.0 Depends: R (>= 3.6.0), SummarizedExperiment, ROCR Imports: BiocParallel, GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges, IVAS, Rsamtools, biomaRt, limma, S4Vectors, stats, DRaWR, GenomeInfoDb, Gviz, Matrix, dplyr, fgsea, reshape2, igraph, graphics, e1071, methods, rtracklayer, scales, grid, ggplot2, mGSZ, utils Suggests: knitr License: GPL-3 MD5sum: ad9f30f825ab2e786c5aca5296b953d9 Package: ASpli Version: 1.14.0 Depends: methods, grDevices, stats, utils, parallel, edgeR Imports: GenomicRanges, GenomicFeatures, BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, AnnotationDbi, Rsamtools, BiocStyle License: GPL MD5sum: 995df4bf907ef55eb0a90f736f65b95b Package: AssessORF Version: 1.6.0 Depends: R (>= 3.5.0), DECIPHER (>= 2.10.0) Imports: Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: e8bf860f1d6912217035ae03c0518a80 Package: ASSET Version: 2.6.0 Depends: MASS, msm, rmeta 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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: f50177444d1e9f3c5a1b8b05b3309486 Package: attract Version: 1.40.0 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: 20255fe54c919fce560e463dc999e46e Package: AUCell Version: 1.10.0 Imports: data.table, graphics, grDevices, GSEABase, methods, mixtools, R.utils, shiny, stats, SummarizedExperiment, BiocGenerics, S4Vectors, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, rbokeh, devtools, Rtsne, tsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: 55e3e579423be920c2eff67e38f945db Package: Autotuner Version: 1.2.0 Depends: R (>= 3.6), methods, Biobase, MSnbase (>= 2.9.3) Imports: RColorBrewer, mzR, assertthat, scales, entropy, cluster, grDevices, graphics, stats, utils Suggests: testthat (>= 2.1.0), covr, devtools, knitr, rmarkdown, mtbls2 License: MIT + file LICENSE MD5sum: bb5dea96c89850f4a72dd54d5e00b5cd Package: AWFisher Version: 1.2.0 Depends: R (>= 3.6) Imports: edgeR, limma, stats Suggests: knitr, tightClust License: GPL-3 MD5sum: aff87638458aacf9529267905e9becf1 Package: BaalChIP Version: 1.14.0 Depends: R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools, Imports: GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy, reshape2, scales, coda, foreach, ggplot2, methods, utils, graphics, stats Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 47913b091b12a25a77e29a3f778aa015 Package: BAC Version: 1.48.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: 75e76b1a562a0264bea0cc5a75ed7c9b Package: bacon Version: 1.16.0 Depends: R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 License: GPL (>= 2) MD5sum: 84c3dbbb09c533e4b04164eecb3511af Package: BADER Version: 1.26.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 MD5sum: 0abe941be76e0b59d19e4d437e0f8e61 Package: BadRegionFinder Version: 1.16.0 Imports: VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 80147c60ca7718991a6d0d8af43bc923 Package: BAGS Version: 2.28.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 MD5sum: 60ac1cb9e7358c24cc92d0953e6a1452 Package: ballgown Version: 2.20.0 Depends: R (>= 3.1.1), methods Imports: GenomicRanges (>= 1.17.25), IRanges (>= 1.99.22), S4Vectors (>= 0.9.39), RColorBrewer, splines, sva, limma, rtracklayer (>= 1.29.25), Biobase (>= 2.25.0), GenomeInfoDb Suggests: testthat, knitr License: Artistic-2.0 MD5sum: 84a11ef78ee1fd8893555d6b0c527769 Package: bamsignals 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prettydoc, yaml Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead Suggests: testthat, BiocStyle License: GPL (>= 3) MD5sum: fe1cd03b4ead331c3f2f0536b0352657 Package: BaseSpaceR Version: 1.32.0 Depends: R (>= 2.15.0), RCurl, RJSONIO Imports: methods Suggests: RUnit, IRanges, Rsamtools License: Apache License 2.0 MD5sum: 19a3f2277f8edb4110ba2e155a73b762 Package: Basic4Cseq Version: 1.24.0 Depends: R (>= 3.4), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805 Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: c9ae803157b0e79b7b91fbc20b574ca7 Package: BASiCS Version: 2.0.0 Depends: R (>= 4.0), SingleCellExperiment Imports: Biobase, BiocGenerics, coda, cowplot, ggExtra, ggplot2, graphics, grDevices, KernSmooth, MASS, methods, Rcpp (>= 0.11.3), S4Vectors, scran, stats, stats4, SummarizedExperiment, viridis, utils, Matrix, matrixStats, assertthat, reshape2, hexbin LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, magick License: GPL (>= 2) MD5sum: a0f3a7df0fd092ee6434cd9ff0886266 Package: BasicSTARRseq Version: 1.16.0 Depends: GenomicRanges,GenomicAlignments Imports: S4Vectors,methods,IRanges,GenomeInfoDb,stats Suggests: knitr License: LGPL-3 MD5sum: 6fef7b2fe305b599f63899fd8f377e5b Package: basilisk Version: 1.0.2 Imports: reticulate, parallel, methods, basilisk.utils Suggests: knitr, rmarkdown, BiocStyle, testthat, callr License: GPL-3 MD5sum: 108bae7b4916af5bd0e221917df8f981 Package: basilisk.utils Version: 1.0.4 Imports: utils, methods, rappdirs Suggests: knitr, rmarkdown, BiocStyle, testthat, BiocFileCache License: GPL-3 MD5sum: fb368f86b0f1c5a7985604a59f7a036b Package: batchelor Version: 1.4.0 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix, DelayedArray, DelayedMatrixStats, scater, BiocParallel LinkingTo: Rcpp, beachmat Suggests: testthat, BiocStyle, knitr, beachmat, scran, scRNAseq License: GPL-3 MD5sum: 963167e8c2ef057f3dcc8bf310361713 Package: BatchQC Version: 1.16.3 Depends: R (>= 3.5.0) Imports: utils, rmarkdown, knitr, pander, gplots, MCMCpack, shiny, sva, corpcor, moments, matrixStats, ggvis, heatmaply, reshape2, limma, grDevices, graphics, stats, methods, Matrix Suggests: testthat License: GPL (>= 2) MD5sum: 666ea495f2b5f3c1dad236e774b7e984 Package: BayesKnockdown Version: 1.14.0 Depends: R (>= 3.3) Imports: stats, Biobase License: GPL-3 MD5sum: a8f222da77b7965a512af6fda918f34b Package: bayNorm Version: 1.6.0 Depends: R (>= 3.5), Imports: Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix, parallel, MASS, locfit, fitdistrplus, stats, methods, graphics, grDevices, SingleCellExperiment, SummarizedExperiment, BiocParallel, utils LinkingTo: Rcpp, RcppArmadillo,RcppProgress Suggests: knitr, rmarkdown, BiocStyle, devtools, 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RcppArmadillo, RcppEigen, stats LinkingTo: Rcpp, RcppArmadillo, RcppEigen Suggests: knitr, rmarkdown, BiocGenerics License: GPL (>= 2) MD5sum: 3008fdea66aa944c489d3bc89385eaff Package: beachmat Version: 2.4.0 Imports: methods, DelayedArray, BiocGenerics, Matrix Suggests: testthat, BiocStyle, knitr, rmarkdown, devtools License: GPL-3 MD5sum: 2412d03ef3560b925c9e4fefa110b181 Package: beadarray Version: 2.38.0 Depends: R (>= 2.13.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), hexbin Imports: BeadDataPackR, limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, illuminaio, methods, ggplot2 Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr License: MIT + file LICENSE MD5sum: ffa1ed2f330a83d8195235e06335862b Package: beadarraySNP Version: 1.54.0 Depends: methods, Biobase (>= 2.14), quantsmooth Suggests: aCGH, affy, limma, snapCGH, beadarray, DNAcopy License: GPL-2 MD5sum: 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rmarkdown, ggplot2 License: GPL-2 MD5sum: 1c023f40c39849d14073dd164e44a54c Package: biotmle Version: 1.12.0 Depends: R (>= 3.4) Imports: stats, methods, dplyr, tibble, ggplot2, ggsci, superheat, assertthat, future, doFuture, drtmle (>= 1.0.4), S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, limma Suggests: testthat, knitr, rmarkdown, BiocStyle, arm, earth, xgboost, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) License: file LICENSE MD5sum: c3e520d0300d14e941ed76c809319496 Package: biovizBase Version: 1.36.0 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: 80dad85594f9d824be1417b1cfd358ba Package: BiRewire Version: 3.20.0 Depends: igraph, slam, tsne, Matrix Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 5c63fa0f8bb3cf0d9e079d1b9822590b Package: biscuiteer Version: 1.2.0 Depends: R (>= 3.6), biscuiteerData, bsseq Imports: readr, qualV, Matrix, impute, HDF5Array, S4Vectors, Rsamtools, data.table, Biobase, GenomicRanges, BiocGenerics, VariantAnnotation, DelayedMatrixStats, SummarizedExperiment, GenomeInfoDb, Mus.musculus, Homo.sapiens, matrixStats, rtracklayer, QDNAseq, dmrseq, methods, utils, R.utils, gtools, BiocParallel Suggests: DSS, covr, knitr, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10 License: GPL-3 MD5sum: 1b6cb334f8081f760956723e6f32a022 Package: BiSeq Version: 1.28.0 Depends: R (>= 2.15.2), methods, S4Vectors, IRanges (>= 1.17.24), GenomicRanges, SummarizedExperiment (>= 0.2.0), Formula Imports: methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer, parallel, betareg, lokern, Formula, globaltest License: LGPL-3 MD5sum: d7aff2d4baf87dc2c063021e49dce1fb Package: BitSeq Version: 1.32.0 Depends: Rsamtools (>= 1.99.3) Imports: S4Vectors, IRanges LinkingTo: Rhtslib (>= 1.15.5) Suggests: edgeR, DESeq, BiocStyle License: Artistic-2.0 + file LICENSE MD5sum: 1d957f071d12b706e94891f809c53347 Package: blacksheepr Version: 1.2.0 Depends: R (>= 3.6) Imports: grid, stats, grDevices, utils, circlize, viridis, RColorBrewer, ComplexHeatmap, SummarizedExperiment, pasilla Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl License: MIT + file LICENSE MD5sum: 4735ebe76a013209819a638f9f2174c6 Package: blima Version: 1.22.0 Depends: R(>= 3.3) Imports: beadarray(>= 2.0.0), Biobase(>= 2.0.0), Rcpp (>= 0.12.8), BiocGenerics, grDevices, stats, graphics LinkingTo: Rcpp Suggests: xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr License: GPL-3 MD5sum: eadb3376b5e42f120766e6e66cd539b3 Package: BLMA Version: 1.12.0 Depends: ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel, Biobase Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: ab47f11c5f7322f98cee7eac62c222ba Package: bnbc Version: 1.10.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, GenomicRanges Imports: Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, GenomeInfoDb, S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 6cd21f783fc3495c5fa626e390812f6f Package: BPRMeth Version: 1.14.1 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: 187cf7c8d2d2d1f2c50534b2b843b3c1 Package: BRAIN Version: 1.34.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 MD5sum: 665b776af11dc03d09e5c068d4f15ac1 Package: brainflowprobes Version: 1.2.0 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), covr License: Artistic-2.0 MD5sum: dade7309980e68b28a20576d038327bb Package: BrainStars Version: 1.32.0 Depends: RCurl, Biobase, methods Imports: RJSONIO, Biobase License: Artistic-2.0 MD5sum: 1e63509f5be7d5aaaab83dfb4c908c38 Package: branchpointer Version: 1.14.0 Depends: caret, R(>= 3.4) Imports: plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt, Biostrings, parallel, utils, stats, BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges, GenomeInfoDb, IRanges, S4Vectors, data.table Suggests: knitr, BiocStyle License: BSD_3_clause + file LICENSE MD5sum: 2aede44bde481c58deaaadbb13c020b6 Package: breakpointR Version: 1.6.0 Depends: R (>= 3.6), GenomicRanges, cowplot, breakpointRdata Imports: methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>= 1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2, BiocGenerics, gtools, doParallel, foreach Suggests: knitr, BiocStyle, testthat License: file LICENSE MD5sum: 5e0306a182738ab9b9b51042598e12be Package: brendaDb Version: 1.2.0 Imports: dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel, crayon, utils, tidyr, curl, xml2, grDevices, rlang, BiocFileCache, rappdirs LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, devtools License: MIT + file LICENSE MD5sum: 7aeb2b04d2b5e003c909ac0a83c78141 Package: BRGenomics Version: 1.0.3 Depends: R (>= 4.0), rtracklayer, GenomeInfoDb, S4Vectors Imports: GenomicRanges, parallel, IRanges, stats, Rsamtools, GenomicAlignments, DESeq2, SummarizedExperiment, utils, methods Suggests: BiocStyle, knitr, rmarkdown, testthat, apeglm, remotes, ggplot2, reshape2, Biostrings License: Artistic-2.0 MD5sum: aa32c8d8e69fecf11f9e9b62510c5ade Package: bridge Version: 1.52.0 Depends: R (>= 1.9.0), rama License: GPL (>= 2) MD5sum: 07880cd7145184f62099f96c2c784d4e Package: BridgeDbR Version: 1.22.0 Depends: R (>= 3.3.0), rJava Imports: curl Suggests: BiocStyle, knitr, rmarkdown, testthat License: AGPL-3 MD5sum: c939f194f905f0e8b01f77c8b5817e67 Package: BrowserViz Version: 2.10.0 Depends: R (>= 3.5.0), jsonlite (>= 1.5), httpuv(>= 1.5.0) Imports: methods, BiocGenerics Suggests: RUnit, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 668879b2dadf0ccf629e15e0c78b177b Package: BSgenome Version: 1.56.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.23.9), GenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), rtracklayer (>= 1.39.7) Imports: methods, utils, stats, matrixStats, BiocGenerics, S4Vectors, IRanges, XVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, rtracklayer Suggests: BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit License: Artistic-2.0 MD5sum: 25622c1e53aba02b7f94238226a41ca1 Package: bsseq Version: 1.24.4 Depends: R (>= 3.5), methods, BiocGenerics, GenomicRanges (>= 1.33.6), SummarizedExperiment (>= 1.17.4) Imports: IRanges (>= 2.22.2), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors (>= 0.25.14), R.utils (>= 2.0.0), DelayedMatrixStats (>= 1.5.2), permute, limma, DelayedArray (>= 0.9.8), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array (>= 1.11.9), rhdf5 LinkingTo: Rcpp, beachmat Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat (>= 1.5.2), BatchJobs License: Artistic-2.0 MD5sum: 8e6feddd66f242c38b957843a4f28c4a Package: BubbleTree Version: 2.18.0 Depends: R (>= 3.5), IRanges, GenomicRanges, plyr, dplyr, magrittr Imports: BiocGenerics (>= 0.31.6), BiocStyle, Biobase, ggplot2, WriteXLS, gtools, RColorBrewer, limma, grid, gtable, gridExtra, biovizBase, e1071, methods, grDevices, stats, utils Suggests: knitr, rmarkdown License: LGPL (>= 3) MD5sum: 34996edfcb20abfdaafb7b1cbf4a5ef7 Package: BufferedMatrix Version: 1.52.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) MD5sum: 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grid, gridExtra, tcltk, Biobase Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 8592454c704392902a3dd92cbfc7e90f Package: CAGEfightR Version: 1.8.0 Depends: R (>= 3.5), GenomicRanges (>= 1.30.1), rtracklayer (>= 1.38.2), SummarizedExperiment (>= 1.8.1) Imports: pryr(>= 0.1.3), assertthat(>= 0.2.0), methods(>= 3.6.3), Matrix(>= 1.2-12), BiocGenerics(>= 0.24.0), S4Vectors(>= 0.16.0), IRanges(>= 2.12.0), GenomeInfoDb(>= 1.14.0), GenomicFeatures(>= 1.29.11), GenomicAlignments(>= 1.22.1), BiocParallel(>= 1.12.0), GenomicFiles(>= 1.14.0), Gviz(>= 1.22.2), InteractionSet(>= 1.9.4), GenomicInteractions(>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-3 + file LICENSE MD5sum: 2815dc8a751becd7a44be3be9abcf578 Package: CAGEr Version: 1.30.3 Depends: methods, MultiAssayExperiment, R (>= 3.5.0) Imports: beanplot, BiocGenerics, BiocParallel, BSgenome, data.table, DelayedArray, formula.tools, GenomeInfoDb, GenomicAlignments, GenomicRanges (>= 1.37.16), ggplot2 (>= 2.2.0), gtools, IRanges (>= 2.18.0), KernSmooth, memoise, plyr, Rsamtools, reshape, rtracklayer, S4Vectors, som, stringdist, stringi, SummarizedExperiment, utils, vegan, VGAM Suggests: BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 59d0f52da71fab8d842ba040e7ebf772 Package: calm Version: 1.2.0 Imports: mgcv, stats, graphics Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 1ea7a80c404fb41d14d67071513ff231 Package: CAMERA Version: 1.44.0 Depends: R (>= 2.1.0), methods, Biobase, xcms (>= 1.13.5) Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph Suggests: faahKO, RUnit, BiocGenerics Enhances: Rmpi, snow License: GPL (>= 2) MD5sum: e59d20e2a58f1c2e88eac5feaa8872a3 Package: CAMTHC Version: 1.6.0 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: 51caa25a2fc856d5ee73ec938c2d99f2 Package: canceR Version: 1.22.01 Depends: R (>= 3.4), tcltk, tcltk2, cgdsr Imports: GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart, survival, Biobase, phenoTest, circlize, plyr, graphics, stats, utils, grDevices Suggests: testthat (>= 0.10.0), R.rsp License: GPL-2 MD5sum: 60eb900cba68e383bcbdaf46f25e6a26 Package: cancerclass Version: 1.32.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 MD5sum: fd10949f6375570f67b3109923ccf491 Package: CancerInSilico Version: 2.8.0 Depends: R (>= 3.4), Rcpp Imports: methods, utils, graphics, stats LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, BiocStyle, Rtsne, viridis, rgl, gplots License: GPL-2 MD5sum: 0a47065e15793628d2a5c5f5d38151ff Package: CancerMutationAnalysis Version: 1.30.0 Depends: R (>= 2.10.0), qvalue Imports: AnnotationDbi, limma, methods, stats Suggests: KEGG.db License: GPL (>= 2) + file LICENSE MD5sum: 5fd082d79fdcea00f3116fbbbd6bae33 Package: CancerSubtypes Version: 1.14.0 Depends: R (>= 3.5.0), sigclust, NMF Imports: SNFtool, iCluster, cluster, impute, limma, ConsensusClusterPlus, grDevices, survival Suggests: BiocGenerics, knitr, RTCGA.mRNA License: GPL (>= 2) MD5sum: 2357096fb047b67ad0995050bdaad808 Package: CAnD Version: 1.20.0 Imports: methods, ggplot2, reshape Suggests: RUnit, BiocGenerics, BiocStyle License: Artistic-2.0 MD5sum: 5daaf11c310a258210d6002d7e3106ed Package: caOmicsV Version: 1.18.0 Depends: R (>= 3.2), igraph (>= 0.7.1), bc3net (>= 1.0.2) License: GPL (>= 2.0) MD5sum: 853139e9dcff1bef2242b4766a9baad3 Package: Cardinal Version: 2.6.0 Depends: BiocGenerics, BiocParallel, EBImage, graphics, methods, S4Vectors (>= 0.23.18), stats, ProtGenerics Imports: Biobase, dplyr, irlba, lattice, Matrix, matter, magrittr, mclust, nlme, parallel, signal, sp, stats4, utils, viridisLite Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 8b04ead30b9fd33d176b5ca201fecd44 Package: CARNIVAL Version: 1.0.0 Depends: R (>= 4.0) Imports: doParallel, readr, viper, AnnotationDbi, Category, ggplot2, UniProt.ws, lpSolve, igraph Suggests: knitr, readxl, testthat (>= 2.1.0) License: Apache License (== 3.0) | file LICENSE MD5sum: 8b05c34e7fc7d0c93faddaebd0f63ffe Package: casper Version: 2.22.0 Depends: R (>= 3.6.0), Biobase, IRanges, methods, GenomicRanges Imports: BiocGenerics (>= 0.31.6), coda, EBarrays, gaga, gtools, GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors (>= 0.9.25), sqldf, survival, VGAM Enhances: parallel License: GPL (>= 2) MD5sum: a0678806d7aeeb9c9081c74b3ba912f2 Package: CATALYST Version: 1.12.2 Depends: R (>= 4.0), SingleCellExperiment Imports: circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot, data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel, ggridges, graphics, grDevices, grid, gridExtra, magrittr, Matrix, matrixStats, methods, nnls, purrr, RColorBrewer, reshape2, Rtsne, SummarizedExperiment, S4Vectors, scales, scater, stats Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat License: GPL (>= 2) MD5sum: 08a817411ff595d7d182de87530e9d07 Package: Category Version: 2.54.0 Depends: methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix Imports: utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGG.db, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db License: Artistic-2.0 MD5sum: ddd8791ae4e4a347ac8b86d19c5db76e Package: categoryCompare Version: 1.32.0 Depends: R (>= 2.10), Biobase, BiocGenerics (>= 0.13.8), Imports: AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1), GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29), methods, grDevices, utils Suggests: knitr, GO.db, KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter License: GPL-2 MD5sum: 95cd28ac09a0037061033626e6012873 Package: CausalR Version: 1.20.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 0c1f70ed7f9a6abaa746afd99b7f03ac Package: cbaf Version: 1.10.1 Depends: R (>= 3.5.0) Imports: BiocFileCache, RColorBrewer, cgdsr, genefilter, gplots, grDevices, stats, utils, xlsx Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: d64d60943554a36a2cc5356c4e121311 Package: cBioPortalData Version: 2.0.10 Depends: R (>= 4.0.0), AnVIL, MultiAssayExperiment Imports: BiocFileCache (>= 1.5.3), digest, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment, RTCGAToolbox (>= 2.15.8), S4Vectors, SummarizedExperiment, stats, tibble, tidyr, TCGAutils, utils Suggests: BiocStyle, knitr, testthat License: AGPL-3 MD5sum: ed4bd1f336f0e7c1370877ece1a602e4 Package: ccfindR Version: 1.8.0 Depends: R (>= 3.6.0) Imports: stats, S4Vectors, utils, 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: 721df334ec09478cabe26474bdcb023b Package: ccmap Version: 1.14.0 Imports: AnnotationDbi (>= 1.36.2), BiocManager (>= 1.30.4), 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: cbe2a2b45914b278429df1f8c545d0dd Package: CCPROMISE Version: 1.14.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: 2a81afe7e868b061bfe415d99bfc3c43 Package: ccrepe Version: 1.24.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat License: MIT + file LICENSE MD5sum: 3c0e358ffde2d964f2a784389ea8e4fa Package: celaref Version: 1.6.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang, BiocGenerics, S4Vectors, readr, tibble, DelayedArray Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat License: GPL-3 MD5sum: 94f5ca92014ae15001bc819af73d1cc7 Package: celda Version: 1.4.7 Depends: R (>= 3.6) Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, gridExtra, methods, reshape2, MAST, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, stringi, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro, pROC, scater (>= 1.14.4), scran, SingleCellExperiment, dbscan, DelayedArray, Seurat, stringr, Matrix LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, M3DExampleData, TENxPBMCData License: MIT + file LICENSE MD5sum: 3ea08a6f24141266ca6b65c7c5bb7e56 Package: cellbaseR Version: 1.12.0 Depends: R(>= 3.4) Imports: methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils, Rsamtools, BiocParallel, foreach, utils, parallel, doParallel Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation License: Apache License (== 2.0) MD5sum: 38c651a213fc64a83837323f06b66a33 Package: CellBench Version: 1.4.1 Depends: R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils Imports: BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, tidyselect, lubridate Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 License: GPL-3 MD5sum: 39a7cfc68fb6fe07c8dc63e462344da5 Package: cellHTS2 Version: 2.52.0 Depends: R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid Imports: prada, GSEABase, Category, stats4, BiocGenerics Suggests: ggplot2 License: Artistic-2.0 MD5sum: 8656da2b5d198e189615f9bc30b37237 Package: cellity Version: 1.16.0 Depends: R (>= 3.3) Imports: AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid, mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats, topGO, utils Suggests: BiocStyle, caret, knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: 76a11f4c1aba469fdf6caa649daca2c4 Package: CellMapper Version: 1.14.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 MD5sum: e6b38eb497a12b4ad0409a4069c62740 Package: CellMixS Version: 1.4.2 Depends: kSamples, R (>= 3.6) Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat, limma License: GPL (>= 2) MD5sum: f0d1314dc20eacc005367b367d9aae37 Package: CellNOptR Version: 1.34.0 Depends: R (>= 3.5.0), RBGL, graph, methods, hash, RCurl, Rgraphviz, XML, ggplot2 Imports: igraph, stringi, stringr, Suggests: data.table, dplyr, tidyr, readr, RUnit, BiocGenerics, Enhances: doParallel License: GPL-3 MD5sum: 2ebbf68e666e88739d3741acb7cb8797 Package: cellscape Version: 1.12.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0), plyr (>= 1.8.3), dplyr (>= 0.4.3), gtools (>= 3.5.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 308f66fda7ba594d05fb7182e7c800ef Package: CellScore Version: 1.8.0 Depends: R (>= 3.5.0) Imports: Biobase (>= 2.39.1), graphics (>= 3.5.0), grDevices (>= 3.5.0), gplots (>= 3.0.1), lsa (>= 0.73.1), methods (>= 3.5.0), RColorBrewer(>= 1.1-2), squash (>= 1.0.8), stats (>= 3.5.0), utils(>= 3.5.0) Suggests: hgu133plus2CellScore, knitr License: GPL-3 MD5sum: f905cd5764bc1b86b0d56a66e023651a Package: CellTrails Version: 1.6.1 Depends: R (>= 3.5), SingleCellExperiment Imports: BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats, ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv, reshape2, Rtsne, stats, splines, SummarizedExperiment, utils Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown License: Artistic-2.0 MD5sum: 1d06d120ee5d75ce65fcf66fffd55d2e Package: cellTree Version: 1.18.0 Depends: R (>= 3.3), topGO Imports: topicmodels, slam, maptpx, igraph, xtable, gplots Suggests: BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db, Biobase, tools License: Artistic-2.0 MD5sum: 95771d090078ef59dfce49311819af26 Package: CEMiTool Version: 1.12.2 Depends: R (>= 4.0) Imports: methods, scales, dplyr, data.table (>= 1.9.4), WGCNA, grid, ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler, fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools, pracma, intergraph, grDevices, utils, network, matrixStats, ggdendro, gridExtra, gtable, fastcluster Suggests: testthat, BiocManager License: GPL-3 MD5sum: dd6eaebe268a86f85a184c1d13f5d487 Package: ceRNAnetsim Version: 1.0.0 Depends: R (>= 4.0.0), dplyr, tidygraph Imports: furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, stats Suggests: knitr, png, rmarkdown, testthat, covr License: GPL (>= 3.0) MD5sum: 95de197d102286718a267f5026a3620e Package: CeTF Version: 1.0.7 Depends: R (>= 4.0), methods Imports: circlize, ComplexHeatmap, clusterProfiler, DESeq2, GenomicTools, GenomicTools.fileHandler, ggnetwork, GGally, ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3, S4Vectors, stats, SummarizedExperiment, utils, WebGestaltR LinkingTo: Rcpp, RcppArmadillo Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat License: GPL-3 MD5sum: a21b74f02af8df60aab0d2bc1973b15b Package: CexoR Version: 1.26.0 Depends: R (>= 2.10.0), S4Vectors, IRanges Imports: Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation Suggests: RUnit, BiocGenerics, BiocStyle License: Artistic-2.0 | GPL-2 + file LICENSE MD5sum: 51afdea50c5782a94d2ea4ff29733b49 Package: CFAssay Version: 1.22.0 Depends: R (>= 2.10.0) License: LGPL MD5sum: f3b327f2eab39ab8413eff30abfe8ac3 Package: CGHbase Version: 1.48.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL MD5sum: 52e5f2acef2fb565f77521c07c6522c1 Package: CGHcall Version: 2.50.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall MD5sum: 99d708607fda9a0e152dd45eecedbbcf Package: cghMCR Version: 1.46.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL MD5sum: 040289a0c6c31d917ee31e66431cd8d5 Package: CGHnormaliter Version: 1.42.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) MD5sum: 05ec6099404f78ac132ec08da8e31cad Package: CGHregions Version: 1.46.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase MD5sum: 307eae5bae29f49022c5535e3d1fde9e Package: ChAMP Version: 2.18.3 Depends: R (>= 3.3), minfi, ChAMPdata (>= 2.6.0),DMRcate, Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest, DT Imports: prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b4.hg19, limma,RPMM, DNAcopy, preprocessCore,impute, marray, wateRmelon, plyr,goseq,missMethyl,kpmt,ggplot2, GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly (>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat Suggests: knitr,rmarkdown License: GPL-3 MD5sum: 6fb63f1399490db3f2e237519dcb0948 Package: ChemmineOB Version: 1.26.0 Depends: R (>= 2.15.1), methods Imports: BiocGenerics, zlibbioc, Rcpp (>= 0.11.0) LinkingTo: BH, Rcpp Suggests: ChemmineR, BiocStyle, knitr, knitcitations, knitrBootstrap, BiocManager Enhances: ChemmineR (>= 2.13.0) License: file LICENSE MD5sum: f96904c68059ecfe94ef65bb84bd9199 Package: ChemmineR Version: 3.40.0 Depends: R (>= 2.10.0), methods Imports: rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp (>= 0.11.0), ggplot2,grid,gridExtra, png,base64enc,DT,rsvg LinkingTo: Rcpp, BH Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineOB (>= 1.16.1), ChemmineDrugs, png,rmarkdown, BiocManager Enhances: ChemmineOB License: Artistic-2.0 MD5sum: bf6ea94f94aa5501dd6647b4ecf5c0f2 Package: CHETAH Version: 1.4.0 Depends: R (>= 3.6), ggplot2, SingleCellExperiment Imports: gplots, shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr License: file LICENSE MD5sum: b67e6ccf22efff369e2f4d62bb55d743 Package: ChIC Version: 1.8.0 Depends: spp, R (>= 3.6) Imports: ChIC.data (>= 1.7.1), caTools, methods,GenomicRanges, IRanges, parallel, progress, caret, grDevices, stats, utils, graphics, S4Vectors, BiocGenerics License: GPL-2 MD5sum: 5ad520aae41f9fa85ec7a803e7d5d735 Package: Chicago Version: 1.16.1 Depends: R (>= 3.2), data.table Imports: matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub License: Artistic-2.0 MD5sum: 48e99fc7021884d3d2916e677092334d Package: chimera Version: 1.30.0 Depends: Biobase, GenomicRanges (>= 1.13.3), Rsamtools (>= 1.13.1), GenomicAlignments, methods, AnnotationDbi, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens Suggests: BiocParallel, geneplotter Enhances: Rsubread, BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: 1fa2e579edbed1f0eb039f3c57132578 Package: ChIPanalyser Version: 1.10.0 Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb Suggests: BSgenome.Dmelanogaster.UCSC.dm3,knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: dbe673d5b821cecc992284f7c812a25d Package: ChIPComp Version: 1.18.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,rtracklayer,GenomeInfoDb,S4Vectors Imports: Rsamtools,limma,BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,BiocGenerics Suggests: BiocStyle,RUnit License: GPL MD5sum: 71dbefc81ef51f36d796839ee8f238c4 Package: chipenrich Version: 2.12.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, chipenrich.data, GenomeInfoDb, GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra, MASS, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer, S4Vectors (>= 0.23.10), stats, stringr, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat License: GPL-3 MD5sum: eeeeccaf92b2db77f335f8dc4d1b39ed Package: ChIPexoQual Version: 1.12.0 Depends: R (>= 3.4.0), GenomicAlignments (>= 1.0.1) Imports: methods, utils, GenomeInfoDb, stats, BiocParallel, GenomicRanges (>= 1.14.4), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools (>= 1.16.1), IRanges (>= 1.6), S4Vectors (>= 0.8), biovizBase (>= 1.18), broom (>= 0.4), RColorBrewer (>= 1.1), dplyr (>= 0.5), scales (>= 0.4.0), viridis (>= 0.3), hexbin (>= 1.27), rmarkdown Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat License: GPL (>= 2) MD5sum: 62463f2c234543c90f5374c3bbcea03a Package: ChIPpeakAnno Version: 3.22.4 Depends: R (>= 3.5), methods, IRanges (>= 2.13.12), Biostrings (>= 2.47.6), GenomicRanges (>= 1.31.8), S4Vectors (>= 0.17.25) Imports: BiocGenerics (>= 0.1.0), GO.db, biomaRt, BSgenome, GenomicFeatures, GenomeInfoDb, grid, matrixStats, AnnotationDbi, limma, multtest, RBGL, graph, BiocManager, stats, regioneR, DBI, ensembldb, Biobase, seqinr, idr, GenomicAlignments, DelayedArray, SummarizedExperiment, rtracklayer, Rsamtools, VennDiagram 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, BSgenome.Hsapiens.UCSC.hg38, 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: 89de8b373c4928c4ce3ed6fb350d812c Package: ChIPQC Version: 1.24.1 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, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene Suggests: BiocStyle License: GPL (>= 3) MD5sum: 8ecac01a0098c43a24472e3d5a918976 Package: ChIPseeker Version: 1.24.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, BiocGenerics, boot, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, graphics, grDevices, gtools, methods, plotrix, dplyr, parallel, magrittr, RColorBrewer, rtracklayer, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils Suggests: clusterProfiler (>= 3.15.4), ggimage, ggplotify, ggupset, ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, tibble License: Artistic-2.0 MD5sum: d8e546f26323b88a005b6cdc8134e46a Package: chipseq Version: 1.38.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), ShortRead Imports: methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges, ShortRead Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene License: Artistic-2.0 MD5sum: a877bcf6c6248825f67bd02fc637ca73 Package: ChIPseqR Version: 1.42.0 Depends: R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25) Imports: Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14), graphics, grDevices, HilbertVis, ShortRead, stats, timsac, utils License: GPL (>= 2) MD5sum: ac14a717f1e553e289212202245d322a Package: ChIPSeqSpike Version: 1.8.0 Depends: R (>= 3.5), rtracklayer (>= 1.37.6) Imports: tools, stringr, Rsamtools, GenomicRanges, IRanges, seqplots, ggplot2, LSD, corrplot, methods, stats, grDevices, graphics, utils, BiocGenerics, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 15bd9f8abbc4f0925807d03c3017a697 Package: ChIPsim Version: 1.42.0 Depends: Biostrings (>= 2.29.2) Imports: IRanges, XVector, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) MD5sum: fc52f4a9c890c14dfa0238ac80530047 Package: ChIPXpress Version: 1.32.0 Depends: R (>= 2.10), ChIPXpressData Imports: Biobase, GEOquery, frma, affy, bigmemory, biganalytics Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: fbd0d923e3e6281b7686e7f904c050fc Package: chopsticks Version: 1.54.0 Imports: graphics, stats, utils, methods, survival Suggests: hexbin License: GPL-3 MD5sum: 371d4cddde289c39c79502d80ea67745 Package: chromDraw Version: 2.18.0 Depends: R (>= 3.0.0) Imports: Rcpp (>= 0.11.1), GenomicRanges (>= 1.17.46) LinkingTo: Rcpp License: GPL-3 MD5sum: 93b1e246a05edb2ef251a4101f7f2666 Package: ChromHeatMap Version: 1.42.0 Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0) Imports: Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer, GenomicRanges Suggests: ALL, hgu95av2.db License: Artistic-2.0 MD5sum: efcdbe7114ba41df5f3f0aff605b442c Package: chromPlot Version: 1.16.0 Depends: stats, utils, graphics, grDevices, datasets, base, biomaRt, GenomicRanges, R (>= 3.1.0) Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 7083b92e4dfb8e88733d9fcb32bc3f2f Package: chromstaR Version: 1.14.1 Depends: R (>= 3.3), GenomicRanges, 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: cb5c32bfad5198d25b8d8bc57713619c Package: chromswitch Version: 1.10.0 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: 9c2fa818490295f453c09d0423b71fae Package: chromVAR Version: 1.10.0 Depends: R (>= 3.4) Imports: IRanges, GenomeInfoDb, GenomicRanges, ggplot2, nabor, BiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools, S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats, utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment, RColorBrewer, BSgenome LinkingTo: Rcpp, RcppArmadillo Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr License: MIT + file LICENSE MD5sum: e097ee8499ed9ca5c5827ed128567ac8 Package: CHRONOS Version: 1.16.0 Depends: R (>= 3.5) Imports: XML, RCurl, RBGL, parallel, foreach, doParallel, openxlsx, igraph, circlize, graph, stats, utils, grDevices, graphics, methods, biomaRt Suggests: RUnit, BiocGenerics, knitr License: GPL-2 MD5sum: b9057ffdcdfb2870d3a9c3e2b1d43286 Package: cicero Version: 1.6.2 Depends: R (>= 3.5.0), monocle, Gviz (>= 1.22.3) Imports: assertthat (>= 0.2.0), Biobase (>= 2.37.2), BiocGenerics (>= 0.23.0), data.table (>= 1.10.4), dplyr (>= 0.7.4), FNN (>= 1.1), GenomicRanges (>= 1.30.3), ggplot2 (>= 2.2.1), glasso (>= 1.8), grDevices, igraph (>= 1.1.0), IRanges (>= 2.10.5), Matrix (>= 1.2-12), methods, parallel, plyr (>= 1.8.4), reshape2 (>= 1.4.3), S4Vectors (>= 0.14.7), stats, stringi, stringr (>= 1.2.0), tibble (>= 1.4.2), tidyr, VGAM (>= 1.0-5), utils Suggests: AnnotationDbi (>= 1.38.2), knitr, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr License: MIT + file LICENSE MD5sum: e1d1764452fb5c939e7efc7b6a2ba042 Package: CINdex Version: 1.16.0 Depends: R (>= 3.3), GenomicRanges Imports: bitops,gplots,grDevices,som, dplyr,gridExtra,png,stringr,S4Vectors, IRanges, GenomeInfoDb,graphics, stats, utils Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens License: GPL (>= 2) MD5sum: 7d754c97f383a114340401eb1adaef60 Package: circRNAprofiler Version: 1.2.1 Depends: R(>= 4.0.0), gwascat Imports: dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2, edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb, universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, Biostrings, BSgenome, Suggests: testthat, knitr, roxygen2, rmarkdown, citr, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager, License: GPL-3 MD5sum: 974b8abf78fdcc43e8efc4c5fd430986 Package: cisPath Version: 1.28.0 Depends: R (>= 2.10.0) Imports: methods, utils License: GPL (>= 3) MD5sum: fa99f2513976e9d2d7227689c60aab27 Package: CiteFuse Version: 1.0.0 Depends: R (>= 4.0) Imports: SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>= 1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid, dbscan, SNFtool, propr, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph, scales, scran (>= 1.14.6), graphics, methods, stats, utils, reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5, rlang Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle License: GPL-3 MD5sum: 6298e1be97f0ed575d09a53afb25d81f Package: ClassifyR Version: 2.8.0 Depends: R (>= 3.5.0), methods, S4Vectors (>= 0.18.0), MultiAssayExperiment (>= 1.6.0), BiocParallel Imports: locfit, grid, utils, plyr Suggests: limma, genefilter, 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: 7997e82191a1647514f0054097fa7801 Package: cleanUpdTSeq Version: 1.26.0 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: 24445a02acaff4ce8f7ae17660603a64 Package: cleaver Version: 1.26.1 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: fa39360b1f12b4e705aa424db908a012 Package: clippda Version: 1.38.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>= 2) MD5sum: 457c5a6f68a3478c09b0ce9b106d4dfa Package: clipper Version: 1.28.0 Depends: R (>= 2.15.0), Matrix, graph Imports: methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor, RBGL Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle Enhances: RCy3 License: AGPL-3 MD5sum: 9e57d892798339879aa9203905b946e0 Package: cliqueMS Version: 1.2.1 Depends: R (>= 3.6.0) Imports: Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, qlcMatrix, matrixStats, methods LinkingTo: Rcpp, BH, RcppArmadillo Suggests: knitr, rmarkdown, testthat, CAMERA License: GPL (>= 2) MD5sum: dc06e47e4ee41a167c998e48c559bf38 Package: Clomial Version: 1.24.0 Depends: R (>= 2.10), matrixStats Imports: methods, permute License: GPL (>= 2) MD5sum: 23ddf1718672a2592669b9b737801da2 Package: Clonality Version: 1.36.0 Depends: R (>= 2.12.2), DNAcopy Imports: grDevices, graphics, stats, utils Suggests: gdata License: GPL-3 MD5sum: 900e81afbce360fae69cfd8c693c6474 Package: clonotypeR Version: 1.26.0 Imports: methods Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan License: file LICENSE MD5sum: 06716daba23f66fe8555335ec83fdc56 Package: clst Version: 1.36.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 MD5sum: 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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: 2a4b90feb214cae5395c0a2a770808e3 Package: ClusterJudge Version: 1.10.0 Depends: R (>= 3.6), stats, utils, graphics, infotheo, lattice, latticeExtra, httr, jsonlite Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt License: Artistic-2.0 MD5sum: 5edd4bc764525c046139f835b991ac0a Package: clusterProfiler Version: 3.16.1 Depends: R (>= 3.4.0) Imports: AnnotationDbi, downloader, DOSE (>= 3.13.1), dplyr, enrichplot (>= 1.7.1), GO.db, GOSemSim, magrittr, methods, plyr, qvalue, rlang, rvcheck, stats, tidyr, utils Suggests: AnnotationHub, knitr, org.Hs.eg.db, prettydoc, ReactomePA, testthat License: Artistic-2.0 MD5sum: 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ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle License: MIT + file LICENSE MD5sum: 08e01e4ce6838dddf862fca90cb25c08 Package: CMA Version: 1.46.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm License: GPL (>= 2) MD5sum: 82e0983475b16dea9b9eb5920cd98064 Package: cmapR Version: 1.0.0 Depends: R (>= 3.5) Imports: methods, rhdf5, data.table, prada, SummarizedExperiment, matrixStats Suggests: knitr, testthat, BiocStyle License: file LICENSE MD5sum: c21c7e67492dde8d09e3fe7fc8ebaa00 Package: cn.farms Version: 1.36.0 Depends: R (>= 3.0), Biobase, methods, ff, oligoClasses, snow Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 License: LGPL (>= 2.0) MD5sum: 9ab6afde67887c461da25cec6725ee44 Package: cn.mops Version: 1.34.0 Depends: R (>= 2.12), methods, utils, stats, graphics, parallel, GenomicRanges Imports: BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb, S4Vectors, exomeCopy Suggests: DNAcopy License: LGPL (>= 2.0) MD5sum: e576eb31cb482ea50a0469c495fd80cd Package: CNAnorm Version: 1.34.0 Depends: R (>= 2.10.1), methods Imports: DNAcopy License: GPL-2 MD5sum: 367287b08b57584c0328773f1ad8bede Package: CNEr Version: 1.24.0 Depends: R (>= 3.4) Imports: Biostrings (>= 2.33.4), DBI (>= 0.7), RSQLite (>= 0.11.4), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.23.16), rtracklayer (>= 1.25.5), XVector (>= 0.5.4), GenomicAlignments (>= 1.1.9), methods, S4Vectors (>= 0.13.13), IRanges (>= 2.5.27), readr (>= 0.2.2), BiocGenerics, tools, parallel, reshape2 (>= 1.4.1), ggplot2 (>= 2.1.0), poweRlaw (>= 0.60.3), annotate (>= 1.50.0), GO.db (>= 3.3.0), R.utils (>= 2.3.0), KEGGREST (>= 1.14.0) LinkingTo: S4Vectors, IRanges, XVector Suggests: Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3 License: GPL-2 | file LICENSE License_restricts_use: yes MD5sum: 6274cff805fff684927171c1e569d245 Package: CNORdt Version: 1.30.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 MD5sum: 4e7621985b08a1fc836438bb2d29beaf Package: CNORfeeder Version: 1.28.0 Depends: R (>= 3.6.0), CellNOptR (>= 1.4.0), graph Suggests: minet, catnet, Rgraphviz, RUnit, BiocGenerics, igraph Enhances: MEIGOR License: GPL-3 MD5sum: 91e9d8876370904f69174d9b03f1ab73 Package: CNORfuzzy Version: 1.30.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 MD5sum: 1ef489dc2d81ff7610e12344b2b34adc Package: CNORode Version: 1.30.0 Depends: CellNOptR (>= 1.5.14), genalg Enhances: MEIGOR License: GPL-2 MD5sum: 225f23c49affd2683249a388766a086d Package: CNTools Version: 1.44.0 Depends: R (>= 2.10), methods, 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BiocGenerics License: GPL-3 MD5sum: eeca3504beeafe66e6d5c76db15bd07d Package: CNVRanger Version: 1.4.3 Depends: GenomicRanges, RaggedExperiment Imports: BiocParallel, GDSArray, GenomeInfoDb, IRanges, S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR, gdsfmt, grDevices, lattice, limma, methods, plyr, qqman, rappdirs, reshape2, stats, utils Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, curatedTCGAData, ensembldb, grid, knitr, regioneR, rmarkdown License: Artistic-2.0 MD5sum: ab8e1d830fe059f126c9b2e5491958f7 Package: CNVrd2 Version: 1.26.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 MD5sum: 028cea128b73cc4ed86221c03aca4054 Package: CoCiteStats Version: 1.60.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL MD5sum: 7b4f9bd981a0e9a3df4a200451411ab6 Package: COCOA 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RUnit, BiocGenerics, knitr License: LGPL MD5sum: 80f8966077ec507e3798d906be2e3e92 Package: CoGAPS Version: 3.8.0 Depends: R (>= 3.5.0) Imports: BiocParallel, cluster, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5 LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL (== 2) MD5sum: 61cfd7b5d8a86e5eff245cb77b609688 Package: cogena Version: 1.22.0 Depends: R (>= 3.6), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools Suggests: knitr, rmarkdown (>= 2.1) License: LGPL-3 MD5sum: 5a7a25be51a769289390bfe5016ad576 Package: coGPS Version: 1.32.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 MD5sum: 980bcb639a3e314fef549dd3aba58c3c Package: COHCAP Version: 1.34.1 Depends: WriteXLS, COHCAPanno, 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Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 366025fd48da3ab749a8e0dfe32fa686 Package: coMET Version: 1.20.0 Depends: R (>= 3.6.0), grid, utils, biomaRt, Gviz, psych Imports: colortools, hash,grDevices, gridExtra, rtracklayer, IRanges, S4Vectors, GenomicRanges, stats, corrplot Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 8ea7e822c6cb9cddbf5ad4a0b7f0f243 Package: compartmap Version: 1.6.0 Depends: R (>= 3.5.0), minfi, Homo.sapiens, mixOmics Imports: SummarizedExperiment, GenomicRanges, gtools, parallel Suggests: covr, testthat, knitr License: GPL-3 + file LICENSE MD5sum: b0f389e7505543bc7abd435c6276aa94 Package: COMPASS Version: 1.26.0 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: 1971bafe9aef13edcdaf9a2ebaf2655c Package: compcodeR Version: 1.24.0 Depends: R (>= 3.0.2), sm Imports: tcltk, knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, gdata, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods Suggests: BiocStyle, EBSeq, DESeq, DESeq2 (>= 1.1.31), baySeq (>= 2.2.0), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), rmarkdown Enhances: rpanel, DSS License: GPL (>= 2) MD5sum: 1443cf34de1185e54542d79aae7e0b29 Package: compEpiTools Version: 1.22.0 Depends: R (>= 3.1.1), methods, topGO, GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, GenomeInfoDb Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer License: GPL MD5sum: bda220f5e81b6fe0a9c64e59d2923a11 Package: CompGO Version: 1.24.0 Depends: RDAVIDWebService Imports: rtracklayer, Rgraphviz, ggplot2, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, pcaMethods, reshape2, pathview License: GPL-2 MD5sum: b060051f7e6dea89a3527f8ed9fa19ee Package: ComplexHeatmap Version: 2.4.3 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, gridtext License: MIT + file LICENSE MD5sum: 22eddcf6d9ba796fda756a5be2f7c3a8 Package: CONFESS Version: 1.16.0 Depends: R (>= 3.3),grDevices,utils,stats,graphics Imports: methods,changepoint,cluster,contrast,data.table(>= 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limma, org.Hs.eg.db, pcaMethods, RColorBrewer, Rsamtools, RUVSeq, S4Vectors, stats, SummarizedExperiment, TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: d8cf6b0de8e99d4bd12f8f1a8240acd5 Package: consensusOV Version: 1.10.0 Depends: R (>= 3.6) Imports: Biobase, GSVA, gdata, genefu, limma, matrixStats, randomForest, stats, utils, methods Suggests: BiocStyle, ggplot2, knitr, rmarkdown License: Artistic-2.0 MD5sum: 3600c1794a35337ba12a058358d36f8a Package: consensusSeekeR Version: 1.16.0 Depends: R (>= 2.10), BiocGenerics, IRanges, GenomicRanges, BiocParallel Imports: GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 7bb6868599545600bf829cd8f94f3b3a Package: contiBAIT Version: 1.16.0 Depends: BH (>= 1.51.0-3), Rsamtools (>= 1.21) Imports: data.table, grDevices, clue, cluster, gplots, BiocGenerics (>= 0.31.6), S4Vectors, IRanges, GenomicRanges, Rcpp, TSP, 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Package: CRISPRseek Version: 1.28.0 Depends: R (>= 3.0.1), BiocGenerics, Biostrings Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges, BSgenome, BiocParallel, hash, methods Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL (>= 2) MD5sum: 44505d3b889c39f4c06f31b663d51827 Package: crisprseekplus Version: 1.14.0 Depends: R (>= 3.3.0), shiny, shinyjs, CRISPRseek Imports: DT, utils, GUIDEseq, GenomicRanges, GenomicFeatures, BiocManager, BSgenome, AnnotationDbi, hash Suggests: testthat, rmarkdown, knitr, R.rsp License: GPL-3 + file LICENSE MD5sum: be3fc2d9862db366cb55df7f6d6cff18 Package: CrispRVariants Version: 1.16.0 Depends: R (>= 3.5), ggplot2 (>= 2.2.0) Imports: AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>= 0.9.38), utils Suggests: BiocStyle, gdata, GenomicFeatures, knitr, rmarkdown, rtracklayer, sangerseqR, testthat, VariantAnnotation License: GPL-2 MD5sum: 52c49783ff348aca0455e4b425ed7f65 Package: crlmm Version: 1.46.0 Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= 1.17.7) Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>= 1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats, VGAM, parallel, graphics, limma, beanplot LinkingTo: preprocessCore (>= 1.17.7) Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats, RUnit License: Artistic-2.0 MD5sum: 2f61a39737a5d462a6ec28adcb0c2b1d Package: CrossICC Version: 1.2.0 Depends: R (>= 3.5), MASS Imports: data.table, methods, MergeMaid, ConsensusClusterPlus, 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 | 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IRanges, GenomeInfoDb, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 MD5sum: 02d77c52b6af45d10b0292e198ba9e30 Package: csaw Version: 1.22.1 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: bf10ad270bd54f4d6060b97b6722bb9c Package: CSSP Version: 1.26.0 Imports: methods, splines, stats, utils Suggests: testthat License: GPL-2 MD5sum: 68d3b996630b04de6fe6f17326cbdd6e Package: CSSQ Version: 1.0.5 Depends: SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, rtracklayer Imports: GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown License: 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pander, rmarkdown, testthat License: GPL-2 MD5sum: f1a906ec5694f993f29b20c4cf1e1457 Package: cummeRbund Version: 2.30.0 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: 512b184b01da8847bfc7daca80b30033 Package: customProDB Version: 1.28.0 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: 812da57158f5be5b45367338928498c8 Package: cycle Version: 1.42.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats 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RcppArmadillo, RcppParallel(>= 4.4.2-1), flowWorkspace Suggests: testthat, flowWorkspaceData , knitr, parallel License: file LICENSE License_restricts_use: yes MD5sum: b6108ad72ae63cc0ec80805a7811a635 Package: dada2 Version: 1.16.0 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: dbc9213a41c08db7b7703d8254ee6a2b Package: dagLogo Version: 1.26.2 Depends: R (>= 3.0.1) Imports: pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils, biomaRt, grid, motifStack, grImport2, methods Suggests: XML, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 96c8816070582c51ed2d8c861d2e8e7b Package: daMA Version: 1.60.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: 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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, tidyverse, vsn, FactoMineR, factoextra, visNetwork Suggests: BiocGenerics, Biobase, testthat, BiocStyle License: Artistic-2.0 MD5sum: 1a9a9a38eb0ecfb33e4b7745e6e0dabb Package: DART Version: 1.36.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: cc33ecffb9a9b6d49f4c7c6c7342d970 Package: DBChIP Version: 1.32.0 Depends: R (>= 2.15.0), edgeR, DESeq Suggests: ShortRead, BiocGenerics License: GPL (>= 2) MD5sum: 9325ac28590cdc4963ac7facaed567b4 Package: dcanr Version: 1.4.0 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: ed344dbe63e5d6b102aab0579ce3515a Package: dcGSA Version: 1.16.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: 2b5553b04b03b8194f67712367454302 Package: DChIPRep Version: 1.18.0 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: e051b11b6d2f874570ae5c515c41d5e1 Package: ddCt Version: 1.44.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: RUnit License: LGPL-3 MD5sum: 3bbb0f1a6bb1d0c2a8611484dea83059 Package: ddPCRclust Version: 1.8.0 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: 16f5e453d3da815a3caffb9c94bb8e6e Package: dearseq Version: 1.0.0 Depends: R (>= 3.6.0) Imports: CompQuadForm, ggplot2, KernSmooth, matrixStats, methods, parallel, pbapply, stats, statmod Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr License: GPL-2 | file LICENSE MD5sum: 8a9236a57c293101789f92f65ccd3fe7 Package: debCAM Version: 1.6.0 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: fe7f0f35ef13b21ccbfff1581b66d0b5 Package: debrowser Version: 1.16.3 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, 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: b84a884508c34ad24884f72567278e0f Package: DECIPHER Version: 2.16.1 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: 5b40f4ac042680cb83c52cae2330dd30 Package: deco Version: 1.4.1 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: e33b3d3a8b9461d70db13b9be2f8c54c Package: DEComplexDisease Version: 1.8.0 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: 8e167cad40003bbd468e40debcc4b1c0 Package: decompTumor2Sig Version: 2.4.1 Depends: R(>= 3.6), ggplot2 Imports: methods, Matrix, quadprog(>= 1.5-5), GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table, GenomeInfoDb Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: c5dccfa0cd2585a4c983208504419b83 Package: DeconRNASeq Version: 1.30.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 MD5sum: 075765ebe3f416b39d463db7105bf817 Package: decontam Version: 1.8.0 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: b726a88ca861ce8dbea0501e0157138c Package: DeepBlueR Version: 1.14.0 Depends: R (>= 3.3), XML, RCurl Imports: GenomicRanges, data.table, stringr, diffr, dplyr, methods, rjson, utils, R.utils, foreach, withr, rtracklayer, GenomeInfoDb, settings, filehash Suggests: knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr, RColorBrewer, matrixStats License: GPL (>= 2.0) MD5sum: 4b2000f02c33b63be571cb61d9913f61 Package: deepSNV Version: 1.34.1 Depends: R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.13.44), Imports: Rhtslib LinkingTo: Rhtslib (>= 1.13.1) Suggests: RColorBrewer, knitr, rmarkdown License: GPL-3 MD5sum: b80fc104b8c5caa625525d9d60bc9b0f Package: DEFormats Version: 1.16.0 Imports: checkmate, data.table, DESeq2, edgeR (>= 3.13.4), GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat License: GPL-3 MD5sum: b98562c3b04814583e9675248cd54565 Package: DEGreport Version: 1.24.1 Depends: R (>= 3.6.0) 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: 14428fcc82d77665f9a8e11c236c0a15 Package: DEGseq Version: 1.42.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: fda903f97216cd3f9a746dfb1b10e288 Package: DelayedArray Version: 0.14.1 Depends: R (>= 3.4), methods, stats4, matrixStats, BiocGenerics (>= 0.31.5), S4Vectors (>= 0.25.15), IRanges (>= 2.17.3) Imports: stats, Matrix LinkingTo: S4Vectors Suggests: BiocParallel, HDF5Array, genefilter, SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit License: Artistic-2.0 MD5sum: 34dde64e65c9b2adaad8034eeda9d35d Package: DelayedDataFrame Version: 1.4.0 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: 56210b77ded4c2ce739ebf3ce963e5cb Package: DelayedMatrixStats Version: 1.10.1 Depends: DelayedArray (>= 0.14.0) Imports: methods, matrixStats (>= 0.56.0), Matrix, S4Vectors (>= 0.17.5), IRanges, HDF5Array (>= 1.16.1), BiocParallel Suggests: testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark, profmem License: MIT + file LICENSE MD5sum: 41b38fc89c0809e0773c9478aef63313 Package: deltaCaptureC Version: 1.2.0 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2 Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 49015e8bd93c519b13ba43f5d5eb3438 Package: deltaGseg Version: 1.28.0 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 MD5sum: abd6480c0b696f96e29c85fc92fd4ef5 Package: DeMAND Version: 1.18.0 Depends: R (>= 2.14.0), KernSmooth, methods License: file LICENSE MD5sum: cc09b9834974302557c91b912edbea2f Package: DeMixT Version: 1.4.0 Depends: R (>= 3.6.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment, knitr, KernSmooth, matrixcalc Imports: matrixStats, stats, truncdist, base64enc, ggplot2 LinkingTo: Rcpp License: GPL-3 MD5sum: 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BiocStyle License: MIT + file LICENSE MD5sum: e80e5c7b7f2f9fe8ea12e9ca86ad5fe8 Package: DEqMS Version: 1.6.0 Depends: R(>= 3.5),graphics,stats,ggplot2,limma(>= 3.34) Suggests: BiocStyle,knitr,rmarkdown,plyr,matrixStats,reshape2,farms,utils,ggrepel,ExperimentHub,LSD License: LGPL MD5sum: 958f2003f33dffe055f83e4900e49006 Package: derfinder Version: 1.22.0 Depends: R (>= 3.5.0) Imports: BiocGenerics (>= 0.25.1), AnnotationDbi (>= 1.27.9), BiocParallel (>= 1.15.15), bumphunter (>= 1.9.2), derfinderHelper (>= 1.1.0), GenomeInfoDb (>= 1.3.3), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges (>= 1.17.40), Hmisc, IRanges (>= 2.3.23), methods, qvalue (>= 1.99.0), Rsamtools (>= 1.25.0), rtracklayer, S4Vectors (>= 0.23.19), stats, utils Suggests: BiocStyle (>= 2.5.19), sessioninfo, derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitcitations (>= 1.0.1), knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat (>= 2.1.0), TxDb.Hsapiens.UCSC.hg19.knownGene, covr License: Artistic-2.0 MD5sum: 84f28ca6c51e0664bb97b8d7655adb76 Package: derfinderHelper Version: 1.22.0 Depends: R(>= 3.2.2) Imports: IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2) Suggests: sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6), BiocStyle (>= 2.5.19), rmarkdown (>= 0.3.3), testthat, covr License: Artistic-2.0 MD5sum: 9d880f928cb5649ae7aa07bb781c6c60 Package: derfinderPlot Version: 1.22.0 Depends: R(>= 3.2) Imports: derfinder (>= 1.1.0), GenomeInfoDb (>= 1.3.3), GenomicFeatures, GenomicRanges (>= 1.17.40), ggbio (>= 1.13.13), ggplot2, graphics, grDevices, IRanges (>= 1.99.28), limma, methods, plyr, RColorBrewer, reshape2, 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, covr License: Artistic-2.0 MD5sum: 791266e2d48ee191a62f7bfe83573eb8 Package: DEScan2 Version: 1.8.0 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: 6fdb3f54f8277f7a9eaad623d7fa23e6 Package: DESeq2 Version: 1.28.1 Depends: S4Vectors (>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter, methods, stats4, locfit, geneplotter, ggplot2, Rcpp (>= 0.11.0) LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10) License: LGPL (>= 3) MD5sum: 245f51e9c130d0063bf91bfa3e22d2f4 Package: DEsingle Version: 1.8.2 Depends: R (>= 3.4.0) Imports: stats, Matrix (>= 1.2-14), MASS (>= 7.3-45), VGAM (>= 1.0-2), bbmle (>= 1.0.18), gamlss (>= 4.4-0), maxLik (>= 1.3-4), pscl (>= 1.4.9), BiocParallel (>= 1.12.0), Suggests: knitr, rmarkdown, SingleCellExperiment License: GPL-2 MD5sum: 194e8190aa2bd04bbb9de2474afae063 Package: DEsubs Version: 1.14.0 Depends: R (>= 3.3), locfit Imports: graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq, DESeq, stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix, jsonlite, tools, DESeq2, methods Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: c3b24316fa29dd9bcca2b2e235aa5c7b Package: DEWSeq Version: 1.2.0 Depends: R(>= 4.0.0), R.utils, DESeq2, BiocParallel Imports: BiocGenerics, data.table(>= 1.11.8), GenomeInfoDb, GenomicRanges, methods, S4Vectors, SummarizedExperiment, stats, utils Suggests: knitr, rmarkdown, testthat, BiocStyle, IHW License: LGPL (>= 3) MD5sum: 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RSQLite, DBI, Rcpp LinkingTo: Rcpp Suggests: knitr, lattice, latticeExtra, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: GPL-3 MD5sum: ac4eca42b8fc8da49d4e8f48189988ee Package: DiffBind Version: 2.16.2 Depends: R (>= 3.5), GenomicRanges, SummarizedExperiment Imports: RColorBrewer, amap, edgeR, gplots, grDevices, limma, GenomicAlignments, locfit, stats, utils, IRanges, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools (>= 1.99.1), DESeq2, methods, graphics, ggrepel LinkingTo: Rhtslib (>= 1.15.3), Rcpp Suggests: DESeq, BiocStyle, testthat Enhances: rgl, XLConnect License: Artistic-2.0 MD5sum: ee5fca81c142e8ce1babc72ae56dbbba Package: diffcoexp Version: 1.8.0 Depends: R (>= 3.5), WGCNA, SummarizedExperiment Imports: stats, DiffCorr, psych, igraph, BiocGenerics Suggests: GEOquery License: GPL (> 2) MD5sum: b7d77123a649259463001e84c799775e Package: diffcyt Version: 1.8.8 Depends: R (>= 3.4.0) Imports: flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma, edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats, methods, utils, grDevices, graphics, ComplexHeatmap, circlize, grid Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST License: MIT + file LICENSE MD5sum: f248bab0839b1b87702463b1a36b1e5c Package: diffGeneAnalysis Version: 1.70.0 Imports: graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils License: GPL MD5sum: 8ba18a538ec203ef9a29631e52a3a547 Package: diffHic Version: 1.20.0 Depends: R (>= 3.5), GenomicRanges, InteractionSet, SummarizedExperiment Imports: Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma, csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb, BiocGenerics, grDevices, graphics, stats, utils, Rcpp, rtracklayer LinkingTo: Rhtslib (>= 1.13.1), zlibbioc, Rcpp Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix, testthat License: GPL-3 MD5sum: 852a3098ea6608182b47ff59ab800c75 Package: DiffLogo Version: 2.12.2 Depends: R (>= 3.4), stats, cba Imports: grDevices, graphics, utils, tools Suggests: knitr, testthat, seqLogo, MotifDb License: GPL (>= 2) MD5sum: 1077749561139ee6a90003090ee2c289 Package: diffloop Version: 1.16.0 Imports: methods, GenomicRanges, foreach, plyr, dplyr, reshape2, ggplot2, matrixStats, Sushi, edgeR, locfit, statmod, biomaRt, GenomeInfoDb, S4Vectors, IRanges, grDevices, graphics, stats, utils, Biobase, readr, data.table, rtracklayer, pbapply, limma Suggests: DESeq2, diffloopdata, ggrepel, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: d985fd0ab8ed51901f08e8a2cce982d9 Package: diffuStats Version: 1.8.0 Depends: R (>= 3.4) Imports: grDevices, stats, methods, Matrix, MASS, expm, igraph, Rcpp, RcppArmadillo, RcppParallel, plyr, precrec LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2 License: GPL-3 MD5sum: e3c3225e36592004fd0566454f47186d Package: diggit Version: 1.20.0 Depends: R (>= 3.0.2), Biobase, methods 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heatmaply, viridis, plotly, DT, gridExtra, methods, stats, SummarizedExperiment, BiocGenerics, S4Vectors, zip, reshape2 Suggests: testthat License: GPL-3 MD5sum: adb20797023592e6c6516b614c91e0f1 Package: distinct Version: 1.0.4 Depends: R (>= 4.0) Imports: Rcpp, stats, SummarizedExperiment, SingleCellExperiment, methods, Matrix, foreach, parallel, doParallel, doRNG, ggplot2, limma, scater LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, testthat, UpSetR License: GPL (>= 3) MD5sum: cb60f5a05d41edcda19bd4a41aa2d2d1 Package: dittoSeq Version: 1.0.2 Depends: ggplot2 Imports: methods, colorspace (>= 1.4), gridExtra, cowplot, reshape2, pheatmap, grDevices, ggrepel, ggridges, stats, utils, SummarizedExperiment, SingleCellExperiment, edgeR, S4Vectors Suggests: plotly, testthat, Seurat (>= 2.2), DESeq2, knitr, BiocStyle, scRNAseq License: MIT + file LICENSE MD5sum: 7a8d45a871e50fc15fb451a2b4ba10fd Package: divergence Version: 1.4.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, 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grDevices, graphics, methods, stats, utils Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 55612fc70ea4d93b2f891fbab3f55c86 Package: DMRcate Version: 2.2.3 Depends: R (>= 3.6.0), minfi, SummarizedExperiment Imports: ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, DSS, missMethyl, GenomicRanges, methods, graphics, plyr, Gviz, IRanges, stats, utils, S4Vectors Suggests: knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: file LICENSE MD5sum: 63514b881e7ff2e6793b1fedd4fc6847 Package: DMRforPairs Version: 1.24.0 Depends: R (>= 2.15.2), Gviz (>= 1.2.1), R2HTML (>= 2.2.1), GenomicRanges (>= 1.10.7), parallel License: GPL (>= 2) MD5sum: 647e0f1f765faaea5ddb22811ce6f203 Package: DMRScan Version: 1.10.0 Depends: R (>= 3.6.0) Imports: Matrix, MASS, RcppRoll,GenomicRanges, IRanges, GenomeInfoDb, methods, mvtnorm, stats, parallel Suggests: knitr, rmarkdown, BiocStyle, BiocManager License: GPL-3 MD5sum: 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rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim License: GPL-3 MD5sum: 9df115ec0f569fa8c0a74d9c328e1f80 Package: ffpe Version: 1.32.0 Depends: R (>= 2.10.0), TTR, methods Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc Suggests: genefilter, ffpeExampleData License: GPL (> 2) MD5sum: 02e69122e72f6473faab20807056f3b2 Package: FGNet Version: 3.22.1 Depends: R (>= 2.15) Imports: igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2, RColorBrewer, png, methods, stats, utils, graphics, grDevices Suggests: RCurl, RDAVIDWebService, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, RGtk2, BiocManager License: GPL (>= 2) MD5sum: 4279a4321b893009f944f88a396e6cce Package: fgsea Version: 1.14.0 Depends: R (>= 3.3) Imports: Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), gridExtra, grid, fastmatch, Matrix, utils LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery License: MIT + file LICENCE MD5sum: c8f7f018f00bf29b6777e4544c98a722 Package: FindMyFriends Version: 1.18.0 Imports: methods, BiocGenerics, Biobase, tools, dplyr, IRanges, Biostrings, S4Vectors, kebabs, igraph, Matrix, digest, filehash, Rcpp, ggplot2, gtable, grid, reshape2, ggdendro, BiocParallel, utils, stats LinkingTo: Rcpp Suggests: BiocStyle, testthat, knitr, rmarkdown, reutils License: GPL (>= 2) MD5sum: 3fc5b590dc6fc6d2aff877e6eafdf8b3 Package: FISHalyseR Version: 1.22.0 Depends: EBImage,abind Suggests: knitr License: Artistic-2.0 MD5sum: d9cd423cf053db6e18fd806906acf2d0 Package: fishpond Version: 1.4.1 Imports: graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, SummarizedExperiment, matrixStats, svMisc, Rcpp, Matrix LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm License: GPL-2 MD5sum: f9d7457943ae78c9b1d32bc5fe75cad5 Package: FitHiC Version: 1.14.0 Imports: data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: a0c5dad823f56581cc7c69dfea5ca3a7 Package: flagme Version: 1.44.0 Depends: gcspikelite, xcms, CAMERA Imports: gplots, graphics, MASS, methods, SparseM, stats, utils License: LGPL (>= 2) MD5sum: 0919c312b01483ac9b51466167a08ba1 Package: flowAI Version: 1.18.5 Depends: R (>= 3.6) Imports: ggplot2, flowCore, plyr, changepoint, knitr, reshape2, RColorBrewer, scales, methods, graphics, stats, utils, rmarkdown Suggests: testthat, shiny License: GPL (>= 2) MD5sum: 4d150a8e8590efa2cf390fe1a62c212e Package: flowBeads Version: 1.26.0 Depends: R (>= 2.15.0), methods, Biobase, rrcov, flowCore Imports: flowCore, rrcov, knitr, xtable Suggests: flowViz License: Artistic-2.0 MD5sum: 596d91bab55a9eb7a9322fde4780f8be Package: flowBin Version: 1.24.0 Depends: methods, flowCore, flowFP, R (>= 2.10) Imports: class, limma, snow, BiocGenerics Suggests: parallel License: Artistic-2.0 MD5sum: 5fc60f779ab0c5d70501f1c67478e4ce Package: flowcatchR Version: 1.22.0 Depends: R (>= 2.10), methods, EBImage Imports: colorRamps, abind, BiocParallel, graphics, stats, utils, plotly, shiny Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 925ac72e7c13a473c35054d626dae68f Package: flowCHIC Version: 1.22.0 Depends: R (>= 3.1.0) Imports: methods, flowCore, EBImage, vegan, hexbin, ggplot2, grid License: GPL-2 MD5sum: 38b4defed146a30e4fe881246cf750b0 Package: flowCL Version: 1.26.0 Depends: R (>= 3.4), Rgraphviz, SPARQL Imports: methods, grDevices, utils, graph Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 46392cd6f5550b943035cf3d147b3994 Package: flowClean Version: 1.26.0 Depends: R (>= 2.15.0), flowCore Imports: bit, changepoint, sfsmisc Suggests: flowViz, grid, gridExtra License: Artistic-2.0 MD5sum: 102d62f349db360a4036258a56fe3595 Package: flowClust Version: 3.26.0 Depends: R(>= 2.5.0) Imports: BiocGenerics, methods, Biobase, graph, ellipse, flowViz, flowCore, clue, corpcor, mnormt, parallel Suggests: testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown, openCyto License: Artistic-2.0 MD5sum: db96b769fc65e637c36d17a1c4194676 Package: flowCore Version: 2.0.1 Depends: R (>= 3.5.0) Imports: Biobase, BiocGenerics (>= 0.29.2), grDevices, graphics, methods, stats, utils, stats4, Rcpp, matrixStats, cytolib (>= 1.9.15) LinkingTo: Rcpp, RcppArmadillo, BH(>= 1.65.0.1), cytolib(>= 1.7.2), RProtoBufLib Suggests: Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat, flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto, gridExtra License: Artistic-2.0 MD5sum: ce2923137693b9b1545df015bd83c182 Package: flowCyBar Version: 1.24.0 Depends: R (>= 3.0.0) Imports: gplots, vegan, methods License: GPL-2 MD5sum: 4bf3d240c8d9459d1596c0a40312dee0 Package: flowDensity Version: 1.22.0 Imports: flowCore, graphics, flowViz (>= 1.46.1), car, sp, rgeos, gplots, RFOC, flowWorkspace (>= 3.33.1), methods, stats, grDevices Suggests: knitr License: Artistic-2.0 MD5sum: 0dc66b904b667c5566af25d71b035702 Package: flowFP Version: 1.46.0 Depends: R (>= 2.10), flowCore, flowViz Imports: Biobase, BiocGenerics (>= 0.1.6), graphics, grDevices, methods, stats, stats4 Suggests: RUnit License: Artistic-2.0 MD5sum: 230448b521aeb7aa3036e582a1deb0d3 Package: flowMap Version: 1.26.0 Depends: R (>= 3.0.1), ade4(>= 1.5-2), doParallel(>= 1.0.3), abind(>= 1.4.0), reshape2(>= 1.2.2), scales(>= 0.2.3), Matrix(>= 1.1-4), methods (>= 2.14) Suggests: BiocStyle, knitr License: GPL (>= 2) MD5sum: 85746f810c7d93c0484136a9245e5d03 Package: flowMatch Version: 1.24.0 Depends: R (>= 3.0.0), Rcpp (>= 0.11.0), methods, flowCore Imports: Biobase LinkingTo: Rcpp Suggests: healthyFlowData License: Artistic-2.0 MD5sum: c23b7c1c30a0468e33bb53e2b783143f Package: flowMeans Version: 1.48.0 Depends: R (>= 2.10.0) Imports: Biobase, graphics, grDevices, methods, rrcov, stats, feature, flowCore License: Artistic-2.0 MD5sum: 8c857e615667d62addef750b9f2afc07 Package: flowMerge Version: 2.36.0 Depends: graph,feature,flowClust,Rgraphviz,foreach,snow Imports: rrcov,flowCore, graphics, methods, stats, utils Suggests: knitr, rmarkdown Enhances: doMC, multicore License: Artistic-2.0 MD5sum: f323b3c46d8cd70d0e9253df15dd214b Package: flowPeaks Version: 1.34.0 Depends: R (>= 2.12.0) Enhances: flowCore License: Artistic-1.0 MD5sum: 7ff1f0c6abbb893b5d54a026af314244 Package: flowPloidy Version: 1.14.0 Imports: flowCore, car, caTools, knitr, rmarkdown, minpack.lm, shiny, methods, graphics, stats, utils Suggests: flowPloidyData, testthat License: GPL-3 MD5sum: cf20edd05e0957dae18b70ebe4f4b552 Package: flowPlots Version: 1.36.0 Depends: R (>= 2.13.0), methods Suggests: vcd License: Artistic-2.0 MD5sum: 9a2cc0092f83fc5daa7c1ce4743118f4 Package: FlowRepositoryR Version: 1.20.0 Depends: R (>= 3.2) Imports: XML, RCurl, tools, utils, jsonlite Suggests: RUnit, BiocGenerics, flowCore, methods License: Artistic-2.0 MD5sum: e342d32df3bdfcfbbee8aee76111193e Package: FlowSOM Version: 1.20.0 Depends: R (>= 3.2), igraph Imports: stats, utils, flowCore, ConsensusClusterPlus, BiocGenerics, tsne, CytoML, flowWorkspace, XML, RColorBrewer Suggests: BiocStyle License: GPL (>= 2) MD5sum: 53a0186f3b0da9f512ea5f38e58fa8d2 Package: flowSpecs Version: 1.2.0 Depends: R (>= 3.6) Imports: ggplot2 (>= 3.1.0), BiocGenerics (>= 0.30.0), BiocParallel (>= 1.18.1), reshape2 (>= 1.4.3), flowCore (>= 1.50.0), zoo (>= 1.8.6), stats (>= 3.6.0), methods (>= 3.6.0) Suggests: testthat, knitr, rmarkdown, BiocStyle, flowVS, DepecheR License: MIT + file LICENSE MD5sum: ae770ec726f5b5142dc7ab1c36c833a9 Package: flowSpy Version: 1.2.3 Depends: R (>= 3.6), igraph Imports: FlowSOM, Rtsne, ggplot2, destiny, gmodels, flowUtils, Biobase, Matrix, flowCore, sva, matrixStats, methods, mclust, prettydoc, RANN(>= 2.5), Rcpp (>= 0.12.0), BiocNeighbors, cluster, pheatmap, scatterpie, umap, scatterplot3d, limma, stringr, grDevices, grid, stats LinkingTo: Rcpp Suggests: BiocGenerics, knitr, RColorBrewer, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: dc461afd881970da665175e7bbe9c58c Package: flowStats Version: 4.0.0 Depends: R (>= 3.0.2) Imports: BiocGenerics, MASS, flowCore (>= 1.99.6), flowWorkspace, ncdfFlow(>= 2.19.5), flowViz, fda (>= 2.2.6), Biobase, methods, grDevices, graphics, stats, cluster, utils, KernSmooth, lattice, ks, RColorBrewer, rrcov Suggests: xtable, testthat, openCyto Enhances: RBGL,graph License: Artistic-2.0 MD5sum: 968533aa3c4cea9bf323239e26b31260 Package: flowTime Version: 1.12.0 Depends: R (>= 3.4), flowCore, plyr Imports: utils Suggests: knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, moments, stats License: Artistic-2.0 MD5sum: 6a134d92a906d2850a0325ef81102456 Package: flowTrans Version: 1.40.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 MD5sum: 892d967c55228d4c45cc7c463b3a6771 Package: flowUtils Version: 1.52.0 Depends: R (>= 2.2.0) Imports: Biobase, graph, methods, stats, utils, corpcor, RUnit, XML, flowCore (>= 1.32.0) Suggests: gatingMLData License: Artistic-2.0 MD5sum: a20f274d81c2d3902d9f3028ebb01d52 Package: flowViz Version: 1.52.0 Depends: R (>= 2.7.0), flowCore(>= 1.41.9), lattice Imports: stats4, Biobase, flowCore, graphics, grDevices, grid, KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer, stats, utils, hexbin,IDPmisc Suggests: colorspace, flowStats, knitr, testthat License: Artistic-2.0 MD5sum: 8533d7ba06e11601cf86c996e1b7e36b Package: flowWorkspace Version: 4.0.6 Depends: R (>= 3.5.0) Imports: Biobase, BiocGenerics, cytolib (>= 1.99.26), lattice, latticeExtra, XML, ggplot2, graph, graphics, grDevices, methods, stats, stats4, utils, RBGL, tools, Rgraphviz, data.table, dplyr, Rcpp, stringr, scales, matrixStats, RcppParallel, RProtoBufLib, digest, flowCore(>= 1.99.20), ncdfFlow(>= 2.25.4) LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib (>= 2.0.1),Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1) Suggests: testthat, flowWorkspaceData (>= 2.23.2), knitr, ggcyto, parallel, CytoML, openCyto License: file LICENSE License_restricts_use: yes MD5sum: fe7b56bd7e16bba57c1a168c8812fcff Package: fmcsR Version: 1.30.0 Depends: R (>= 2.10.0), ChemmineR, methods Imports: RUnit, methods, ChemmineR, BiocGenerics, parallel Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap License: Artistic-2.0 MD5sum: b490907c4c1cdd456d004b12f922c13c Package: FoldGO Version: 1.6.0 Depends: R (>= 4.0) Imports: topGO (>= 2.30.1), ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), stats, methods Suggests: knitr, rmarkdown, devtools, kableExtra License: GPL-3 MD5sum: d535ee450e8265b73e98aefcde62e6d8 Package: FourCSeq Version: 1.22.1 Depends: R (>= 3.0), splines, LSD, DESeq2 (>= 1.9.11), ggplot2 Imports: Biobase, Biostrings, GenomicRanges, SummarizedExperiment, Rsamtools, ggbio, reshape2, rtracklayer, fda, GenomicAlignments, gtools, Matrix, methods Suggests: BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene License: GPL (>= 3) MD5sum: 1221cb31765c50ae10f27c35a3556555 Package: FRASER Version: 1.0.2 Depends: BiocParallel, data.table, Rsamtools, SummarizedExperiment Imports: AnnotationDbi, BBmisc, Biobase, BiocGenerics, biomaRt, BSgenome, cowplot, DelayedArray (>= 0.5.11), DelayedMatrixStats, extraDistr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges, grDevices, ggplot2, ggrepel, HDF5Array, matrixStats, methods, pcaMethods, pheatmap, plotly, PRROC, RColorBrewer, rhdf5, Rsubread, R.utils, S4Vectors, stats, tibble, tools, utils, VGAM LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, License: MIT + file LICENSE MD5sum: 85d2959357e9daabdaa0323e6c570d55 Package: frenchFISH Version: 1.0.0 Imports: utils, MCMCpack, NHPoisson Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: eb886b9a0cf2b8f9936c762d2c2677a1 Package: FRGEpistasis Version: 1.24.0 Depends: R (>= 2.15), MASS, fda, methods, stats Imports: utils License: GPL-2 MD5sum: c5cefb4f574386829dc7b8e87044d7d6 Package: frma Version: 1.40.0 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: f4ec555a650f11fc00a78e4179b92b77 Package: frmaTools Version: 1.40.0 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: 550b952ced780dead27889d669936005 Package: FunChIP Version: 1.14.0 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: 20c2e43276afab6d25a7ef462b6e7dcf Package: FunciSNP Version: 1.32.0 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: 0cab8ed3f777d3b5cf03db7bf5c0dae4 Package: funtooNorm Version: 1.12.0 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: f704863482367e9f083762cc6df9f247 Package: GA4GHclient Version: 1.12.0 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: 20b994da8a76a8c4df1b50354c4346b7 Package: GA4GHshiny Version: 1.10.0 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: ec9631d6be78ff1304020c09b13b2234 Package: gaga Version: 2.34.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: parallel License: GPL (>= 2) MD5sum: 6b6f63bc428392a8bd32fc2a81aa37d3 Package: gage Version: 2.38.3 Depends: R (>= 2.10) Imports: graph, KEGGREST, AnnotationDbi, GO.db Suggests: pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq, DESeq2, edgeR, limma License: GPL (>= 2.0) MD5sum: 079abe3fbb2a3d0c8046f09aa2c329a4 Package: gaggle Version: 1.56.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>= 0.4.17) License: GPL (>= 2) MD5sum: 30369cd77970413abafa731ca533df9c Package: gaia Version: 2.32.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: 0d6e4889841931fc689c6bdde988ccf2 Package: GAPGOM Version: 1.4.0 Depends: R (>= 4.0) 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: b4c513ebc4cc458d0fffa0f9a354d5be Package: GAprediction Version: 1.14.0 Depends: R (>= 3.3) Imports: glmnet, stats, utils, Matrix Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 1cdf52736aca6d1c6cdacdf411ef68e4 Package: garfield Version: 1.16.0 Suggests: knitr License: GPL-3 MD5sum: 5af73c40763da7f1282996562ec6f861 Package: GARS Version: 1.8.0 Depends: R (>= 3.5), ggplot2, cluster Imports: DaMiRseq, MLSeq, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: cfa7f92ea4c2a89373d9ed2de9a7e95d Package: GateFinder Version: 1.8.0 Imports: splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: eb7335422b316b581a11fd64d7a525ac Package: gcapc Version: 1.12.0 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: bde87e38cd3eebd7d0cc81c601141c66 Package: gcatest Version: 1.18.0 Depends: R (>= 3.2) Imports: lfa Suggests: knitr, ggplot2 License: GPL-3 MD5sum: 377a6604426bee4dec47e37f8cf7d2ad Package: gCMAP Version: 1.32.0 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, reactome.db, RUnit, GO.db, mgsa License: Artistic-2.0 OS_type: unix MD5sum: 3a419ec86d7e6688c972d5a201680c23 Package: gCrisprTools Version: 1.16.0 Depends: R (>= 3.6) Imports: Biobase, limma, RobustRankAggreg, ggplot2, PANTHER.db, rmarkdown, grDevices, graphics, stats, utils, parallel, SummarizedExperiment Suggests: edgeR, knitr, grid, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: f4f1fce522ced81777371557138855ff Package: gcrma Version: 2.60.0 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: 7ad9655c7eb7acdbf2dc5658d0b0bc2a Package: GCSConnection Version: 1.0.1 Depends: R (>= 4.0.0) Imports: Rcpp (>= 1.0.2), httr, googleAuthR, googleCloudStorageR, methods, jsonlite, utils LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 170aef6980ca441b32a3779f201bdfdc Package: GCSscore Version: 1.2.0 Depends: R (>= 3.6) Imports: BiocManager, Biobase, utils, methods, RSQLite, devtools, dplR, stringr, graphics, stats, affxparser, data.table Suggests: siggenes, GEOquery, R.utils License: GPL (>= 3) MD5sum: 578526f04c62789c00353c91ce049020 Package: GDCRNATools Version: 1.8.0 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: 6b18d3f4136fe75e24d95a97d8aa04dc Package: GDSArray Version: 1.8.0 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: a20cd95c74ca3e71507cc74c3250f8c8 Package: gdsfmt Version: 1.24.1 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, Matrix, RUnit, knitr, crayon, BiocGenerics License: LGPL-3 MD5sum: 3c437aeececd51046d4657d5ee5349b2 Package: GEM Version: 1.14.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics License: Artistic-2.0 MD5sum: 0f12fb23a53abe13193713355e36d7b4 Package: gemini Version: 1.2.0 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: f490a4df1b46fad2e0d1c55e31e844cf Package: genArise Version: 1.64.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: 94b7011e8ef28775d45e3c3987334aee Package: genbankr Version: 1.16.0 Depends: methods Imports: BiocGenerics, IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), GenomicFeatures (>= 1.31.5), Biostrings, VariantAnnotation, rtracklayer, S4Vectors (>= 0.17.28), GenomeInfoDb, Biobase Suggests: RUnit, rentrez, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 9c43fae80e7ff40acc80b462c103ffd3 Package: GeneAccord Version: 1.6.0 Depends: R (>= 3.5) Imports: biomaRt, caTools, dplyr, ggplot2, graphics, grDevices, gtools, ggpubr, magrittr, maxLik, RColorBrewer, reshape2, stats, tibble, utils Suggests: assertthat, BiocStyle, devtools, knitr, rmarkdown, testthat License: file LICENSE MD5sum: b4d65c43ddb6218a6f7ac3af66ff1ba3 Package: GeneAnswers Version: 2.30.0 Depends: R (>= 3.0.0), igraph, RCurl, annotate, Biobase (>= 1.12.0), methods, XML, RSQLite, MASS, Heatplus, RColorBrewer Imports: RBGL, annotate, downloader Suggests: GO.db, KEGG.db, reactome.db, biomaRt, AnnotationDbi, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db, graph License: LGPL (>= 2) MD5sum: b4aae3f08b6e99db31c10fcec3921f95 Package: geneAttribution Version: 1.14.0 Imports: utils, GenomicRanges, 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: 7ae9cbb39e6f9bfbeb2ed24d1a63198e Package: GeneBreak Version: 1.18.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: f40fb2ebedc18bdc238bec4b3cbe3323 Package: geneClassifiers Version: 1.12.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: 6d666e06fd606d4f7fe1e4defac40300 Package: GeneExpressionSignature Version: 1.34.0 Depends: R (>= 2.13), Biobase, PGSEA Suggests: apcluster,GEOquery License: GPL-2 MD5sum: a1e016d4a77db7dd819b50433a79ed57 Package: genefilter Version: 1.70.0 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: 769f57e021cf7c50196c68a370d4b3c4 Package: genefu Version: 2.20.0 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: 2cb2a7899aff668f658538dcf418f113 Package: GeneGA Version: 1.38.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: 605caa88b4abd90979b7ed65b6d44591 Package: GeneGeneInteR Version: 1.14.0 Depends: R (>= 4.0) Imports: snpStats, mvtnorm, GGtools, Rsamtools, igraph, kernlab, FactoMineR, plspm, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods License: GPL (>= 2) MD5sum: 20c6f5e723e727ff897f7e1bc205a8c7 Package: GeneMeta Version: 1.60.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: c9221d89f91f21d9f2be06148a9b15d0 Package: GeneNetworkBuilder Version: 1.30.0 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick License: GPL (>= 2) MD5sum: 133b060a3713d599ccbf07f90961e7e6 Package: GeneOverlap Version: 1.24.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: e8ea22f66f446292bbbc9a7b187ebfba Package: geneplast Version: 1.14.0 Depends: R (>= 3.3), methods Imports: igraph, snow, ape, grDevices, graphics, stats, utils, data.table Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: 27799ff203ece27a13d9f7e1dd12a92f Package: geneplotter Version: 1.66.0 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: c5cf553386bd84444e37b5358a1fb71d Package: geneRecommender Version: 1.60.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: d76f88341be4df9ff715d0e647f4e352 Package: GeneRegionScan Version: 1.44.0 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: 0ed904637264e9c03aee16b91a51e91f Package: geneRxCluster Version: 1.24.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: ddc2bb6825bfec6b2456f8bb3e9ed1fd Package: GeneSelectMMD Version: 2.32.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: 15d98dbcede82c353541aee79eeb49a6 Package: GENESIS Version: 2.18.0 Imports: Biobase, BiocGenerics, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, dplyr, foreach, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: f4b30ea881d4aeb7a95d797dfa6e6b11 Package: GeneStructureTools Version: 1.8.0 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: 469bf0a56c19c771f0500f153661bd2e Package: geNetClassifier Version: 1.28.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics, grDevices Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) MD5sum: ebd280f9d67615c947c55d17fff1d332 Package: GeneticsPed Version: 1.50.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: debe84d3cd77007804c49543f8ac1a68 Package: GeneTonic Version: 1.0.1 Depends: R (>= 4.0.0) Imports: AnnotationDbi, bs4Dash, ComplexHeatmap, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, ggforce, ggplot2, ggrepel, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tools, utils, viridis, visNetwork Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: a8abea8833dd89004216235ed3578917 Package: geneXtendeR Version: 1.14.0 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: a63146177e3b5a71d12dbe15c9df45d9 Package: GENIE3 Version: 1.10.0 Imports: stats, reshape2 Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods License: GPL (>= 2) MD5sum: a00fbdd62e99cac841eb9dcacd9ca013 Package: genoCN Version: 1.40.0 Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: 0c82103b34a95223437895b8f0c471ca Package: GenoGAM Version: 2.6.0 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: 4590679ceca203df4b10ed39bcaaa3ac Package: genomation Version: 1.20.0 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: 57b826e4e769464dbf6c215f61022920 Package: GenomeInfoDb Version: 1.24.2 Depends: R (>= 3.1), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.25.12), IRanges (>= 2.13.12) Imports: stats, stats4, utils, RCurl, GenomeInfoDbData Suggests: GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 2f636cb7adc83500efca2782656c31d2 Package: genomeIntervals Version: 1.44.2 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: ed1ff03f15c7a710de175018f074b00e Package: genomes Version: 3.18.0 Depends: readr, curl License: GPL-3 MD5sum: 34545dee6f53ad3e92b7291d3d29eabf Package: GenomicAlignments Version: 1.24.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.25.14), IRanges (>= 2.21.6), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.39.3), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.55.7), 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: c0d36ab59e1add8802091858e993c3cd Package: GenomicDataCommons Version: 1.12.0 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: 60b2f12595f4a0e7da2a1d890c66c67c Package: GenomicFeatures Version: 1.40.1 Depends: BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29), IRanges (>= 2.13.23), GenomeInfoDb (>= 1.23.10), GenomicRanges (>= 1.31.17), AnnotationDbi (>= 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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, snpStats, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens License: Artistic-2.0 MD5sum: 5c28c48fbd11736424400d1ee7d27a2e Package: GenomicInteractions Version: 1.22.0 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: f0b3b62b42326eb144cc0a6093822890 Package: GenomicOZone Version: 1.2.0 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: 86b0e298343d2572349cd9f8722b7e73 Package: GenomicRanges Version: 1.40.0 Depends: R (>= 2.10), methods, stats4, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.25.14), IRanges (>= 2.21.6), GenomeInfoDb (>= 1.15.2) Imports: utils, stats, XVector (>= 0.27.2) 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: 0202594fe5dcd2d8b14eae9552398ab7 Package: GenomicScores Version: 2.0.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: stats, utils, XML, Biobase, IRanges (>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub, rhdf5, DelayedArray, HDF5Array 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, shiny, shinythemes, shinyjs, shinycustomloader, data.table, DT License: Artistic-2.0 MD5sum: 7880d725068ea1b0742826d35b29e7de Package: GenomicTuples Version: 1.22.1 Depends: R (>= 4.0), 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, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: bb4c46356b34ff6dd204aef6c57c3da7 Package: genoset Version: 1.44.0 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: 5d14e81cb725d75a81179a0797a9ce06 Package: genotypeeval Version: 1.20.0 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: 2031709498354de659e0e9b520a6694c Package: genphen Version: 1.16.0 Depends: R (>= 3.5.0), Rcpp (>= 0.12.17), methods, stats, graphics Imports: rstan (>= 2.17.3), ranger, parallel, foreach, doParallel, e1071, Biostrings, 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methods, snpStats Imports: limma, genefilter, Biobase, BiocGenerics, S4Vectors, IRanges, Matrix, AnnotationDbi, digest, GenomicRanges, SummarizedExperiment Suggests: GGtools, illuminaHumanv1.db, knitr License: Artistic-2.0 MD5sum: 071d7707c83a01562d6958d2cfc539a8 Package: ggbio Version: 1.36.0 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, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, 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XML Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: d8384755c966fc5a24e4fd8643156092 Package: Glimma Version: 1.16.0 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: 0a22759b93f675e53bb44b4d49f487c2 Package: glmGamPoi Version: 1.0.0 Imports: Rcpp, pracma, DelayedMatrixStats, DelayedArray, HDF5Array, SummarizedExperiment, methods, stats, utils LinkingTo: Rcpp, RcppArmadillo, beachmat (>= 2.0.0) Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, beachmat, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData License: GPL-3 MD5sum: 0d3f6c480f66a656d9a16aca110585f4 Package: glmSparseNet Version: 1.6.0 Depends: R (>= 3.5), Matrix, MultiAssayExperiment, glmnet Imports: SummarizedExperiment, STRINGdb, biomaRt, futile.logger, sparsebn, 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LICENSE MD5sum: b36833cfaf43a84821b396dcadfa09e4 Package: gmoviz Version: 1.0.1 Depends: circlize, GenomicRanges, graphics, R (>= 4.0) Imports: grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics, Biostrings, GenomeInfoDb, methods, GenomicAlignments, GenomicFeatures, IRanges, rtracklayer, pracma, colorspace, S4Vectors Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager License: GPL-3 MD5sum: 4b0b0601903c46db1842d56167384b25 Package: GMRP Version: 1.16.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: 61ee8f4da4b56205e424c1aa3f397a02 Package: GNET2 Version: 1.4.0 Depends: R (>= 3.3) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment,dplyr,igraph, grDevices LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 MD5sum: 16cbeab7ae5fd0581238fab0b14f09f2 Package: GOexpress Version: 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Imports: BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils, stats, GenomeInfoDb Suggests: HiCDataLymphoblast Enhances: parallel License: GPL-3 MD5sum: 9d5c3691ffb7efdb9c774649930ace65 Package: goTools Version: 1.62.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 MD5sum: bac246a8edfa3092f5b8250982d932ab Package: GPA Version: 1.0.0 Depends: R (>= 4.0.0), methods, graphics, Rcpp Imports: parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS, stats, utils, grDevices LinkingTo: Rcpp Suggests: gpaExample License: GPL (>= 2) MD5sum: 8ef80a7d2cdb81f5e875d4e1fcb67fd7 Package: gpart Version: 1.6.0 Depends: R (>= 3.5.0), grid, Homo.sapiens, 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: 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tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle License: GPL (>= 2) MD5sum: 50a038273ee41ca6bd3aadb324df072b Package: gscreend Version: 1.2.0 Depends: R (>= 3.6) Imports: SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics Suggests: knitr, testthat License: GPL-3 MD5sum: 59dde213882fba7d1cdeb34374449bd4 Package: GSEABase Version: 1.50.1 Depends: R (>= 2.6.0), BiocGenerics (>= 0.13.8), Biobase (>= 2.17.8), annotate (>= 1.45.3), methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: 8eec1ae11e16ba96628f7b5c356d220e Package: GSEABenchmarkeR Version: 1.8.0 Depends: Biobase, SummarizedExperiment Imports: AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, rappdirs, 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IRanges, GenomicAlignments, GenomicRanges, rtracklayer, SummarizedExperiment, VariantAnnotation, limma, edgeR, csaw, DESeq2, TxDb.Dmelanogaster.UCSC.dm6.ensGene Suggests: knitr, rmarkdown, Rsubread (>= 1.29.0), testthat License: GPL-3 + file LICENSE MD5sum: 3759efe88a9b73134d66d2ee47b98400 Package: iCheck Version: 1.18.0 Depends: R (>= 3.2.0), Biobase, lumi, gplots Imports: stats, graphics, preprocessCore, grDevices, randomForest, affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest, scatterplot3d, utils License: GPL (>= 2) MD5sum: 62809d147b37b7c7ce2a504f0810b502 Package: iChip Version: 1.42.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) MD5sum: f74e53ffe8f3b6a1277060af3d495f63 Package: iClusterPlus Version: 1.24.0 Depends: R (>= 3.3.0), parallel Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: e7e2249d912f13a76ad4524a271cf056 Package: iCNV Version: 1.8.0 Depends: R (>= 3.3.1), CODEX Imports: fields, ggplot2, truncnorm, tidyr, data.table, dplyr, grDevices, graphics, stats, utils, rlang Suggests: knitr, rmarkdown, WES.1KG.WUGSC License: GPL-2 MD5sum: 10e2474b0dcb95c47ff463e22a63f28f Package: iCOBRA Version: 1.16.0 Depends: R (>= 3.4) Imports: shiny (>= 0.9.1.9008), shinydashboard, shinyBS, reshape2, ggplot2 (>= 2.0.0), scales, ROCR, dplyr, DT, limma, methods, UpSetR Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 259bbc6d498e154152f33d063d5cb83e Package: ideal Version: 1.12.1 Depends: topGO Imports: DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0), heatmaply, plotly, pheatmap, pcaExplorer, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, DT, rentrez, rintrojs, ggrepel, knitr, rmarkdown, shinyAce, BiocParallel, grDevices, base64enc, methods Suggests: testthat, BiocStyle, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR License: MIT + file LICENSE MD5sum: 560588fddb9df64e27772e97db62aa5b Package: IdeoViz Version: 1.24.0 Depends: Biobase, IRanges, GenomicRanges, RColorBrewer, rtracklayer,graphics,GenomeInfoDb License: GPL-2 MD5sum: e7a05b00cd474ce026c4dd24f2f8cb9a Package: idiogram Version: 1.64.0 Depends: R (>= 2.10), methods, Biobase, annotate, plotrix Suggests: hu6800.db, hgu95av2.db, golubEsets License: GPL-2 MD5sum: 27f11e3f7d52b3e6d6f14862012f6507 Package: idr2d Version: 1.2.2 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.6), futile.logger (>= 1.4.3), GenomeInfoDb (>= 1.14.0), GenomicRanges (>= 1.30), ggplot2 (>= 3.1.1), grDevices, idr (>= 1.2), IRanges (>= 2.18.0), magrittr (>= 1.5), methods, reticulate (>= 1.13), scales (>= 1.0.0), stats, stringr (>= 1.3.1), utils Suggests: DT (>= 0.4), htmltools (>= 0.3.6), knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: a037526c3441321347fdf3db76e8f451 Package: iGC Version: 1.18.0 Depends: R (>= 3.2.0) Imports: plyr, data.table Suggests: BiocStyle, knitr, rmarkdown Enhances: doMC License: GPL-2 MD5sum: b99d1d605c2a4949e6117d936b4795d0 Package: IgGeneUsage Version: 1.2.2 Depends: methods, R (>= 3.6.0), Rcpp (>= 0.12.0), SummarizedExperiment, StanHeaders (> 2.18.1) Imports: rstan (>= 2.19.2), reshape2 (>= 1.4.3) Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, gridExtra, ggrepel License: file LICENSE MD5sum: 4065b70ece329026f1e2734ab8e481c4 Package: igvR Version: 1.8.2 Depends: R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz (>= 2.9.1) Imports: methods, BiocGenerics, httpuv, utils, MotifDb, seqLogo, rtracklayer, VariantAnnotation, RColorBrewer Suggests: RUnit, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: c80b30e6f04eda866b293a49d7bbf304 Package: IHW Version: 1.16.0 Depends: R (>= 3.3.0) Imports: methods, slam, lpsymphony, fdrtool, BiocGenerics Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools License: Artistic-2.0 MD5sum: 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shinyBS, shinyFiles, shinythemes, ggplot2 Suggests: knitr, BiocStyle, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: 64b4a7e84c759b6ea5eb18defbecb0e8 Package: IMMAN Version: 1.8.2 Imports: STRINGdb, Biostrings, igraph, graphics, utils, seqinr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 392937675348b27bf3bdad4a24f14eda Package: ImmuneSpaceR Version: 1.16.0 Depends: R (>= 3.5.0) Imports: utils, R6, data.table, curl, httr, Rlabkey (>= 2.3.1), Biobase, pheatmap, ggplot2 (>= 3.2.0), scales, stats, gplots, plotly, heatmaply (>= 0.7.0), jsonlite, rmarkdown, preprocessCore, flowCore, flowWorkspace, digest Suggests: knitr, testthat License: GPL-2 MD5sum: be377db31a985df390376d3d369f73ac Package: immunoClust Version: 1.20.1 Depends: R(>= 3.6), methods, stats, graphics, grid, lattice, grDevices, flowCore Suggests: BiocStyle, utils License: Artistic-2.0 MD5sum: d0034e3cbf94b8d4a3268fa39e551114 Package: IMPCdata Version: 1.24.0 Depends: R (>= 2.3.0) Imports: rjson 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SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 71b501504d07aec5f4129d86ef4e29ba Package: InTAD Version: 1.8.0 Depends: R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges, MultiAssayExperiment, SummarizedExperiment,stats Imports: BiocGenerics,Biobase,rtracklayer,parallel,graphics,mclust,qvalue, ggplot2,utils,ggpubr Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: d136a64b59585f33e3d48521f231c28f Package: intansv Version: 1.28.0 Depends: R (>= 2.14.0), plyr, ggbio, GenomicRanges Imports: BiocGenerics, IRanges License: MIT + file LICENSE MD5sum: ad48d0eb262e58b75d6ccbd70bad66a6 Package: InteractionSet Version: 1.16.0 Depends: GenomicRanges, SummarizedExperiment Imports: methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.25.14), IRanges, GenomeInfoDb LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 56fcae2313bbb6969035c73c76edefb4 Package: 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knitr, BSgenome.Hsapiens.UCSC.hg19 License: GPL-2 MD5sum: 4833e5757d2b2f4a020b051f871c8347 Package: InterMineR Version: 1.10.0 Depends: R (>= 3.4.1) Imports: Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, igraph, httr, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, methods Suggests: BiocStyle, Gviz, knitr, rmarkdown, GeneAnswers, GO.db, org.Hs.eg.db License: LGPL MD5sum: 4d00a7318ea5dfd4a6d656f37f6faea1 Package: IntramiRExploreR Version: 1.10.0 Depends: R (>= 3.4) Imports: igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats, utils, grDevices, graphics Suggests: RDAVIDWebService, gProfileR, topGO, KEGGprofile, org.Dm.eg.db, rmarkdown, testthat License: GPL-2 MD5sum: 9b0d22a58575a031ccd30dc5176f4b4d Package: inveRsion Version: 1.36.0 Depends: methods, haplo.stats Imports: graphics, methods, utils License: GPL (>= 2) MD5sum: d64fc7111e93f6be64fc649f8b92678a Package: IONiseR Version: 2.12.0 Depends: R (>= 3.4) Imports: rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2, methods, BiocGenerics, XVector, tibble, stats, BiocParallel, bit64, stringr, utils Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData License: MIT + file LICENSE MD5sum: 86360e874d2cdec63ab3cda79c01d334 Package: iPAC Version: 1.32.0 Depends: R(>= 2.15),gdata, scatterplot3d, Biostrings, multtest License: GPL-2 MD5sum: 3a6707ec8cbd66b80b088e8f6057f8d2 Package: ipdDb Version: 1.6.0 Depends: R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1), AnnotationHub Imports: Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats, assertthat Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 7abbd0c090e707ecb015ffff538902ae Package: IPO Version: 1.14.0 Depends: xcms (>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats, utils Imports: BiocParallel Suggests: RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr Enhances: parallel License: GPL (>= 2) + file LICENSE MD5sum: e2498f16657e9816189e0fc25cffe948 Package: IRanges Version: 2.22.2 Depends: R (>= 3.1.0), methods, utils, stats, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.25.14) Imports: stats4 LinkingTo: S4Vectors Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 19b91838a113c7ce589f4725b09e2413 Package: iSEE Version: 2.0.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, ComplexHeatmap, circlize Suggests: testthat, BiocStyle, knitr, rmarkdown, scRNAseq, scater, DelayedArray, RColorBrewer, viridis, htmltools License: MIT + file LICENSE MD5sum: 896f9ff64ed6a614ce3c28941b7e17d5 Package: iSEEu Version: 1.0.1 Depends: iSEE Imports: methods, S4Vectors, shiny, SummarizedExperiment, SingleCellExperiment, ggplot2, DT, stats Suggests: scRNAseq, scater, scran, airway, edgeR, AnnotationDbi, org.Hs.eg.db, GO.db, knitr, rmarkdown, BiocStyle, htmltools, Rtsne, uwot, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 454764442118963b2d25a34e5cc542e7 Package: iSeq Version: 1.40.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 622d1b8d4ea60ef59bccabe86856d03d Package: isobar Version: 1.34.0 Depends: R (>= 2.10.0), Biobase, stats, methods Imports: distr, plyr, biomaRt, ggplot2 Suggests: MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS License: LGPL-2 MD5sum: 13f32ece14cb69551fbe8744a29d30ab Package: IsoCorrectoR Version: 1.6.2 Depends: R (>= 3.5) Imports: dplyr, magrittr, methods, quadprog, readr, readxl, stringr, tibble, tools, utils, pracma, WriteXLS Suggests: IsoCorrectoRGUI, knitr, rmarkdown, testthat License: GPL-3 MD5sum: bf9ca7387abb319edb51004fd7242c53 Package: IsoCorrectoRGUI Version: 1.4.0 Depends: R (>= 3.6) Imports: IsoCorrectoR, readxl, tcltk2, tcltk, utils 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Biobase, broom, cluster, cowplot, DEGreport, DESeq2, IRanges, dplyr, GenomicRanges, gplots, ggplot2, gtools, gridExtra, grid, grDevices, graphics, GGally, limma, methods, RColorBrewer, readr, reshape, rlang, stats, stringr, S4Vectors, tidyr, tibble Suggests: knitr, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 394d0ba21b47d46b794f6fcabf01968d Package: ITALICS Version: 2.48.0 Depends: R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser, pd.mapping50k.xba240 Imports: affxparser, DBI, GLAD, oligo, oligoClasses, stats Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp License: GPL-2 MD5sum: f92fdc450b202313f49d9edb222dad4c Package: iterativeBMA Version: 1.46.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 2217f98df569aa87b2bc976b3004b46d Package: iterativeBMAsurv Version: 1.46.0 Depends: BMA, leaps, survival, splines Imports: graphics, grDevices, stats, survival, utils License: GPL (>= 2) MD5sum: 77caefd1764454a4311c4ac3548902e6 Package: iterClust Version: 1.10.0 Depends: R (>= 3.4.1) Imports: Biobase, cluster, stats, methods Suggests: tsne, bcellViper License: file LICENSE MD5sum: 0f43df21c8323b09a0aa6cacf74392a4 Package: iteremoval Version: 1.8.0 Depends: R (>= 3.5.0), ggplot2 (>= 2.2.1) Imports: magrittr, graphics, utils, GenomicRanges, SummarizedExperiment Suggests: testthat, knitr License: GPL-2 MD5sum: 3f48d69198b9a00979e94c7241a2fecc Package: IVAS Version: 2.8.0 Depends: R (> 3.0.0),GenomicFeatures, ggplot2, Biobase Imports: doParallel, lme4, BiocGenerics, GenomicRanges, IRanges, foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, ggfortify, grDevices, methods, Matrix, BiocParallel,utils, stats Suggests: BiocStyle License: GPL-2 MD5sum: 463d4af07b143adcff5259cc3032a184 Package: ivygapSE Version: 1.10.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: shiny, survival, survminer, hwriter, plotly, ggplot2, S4Vectors, graphics, stats, utils, UpSetR Suggests: knitr, png, limma, grid, DT, randomForest, digest, testthat License: Artistic-2.0 MD5sum: 8d47553f0754ef2b12d0d11b835ce45d Package: IWTomics Version: 1.12.0 Depends: GenomicRanges Imports: parallel,gtable,grid,graphics,methods,IRanges,KernSmooth,fda,S4Vectors,grDevices,stats,utils,tools Suggests: knitr License: GPL (>= 2) MD5sum: f378928c2c188568f342c67648e9499c Package: karyoploteR Version: 1.14.1 Depends: R (>= 3.4), regioneR, GenomicRanges, methods Imports: regioneR, GenomicRanges, IRanges, Rsamtools, stats, graphics, memoise, rtracklayer, GenomeInfoDb, S4Vectors, biovizBase, digest, bezier, GenomicFeatures, bamsignals, AnnotationDbi, grDevices, VariantAnnotation Suggests: BiocStyle, knitr, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db, pasillaBamSubset License: Artistic-2.0 MD5sum: d02a2d2eb8a776dabe243a229d887a2f Package: KCsmart Version: 2.46.0 Depends: siggenes, multtest, KernSmooth Imports: methods, BiocGenerics Enhances: Biobase, CGHbase License: GPL-3 MD5sum: a1d503f0277a6964c07e61e056045eb7 Package: kebabs Version: 1.22.0 Depends: R (>= 3.2.0), Biostrings (>= 2.35.5), kernlab Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.7.3), S4Vectors (>= 0.5.11), e1071, LiblineaR, graphics, grDevices, utils, apcluster LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors Suggests: SparseM, Biobase, BiocGenerics, knitr License: GPL (>= 2.1) MD5sum: c374cb8537570823866994ed52147c74 Package: KEGGgraph Version: 1.48.0 Depends: R (>= 2.10.0) Imports: methods, XML (>= 2.3-0), graph, utils, RCurl Suggests: Rgraphviz, RBGL, testthat, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) MD5sum: 3cbd3b6cce62c41bb30bd8614061a5c2 Package: KEGGlincs Version: 1.14.0 Depends: R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db (>= 3.3.0) Imports: AnnotationDbi,KEGGgraph,igraph,plyr,gtools,httr,RJSONIO,KEGGREST, methods,graphics,stats,utils, XML, grDevices Suggests: BiocManager (>= 1.20.3), knitr, graph License: GPL-3 MD5sum: 81b39e7e94d5fd5a1ed6741cea6be353 Package: keggorthology Version: 2.40.0 Depends: R (>= 2.5.0),stats,graph,hgu95av2.db Imports: AnnotationDbi,graph,DBI, graph, grDevices, methods, stats, tools, utils Suggests: RBGL,ALL License: Artistic-2.0 MD5sum: 74b723c3b390d365fad82c9406fda966 Package: KEGGprofile Version: 1.30.0 Imports: AnnotationDbi,png,TeachingDemos,XML,KEGG.db,KEGGREST,biomaRt,RCurl,ggplot2,reshape2 License: GPL (>= 2) MD5sum: 08a7b6e102075057e0f097695e4720cc Package: KEGGREST Version: 1.28.0 Imports: methods, httr, png, Biostrings Suggests: RUnit, BiocGenerics, knitr License: Artistic-2.0 MD5sum: 30cce2ce65ce87ce9cb962ceb5c2f2fc Package: KinSwingR Version: 1.6.0 Depends: R (>= 3.5) Imports: data.table, BiocParallel, sqldf, stats, grid, grDevices Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 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parallel, plot3D, plyr, RCurl, ROCR, testthat License: MIT | file LICENSE MD5sum: 2c7b948ebc8e346b76c7b20434275357 Package: les Version: 1.38.0 Depends: R (>= 2.13.2), methods, graphics, fdrtool Imports: boot, gplots, RColorBrewer Suggests: Biobase, limma Enhances: parallel License: GPL-3 MD5sum: 73dead07f2a7f10f968bbd40b76fdb5b Package: levi Version: 1.6.0 Imports: DT(>= 0.4), RColorBrewer(>= 1.1-2), colorspace(>= 1.3-2), dplyr(>= 0.7.4), ggplot2(>= 2.2.1), httr(>= 1.3.1), igraph(>= 1.2.1), reshape2(>= 1.4.3), shiny(>= 1.0.5), shinydashboard(>= 0.7.0), shinyjs(>= 1.0), xml2(>= 1.2.0), knitr, Rcpp (>= 0.12.18), grid, grDevices, stats, utils, testthat, methods LinkingTo: Rcpp License: GPL (>= 2) MD5sum: 46b4c2224fc312c50a6dddfa2bfbe972 Package: lfa Version: 1.18.0 Depends: R (>= 3.2) Imports: corpcor Suggests: knitr, ggplot2 License: GPL-3 MD5sum: 536f9e6e55a63823167cbdc719354122 Package: limma Version: 3.44.3 Depends: R (>= 3.6.0) Imports: grDevices, graphics, stats, utils, methods Suggests: affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn License: GPL (>= 2) MD5sum: 005a7011f84b6fb1a8f5529b4216c53c Package: limmaGUI Version: 1.64.0 Imports: methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot, xtable, utils License: GPL (>= 2) MD5sum: c62b1e0445bc2a20fd3533940d67f92a Package: LineagePulse Version: 1.8.0 Imports: BiocParallel, circlize, compiler, ComplexHeatmap, ggplot2, gplots, grDevices, grid, knitr, Matrix, methods, RColorBrewer, SingleCellExperiment, splines, stats, SummarizedExperiment, utils License: Artistic-2.0 MD5sum: e687bcf56c7eee15fd70a927d19305de Package: LinkHD Version: 1.2.0 Depends: R(>= 3.6.0), methods, ggplot2, stats Imports: scales, cluster, graphics, ggpubr, gridExtra, vegan, rio, MultiAssayExperiment, emmeans, reshape2, data.table Suggests: MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: e6d472be97da2b8bd4bfcbe69b65eae2 Package: 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grDevices, utils, zlibbioc, vcfR Suggests: knitr License: GPL (>= 2) MD5sum: 1a4f0e9222170c91a16d036793da334b Package: maftools Version: 2.4.12 Depends: R (>= 3.3) Imports: data.table, RColorBrewer, methods, grDevices, survival Suggests: knitr, rmarkdown, BSgenome, Biostrings, NMF, mclust, berryFunctions License: MIT + file LICENSE MD5sum: f47dee7df4621cdbb4ab3ee177ecd20b Package: MAGeCKFlute Version: 1.8.0 Depends: R (>= 3.5) Imports: clusterProfiler, DOSE, enrichplot, gridExtra, biomaRt, sva, ggsci, ggplot2, ggrepel, ggpubr, data.table, pheatmap, png, grDevices, grid, stats, utils, dendextend, scales, Biobase, msigdbr, KEGGgraph, KEGGREST, graph, graphics, pathview, XML Suggests: knitr, testthat, BiocStyle License: GPL (>= 3) MD5sum: 8f49e8e4f7c3312d542a4a1c7fc64f86 Package: maigesPack Version: 1.52.0 Depends: R (>= 2.10), convert, graph, limma, marray, methods Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML, rgl, som License: GPL (>= 2) MD5sum: 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Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 MD5sum: 5dca15424231388e30708609dbfd93e0 Package: methrix Version: 1.2.06 Depends: R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment Imports: DelayedArray, HDF5Array, BSgenome, rjson, DelayedMatrixStats, parallel, methods, ggplot2, matrixStats, graphics, stats, utils Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, GenomicScores, Biostrings, RColorBrewer, GenomicRanges, GenomeInfoDb, IRanges, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: f3d4e584d7eff628c1032966e7bdbb85 Package: MethTargetedNGS Version: 1.20.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings License: Artistic-2.0 MD5sum: dff83f8acd5a31b64b38646fe2096b77 Package: methyAnalysis Version: 1.30.0 Depends: R (>= 2.10), grid, BiocGenerics, IRanges, GenomeInfoDb (>= 1.22.0), 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: 0e69dd7a77cbd935c84b594ec1139ac5 Package: MethylAid Version: 1.22.0 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: cfe64d848ed085449ebab77daab13a48 Package: methylCC Version: 1.2.0 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: 61636a1d5b5779e89d5c9e1da43517dd Package: methylGSA Version: 1.6.1 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: c183a110bb5fb0bf2b1e07b7549eb664 Package: methylInheritance Version: 1.12.0 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: 610b7a6f49574b71808a90d7087d1dab Package: methylKit Version: 1.14.2 Depends: R (>= 3.5.0), 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 (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager License: Artistic-2.0 MD5sum: 7c95677b2a237839cbe02efdc99fbed4 Package: MethylMix Version: 2.18.0 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: fe8a800860da0e3d8bb0fce9890a4e69 Package: methylMnM Version: 1.26.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: 45632b0dbcfe260aa9e3101ff1cf14e2 Package: methylPipe Version: 1.22.0 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: 22163eaa3cd4f0af1196e35a824b4c03 Package: MethylSeekR Version: 1.28.0 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: 0ff34a14bd8ee13afb061657008d79ae Package: methylSig Version: 1.0.0 Depends: R (>= 3.6) Imports: bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, GenomeInfoDb, GenomicRanges, methods, parallel, stats, S4Vectors Suggests: BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr License: GPL-3 MD5sum: 400d4afc48d6f50becfeb866cefad919 Package: methylumi Version: 2.34.0 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: 4c772f21586cc86f738dc7d489322295 Package: methyvim Version: 1.10.0 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: 08eb2fff60fa302419dbacd6de13f114 Package: MetID Version: 1.6.0 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: cc19831bfe8323216c5fdfbe8e897744 Package: MetNet Version: 1.6.0 Depends: R (>= 3.6) 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 (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1) License: GPL (>= 3) MD5sum: e662b18f363676531302646e3535600c Package: mfa Version: 1.10.0 Depends: R (>= 3.4.0) Imports: methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack, MCMCglmm, coda, magrittr, tibble, Biobase LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: 5195822eb1522c99afee0104c9952696 Package: Mfuzz Version: 2.48.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 MD5sum: 7d21c02bbf37b348c7b67e204bf41151 Package: MGFM Version: 1.22.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 MD5sum: 293ada4783a47c2c4d9b83dc8b7f2ded Package: MGFR Version: 1.14.0 Depends: R (>= 3.5) Imports: biomaRt, annotate License: GPL-3 MD5sum: 8f1de6ad9124db208e42a46f6d520ee1 Package: mgsa Version: 1.36.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: 63443bfab840ede85be1325b16f14abb Package: MiChip Version: 1.42.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: 3c4f2cab8286f6456445f328e469e15b Package: microbiome Version: 1.10.0 Depends: R (>= 3.6.0), phyloseq, ggplot2 Imports: dplyr, reshape2, Rtsne, scales, stats, tibble, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitcitations, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE MD5sum: 446b8949c170db2fc5619b601e78159b Package: microbiomeDASim Version: 1.2.0 Depends: R (>= 3.6.0) Imports: graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase Suggests: testthat (>= 2.1.0), knitr, devtools License: MIT + file LICENSE MD5sum: 40bb0e5fec16fb8ae80cd52db6e4c383 Package: MicrobiotaProcess Version: 1.0.5 Depends: R (>= 4.0.0) Imports: ape, plyr, tidyr, ggplot2, phyloseq, magrittr, dplyr, Biostrings, ggrepel, vegan, rentrez, reshape, zoo, ggtree, tidytree, gtools, MASS, methods, randomForest, rlang, tibble, grDevices, stats, utils, coin, ggsignif, scales, Rmisc, DECIPHER, biomformat, yaml, phangorn, patchwork Suggests: DT, prettydoc, treeio, tidyverse, testthat, knitr, nlme License: GPL (>= 3.0) MD5sum: 4e3fd04cdb6df13e7e43b6494745873e Package: microRNA Version: 1.46.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: 3f889017d14c3b7a9307901503bcbe88 Package: MIGSA Version: 1.12.0 Depends: R (>= 3.4), methods, BiocGenerics Imports: AnnotationDbi, Biobase, BiocParallel, compiler, data.table, edgeR, futile.logger, ggdendro, ggplot2, GO.db, GOstats, graph, graphics, grDevices, grid, GSEABase, ismev, limma, matrixStats, org.Hs.eg.db, RBGL, reshape2, Rgraphviz, RJSONIO, stats, utils, vegan Suggests: BiocStyle, breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, knitr, mGSZ, MIGSAdata License: GPL (>= 2) MD5sum: 24591f68e860571118f00fe519bb62e8 Package: mimager Version: 1.12.0 Depends: Biobase Imports: BiocGenerics, S4Vectors, preprocessCore, grDevices, methods, grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 License: MIT + file LICENSE MD5sum: 811f71e72fc54fd88147df35954bbcda Package: MIMOSA Version: 1.26.0 Depends: R (>= 3.0.2), MASS, plyr, reshape, Biobase, ggplot2 Imports: methods, Formula, data.table, pracma, MCMCpack, coda, modeest, testthat, Rcpp, scales, dplyr, tidyr, rlang LinkingTo: Rcpp, RcppArmadillo Suggests: parallel, knitr License: MIT + file LICENSE MD5sum: 47e7d15527f0833f44d97171cee24790 Package: MineICA Version: 1.28.0 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, future, future.apply Enhances: doMC License: GPL-2 MD5sum: 8137abb03a449f6cb4b5a1708f81c0b8 Package: minet Version: 3.46.0 Imports: infotheo License: Artistic-2.0 MD5sum: 74e2f43cce779790a3c79dbfd77980d5 Package: minfi Version: 1.34.0 Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges, SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>= 1.1.9) Imports: S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray (>= 0.9.8), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools License: Artistic-2.0 MD5sum: 28d943eb50aea56a37173f6863995fb6 Package: MinimumDistance Version: 1.32.0 Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1) Imports: methods, BiocGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: 8aca1d21ca69bee11e7b592862be2192 Package: MiPP Version: 1.60.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: 967826792c89689ab06a3ca43c112111 Package: MIRA Version: 1.10.0 Depends: R (>= 3.5) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: f17c5caabbee4a36058a0083f5362fd3 Package: MiRaGE Version: 1.30.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: BiocGenerics, S4Vectors, AnnotationDbi, BiocManager Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL MD5sum: 4cdcc2bc8ebd8538549d52c09e819f5d Package: miRBaseConverter Version: 1.12.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils License: GPL (>= 2) MD5sum: 27c9e8036ee02361539ef527bdfc4072 Package: miRcomp Version: 1.18.0 Depends: R (>= 3.2), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: e144a4d16f86f4e77769708c6e6bd381 Package: mirIntegrator Version: 1.18.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: 3aec7a4e246c751627cc342c2ee7fec4 Package: miRLAB Version: 1.18.0 Imports: methods, stats, utils, RCurl, httr, stringr, Hmisc, energy, entropy, Roleswitch, gplots, glmnet, impute, limma, pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc, heatmap.plus, InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit License: GPL (>= 2) MD5sum: 5fcaea60000181e137fd3c4a573ae839 Package: miRmine Version: 1.10.0 Depends: R (>= 3.4), SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, DESeq2 License: GPL (>= 3) MD5sum: 45f35fde8192ab2789d8cee660aa9d1e Package: miRNAmeConverter Version: 1.16.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: f4df927387e24b8d737d01e26c21262d Package: 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utils, Rcpp, org.Hs.eg.db Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 051a1265036a4037c22666ee583a85ca Package: missMethyl Version: 1.22.0 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData License: GPL-2 MD5sum: cf81f31446a6c5b07f936282875e8151 Package: missRows Version: 1.8.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 02f19576f7fbcbd370cd41125e28c2c8 Package: mitch Version: 1.0.10 Depends: R (>= 4.0) Imports: stats, grDevices, graphics, utils, MASS, plyr, reshape2, parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r Suggests: stringi, testthat (>= 2.1.0) License: CC BY-SA 4.0 + file LICENSE MD5sum: 01210b01c834cfd5b4aa799ff676101c Package: mitoODE Version: 1.26.1 Depends: R (>= 2.14.0), minpack.lm, MASS, parallel, mitoODEdata, KernSmooth License: LGPL MD5sum: 03b86610f608a1a4648fb7da22519480 Package: mixOmics Version: 6.12.2 Depends: R (>= 3.5.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rgl License: GPL (>= 2) MD5sum: c012d40e5a07f4b4e7293755072ffd35 Package: MLInterfaces Version: 1.68.0 Depends: R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4, tools, grDevices, graphics, stats Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, testthat Enhances: parallel, rda License: LGPL MD5sum: 98ce6051da75c2802504bd9bedde1edd Package: MLP Version: 1.36.0 Depends: AnnotationDbi, affy, plotrix, gplots, gmodels, gdata, gtools Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, KEGG.db, annotate, Rgraphviz, GOstats, limma, mouse4302.db, reactome.db License: GPL-3 MD5sum: a6e733b26bcb228fe7ab0dae9eab2a86 Package: MLSeq Version: 2.6.0 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: 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Suggests: testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter License: MIT + file LICENSE MD5sum: 2ef85628164defc4ab16f57294113a1c Package: mnem Version: 1.4.5 Depends: R (>= 3.6) Imports: cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071 LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM License: GPL-3 MD5sum: d8b42d4a6445c0a7e2dc4bdfbfe9c495 Package: MODA Version: 1.14.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: b6fec9bd4cad29d4c919464214b43013 Package: Modstrings Version: 1.4.1 Depends: R (>= 3.6), Biostrings (>= 2.51.5) Imports: methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: be8b788aac1ded03be9762805c2ecbe8 Package: MOFA Version: 1.4.0 Depends: R (>= 3.5) Imports: rhdf5, dplyr, reshape2, pheatmap, corrplot, ggplot2, ggbeeswarm, methods, scales, GGally, RColorBrewer, cowplot, ggrepel, MultiAssayExperiment, Biobase, doParallel, foreach, reticulate, grDevices, stats, utils Suggests: knitr, MOFAdata License: LGPL-3 | file LICENSE MD5sum: 1f36153dc3923a3242f536ea30a40418 Package: mogsa Version: 1.22.1 Depends: R (>= 3.4.0) Imports: methods, graphite, genefilter, BiocGenerics, gplots, GSEABase, Biobase, parallel, corpcor, svd, cluster, grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, org.Hs.eg.db License: GPL-2 MD5sum: fa06275c10a0f811fe6241af144af658 Package: MOMA Version: 1.0.2 Depends: R (>= 4.0) Imports: circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics, grid, grDevices, magrittr, methods, MKmisc, MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr, reshape2, rlang, stats, stringr, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, viper License: GPL-3 MD5sum: 6b2ddb889b8ce6dc7bfe4bc4a5adae4a Package: monocle Version: 2.16.0 Depends: R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-6), DDRTree (>= 0.1.4), Imports: parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, densityClust (>= 0.3), Rtsne, MASS, reshape2, limma, tibble, dplyr, qlcMatrix, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0) LinkingTo: Rcpp Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat License: Artistic-2.0 MD5sum: 26684cde03ee3d81ac01570af173a3e7 Package: MoonlightR Version: 1.14.1 Depends: R (>= 3.5), doParallel, foreach Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png License: GPL (>= 3) MD5sum: 6b4ed04bc835197d8c9b4215ca262541 Package: mosaics Version: 2.26.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: 7eb49f4925984b4a2efbee646f721e28 Package: MOSim Version: 1.2.0 Depends: R (>= 3.6) Imports: HiddenMarkov, zoo, methods, matrixStats, dplyr, stringi, lazyeval, rlang, stats, utils, purrr, scales, stringr, tibble, tidyr, ggplot2, Biobase, IRanges, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 79bdd97edc9918de8af2bf31130d60a7 Package: motifbreakR Version: 2.2.0 Depends: R (>= 3.5.0), grid, MotifDb Imports: methods, compiler, grDevices, grImport, stringr, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, 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: ff234c3a12cbf6ca2019729fc11603f3 Package: motifcounter Version: 1.12.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: 5655def4f411bdfd1fe05b7697a8b44e Package: MotifDb Version: 1.30.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes MD5sum: 52dc6284ee053d86b93f3d89aa94c22a Package: motifmatchr Version: 1.10.0 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, GenomeInfoDb LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 + file LICENSE MD5sum: 973b12854609a9355331691cb6d65cdb Package: motifStack Version: 1.32.1 Depends: R (>= 2.15.1), methods, grImport2, grid, MotIV, ade4, Biostrings Imports: XML, scales, htmlwidgets,grDevices, stats, stats4, graphics, utils, ggplot2 Suggests: RUnit, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, httr, htmltools License: GPL (>= 2) MD5sum: a99598f295e4f10b7524be4834792325 Package: MPFE Version: 1.24.1 License: GPL (>= 3) MD5sum: 3a2c95cdcaa7a2f67221e2b5c98d48c0 Package: mpra Version: 1.10.0 Depends: R (>= 3.4.0), methods, BiocGenerics, SummarizedExperiment, limma Imports: S4Vectors, scales, stats, graphics, statmod Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 7f899bbff60b23e34420d8535b85e817 Package: MPRAnalyze Version: 1.6.0 Imports: BiocParallel, methods, progress, stats, SummarizedExperiment Suggests: knitr License: GPL-3 MD5sum: 2ae069ec0bf310c9f86c1e9fe7b998c4 Package: msa Version: 1.20.1 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.40.0) Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors, tools LinkingTo: Rcpp Suggests: Biobase, knitr, seqinr, ape, phangorn License: GPL (>= 2) MD5sum: dee047bfa40dee5a0b227fe9aca2efd4 Package: MsCoreUtils Version: 1.0.0 Depends: R (>= 3.6.0) Imports: methods, S4Vectors, MASS, stats LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, pcaMethods, vsn, preprocessCore License: Artistic-2.0 MD5sum: a1c8869b2935c9a48f100365addac355 Package: msgbsR Version: 1.12.0 Depends: R (>= 3.4), GenomicRanges, methods Imports: BSgenome, easyRNASeq, edgeR, GenomicAlignments, GenomicFeatures, 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Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr, SummarizedExperiment License: Artistic-2.0 MD5sum: a74491189e9eb0b42192986b839eba4e Package: MSnID Version: 1.22.0 Depends: R (>= 2.10), Rcpp Imports: MSnbase (>= 1.12.1), mzID (>= 1.3.5), R.cache, foreach, doParallel, parallel, methods, iterators, data.table, Biobase, ProtGenerics, reshape2, dplyr, mzR Suggests: BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: d4c34a912cc9d4321487baa3793d9843 Package: msPurity Version: 1.14.1 Depends: Rcpp Imports: plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite, uuid, jsonlite Suggests: testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL License: GPL (>= 2) MD5sum: 0aece9fa1c11dac9d81d11f53f911a24 Package: MSstats Version: 3.20.3 Depends: R (>= 3.6) 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rmarkdown, testthat License: Artistic-2.0 MD5sum: a80880029db8da0357cc966d4cdbbd9e Package: MSstatsTMT Version: 1.6.6 Depends: R (>= 4.0) 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: ea03930009089841be595f9365f78cdc Package: Mulcom Version: 1.38.0 Depends: R (>= 2.10), Biobase Imports: graphics, grDevices, stats, methods, fields License: GPL-2 MD5sum: d917f5b7011eb90ef5172ee889cdb394 Package: MultiAssayExperiment Version: 1.14.0 Depends: R (>= 3.6.0), SummarizedExperiment (>= 1.3.81) Imports: methods, GenomicRanges (>= 1.25.93), BiocGenerics, S4Vectors (>= 0.23.19), IRanges, Biobase, stats, tidyr, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, R.rsp, HDF5Array, RaggedExperiment, UpSetR, survival, survminer License: Artistic-2.0 MD5sum: 2143ee121b7a306593de8983f2467f63 Package: multiClust Version: 1.18.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) MD5sum: 1f1f0f233c00214862e6e9d437d8fd9d Package: MultiDataSet Version: 1.16.0 Depends: R (>= 3.3), Biobase Imports: BiocGenerics, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman, limma Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment License: file LICENSE MD5sum: 317ed595fa1005ab670ee3af6846e136 Package: multiHiCcompare Version: 1.6.0 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: 072b3d4425c00f39a80919ff5d9160cc Package: 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GenomicRanges, S4Vectors, SummarizedExperiment Imports: graphics, methods, baseline, signal, GenomicAlignments, GenomeInfoDb, rtracklayer, limma, trackViewer, stats, utils, Rsamtools, metap, EmpiricalBrownsMethod,ATACseqQC, corrplot, csaw Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager License: GPL (>= 2) MD5sum: fef0fd78c44b2c1e05fa478eab5d93e1 Package: NanoStringDiff Version: 1.18.0 Depends: Biobase Imports: matrixStats, methods, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle License: GPL MD5sum: 13f7fbf7fb227a09b86d4633b7dc1b23 Package: NanoStringQCPro Version: 1.20.0 Depends: R (>= 3.2), methods Imports: AnnotationDbi (>= 1.26.0), org.Hs.eg.db (>= 2.14.0), Biobase (>= 2.24.0), knitr (>= 1.12), NMF (>= 0.20.5), RColorBrewer (>= 1.0-5), png (>= 0.1-7) Suggests: roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: e5cd777a4c491b21e7ae1e9c4c85f66d Package: nanotatoR Version: 1.4.0 Depends: R (>= 3.6) Imports: hash(>= 2.2.6), openxlsx(>= 4.0.17), rentrez(>= 1.1.0), stats, grDevices, graphics, stringr, knitr, testthat, utils, AnnotationDbi, httr, org.Hs.eg.db, rtracklayer Suggests: rmarkdown, yaml License: file LICENSE MD5sum: 6bc58304c548bff952f42a6dcce3dd5c Package: NBAMSeq Version: 1.4.1 Depends: R (>= 3.6), SummarizedExperiment, S4Vectors Imports: DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods, stats, Suggests: knitr, rmarkdown, testthat, ggplot2 License: GPL-2 MD5sum: eabc238efc45e60d30308bcf0739b5bc Package: NBSplice Version: 1.6.0 Depends: R (>= 3.5), methods Imports: edgeR, stats, MASS, car, mppa, BiocParallel, ggplot2, reshape2 Suggests: knitr, RUnit, BiocGenerics, BiocStyle License: GPL (>= 2) MD5sum: 3b39dda2edca0c80b733936a33a060d4 Package: ncdfFlow Version: 2.34.0 Depends: R (>= 2.14.0), flowCore(>= 1.51.7), RcppArmadillo, methods, BH Imports: Biobase,BiocGenerics,flowCore,zlibbioc LinkingTo: Rcpp,RcppArmadillo,BH, Rhdf5lib Suggests: testthat,parallel,flowStats,knitr License: Artistic-2.0 MD5sum: ae966e546bf8fea559046b89b601d2be Package: ncGTW Version: 1.2.0 Depends: methods, BiocParallel, xcms Imports: Rcpp, grDevices, graphics, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-2 MD5sum: f2f6fd9299a9f8cbf9831af9a427bc1b Package: ndexr Version: 1.10.0 Depends: igraph Imports: httr, jsonlite, plyr, tidyr Suggests: BiocStyle, testthat, knitr, rmarkdown License: BSD MD5sum: 0a6c81ce62831b7d6d8c9d3441888b7d Package: NeighborNet Version: 1.6.0 Depends: methods Imports: graph, stats License: CC BY-NC-ND 4.0 MD5sum: 45ece553c3046bd036aa7ead238f5c59 Package: netbiov Version: 1.22.0 Depends: R (>= 3.1.0), igraph (>= 0.7.1) Suggests: BiocStyle,RUnit,BiocGenerics,Matrix License: GPL (>= 2) MD5sum: 447db57fced31241bc5b077856d49e84 Package: netboost Version: 1.4.0 Depends: R (>= 3.6.0) Imports: Rcpp, RcppParallel, parallel, grDevices, graphics, stats, utils, dynamicTreeCut, WGCNA, impute, colorspace, methods, R.utils LinkingTo: Rcpp, RcppParallel Suggests: knitr License: GPL-3 OS_type: unix MD5sum: 35dc714c26a306691d8d67946332dc1d Package: netboxr Version: 1.0.1 Depends: R (>= 4.0.0), igraph (>= 1.2.4.1), parallel Imports: RColorBrewer, DT, stats, clusterProfiler, data.table, gplots, jsonlite, plyr Suggests: paxtoolsr, BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, cgdsr License: LGPL-3 + file LICENSE MD5sum: 323ad1e36cb122cf704a065add9e05d2 Package: netDx Version: 0.99.18 Depends: R (>= 3.6) Imports: ROCR,pracma,ggplot2,RCy3,glmnet,igraph,reshape2,parallel,stats,utils,MultiAssayExperiment,graphics,grDevices,methods,BiocFileCache,GenomicRanges,bigmemory,doParallel,foreach,combinat,rappdirs,GenomeInfoDb,S4Vectors,IRanges,RColorBrewer Suggests: curatedTCGAData, testthat, knitr, biomaRt License: MIT + file LICENSE MD5sum: d616e9e06707b985bda8f00689ecc108 Package: nethet Version: 1.20.1 Imports: glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network, ggplot2, grDevices, graphics, stats, utils Suggests: knitr, xtable, BiocStyle, testthat License: GPL-2 MD5sum: 2ba0ebfd85a992b2a2457ff4a0bc0d6c Package: NetPathMiner Version: 1.24.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: a991199ca8fa681524c6b51d34ccc7ff Package: netprioR Version: 1.14.0 Depends: methods, graphics, R(>= 3.3) Imports: stats, Matrix, dplyr, doParallel, foreach, parallel, sparseMVN, ggplot2, gridExtra, pROC Suggests: knitr, BiocStyle, pander License: GPL-3 MD5sum: f2d0ffde71bd884e63c8c1ea97306ffd Package: netresponse Version: 1.48.0 Depends: R (>= 2.15.1), Rgraphviz, methods, minet, mclust, reshape2 Imports: dmt, ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer Suggests: knitr License: GPL (>= 2) MD5sum: 9416b54530d21f56ed9b06f79893fdac Package: NetSAM Version: 1.28.0 Depends: R (>= 2.15.1), methods, igraph (>= 0.6-1), seriation (>= 1.0-6), graph (>= 1.34.0) Imports: methods Suggests: RUnit, BiocGenerics License: LGPL MD5sum: 3fb781d545f181fb796a109bed0f33a0 Package: netSmooth Version: 1.8.0 Depends: R (>= 3.5), scater (>= 1.15.11), clusterExperiment (>= 2.1.6) Imports: entropy, SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods, DelayedArray, HDF5Array (>= 1.15.13) Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot License: GPL-3 MD5sum: e525cec50935de5eada0023af6cfe528 Package: networkBMA Version: 2.28.0 Depends: R (>= 2.15.0), stats, utils, BMA, Rcpp (>= 0.10.3), RcppArmadillo (>= 0.3.810.2), RcppEigen (>= 0.3.1.2.1), leaps LinkingTo: Rcpp, RcppArmadillo, RcppEigen, BH License: GPL (>= 2) MD5sum: 2bfa6763c7f96f52b58e12cf1f7f57c7 Package: ngsReports Version: 1.4.2 Depends: R (>= 3.6.0), BiocGenerics, ggplot2, tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 0.8.0), DT, FactoMineR, forcats, ggdendro, grDevices, grid, lubridate, methods, pander, parallel, plotly, readr, reshape2, rmarkdown, Rsamtools, scales, ShortRead, stats, stringr, tidyr, tidyselect (>= 0.2.3), truncnorm, utils, viridisLite, XVector, zoo Suggests: BiocStyle, Cairo, knitr, testthat License: file LICENSE MD5sum: 1be506424ba594c0b265ae3e7cbda3cf Package: nnNorm Version: 2.52.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: b04faf17a1b643120f11e686090310a2 Package: nondetects Version: 2.18.0 Depends: R (>= 3.2), Biobase (>= 2.22.0) Imports: limma, mvtnorm, utils, methods, arm, HTqPCR (>= 1.16.0) Suggests: knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics (>= 0.8.0) License: GPL-3 MD5sum: 61b896fbfa6fc5d4018856760128a312 Package: NoRCE Version: 1.0.0 Depends: R (>= 4.0) Imports: KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices, S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl, dbplyr,utils,ggplot2,igraph,stats,reshape2,readr, GO.db,zlibbioc, biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi Suggests: knitr, TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene, testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown, TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene, org.Mm.eg.db, org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics, org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, methods, License: MIT + file LICENSE MD5sum: 2e98dbe607fd0990296a21aff967df76 Package: normalize450K Version: 1.16.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 9f45f65bb8cdc118fe14064a741a9c80 Package: NormalyzerDE Version: 1.6.0 Depends: R (>= 3.6) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, Biobase, RcmdrMisc, raster, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 MD5sum: e57f0aa343949471057cee52daf52397 Package: NormqPCR Version: 1.34.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: b31bd6bdc03caedbb2be54dd59bffd96 Package: normr Version: 1.14.0 Depends: R (>= 3.3.0) Imports: methods, stats, utils, grDevices, parallel, GenomeInfoDb, GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2), bamsignals (>= 1.4), rtracklayer (>= 1.32) LinkingTo: Rcpp Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown Enhances: BiocParallel License: GPL-2 MD5sum: d8b692d5ccfc76c007f2b4b46b7b7a1a Package: NPARC Version: 1.0.1 Depends: R (>= 4.0.0) Imports: dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr, stats, methods Suggests: testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2, BiocStyle License: GPL-3 MD5sum: 2cc3a1bf7e449e8067c3e1d30dabc547 Package: npGSEA Version: 1.24.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: 856fa67e17824042a0b62cad4eb22b7d Package: NTW Version: 1.38.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 MD5sum: 76fd072addcafcfe128e87899e776ad4 Package: nucleoSim Version: 1.16.0 Imports: stats, IRanges, S4Vectors, graphics, methods Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 3a81135c33677b2567bc3324e0e7c189 Package: nuCpos Version: 1.6.0 Depends: R (>= 3.6) Imports: graphics, methods Suggests: NuPoP, Biostrings, testthat License: file LICENSE MD5sum: 38303ccea11923b833f03fa2412fd9eb Package: NuPoP Version: 1.38.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: 5ed7cad6983bc5ca5e35430be156755f Package: occugene Version: 1.48.0 Depends: R (>= 2.0.0) License: GPL (>= 2) MD5sum: e9cacaa4572c8b61612cf36f3af6c7c0 Package: OCplus Version: 1.62.0 Depends: R (>= 2.1.0) Imports: multtest (>= 1.7.3), graphics, grDevices, stats, akima License: LGPL MD5sum: fb7c11fc122b07470f3846660eb72ae1 Package: odseq Version: 1.16.0 Depends: R (>= 3.2.3) Imports: msa (>= 1.2.1), kebabs (>= 1.4.1), mclust (>= 5.1) Suggests: knitr(>= 1.11) License: MIT + file LICENSE MD5sum: f9fb57d2230a372320fe306750ef6a55 Package: oligo Version: 1.52.1 Depends: R (>= 3.2.0), BiocGenerics (>= 0.13.11), oligoClasses (>= 1.29.6), Biobase (>= 2.27.3), Biostrings (>= 2.35.12) Imports: affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, zlibbioc LinkingTo: preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl Enhances: doMC, doMPI License: LGPL (>= 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(>= 3.4), Biobase Imports: stats, utils, grDevices, graphics, methods, rexposome, limma, sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet, SmartSVA, isva, parallel, SummarizedExperiment, stringr Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata License: MIT + file LICENSE MD5sum: 8a142dda2152c2e1d486a0870b92ca0f Package: OmicsLonDA Version: 1.4.0 Depends: R(>= 3.6) Imports: SummarizedExperiment, gss, plyr, zoo, pracma, ggplot2, BiocParallel, parallel, grDevices, graphics, stats, utils, methods, BiocGenerics Suggests: knitr, rmarkdown, testthat, devtools, BiocManager License: MIT + file LICENSE MD5sum: 413abfbe48f2f1a1feb843890e058b09 Package: OMICsPCA Version: 1.6.0 Depends: R (>= 3.5.0), OMICsPCAdata Imports: HelloRanges, fpc, stats, MultiAssayExperiment, pdftools, methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown, kableExtra, rtracklayer, IRanges, GenomeInfoDb, reshape2, ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR, PerformanceAnalytics, tidyr, data.table, cluster, magick Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: dfcca0f70c95552efcdf4e75618472ef Package: omicsPrint Version: 1.8.0 Depends: R (>= 3.5), MASS Imports: methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 2) MD5sum: 830843f76dcb5dbfcc71a72823700e33 Package: OmnipathR Version: 1.2.1 Depends: R(>= 3.6.0), igraph, graphics, methods, utils Imports: dplyr, rlang Suggests: tidyr, dnet, gprofiler2, BiocStyle, testthat, knitr, rmarkdown, ggplot2, ggraph License: MIT + file LICENSE MD5sum: e11b3c8559e0b86676f657c459138b27 Package: Onassis Version: 1.10.0 Depends: R (>= 4.0), 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: bfd9a0715bbaa2d53f16692a20de4636 Package: oncomix Version: 1.10.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: 984200ff370d1c72dbeac24344fb3e35 Package: OncoScore Version: 1.16.0 Depends: R (>= 4.0.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: 10a3b838cbf45ca89cb9e8e46ae1a521 Package: OncoSimulR Version: 2.18.0 Depends: R (>= 3.3.0) Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel LinkingTo: Rcpp Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander License: GPL (>= 3) MD5sum: 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splines, igraph, foreach, parallel, doParallel, diffusr, lazyeval, tibble, grid, utils, graphics, scales, magrittr, formula.tools, rlang Suggests: testthat, lintr, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: ab3864ae05eaeefdd6a6f469402c3dc4 Package: PGA Version: 1.18.1 Depends: R (>= 3.5.0), IRanges, GenomicRanges, Biostrings (>= 2.26.3), data.table, rTANDEM Imports: S4Vectors (>= 0.9.25), Rsamtools (>= 1.10.2), GenomicFeatures (>= 1.19.8), biomaRt (>= 2.17.1), stringr, RCurl, Nozzle.R1, VariantAnnotation (>= 1.7.28), rtracklayer, RSQLite, ggplot2, AnnotationDbi, customProDB (>= 1.21.5), pheatmap, dplyr, processx, readr, seqinr Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics, BiocStyle, knitr, R.utils License: GPL-2 MD5sum: 13231f5c1d4bb45708dd53a391ef5623 Package: pgca Version: 1.12.0 Imports: utils, stats Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 28ab4320e3f2f21dc60eb6fc06b1cb1d Package: phantasus Version: 1.8.0 Depends: R (>= 3.5) Imports: ggplot2, protolite, Biobase, GEOquery, Rook, htmltools, httpuv, jsonlite, limma, opencpu, assertthat, methods, httr, rhdf5, utils, parallel, stringr, fgsea (>= 1.9.4), svglite, gtable, stats, Matrix, pheatmap, scales, ccaPP, grid, grDevices, AnnotationDbi, DESeq2 Suggests: testthat, BiocStyle, knitr, rmarkdown, data.table License: MIT + file LICENSE MD5sum: a533f9c7b3fed7f14b82a7708948bdf7 Package: PharmacoGx Version: 2.0.9 Depends: R (>= 3.6), CoreGx Imports: Biobase, S4Vectors, SummarizedExperiment, BiocParallel, ggplot2, magicaxis, RColorBrewer, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, testthat, jsonlite Suggests: pander, rmarkdown, knitr, knitcitations License: Artistic-2.0 MD5sum: a27054f0f6f0e777a60739e33970e68c Package: phemd Version: 1.4.0 Depends: R (>= 3.5), monocle Imports: SingleCellExperiment, RColorBrewer, igraph, transport, pracma, cluster, Rtsne, destiny, Seurat, RANN, ggplot2, maptree, pheatmap, scatterplot3d, VGAM, methods, grDevices, graphics, stats, utils, cowplot, S4Vectors, BiocGenerics, SummarizedExperiment, Biobase, phateR, reticulate Suggests: knitr License: GPL-2 MD5sum: 323eec55efc67eecccc01b974edb46cd Package: phenopath Version: 1.12.0 Imports: Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr, tibble, ggplot2, tidyr LinkingTo: Rcpp Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment License: Apache License (== 2.0) MD5sum: ff2f014814de148ee02035ad39619c44 Package: phenoTest Version: 1.36.0 Depends: R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2, Hmisc Imports: survival, limma, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, hgu133a.db, ellipse Suggests: GSEABase, KEGG.db, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) MD5sum: 3a97f96b3e91d7c7c7945ffa3565da72 Package: PhenStat Version: 2.24.0 Depends: R (>= 3.5.0) Imports: SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf, knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4, graphics, grDevices, utils, stats Suggests: RUnit, BiocGenerics License: file LICENSE MD5sum: 1ecb396c7f7ee292df4645b2348a9e33 Package: philr Version: 1.14.0 Imports: ape, phangorn, tidyr, ggplot2, ggtree Suggests: testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet, dplyr License: GPL-3 MD5sum: 470bad8bdab93722f44665bdbbdc3057 Package: phosphonormalizer Version: 1.12.0 Depends: R (>= 3.4.0) Imports: plyr, stats, graphics, matrixStats Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) MD5sum: 3d13581f370d096a6d4b8ef928bfaff2 Package: PhyloProfile Version: 1.2.8 Depends: R (>= 4.0.0) Imports: ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, DT, energy, ExperimentHub, ggplot2, gridExtra, pbapply, RColorBrewer, shiny, shinyBS, shinyjs, OmaDB, plyr, xml2, zoo Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: bb93c953e01605fe76169ac86816e1c9 Package: phyloseq Version: 1.32.0 Depends: R (>= 3.3.0) Imports: ade4 (>= 1.7.4), ape (>= 5.0), Biobase (>= 2.36.2), BiocGenerics (>= 0.22.0), biomformat (>= 1.0.0), Biostrings (>= 2.40.0), cluster (>= 2.0.4), data.table (>= 1.10.4), foreach (>= 1.4.3), ggplot2 (>= 2.1.0), igraph (>= 1.0.1), methods (>= 3.3.0), multtest (>= 2.28.0), plyr (>= 1.8.3), reshape2 (>= 1.4.1), scales (>= 0.4.0), vegan (>= 2.5) Suggests: BiocStyle (>= 2.4), DESeq2 (>= 1.16.1), genefilter (>= 1.58), knitr (>= 1.16), magrittr (>= 1.5), metagenomeSeq (>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2) Enhances: doParallel (>= 1.0.10) License: AGPL-3 MD5sum: a53fb6170d7b288843b5bd786f44bca7 Package: Pi Version: 2.0.3 Depends: igraph, dnet, ggplot2, graphics Imports: Matrix, ggbio, GenomicRanges, GenomeInfoDb, supraHex, scales, grDevices, ggrepel, ROCR, randomForest, glmnet, Gviz, lattice, caret, plot3D, stats, methods, MASS, IRanges, BiocGenerics, dplyr, tidyr, ggnetwork, osfr, RCircos, purrr, readr, tibble Suggests: foreach, doParallel, BiocStyle, knitr, rmarkdown, png, GGally, gridExtra, ggforce, fgsea, RColorBrewer, ggpubr, rtracklayer License: GPL-3 MD5sum: 86ba03771316d83f781a3aed3dfb337b Package: piano Version: 2.4.0 Depends: R (>= 3.5) Imports: BiocGenerics, Biobase, gplots, igraph, relations, marray, fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard, visNetwork, scales, grDevices, graphics, stats, utils, methods Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: a6cb7119848fd9f8eefac01d92a24ef6 Package: pickgene Version: 1.60.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: 760c14f392f286bba3ce4a03d9fa7a97 Package: PICS Version: 2.32.0 Depends: R (>= 3.0.0) Imports: utils, stats, graphics, grDevices, methods, IRanges, GenomicRanges, Rsamtools, GenomicAlignments Suggests: rtracklayer, parallel, knitr License: Artistic-2.0 MD5sum: 7b73b67d87ccc9db8c7f08fd44ecfafb Package: Pigengene Version: 1.14.0 Depends: R (>= 3.5.0), graph Imports: bnlearn (>= 4.4.1), C50 (>= 0.1.2), MASS, matrixStats, partykit, Rgraphviz, WGCNA, GO.db, impute, preprocessCore, grDevices, graphics, stats, utils, parallel, pheatmap (>= 1.0.8), dplyr, gdata Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>= 2.30.0), knitr, BiocStyle, AnnotationDbi, energy License: GPL (>= 2) MD5sum: 05b78c699d4f6cb6cd8583c6b1a38d8a Package: PING Version: 2.32.0 Depends: R(>= 3.5.0) Imports: methods, PICS, graphics, grDevices, stats, Gviz, fda, BSgenome, stats4, BiocGenerics, IRanges, GenomicRanges, S4Vectors Suggests: parallel, ShortRead, rtracklayer License: Artistic-2.0 MD5sum: f84da29ac93d83395a6a32588852a12d Package: pipeFrame Version: 1.4.0 Depends: R (>= 3.6.1), Imports: BSgenome, digest, visNetwork, magrittr, methods, Biostrings, GenomeInfoDb, parallel, stats, utils Suggests: BiocManager, knitr, 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BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr License: GPL (>= 2) MD5sum: 60012521f746053ea2c448a0bafd4ab6 Package: pogos Version: 1.8.0 Depends: R (>= 3.5.0), rjson (>= 0.2.15), httr (>= 1.3.1) Imports: methods, S4Vectors, utils, shiny, ontoProc, ggplot2, graphics Suggests: knitr, DT, ontologyPlot, testthat License: Artistic-2.0 MD5sum: 702765c7f29f4e77b83e377e5ca1593a Package: polyester Version: 1.24.0 Depends: R (>= 3.0.0) Imports: Biostrings (>= 2.32.0), IRanges, S4Vectors, logspline, limma, zlibbioc Suggests: knitr, ballgown License: Artistic-2.0 MD5sum: 80efd1466022d05f88561f511c9dce18 Package: Polyfit Version: 1.22.0 Depends: DESeq Suggests: BiocStyle License: GPL (>= 3) MD5sum: 83cdcbd68490c9c10c735a578e445d63 Package: POST Version: 1.12.0 Depends: R (>= 3.4.0) Imports: stats, CompQuadForm, Matrix, survival, Biobase, GSEABase License: GPL (>= 2) 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pqsfinder Version: 2.4.0 Depends: Biostrings Imports: Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods LinkingTo: Rcpp, BH (>= 1.69.0) Suggests: BiocStyle, knitr, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi License: BSD_2_clause + file LICENSE MD5sum: 9cbd1b56f3b48dc25baab8c1f1a9ef74 Package: pram Version: 1.4.0 Depends: R (>= 3.6) Imports: methods, BiocParallel, tools, utils, data.table (>= 1.11.8), GenomicAlignments (>= 1.16.0), rtracklayer (>= 1.40.6), BiocGenerics (>= 0.26.0), GenomeInfoDb (>= 1.16.0), GenomicRanges (>= 1.32.0), IRanges (>= 2.14.12), Rsamtools (>= 1.32.3), S4Vectors (>= 0.18.3) Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 3) MD5sum: edeb9dd979d230fe61b58c05dc874419 Package: prebs Version: 1.28.0 Depends: R (>= 2.14.0), GenomicAlignments, affy, RPA Imports: parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges, Biobase, GenomeInfoDb, S4Vectors Suggests: prebsdata, hgu133plus2cdf, 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testthat (>= 2.1.0) License: Apache License (== 2.0) | file LICENSE MD5sum: 24c3403dc740981a30da867373fbb15f Package: projectR Version: 1.4.0 Imports: methods, cluster, stats, limma, CoGAPS, NMF, ROCR, ggalluvial, RColorBrewer, dplyr, reshape2, viridis, scales, ggplot2 Suggests: BiocStyle, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap License: GPL (== 2) MD5sum: 699542477bf086b30f498d32e3768bef Package: pRoloc Version: 1.28.0 Depends: R (>= 2.15), MSnbase (>= 1.19.20), MLInterfaces (>= 1.67.10), methods, Rcpp (>= 0.10.3), BiocParallel Imports: stats4, Biobase, mclust (>= 4.3), caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS, knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools, plyr, ggplot2, biomaRt, utils, grDevices, graphics LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, synapter, xtable, rgl, BiocStyle (>= 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rstudioapi, spelling License: MIT + file LICENSE MD5sum: d88d148772c0be806d071f4023de479a Package: PSICQUIC Version: 1.26.1 Depends: R (>= 3.2.0), methods, IRanges, biomaRt (>= 2.34.1), BiocGenerics, httr, plyr Imports: RCurl Suggests: org.Hs.eg.db License: Apache License 2.0 MD5sum: 1a40d80c563e3c4b253f4a59064ce105 Package: psygenet2r Version: 1.20.0 Depends: R (>= 3.4) Imports: stringr, RCurl, igraph, ggplot2, reshape2, grid, parallel, biomaRt, BgeeDB, topGO, BiocManager, Biobase, labeling, GO.db Suggests: testthat, knitr License: MIT + file LICENSE MD5sum: 45b61d4cd43d1764d7563999b74e62c8 Package: PubScore Version: 1.0.0 Depends: R (>= 4.0.0) Imports: ggplot2, igraph, ggrepel,rentrez, progress, graphics, dplyr, utils, methods, intergraph, network, sna Suggests: FCBF, plotly, SummarizedExperiment, SingleCellExperiment, knitr, rmarkdown, testthat (>= 2.1.0), BiocManager, biomaRt License: MIT + file LICENSE MD5sum: f6f93350b718045ab26c1bf1eae612fc Package: pulsedSilac Version: 1.2.0 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BiocParallel, BiocStyle, PSCBS, TxDb.Hsapiens.UCSC.hg19.knownGene, copynumber, covr, knitr, optparse, org.Hs.eg.db, rmarkdown, testthat License: Artistic-2.0 MD5sum: 1b3466704af132754c57509f3ab479a5 Package: pvac Version: 1.36.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) MD5sum: d0b932794f90364ea776680443c314a6 Package: pvca Version: 1.28.0 Depends: R (>= 2.15.1) Imports: Matrix, Biobase, vsn, stats, lme4 Suggests: golubEsets License: LGPL (>= 2.0) MD5sum: 2a9451216d685ebd64cf823a2a3ff312 Package: Pviz Version: 1.22.0 Depends: R(>= 3.0.0), Gviz(>= 1.7.10) Imports: biovizBase, Biostrings, GenomicRanges, IRanges, data.table, methods Suggests: knitr, pepDat License: Artistic-2.0 MD5sum: 77370eca6162619a9415f49ff83d0cd2 Package: PWMEnrich Version: 4.24.2 Depends: methods, grid, BiocGenerics, Biostrings, Imports: seqLogo, gdata, evd, BSgenome Suggests: MotifDb, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr License: LGPL (>= 2) MD5sum: 92e079b4321c383c6f265eec7a31aace Package: pwOmics Version: 1.20.0 Depends: R (>= 3.2) Imports: data.table, rBiopaxParser, igraph, STRINGdb, graphics, gplots, Biobase, BiocGenerics, AnnotationDbi, biomaRt, AnnotationHub, GenomicRanges, graph, grDevices, stats, utils Suggests: ebdbNet, longitudinal, Mfuzz License: GPL (>= 2) MD5sum: ed85c367b36fbf8c61a8e09b61cfc96d Package: pwrEWAS Version: 1.2.0 Depends: shinyBS, foreach Imports: doParallel, abind, truncnorm, CpGassoc, shiny, ggplot2, parallel, shinyWidgets, BiocManager, doSNOW, limma, genefilter, stats, grDevices, methods, utils, graphics, pwrEWAS.data Suggests: knitr, RUnit, BiocGenerics, rmarkdown License: Artistic-2.0 MD5sum: cbd330cb10b8dc803ec875243873dd15 Package: qckitfastq Version: 1.4.0 Imports: magrittr, ggplot2, dplyr, seqTools, zlibbioc, data.table, reshape2, grDevices, graphics, stats, utils, Rcpp, rlang, RSeqAn LinkingTo: Rcpp, RSeqAn Suggests: knitr, rmarkdown, kableExtra, testthat License: Artistic-2.0 MD5sum: 1bcffc06b77ecbf4299efc23251f679b Package: qcmetrics Version: 1.26.0 Depends: R (>= 3.3) Imports: Biobase, methods, knitr, tools, Nozzle.R1, xtable, pander, S4Vectors Suggests: affy, MSnbase, ggplot2, lattice, yaqcaffy, MAQCsubsetAFX, RforProteomics, AnnotationDbi, mzR, hgu133plus2cdf, BiocStyle License: GPL-2 MD5sum: 7fa691ff9ace3dccedb84c6d4f48373d Package: QDNAseq Version: 1.24.0 Depends: R (>= 3.1.0) Imports: graphics, methods, stats, utils, Biobase (>= 2.18.0), CGHbase (>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0), GenomicRanges (>= 1.20), IRanges (>= 2.2), matrixStats (>= 0.54.0), R.utils (>= 2.9.0), Rsamtools (>= 1.20), future (>= 1.14.0), future.apply (>= 1.3.0) Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>= 0.6.20), GenomeInfoDb (>= 1.6.0), R.cache (>= 0.13.0), QDNAseq.hg19, QDNAseq.mm10 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R (>= 4.0), parallel, GenomicRanges, Rbowtie Imports: methods, grDevices, graphics, utils, BiocGenerics, S4Vectors, IRanges, BiocManager, Biobase, Biostrings, BSgenome, Rsamtools, GenomicFeatures, ShortRead, GenomicAlignments, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, Rhisat2, AnnotationDbi LinkingTo: Rhtslib Suggests: Gviz, BiocStyle, knitr, rmarkdown, covr, testthat License: GPL-2 Archs: x64 MD5sum: 3e732161ddbb063b1d102ef3b7f1c6dc Package: QuaternaryProd Version: 1.22.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.3), dplyr, yaml (>= 2.1.18) LinkingTo: Rcpp Suggests: knitr License: GPL (>= 3) MD5sum: 09c83b4c9d3af3282fb6987cfd15107b Package: QUBIC Version: 1.16.0 Depends: R (>= 3.1), biclust Imports: Rcpp (>= 0.11.0), methods, Matrix LinkingTo: Rcpp, RcppArmadillo Suggests: QUBICdata, qgraph, fields, knitr, rmarkdown Enhances: RColorBrewer License: CC BY-NC-ND 4.0 + file LICENSE MD5sum: 8233ddb343b5b7da3daec3a56b0db483 Package: qusage Version: 2.22.0 Depends: R (>= 2.10), limma 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TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment License: GPL-3 MD5sum: 3cf00cd5fce1fa62862979ff13484172 Package: ribor Version: 1.0.0 Depends: R (>= 3.6.0) Imports: dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors, tidyr, tools, yaml Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: b8173b27cec7d631ff9df399734c57aa Package: riboSeqR Version: 1.22.0 Depends: R (>= 3.0.2), methods, GenomicRanges, abind Imports: Rsamtools, IRanges, baySeq, GenomeInfoDb, seqLogo Suggests: BiocStyle, RUnit, BiocGenerics License: GPL-3 MD5sum: 48f8b7d90f237724d3d9d9aa00f12732 Package: ribosomeProfilingQC Version: 1.0.6 Depends: R (>= 4.0), GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq, GenomicAlignments, GenomicFeatures, GenomeInfoDb, IRanges, methods, motifStack, rtracklayer, Rsamtools, RUVSeq, Rsubread, S4Vectors, XVector, ggplot2, ggfittext, scales, ggrepel, utils, cluster, stats, graphics, grid Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, limma, testthat License: GPL (>= 3) + file LICENSE MD5sum: 8a7b217db43c9a6081fa52f2cb274177 Package: RImmPort Version: 1.16.0 Imports: plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools, utils, RSQLite Suggests: knitr License: GPL-3 MD5sum: 593acb0f2559cd8ee8187f6b919b4a4b Package: Ringo Version: 1.52.0 Depends: methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix, grid, lattice Imports: BiocGenerics (>= 0.1.11), genefilter, limma, vsn, stats4 Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0) License: Artistic-2.0 MD5sum: 978320d5e618e2d9c2c0769ebb4e4b7c Package: Risa Version: 1.30.0 Depends: R (>= 2.0.9), Biobase (>= 2.4.0), methods, Rcpp (>= 0.9.13), biocViews, affy Imports: xcms Suggests: faahKO (>= 1.2.11) License: LGPL MD5sum: 1618e783f7ec7a1df7413005b3373f3f Package: RITAN Version: 1.12.0 Depends: R (>= 3.4), Imports: graphics, stats, utils, grid, gridExtra, reshape2, gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL, linkcomm, dynamicTreeCut, gsubfn, hash, png, sqldf, igraph, BgeeDB, knitr, RITANdata Suggests: rmarkdown License: file LICENSE MD5sum: 5fb0574f0ea9083dc1c2fef84bd6f647 Package: RIVER Version: 1.12.0 Depends: R (>= 3.3.2) Imports: glmnet, pROC, ggplot2, graphics, stats, Biobase, methods, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools License: GPL (>= 2) MD5sum: ffc26425dc25c51dc18c33ee4de1b526 Package: RJMCMCNucleosomes Version: 1.12.0 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: 29eeb4f69e634932d9248feccb931cf1 Package: RLMM Version: 1.50.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) MD5sum: 61196a59b3a3366c0b8c7e2f13496369 Package: Rmagpie Version: 1.44.0 Depends: R (>= 2.6.1), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab, methods, pamr, stats, utils Suggests: xtable License: GPL (>= 3) MD5sum: c9ef471b9db34a32c761d8c7cd8289de Package: RMassBank Version: 2.16.0 Depends: Rcpp Imports: XML,RCurl,rjson,S4Vectors,digest, rcdk,yaml,mzR,methods,Biobase,MSnbase,httr, enviPat Suggests: gplots,RMassBankData, xcms (>= 1.37.1), CAMERA, RUnit License: Artistic-2.0 MD5sum: 7f70155e91ba10c7c826281150c92b80 Package: rmelting Version: 1.4.0 Depends: R (>= 3.6) Imports: Rdpack, rJava (>= 0.5-0) Suggests: readxl, knitr, rmarkdown, reshape2, pander, testthat License: GPL-2 | GPL-3 MD5sum: 5009b7121ee1464d46cb7c284fdcb8c7 Package: RmiR Version: 1.44.0 Depends: R (>= 2.7.0), RmiR.Hs.miRNA, RSVGTipsDevice Imports: DBI, methods, stats Suggests: hgug4112a.db,org.Hs.eg.db License: Artistic-2.0 MD5sum: 047f036750f8d1f9d5503a2c436aab53 Package: Rmmquant Version: 1.6.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.12.8), methods, S4Vectors, GenomicRanges, SummarizedExperiment, devtools, TBX20BamSubset, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, DESeq2, BiocStyle LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 961fbfcc33b62117b5cc295b9dbf39c0 Package: RNAAgeCalc Version: 1.0.2 Depends: R (>= 4.0) Imports: ggplot2, recount, impute, AnnotationDbi, org.Hs.eg.db, stats, SummarizedExperiment, methods Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: f0e41ed1e9928577f15f619ac8c6aeae Package: RNAdecay Version: 1.8.0 Depends: R (>= 3.5) Imports: stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr, scales Suggests: parallel, knitr, reshape2, rmarkdown License: GPL-2 MD5sum: 0ae95150009f4bf0e12e0c989b8b4151 Package: RNAinteract Version: 1.36.0 Depends: R (>= 2.12.0), abind, locfit, Biobase Imports: RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid, hwriter, lattice, latticeExtra, limma, methods, splots (>= 1.13.12) License: Artistic-2.0 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utils Suggests: BiocStyle License: GPL (>= 2) MD5sum: 5cc8391e8e3f45d8202fef6b0827391d Package: RNAsense Version: 1.2.0 Depends: R (>= 3.6) Imports: ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment, stats, utils, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 916ef5da7200acb588b330f931013496 Package: rnaseqcomp Version: 1.18.0 Depends: R (>= 3.2.0) Imports: RColorBrewer, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 69662ae05b6fcc657711bacd13e08dd9 Package: rnaSeqMap Version: 2.46.0 Depends: R (>= 2.11.0), methods, Biobase, Rsamtools, GenomicAlignments Imports: GenomicRanges , IRanges, edgeR, DESeq, DBI License: GPL-2 MD5sum: 113eb1a7db366d2af193d905632deca6 Package: RNASeqPower Version: 1.28.0 License: LGPL (>= 2) MD5sum: d567b8c998bac85c6a8e1c53683c6643 Package: RNASeqR Version: 1.6.0 Depends: R(>= 3.5.0), ggplot2, pathview, edgeR, methods Imports: Rsamtools, tools, reticulate, ballgown, gridExtra, rafalib, FactoMineR, factoextra, corrplot, PerformanceAnalytics, reshape2, DESeq2, systemPipeR, systemPipeRdata, clusterProfiler, org.Hs.eg.db, org.Sc.sgd.db, stringr, pheatmap, grDevices, graphics, stats, utils, DOSE, Biostrings, parallel Suggests: knitr, png, grid, RNASeqRData License: Artistic-2.0 MD5sum: df8353abda5c3849ffbfe3f6a44fcecb Package: RnBeads Version: 2.6.0 Depends: R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25), GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr Imports: IRanges Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RefFreeEWAS, RnBeads.hg19, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, GLAD, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR License: GPL-3 MD5sum: e0a4f66364f81f324b819fdc31b109dd Package: Rnits Version: 1.22.0 Depends: R (>= 3.6.0), Biobase, ggplot2, limma, methods Imports: affy, boot, impute, splines, graphics, qvalue, reshape2 Suggests: BiocStyle, knitr, GEOquery, stringr License: GPL-3 MD5sum: f0e15431d3a4f3422eab3eb816dc307d Package: roar Version: 1.24.0 Depends: R (>= 3.0.1) Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, GenomicAlignments (>= 0.99.4), rtracklayer, GenomeInfoDb Suggests: RNAseqData.HNRNPC.bam.chr14, testthat License: GPL-3 MD5sum: fe2281e9a6d8fef5dc6a5b33e8fed8e1 Package: ROC Version: 1.64.0 Depends: R (>= 1.9.0), utils, methods Imports: knitr Suggests: Biobase License: Artistic-2.0 MD5sum: 68c214bc27ff71abd536f4e75f813979 Package: ROCpAI Version: 1.0.0 Depends: boot, SummarizedExperiment, fission, knitr, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 092afb2ad61ac0f1111a1f4541063dc9 Package: rols Version: 2.16.4 Depends: 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stats LinkingTo: Rhtslib (>= 1.17.7), S4Vectors, IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, 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: a0cd0b9a2cfeb9ac27a4c8a16ff0b709 Package: rScudo Version: 1.4.0 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: 3ba4aeec82dc0e0ec64f7c82fdea3ce3 Package: RSeqAn Version: 1.8.0 Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: d575f8251522b902605d97d3ea19a8e6 Package: Rsubread Version: 2.2.6 Imports: grDevices, stats, utils, Matrix License: GPL (>= 3) MD5sum: 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RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, RTCGA.PANCAN12, magrittr, tidyr License: GPL-2 MD5sum: b0f0af5149daa782bfcc2d2935f5e062 Package: RTCGAToolbox Version: 2.18.0 Depends: R (>= 3.5.0) Imports: BiocGenerics, data.table, DelayedArray, GenomicRanges, GenomeInfoDb, httr, limma, methods, RaggedExperiment, RCircos, RCurl, RJSONIO, S4Vectors (>= 0.23.10), stats, stringr, SummarizedExperiment, survival, TCGAutils, XML Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown License: file LICENSE MD5sum: 0cbf03fa23d633282b65c0a54c4ad043 Package: RTN Version: 2.12.1 Depends: R (>= 3.5.0), methods, Imports: RedeR, minet, viper, mixtools, snow, stats, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr, pheatmap, grDevices, graphics, utils Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 8733c7fcc86dac8d0be8d18aaed44343 Package: RTNduals Version: 1.12.2 Depends: R(>= 3.5), RTN(>= 2.12.1), methods Imports: graphics, 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Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), tools LinkingTo: S4Vectors, IRanges, XVector Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit License: Artistic-2.0 + file LICENSE MD5sum: ef65324d20e784fc33c7b49af35c75b6 Package: Rtreemix Version: 1.50.0 Depends: R (>= 2.5.0) Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz License: LGPL MD5sum: 3ea8521a629eac18f059914c18129417 Package: rTRM Version: 1.26.0 Depends: R (>= 2.10), igraph (>= 1.0) Imports: AnnotationDbi, DBI, RSQLite Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2 License: GPL-3 MD5sum: c4d45aa8e9192556ecafbd4f37e3d7c9 Package: rTRMui Version: 1.26.0 Imports: shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 35995fed98379d75d905d48baa122be4 Package: RUVcorr Version: 1.20.0 Imports: corrplot, MASS, stats, lattice, grDevices, gridExtra, snowfall, psych, BiocParallel, grid, bladderbatch, reshape2, graphics Suggests: knitr, hgu133a2.db License: GPL-2 MD5sum: c9c688c0e173c5d1517ba437cf64273e Package: RUVnormalize Version: 1.22.0 Depends: R (>= 2.10.0) Imports: RUVnormalizeData, Biobase Enhances: spams License: GPL-3 MD5sum: 50f4f4c750d083f7bfc1bf9df92552d2 Package: RUVSeq Version: 1.22.0 Depends: Biobase, EDASeq (>= 1.99.1), edgeR Imports: methods, MASS Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 License: Artistic-2.0 MD5sum: 0b639f9fef2e4d22979f2338bce399c6 Package: RVS Version: 1.10.0 Depends: R (>= 3.5.0) Imports: GENLIB, gRain, snpStats, kinship2, methods, stats, utils Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation License: GPL-2 MD5sum: 68fca00a12dd3987c2563545e63f34c8 Package: rWikiPathways Version: 1.8.5 Imports: httr, utils, XML, rjson, data.table, tidyr Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 929f1f8353a600c578056e99bec55ea1 Package: S4Vectors Version: 0.26.1 Depends: R (>= 3.3.0), methods, utils, stats, stats4, BiocGenerics (>= 0.31.1) Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 5a1cfdf45bb7fac5073bf1913dc3bdd8 Package: safe Version: 3.28.1 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: GPL (>= 2) MD5sum: c977719c50298547d1ec5ffaae317e3a Package: sagenhaft Version: 1.58.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: 5371ae62cee205d7c3b8d3c7fcb52204 Package: SAGx Version: 1.62.0 Depends: R (>= 2.5.0), stats, multtest, methods Imports: Biobase, stats4 Suggests: KEGG.db, hu6800.db, MASS License: GPL-3 MD5sum: 337daa9de0bd521ea4020043ec23b541 Package: SAIGEgds Version: 1.2.3 Depends: R (>= 3.5.0), gdsfmt (>= 1.20.0), SeqArray (>= 1.24.1), Rcpp Imports: methods, stats, utils, RcppParallel, SPAtest (>= 3.0.0) LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: parallel, crayon, RUnit, knitr, BiocGenerics, SNPRelate License: GPL-3 MD5sum: 42e830d0fec52c012eb276b6467188da Package: samExploreR Version: 1.12.0 Depends: ggplot2,Rsubread,RNAseqData.HNRNPC.bam.chr14,edgeR,R (>= 3.4.0) Imports: grDevices, stats, graphics Suggests: BiocStyle,RUnit,BiocGenerics,Matrix License: GPL-3 MD5sum: ab70c0806f58793afef41a359e03a4af Package: SamSPECTRAL Version: 1.42.0 Depends: R (>= 3.3.3) Imports: methods License: GPL (>= 2) MD5sum: 0722999b26b81187d2e1c1e18189bc75 Package: sangerseqR Version: 1.24.0 Depends: R (>= 3.0.2), Biostrings Imports: methods, shiny Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 MD5sum: 3eec1ebba726f2cf3ea755b9710ea97d Package: sapFinder Version: 1.26.0 Depends: R (>= 3.0.0),rTANDEM (>= 1.3.5) Imports: pheatmap,Rcpp (>= 0.10.6),graphics,grDevices,stats, utils LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-2 MD5sum: 909ca1c02401273eec56fc11d54febb5 Package: sarks Version: 1.0.0 Depends: R (>= 4.0) Imports: rJava, Biostrings, IRanges, utils, stats, cluster, binom Suggests: RUnit, BiocGenerics, ggplot2 License: BSD_3_clause + file LICENSE MD5sum: 340c156279dc89393d176376f8615403 Package: savR Version: 1.26.0 Depends: ggplot2 Imports: methods, reshape2, scales, gridExtra, XML Suggests: Cairo, testthat License: AGPL-3 MD5sum: 36bab1a8647e1792babd618c69946293 Package: SBGNview Version: 1.2.0 Depends: R (>= 3.6), pathview, SBGNview.data Imports: Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi Suggests: testthat, gage License: AGPL-3 MD5sum: f032173ea4c65dcbf5dd648f03eae4ff Package: SC3 Version: 1.16.0 Depends: R(>= 3.3) Imports: graphics, stats, utils, methods, e1071, parallel, foreach, doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR, robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1), SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, mclust, scater License: GPL-3 MD5sum: 9fbd262d634821770bece7f0c2a3a006 Package: Scale4C Version: 1.10.0 Depends: R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: 52a586f05b5d4dbacf86b575f3c579e2 Package: SCAN.UPC Version: 2.30.0 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva Imports: utils, methods, MASS, tools, IRanges Suggests: pd.hg.u95a License: MIT MD5sum: 5166593c4eb19cbc014f61fb36fe228e Package: SCANVIS Version: 1.2.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file LICENSE MD5sum: 8460353bdf45f368daab658e6ad69b4f Package: scater Version: 1.16.2 Depends: SingleCellExperiment, ggplot2 Imports: BiocGenerics, SummarizedExperiment, Matrix, ggbeeswarm, rlang, grid, DelayedArray, DelayedMatrixStats, methods, S4Vectors, stats, utils, viridis, Rcpp, BiocNeighbors, BiocSingular, BiocParallel LinkingTo: Rcpp, beachmat Suggests: BiocStyle, BiocFileCache, biomaRt, beachmat, cowplot, destiny, knitr, scRNAseq, robustbase, rmarkdown, Rtsne, uwot, NMF, testthat, pheatmap, Biobase, limma, DropletUtils License: GPL-3 MD5sum: cbcbfd5ca38cee17ee32a30d38a0bc02 Package: scBFA Version: 1.2.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods, Matrix Suggests: knitr, rmarkdown, testthat, Rtsne License: GPL-3 + file LICENSE MD5sum: 727ad5d9f7c29b439121a7ea9dff0752 Package: SCBN Version: 1.6.0 Depends: R (>= 3.5.0) Imports: stats Suggests: knitr,rmarkdown License: GPL-2 MD5sum: 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MD5sum: 1d9ee863283cfa343a5e432f1de2593c Package: scde Version: 2.16.0 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: 6937d33f9a97d9fc3b57977fdb5b35cf Package: scds Version: 1.4.0 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: af4017c2693365ee6c8100811a796d9d Package: scFeatureFilter Version: 1.8.0 Depends: R (>= 3.6) 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, BiocStyle, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE MD5sum: b7f48531f6f9e8595648d92d5a691d43 Package: scGPS Version: 1.2.0 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: 03b534748485a8144f9f02cf69b8a7bc Package: schex Version: 1.2.0 Depends: SingleCellExperiment (>= 1.7.4), Seurat, ggplot2 (>= 3.2.1), shiny Imports: hexbin, stats, methods, cluster, dplyr, entropy, ggforce, scales, grid, concaveman Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran License: GPL-3 MD5sum: 7001211cb83cfb05bd1a35cb0272a743 Package: scHOT Version: 1.0.0 Depends: R (>= 4.0) Imports: S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix, SummarizedExperiment, IRanges, methods, stats, BiocParallel, reshape, ggplot2, igraph, grDevices, ggforce, graphics Suggests: knitr, rmarkdown, scater, scattermore, scales, matrixStats, deldir License: GPL-3 MD5sum: 8b8aaad3aa4ac304a895c844e15fe948 Package: ScISI Version: 1.60.0 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: 8320b8c9eba28373c59e0681beace004 Package: scMAGeCK Version: 1.0.0 Imports: Seurat, stats, utils Suggests: knitr, rmarkdown License: BSD_2_clause MD5sum: 2d3743115218ec4d809f5f2d8778022e Package: scmap Version: 1.10.0 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: 66b4e55241638d47284b909c77c68a5d Package: scMerge Version: 1.4.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, cluster, DelayedArray, DelayedMatrixStats, distr, dplyr, 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: 1167388f35f4c9f31488e25e12611176 Package: scmeth Version: 1.8.0 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: 36bff922e30d6d761f11120c741cf3bc Package: SCnorm Version: 1.10.0 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: a8b58e8cc87741705280b02a87868c0c Package: scone Version: 1.12.0 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: ad4092a26e6ba0e120ab758883e30813 Package: Sconify Version: 1.8.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: bd30c91e65e41b6f6042172208781c59 Package: SCOPE Version: 1.0.0 Depends: R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19 Imports: stats, grDevices, graphics, utils, DescTools, RColorBrewer, gplots, foreach, parallel, doParallel, DNAcopy, BSgenome, Biostrings, BiocGenerics, S4Vectors Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) License: GPL-2 MD5sum: fa32fa841b66c7dfa21713c4bc6622c6 Package: scoreInvHap Version: 1.10.0 Depends: R (>= 3.4.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: e115aa8079e0e4437ebdab6261ca1194 Package: scPCA Version: 1.2.0 Depends: R (>= 3.6) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca, cluster, kernlab, origami Suggests: testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, Matrix, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark License: MIT + file LICENSE MD5sum: 1cc592b855f55128b7e37081eafad15d Package: scPipe Version: 1.10.0 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, hash, dplyr, GenomicRanges, magrittr, glue (>= 1.3.0), rlang, scater (>= 1.11.0) LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat Suggests: Rsubread, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 04401f06c80af1bfe38937869d547b14 Package: scran Version: 1.16.0 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, IRanges, 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, pheatmap License: GPL-3 MD5sum: 9febea7f18479873b66b3fa76b4bf460 Package: scRecover Version: 1.4.1 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: ae68a04c8dbf82ab208cd3f19d5a9cc1 Package: scruff Version: 1.6.0 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, Rsubread Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 2c22dface785652f6c6668f93c249728 Package: scry Version: 1.0.1 Depends: R (>= 4.0), stats, methods Imports: glmpca (>= 0.2.0), Matrix, SingleCellExperiment, SummarizedExperiment Suggests: BiocGenerics, knitr, testthat, covr, rmarkdown, ggplot2, DuoClustering2018 License: Artistic-2.0 MD5sum: 8f4d828b1c01232bab121ec789f5c93a Package: scTensor Version: 1.4.3 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, schex, ggplot2 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: af1f1dc5dbde08510780f3d78868f830 Package: scTGIF Version: 1.2.2 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, schex, tibble, ggplot2, igraph Suggests: testthat License: Artistic-2.0 MD5sum: c0643f1f6f7fd1581985a7c6e05b541a Package: scTHI Version: 1.0.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown License: GPL-2 MD5sum: f502b3b258d59ad2f48f7ad02c586147 Package: SDAMS Version: 1.8.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: 096142142e95901add87c4206536edd8 Package: segmentSeq Version: 2.22.0 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: a2274142225ca062548b89887e9fce11 Package: selectKSigs Version: 1.0.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: fde0c42c8f9eac99eb04ff49b5c47731 Package: SELEX Version: 1.20.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: 46e75daad41765998ea60fd8b91b0f43 Package: SemDist Version: 1.22.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) MD5sum: 702c194b81a6152bfbc0267b9fc1f7e4 Package: semisup Version: 1.12.4 Depends: R (>= 3.0.0) Imports: VGAM Suggests: knitr, testthat, SummarizedExperiment License: GPL-3 MD5sum: c1c387a241f51cd6d48c6762b130f5e3 Package: SEPIRA Version: 1.8.0 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: 46b5f26faf083df5ce1eaf0ac895a6b8 Package: seq2pathway Version: 1.20.0 Depends: R (>= 2.10.0) Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data License: GPL-2 MD5sum: f13301f9e3e2e01a5e98eff3e8c90768 Package: SeqArray Version: 1.28.1 Depends: R (>= 3.5.0), gdsfmt (>= 1.23.5) 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: d99b959c1ab84baa4b8f9d543b860d5a Package: seqbias Version: 1.36.0 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: ef3f7bcd3606d953b1efd557f8a26fbd Package: seqCAT Version: 1.10.0 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: c6352b910da2abb5afe65698e437131c Package: seqCNA Version: 1.34.0 Depends: R (>= 3.0), GLAD (>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot (>= 0.99), methods License: GPL-3 MD5sum: 32b415bd1359607b6487901eeb7bb8ff Package: seqcombo Version: 1.10.0 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: 714130fd4df8a4cdcb7fb79fb9e5405d Package: SeqGSEA Version: 1.28.0 Depends: Biobase, doParallel, DESeq Imports: methods, biomaRt Suggests: easyRNASeq, GenomicRanges License: GPL (>= 3) MD5sum: 9ffbf937c20f142d395b7435982cc187 Package: seqLogo Version: 1.54.3 Depends: methods, grid Imports: stats4 License: LGPL (>= 2) MD5sum: 88e46b01560bcbf4713c6cb2ef1a1ee3 Package: seqPattern Version: 1.20.0 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: 5f600e73a9f2609e57cb29a74f2dfb29 Package: seqplots Version: 1.26.0 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: 90f6d8b4940147345bbce90b96dd7b07 Package: seqsetvis Version: 1.8.0 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: 0c5d9a4c324d4c7b18904864a8419ccc Package: SeqSQC Version: 1.10.0 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: 1db572a8a0d6aeafe67fa10b3c338aa1 Package: seqTools Version: 1.22.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 581bd28483c34421265e71c406beca7a Package: SeqVarTools Version: 1.26.0 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: 5e8925f7923b5ec58aaaa0228da3c82c Package: sesame Version: 1.6.0 Depends: R (>= 3.6), sesameData, methods Imports: BiocParallel, grDevices, utils, illuminaio, MASS, GenomicRanges, IRanges, grid, preprocessCore, stats, S4Vectors, randomForest, wheatmap, ggplot2, parallel, matrixStats, DNAcopy, HDF5Array, SummarizedExperiment Suggests: scales, knitr, rmarkdown, testthat, minfi, FlowSorted.CordBloodNorway.450k, 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Package: SIAMCAT Version: 1.8.1 Depends: R (>= 3.6.0), mlr, phyloseq Imports: beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, ParamHelpers, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot Suggests: BiocStyle, optparse, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 9274342decaaaca91726aa22692a7af0 Package: SICtools Version: 1.18.0 Depends: R (>= 3.0.0), methods, Rsamtools (>= 1.18.1), doParallel (>= 1.0.8), Biostrings (>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges (>= 1.22.4), IRanges (>= 2.4.8) Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 089b49febc421bcce927c664fcec4869 Package: SigCheck Version: 2.20.0 Depends: R (>= 3.2.0), MLInterfaces, Biobase, e1071, BiocParallel, survival Imports: graphics, stats, utils, methods Suggests: BiocStyle, breastCancerNKI, qusage License: Artistic-2.0 MD5sum: 2018b7362dc7ed41bfe3e3eafbd3b167 Package: sigFeature Version: 1.6.0 Depends: R (>= 3.5.0) Imports: biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer, Matrix, SparseM, graphics, stats, utils, SummarizedExperiment, BiocParallel, methods Suggests: RUnit, BiocGenerics, knitr License: GPL MD5sum: a37ae8417b39adaaae0ad32933d4a9bc Package: SigFuge Version: 1.26.0 Depends: R (>= 3.1.1), GenomicRanges Imports: ggplot2, matlab, reshape, sigclust Suggests: org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle License: GPL-3 MD5sum: 3dbb2f70fa7c1b988ec66a02b77c081a Package: siggenes Version: 1.62.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: 74d8f692cb855ca640cf07a4aa492974 Package: sights Version: 1.14.0 Depends: R(>= 3.3) Imports: MASS(>= 7.3), qvalue(>= 2.2), ggplot2(>= 2.0), reshape2(>= 1.4), lattice(>= 0.2), stats(>= 3.3) Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx License: GPL-3 | file LICENSE MD5sum: 6b141696db8c0fdf9478096250f73676 Package: signatureSearch Version: 1.2.5 Depends: R(>= 3.6.0), Rcpp, SummarizedExperiment Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, utils, reshape2, visNetwork, BiocParallel, fastmatch, Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, org.Hs.eg.db License: Artistic-2.0 MD5sum: e87326eeebddc657491c8595fd328efb Package: signeR Version: 1.14.0 Depends: VariantAnnotation, NMF Imports: BiocGenerics, Biostrings, class, graphics, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMR LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: 7b59dad46406c2be9c9f546f655a65ed Package: sigPathway 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License: GPL-3 + file LICENSE MD5sum: 9deae8fda4f235d220d2dac002249be1 Package: singscore Version: 1.8.0 Depends: R (>= 3.6) Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, reshape2, S4Vectors Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 1f13f8d6c6f162b97ffbaaa656378794 Package: SISPA Version: 1.18.0 Depends: R (>= 3.2),genefilter,GSVA,changepoint Imports: data.table, plyr, ggplot2 Suggests: knitr License: GPL-2 MD5sum: fb8345ad5330a7777ce7aec8cbe0cf7d Package: sitePath Version: 1.4.2 Depends: R (>= 3.6.0) Imports: ape, seqinr, Rcpp, methods, graphics, utils, stats LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 417a22e5d3b877e78b102d58521c1f20 Package: sizepower Version: 1.58.0 Depends: stats License: LGPL MD5sum: 70bb3a7f352633043d2e99d7740e0fa0 Package: skewr Version: 1.20.0 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2fb7e0cb90b0892b32322e0414256f81 Package: Structstrings Version: 1.4.1 Depends: R (>= 3.6), S4Vectors (>= 0.25.14), IRanges (>= 2.21.6), Biostrings (>= 2.55.7) Imports: methods, BiocGenerics, XVector, stringr, stringi, crayon, grDevices LinkingTo: IRanges, S4Vectors Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle License: Artistic-2.0 MD5sum: a318ba74f471f233f907026dc9414918 Package: structToolbox Version: 1.0.1 Depends: R (>= 4.0), struct (>= 0.99.10) Imports: ggplot2, ggthemes, grid, gridExtra, methods, scales, sp, stats Suggests: agricolae, BiocFileCache, BiocStyle, car, covr, cowplot, e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls, pmp, reshape2, ropls, rmarkdown, Rtsne, testthat License: GPL-3 MD5sum: f69440ff4c104e8ac919c6db7f15da7e Package: StructuralVariantAnnotation Version: 1.4.0 Depends: GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 3.6.0) Imports: assertthat, Biostrings, stringr, dplyr, methods, rlang Suggests: BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat, roxygen2, covr, knitr, plyranges, ggbio, biovizBase, circlize, tictoc, GenomeInfoDb, IRanges, S4Vectors, SummarizedExperiment License: GPL-3 MD5sum: 8ffc6f114660ad8a80e36a4e73ccbb8b Package: SubCellBarCode Version: 1.4.0 Depends: R (>= 3.6) Imports: Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra, networkD3, ggrepel, graphics, stats, org.Hs.eg.db, AnnotationDbi Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 960ba3059c2ccec13dbb16db99fca494 Package: subSeq Version: 1.18.0 Depends: R (>= 3.2) Imports: data.table, dplyr, tidyr, ggplot2, magrittr, qvalue (>= 1.99), digest, Biobase Suggests: limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr License: MIT + file LICENSE MD5sum: f71c9dc953229b11d31b6bed96446257 Package: SummarizedBenchmark Version: 2.6.0 Depends: R (>= 3.6), tidyr, SummarizedExperiment, S4Vectors, BiocGenerics, methods, UpSetR, rlang, stringr, utils, BiocParallel, ggplot2, mclust, dplyr, digest, sessioninfo, crayon, tibble Suggests: iCOBRA, BiocStyle, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt License: GPL (>= 3) MD5sum: 2005af967d5d0efb0eb0ad7f2ca33484 Package: SummarizedExperiment Version: 1.18.2 Depends: R (>= 3.2), methods, GenomicRanges (>= 1.33.6), Biobase, DelayedArray (>= 0.3.20) Imports: utils, stats, tools, Matrix, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.25.14), IRanges (>= 2.21.6), GenomeInfoDb (>= 1.13.1) Suggests: annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, jsonlite, rhdf5, HDF5Array (>= 1.7.5), airway, RUnit, testthat License: Artistic-2.0 MD5sum: c0aad0f8107efa793c8ea2614f302744 Package: supraHex Version: 1.26.0 Depends: R (>= 3.6), hexbin Imports: ape, MASS, grDevices, graphics, stats, utils, methods License: GPL-2 MD5sum: 7730e9e05ff467db3f76e9de324afb69 Package: survcomp Version: 1.38.0 Depends: survival, prodlim, R (>= 3.4) Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta, stats, graphics Suggests: Hmisc, CPE, clinfun, xtable, Biobase, BiocManager License: Artistic-2.0 MD5sum: ea071ffcd8b2e4253cdadd5075abc036 Package: survtype Version: 1.4.0 Depends: SummarizedExperiment, pheatmap, survival, survminer, clustvarsel, stats, utils Suggests: maftools, scales, knitr License: Artistic-2.0 MD5sum: 6a84f1e9b305576d99efea17f57c7efc Package: Sushi Version: 1.26.0 Depends: R (>= 2.10), zoo,biomaRt Imports: graphics, grDevices License: GPL (>= 2) MD5sum: c0570e181115d2394cbff8a6a1ea4658 Package: sva Version: 3.36.0 Depends: R (>= 3.2), mgcv, genefilter, BiocParallel Imports: matrixStats, stats, graphics, utils, limma, edgeR Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat License: Artistic-2.0 MD5sum: 203fae3d70c4db0e678c1de2b1ab3d25 Package: SWATH2stats Version: 1.18.0 Depends: R(>= 2.10.0) Imports: data.table, reshape2, grid, ggplot2, stats, grDevices, graphics, utils, biomaRt Suggests: testthat, knitr Enhances: imsbInfer, MSstats, PECA, aLFQ License: GPL-3 MD5sum: de3f9cb48b817b5cb0b1612b75f93aa1 Package: SwathXtend Version: 2.10.0 Depends: e1071, openxlsx, VennDiagram, lattice License: GPL-2 MD5sum: b5c2ddf8a0a9da473e861c1a50def94a Package: swfdr Version: 1.14.0 Depends: R (>= 3.4) Imports: methods, splines, stats4, stats Suggests: dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2, rmarkdown, testthat License: GPL (>= 3) MD5sum: b660991c56fa1e582fa90727fdd13400 Package: SwimR Version: 1.26.0 Depends: R (>= 3.0.0), methods, gplots (>= 2.10.1), heatmap.plus (>= 1.3), signal (>= 0.7), R2HTML (>= 2.2.1) Imports: methods License: LGPL-2 MD5sum: f88fcea32539e9e7f23c9b1cae173a49 Package: switchBox Version: 1.24.0 Depends: R (>= 2.13.1), pROC, gplots License: GPL-2 MD5sum: cbbc4170fe48c548fbc5169cd45522c8 Package: switchde Version: 1.14.0 Depends: R (>= 3.4), SingleCellExperiment Imports: SummarizedExperiment, dplyr, ggplot2, methods, stats Suggests: knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr License: GPL (>= 2) MD5sum: b4c0f5f0c3278aee9c37cbf05b3c8379 Package: synapter Version: 2.12.0 Depends: R (>= 3.1.0), methods, MSnbase (>= 2.1.2) Imports: RColorBrewer, lattice, qvalue, multtest, utils, tools, Biobase, knitr, Biostrings, cleaver (>= 1.3.3), readr (>= 0.2), rmarkdown (>= 1.0) Suggests: synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle License: GPL-2 MD5sum: 73c3ebf3ecdb82a5295efbc1303d2c01 Package: synergyfinder Version: 2.2.4 Depends: R (>= 3.6.0), methods Imports: drc (>= 2.5-12), reshape2 (>= 1.4.1), ggplot2 (>= 2.1.0), grid (>= 3.2.4), lattice (>= 0.20-33), nleqslv(>= 3.0), stats (>= 3.3.0), graphics (>= 3.3.0), grDevices (>= 3.3.0) Suggests: knitr, rmarkdown License: Mozilla Public License 2.0 MD5sum: bbda9ff735a78fd6d8221a32be436f6c Package: SynExtend Version: 1.0.0 Depends: R (>= 4.0.0), DECIPHER (>= 2.14.0), igraph (>= 1.2.4.1) Imports: methods, Biostrings, S4Vectors, IRanges, utils, stats Suggests: knitr License: GPL-3 MD5sum: 71a2f2cebc339b5f0476fd04a95e2ea7 Package: synlet Version: 1.18.0 Depends: R (>= 3.2.0), ggplot2 Imports: doBy, dplyr, grid, magrittr, RColorBrewer, RankProd, reshape2 Suggests: knitr, testthat License: GPL-3 MD5sum: 943ff55c3b3c3df114c5c4d7b50fc72c Package: SynMut Version: 1.4.0 Imports: seqinr, methods, Biostrings, stringr, BiocGenerics Suggests: BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc, glue License: GPL-2 MD5sum: 73db6ddf38f5c74eefa0b4a0c1fa3e2e Package: systemPipeR Version: 1.22.0 Depends: Rsamtools (>= 1.31.2), Biostrings, ShortRead (>= 1.37.1), methods Imports: GenomicRanges, GenomicFeatures (>= 1.31.3), SummarizedExperiment, VariantAnnotation (>= 1.25.11), rjson, ggplot2, grid, limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap, batchtools, yaml, stringr, assertthat, magrittr, DOT, rsvg Suggests: BiocGenerics, ape, RUnit, BiocStyle, knitr, rmarkdown, biomaRt, BiocParallel, BiocManager, systemPipeRdata, GenomicAlignments License: Artistic-2.0 MD5sum: c3e5b7673ac2ef8df11a64a68b7e9428 Package: TAPseq Version: 1.0.0 Depends: R (>= 4.0) Imports: methods, GenomicAlignments, GenomicRanges, IRanges, BiocGenerics, S4Vectors (>= 0.20.1), GenomeInfoDb, BSgenome, GenomicFeatures, Biostrings, dplyr, tidyr, BiocParallel Suggests: testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer License: MIT + file LICENSE MD5sum: 23ebe18c143c8365c46d48c27c34b2a9 Package: target Version: 1.2.0 Depends: R (>= 3.6) Imports: BiocGenerics, GenomicRanges, IRanges, matrixStats, methods, stats, graphics, shiny Suggests: testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS, covr License: GPL-3 MD5sum: 2ffb61dd613d3f102b1180b3d1febefe Package: TargetScore Version: 1.26.0 Depends: pracma, Matrix Suggests: TargetScoreData, gplots, Biobase, GEOquery License: GPL-2 MD5sum: 2a4cf71389def68382f2e24a2df2a071 Package: TargetSearch Version: 1.44.0 Depends: ncdf4 Imports: graphics, grDevices, methods, stats, utils, stringr, assertthat Suggests: TargetSearchData, BiocStyle, knitr License: GPL (>= 2) MD5sum: b98ee8ec7d0dce4acbc26e0cea7b292d Package: TarSeqQC Version: 1.18.0 Depends: R (>= 3.5.1), methods, GenomicRanges, Rsamtools (>= 1.9.2), ggplot2, plyr, openxlsx Imports: grDevices, stats, utils, S4Vectors, IRanges, BiocGenerics, reshape2, GenomeInfoDb, BiocParallel, Biostrings, cowplot, graphics, GenomicAlignments, Hmisc Suggests: BiocManager, RUnit License: GPL (>= 2) MD5sum: 205c2daaae7a12332c6427f99dadbf09 Package: TBSignatureProfiler Version: 1.0.0 Depends: R (>= 4.0.0) Imports: ASSIGN (>= 1.23.1), GSVA, SummarizedExperiment, S4Vectors, methods, BiocParallel, ComplexHeatmap, RColorBrewer, ggplot2, reshape2, circlize, glmnet, ROCit, bioDist, readr, boot, DESeq2, caret, ggfortify, e1071, DT, edgeR, singscore, gdata, shiny Suggests: testthat, spelling, lintr, covr, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 907c36e280d5c2d01bddd5fcd52c4525 Package: TCC Version: 1.28.0 Depends: R (>= 3.0), methods, DESeq, DESeq2, edgeR, baySeq, ROC Suggests: RUnit, BiocGenerics Enhances: snow License: GPL-2 MD5sum: afcb98c0a58f79c1df4f14f7aa458805 Package: TCGAbiolinks Version: 2.16.4 Depends: R (>= 3.5) Imports: downloader (>= 0.4), grDevices, dplyr, graphics, tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite (>= 1.0.0), plyr, knitr, methods, biomaRt, ggplot2, stringr (>= 1.0.0), IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils, SummarizedExperiment (>= 1.4.0), readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1) Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame, pathview, clusterProfiler, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, TCGAbiolinksGUI.data, supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid License: GPL (>= 3) MD5sum: b3f8b3ed1c97e368603c054af24a9344 Package: TCGAbiolinksGUI Version: 1.14.0 Depends: R (>= 3.3.1), shinydashboard (>= 0.5.3), TCGAbiolinksGUI.data Imports: shiny (>= 0.14.1), downloader (>= 0.4), grid, DT, plotly, readr, maftools, stringr (>= 1.1.0), SummarizedExperiment, ggrepel, data.table, caret, shinyFiles (>= 0.6.2), ggplot2 (>= 2.1.0), pathview, ELMER (>= 2.0.0), clusterProfiler, parallel, TCGAbiolinks (>= 2.5.5), shinyjs (>= 0.7), colourpicker, sesame, shinyBS (>= 0.61) Suggests: testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2, BiocStyle, animation, pander License: GPL (>= 3) MD5sum: cd7339363fc0d811e7c1885ec593ba85 Package: TCGAutils Version: 1.8.1 Depends: R (>= 3.6.0) Imports: AnnotationDbi, BiocGenerics, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment (>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2 Suggests: BiocFileCache, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: cb54b1a7023a6b8ef8c4ed6f4c9b7698 Package: TCseq Version: 1.12.1 Depends: R (>= 3.4) Imports: edgeR, BiocGenerics, reshape2, GenomicRanges, IRanges, SummarizedExperiment, GenomicAlignments, Rsamtools, e1071, cluster, ggplot2, grid, grDevices, stats, utils, methods, locfit Suggests: testthat License: GPL (>= 2) MD5sum: 45584b9365440c6ed7c363fa405db4f9 Package: TDARACNE Version: 1.38.0 Depends: GenKern, Rgraphviz, Biobase License: GPL-2 MD5sum: 5bfc9c0dd2837c850558541c9c65172c Package: tenXplore Version: 1.10.0 Depends: R (>= 3.4), shiny, restfulSE (>= 0.99.12) Imports: methods, ontoProc (>= 0.99.7), SummarizedExperiment, AnnotationDbi, matrixStats, org.Mm.eg.db, stats, utils Suggests: org.Hs.eg.db, testthat, knitr License: Artistic-2.0 MD5sum: 5e3b71811a97a2d19a4c5f13f2b4a3fb Package: ternarynet Version: 1.32.0 Depends: R (>= 2.10.0), methods Imports: utils, igraph License: GPL (>= 2) MD5sum: 9d2f4c8a70c426a2acdf34b8049e74b0 Package: TFARM Version: 1.10.0 Depends: R (>= 3.4) Imports: arules, fields, GenomicRanges, graphics, stringr, methods, stats, gplots Suggests: BiocStyle, knitr, plyr License: Artistic-2.0 MD5sum: fadfe46c55efa73c91534aa4eca6f756 Package: TFBSTools Version: 1.26.0 Depends: R (>= 3.2.2) Imports: Biobase(>= 2.28), Biostrings(>= 2.36.4), BiocGenerics(>= 0.14.0), BiocParallel(>= 1.2.21), BSgenome(>= 1.36.3), caTools(>= 1.17.1), CNEr(>= 1.4.0), DirichletMultinomial(>= 1.10.0), GenomeInfoDb(>= 1.6.1), GenomicRanges(>= 1.20.6), gtools(>= 3.5.0), grid, IRanges(>= 2.2.7), methods, DBI (>= 0.6), RSQLite(>= 1.0.0), rtracklayer(>= 1.28.10), seqLogo(>= 1.34.0), S4Vectors(>= 0.9.25), TFMPvalue(>= 0.0.5), XML(>= 3.98-1.3), XVector(>= 0.8.0), parallel Suggests: BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr(>= 1.11), testthat, JASPAR2016(>= 1.0.0), JASPAR2018(>= 1.0.0) License: GPL-2 MD5sum: 83c78203434625260508fb695fd4b201 Package: TFEA.ChIP Version: 1.8.0 Depends: R (>= 3.3) Imports: GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices, dplyr, stats, utils, R.utils, methods, org.Hs.eg.db Suggests: knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, GSEABase, DESeq2, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: c4643e6c98eee0844a629a219a3291ef Package: TFHAZ Version: 1.10.0 Depends: R(>= 3.4) Imports: GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 2709b1a5d70d9b9a0e62b96ffe4bbd5f Package: TFutils Version: 1.8.0 Depends: R (>= 3.5.0) Imports: methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase Suggests: knitr, data.table, testthat, AnnotationDbi, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, Rsamtools, S4Vectors, org.Hs.eg.db, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer License: Artistic-2.0 MD5sum: db52451544f73b5dc0740778c7760c7c Package: tidybulk Version: 1.0.2 Depends: R (>= 4.0.0) Imports: tibble, readr, dplyr, magrittr, tidyr, rlang, purrr, preprocessCore, stats, parallel, utils, lifecycle Suggests: testthat, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, EGSEA, SummarizedExperiment, S4Vectors, ggplot2, widyr, clusterProfiler, msigdbr License: GPL-3 MD5sum: 6acb0fe15e2de8e537b3f7f7bb9bbadb Package: tigre Version: 1.42.0 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, AnnotationDbi, gplots, graphics, grDevices, stats, utils, annotate, DBI, RSQLite Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager License: AGPL-3 MD5sum: 9202c2c3e9fc018c3564b03076c39b5a Package: tilingArray Version: 1.66.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 MD5sum: 0bcb16f6b71d882fb4037214ef830514 Package: timecourse Version: 1.60.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL MD5sum: 36660a0ad195884bc19b823b661dd9af Package: timeOmics Version: 1.0.1 Depends: mixOmics, lmms, R (>= 4.0) Imports: dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, propr, lmtest Suggests: BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots License: GPL-3 MD5sum: 88cd340c23820af95b5918b8c37d4391 Package: timescape Version: 1.12.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), stringr (>= 1.0.0), dplyr (>= 0.4.3), gtools (>= 3.5.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 6323a6929a3fe60dd2b557c32d62532f Package: TimeSeriesExperiment Version: 1.6.0 Depends: R (>= 3.5.0), S4Vectors (>= 0.19.23), SummarizedExperiment (>= 1.11.6) Imports: dynamicTreeCut, dplyr, edgeR, DESeq2, ggplot2 (>= 3.0.0), graphics, Hmisc, limma, methods, magrittr, proxy, stats, tibble, tidyr, vegan, viridis, utils 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: 634024849017c2b36f4a507f424ea6ca Package: TIN Version: 1.20.0 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: d5962312fcef9a24ac655644d2046ce2 Package: TissueEnrich Version: 1.8.0 Depends: R (>= 3.5), ensurer (>= 1.1.0), ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), SummarizedExperiment (>= 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Depends: R (>= 3.6.0), e1071, quadprog, SummarizedExperiment Imports: GSVA (>= 1.26.0), pheatmap, grDevices, RColorBrewer, pracma, GGally, R.utils, forestplot, ggplot2, ggpubr, survival, grid, stats, methods Suggests: knitr License: GPL-3 MD5sum: f4dc0f61010f20328d3616d026e76873 Package: TnT Version: 1.10.0 Depends: R (>= 3.4), GenomicRanges Imports: methods, stats, utils, grDevices, htmlwidgets, jsonlite, data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr Suggests: GenomicFeatures, shiny, BiocManager, rmarkdown, testthat License: AGPL-3 MD5sum: e48f0a01227d5bce1aa5a9df72458663 Package: TOAST Version: 1.2.0 Depends: R (>= 3.6), RefFreeEWAS, EpiDISH, limma, nnls Imports: stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, csSAM, gplots, matrixStats, Matrix License: GPL-2 MD5sum: b71df6cde1a88523875d335c13a8cef0 Package: tofsims Version: 1.16.0 Depends: R (>= 3.3.0), methods, utils, ProtGenerics Imports: Rcpp (>= 0.11.2), ALS, ChemometricsWithR, signal, KernSmooth, graphics, grDevices, stats LinkingTo: Rcpp, RcppArmadillo Suggests: EBImage, knitr, rmarkdown, testthat, tofsimsData, BiocParallel, RColorBrewer Enhances: parallel License: GPL-3 MD5sum: fe8daf470a60f6009dd9ea3328406ccb Package: ToPASeq Version: 1.22.0 Depends: R(>= 3.5.0), graphite Imports: Rcpp, graph, methods, Biobase, RBGL, SummarizedExperiment, gRbase, limma, corpcor LinkingTo: Rcpp Suggests: BiocStyle, airway, knitr, rmarkdown, DESeq2, DESeq, edgeR, plotrix, breastCancerVDX, EnrichmentBrowser License: AGPL-3 MD5sum: 0146ab7cb75cf1b27315aefcd7b4bd80 Package: topconfects Version: 1.4.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, assertthat, ggplot2 Suggests: limma, edgeR, DESeq2, NBPSeq, dplyr, testthat, knitr, rmarkdown, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi License: LGPL-2.1 | file LICENSE MD5sum: 35ecb281aa31541a57357340c1492635 Package: topdownr Version: 1.10.0 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.20.0), ProtGenerics (>= 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rmarkdown, splines, stats, stringr, tibble, utils, VennDiagram, VGAM Suggests: BiocStyle, testthat License: Artistic-2.0 MD5sum: 7d049b4fe00af064d19a014cf0a2d171 Package: TPP2D Version: 1.4.1 Depends: R (>= 3.6.0), stats, utils, dplyr, methods Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl, parallel, MASS, BiocParallel, limma Suggests: knitr, testthat License: GPL-3 MD5sum: 39467c937808f6cbb0251e868daa91c7 Package: tracktables Version: 1.22.0 Depends: R (>= 3.0.0) Imports: IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base, stringr, RColorBrewer, methods Suggests: knitr, BiocStyle License: GPL (>= 3) MD5sum: a1243886c2b3877076222a6818ed7a54 Package: trackViewer Version: 1.24.2 Depends: R (>= 3.5.0), grDevices, methods, GenomicRanges, grid Imports: GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, plotrix, Rgraphviz, InteractionSet, graph, utils Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools License: GPL (>= 2) MD5sum: e3bf48e60caed538cf7fef417ba67925 Package: tradeSeq Version: 1.2.01 Depends: R (>= 3.6) Imports: mgcv, edgeR, SingleCellExperiment, SummarizedExperiment, slingshot, magrittr, RColorBrewer, BiocParallel, Biobase, pbapply, ggplot2, princurve, methods, S4Vectors, tibble, dplyr, monocle, igraph, clusterExperiment Suggests: knitr, rmarkdown, cowplot, tidyr, testthat, covr License: MIT + file LICENSE MD5sum: 602926de77a9c16c8541552dc06c6bef Package: transcriptogramer Version: 1.10.0 Depends: R (>= 3.4), methods Imports: biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 79443ba1761227580da4dbb7fcc7d5fd Package: transcriptR Version: 1.16.0 Depends: methods, R (>= 3.3) Imports: BiocGenerics, caret, chipseq, e1071, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2, Rsamtools, rtracklayer, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat License: GPL-3 MD5sum: a6b323b759f26e4650bd207d1bd00b35 Package: transite Version: 1.6.2 Depends: R (>= 3.5) Imports: BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0), ggseqlogo (>= 0.1), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 0.12.18), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils LinkingTo: Rcpp (>= 0.12.18), RcppArmadillo Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 25f246ceb7b808550bf6c4909508e4d9 Package: tRanslatome Version: 1.26.0 Depends: R (>= 2.15.0), methods, limma, sigPathway, anota, DESeq, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 MD5sum: d38dc0a8d9f1ca5709531d6cd46146bf Package: TransView Version: 1.32.0 Depends: methods, GenomicRanges Imports: BiocGenerics, S4Vectors (>= 0.9.25), IRanges, zlibbioc, gplots LinkingTo: Rhtslib (>= 1.15.3) Suggests: RUnit, pasillaBamSubset, BiocManager License: GPL-3 MD5sum: bd1de4b38e11525df424d9b7491d9c54 Package: traseR Version: 1.18.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL MD5sum: 93fe279b57ba2056f354f1d12865e327 Package: TreeAndLeaf Version: 1.0.0 Depends: R (>= 4.0) Imports: RedeR, igraph, ape, methods Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, RColorBrewer, geneplast License: Artistic-2.0 MD5sum: 466486b209c994bc05146be33bdaa5bc Package: treeio Version: 1.12.0 Depends: R (>= 3.4.0) Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, tibble, tidytree (>= 0.2.6), utils Suggests: Biostrings, ggplot2, ggtree, igraph, knitr, phangorn, prettydoc, testthat, tidyr, vroom, xml2 License: Artistic-2.0 MD5sum: e8848eaf7e1be001d3aa34576ff87182 Package: TreeSummarizedExperiment Version: 1.4.8 Depends: R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18) Imports: methods, BiocGenerics, utils, ape, rlang, dplyr, SummarizedExperiment Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: de191fda3af3058b6c413a48311c758c Package: trena Version: 1.10.2 Depends: R (>= 3.5.0), utils, glmnet (>= 2.0.3), MotifDb (>= 1.19.17) Imports: RSQLite, RMySQL, lassopv, randomForest, vbsr, xgboost, BiocParallel, RPostgreSQL, methods, DBI, BSgenome, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, SNPlocs.Hsapiens.dbSNP150.GRCh38, org.Hs.eg.db, Biostrings, GenomicRanges, biomaRt, AnnotationDbi Suggests: RUnit, plyr, knitr, BiocGenerics, rmarkdown, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 MD5sum: 40de1f2299dc000615e85711f9fd82a4 Package: Trendy Version: 1.10.0 Depends: R (>= 3.4) Imports: stats, utils, graphics, grDevices, segmented, gplots, parallel, magrittr, BiocParallel, DT, S4Vectors, SummarizedExperiment, methods, shiny, shinyFiles Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL-3 MD5sum: e0de63cf64844bc75dda5d8cdb709dd6 Package: trigger Version: 1.34.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 MD5sum: 5e3b5f702e363a339dba0453a444300a Package: trio Version: 3.26.0 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: a016f3a7fdc69dd221064c8e95973dd8 Package: triplex Version: 1.28.0 Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27), XVector (>= 0.11.6), Biostrings (>= 2.39.10) Imports: methods, grid, GenomicRanges LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer License: BSD_2_clause + file LICENSE MD5sum: ccd26748fd4db432e448a0434f44f3e3 Package: tRNA Version: 1.6.1 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE MD5sum: 5c19676c03b390e18aa30d418fe955dc Package: tRNAdbImport Version: 1.6.1 Depends: R (>= 3.5), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, BiocGenerics, stringr, xml2, S4Vectors, methods, httr, IRanges, utils Suggests: knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE MD5sum: 25aa0405e2314d034b4f7402599921d7 Package: tRNAscanImport Version: 1.8.1 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, stringr, BiocGenerics, Biostrings, Structstrings, S4Vectors, IRanges, XVector, GenomeInfoDb, rtracklayer, BSgenome, Rsamtools Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 + file LICENSE MD5sum: 3e5beb5a96a39895bcb3ae8405587477 Package: TRONCO Version: 2.20.1 Depends: R (>= 4.0.0), Imports: bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, cgdsr, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways License: GPL-3 MD5sum: ede5b04c57290d17a13bee2c6827dd6e Package: TSCAN Version: 1.26.0 Depends: R(>= 2.10.0) Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots Suggests: knitr License: GPL (>= 2) MD5sum: fce9f60ba97fa8d5735230615dda73fa Package: tscR Version: 1.0.1 Depends: R (>= 4.0), dplyr Imports: gridExtra, methods, dtw, class, kmlShape, graphics, cluster, RColorBrewer, grDevices, knitr, rmarkdown, prettydoc, grid, ggplot2, latex2exp, stats, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors Suggests: testthat License: GPL (>= 2) MD5sum: 69818a22683ee7bed9588b92c828fff7 Package: tspair Version: 1.46.0 Depends: R (>= 2.10), Biobase (>= 2.4.0) License: GPL-2 MD5sum: 24fe42e2d82a7bed816e31a0fe2360ff Package: TSRchitect Version: 1.14.0 Depends: R (>= 3.5) Imports: AnnotationHub, BiocGenerics, BiocParallel, dplyr, GenomicAlignments, GenomeInfoDb, GenomicRanges, gtools, IRanges, methods, readxl, Rsamtools (>= 1.14.3), rtracklayer, S4Vectors, SummarizedExperiment, tools, utils Suggests: ENCODExplorer, ggplot2, knitr, rmarkdown License: GPL-3 MD5sum: e0ca7c7dc64de75b74d039d61746ae66 Package: TTMap Version: 1.10.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 MD5sum: 192e5d5156279ec560fea4686acc9351 Package: TurboNorm Version: 1.36.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata License: LGPL MD5sum: ba859ab5abd8aeb55b787d502f4bd08e Package: TVTB Version: 1.14.0 Depends: R (>= 3.4), methods, utils, stats Imports: AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel, Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges (>= 2.21.6), reshape2, Rsamtools, S4Vectors (>= 0.25.14), SummarizedExperiment, VariantAnnotation (>= 1.19.9) Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander License: Artistic-2.0 MD5sum: b675140ee57d04b3c1d1ac6449c16966 Package: tweeDEseq Version: 1.34.0 Depends: R (>= 2.12.0) Imports: MASS, limma, edgeR, parallel, cqn Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) MD5sum: 05ecefa84ba45748e7a109406bccca30 Package: twilight Version: 1.64.0 Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, grDevices, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) MD5sum: 07d9e673ff362bcf88fb2cf09e52aa26 Package: twoddpcr Version: 1.12.0 Depends: R (>= 3.4) Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 88956ce49f43145424bd095966de67cd Package: tximeta Version: 1.6.3 Imports: SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, rappdirs, utils, methods, Matrix Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, edgeR, limma, devtools License: GPL-2 MD5sum: 2bd15e271b48df465d8f1aff35ec10d8 Package: tximport Version: 1.16.1 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, csaw, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, fishpond License: GPL (>= 2) MD5sum: 8755e4696098c2a2065d5882dd249479 Package: TxRegInfra Version: 1.8.0 Depends: R (>= 3.5), RaggedExperiment (>= 1.3.11), mongolite Imports: methods, rjson, GenomicRanges, IRanges, BiocParallel, GenomeInfoDb, S4Vectors, SummarizedExperiment, utils Suggests: knitr, GenomicFiles, EnsDb.Hsapiens.v75, testthat, shiny, biovizBase (>= 1.27.2), Gviz, AnnotationFilter, ensembldb, ontoProc, rjson, graph, TFutils (>= 1.5.4) License: Artistic-2.0 MD5sum: 7abd73a7f237faae7a8df27dab46450d Package: TypeInfo Version: 1.54.0 Depends: methods Suggests: Biobase License: BSD MD5sum: 411248c2a6e8e2da75f2c090e6598767 Package: Ularcirc Version: 1.6.0 Depends: R (>= 3.4.0) Imports: AnnotationHub, 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: 2118eb5658c1c50d914ece175151cdbd Package: UNDO Version: 1.30.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: fc18e66e6d480a64f182fcc6b8363813 Package: unifiedWMWqPCR Version: 1.24.0 Depends: methods Imports: BiocGenerics, stats, graphics, HTqPCR License: GPL (>= 2) MD5sum: 6953f8c8a887abdcf740f6e3dfa93902 Package: UniProt.ws Version: 2.28.0 Depends: methods, utils, RSQLite, RCurl, BiocGenerics (>= 0.13.8) Imports: AnnotationDbi, BiocFileCache, rappdirs Suggests: RUnit, BiocStyle, knitr License: Artistic License 2.0 MD5sum: 6820f1360b778ef87e54dad9702c65d8 Package: Uniquorn Version: 2.8.0 Depends: R (>= 3.5) Imports: stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation Suggests: testthat, knitr, rmarkdown, BiocGenerics, RUnit License: Artistic-2.0 MD5sum: 6bd04390e0498f7c153337c6256e02de Package: universalmotif Version: 1.6.4 Depends: R (>= 3.5.0) Imports: methods, stats, utils, MASS, ggplot2, ape, ggtree, ggseqlogo, yaml, Rcpp, Rdpack (>= 0.7), Biostrings, BiocGenerics, processx, S4Vectors, rlang LinkingTo: Rcpp, RcppThread Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, Logolas, BiocParallel, seqLogo, motifStack, dplyr Enhances: MotIV, PWMEnrich, rGADEM, motifRG License: GPL-3 MD5sum: be295864adff7c8198d223cc3cf29a69 Package: uSORT Version: 1.14.0 Depends: R (>= 3.3.0), tcltk Imports: igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 MD5sum: b7615de7645e50f5491b694a02200191 Package: VanillaICE Version: 1.50.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, human610quadv1bCrlmm, ArrayTV Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 MD5sum: 7395476675c97feebab6939c4143b44b Package: variancePartition Version: 1.18.3 Depends: R (>= 3.6.0), ggplot2, limma, foreach, scales, Biobase, methods Imports: MASS, 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: 6436f3d5d79a0c6481313994067b0949 Package: VariantAnnotation Version: 1.34.0 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: 565d506d0c929e15acff21f5b1d7c372 Package: VariantExperiment Version: 1.2.0 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: f4eab0e3e5e44495c578f47e9af988bc Package: VariantFiltering Version: 1.24.0 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, Rsamtools (>= 1.17.8), BSgenome, GenomicScores (>= 1.0.0), Gviz, shiny, shinythemes, shinyjs, DT, shinyTree LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 License: Artistic-2.0 MD5sum: 53189c31f7ad36bb9eadc00f21e5a0a1 Package: VariantTools Version: 1.30.0 Depends: S4Vectors (>= 0.17.33), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), VariantAnnotation (>= 1.11.16), methods Imports: Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel, GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7), BiocParallel, GenomeInfoDb, BSgenome, Biobase Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3) License: Artistic-2.0 MD5sum: 9b83429923ca2ae735c5d423fc6eb5ad Package: vasp Version: 1.0.0 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, Sushi, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 30d76c5138ff8e7093470cd1753937af Package: vbmp Version: 1.56.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: 275a23dcf15ff9651e425d2669d676b9 Package: VCFArray Version: 1.4.0 Depends: R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28) Imports: tools, GenomicRanges, VariantAnnotation (>= 1.29.3), GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 0693c68e82131a66dcbe20738a09a621 Package: VegaMC Version: 3.26.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods, genoset License: GPL-2 MD5sum: e42655aff057921acffb243c997138a5 Package: VennDetail Version: 1.4.0 Imports: utils, grDevices, stats, methods, dplyr, purrr, tibble, magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 327ac7ec409028c3d3ed5becc52e1454 Package: vidger Version: 1.8.0 Depends: R (>= 3.5) Imports: Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr, RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, testthat License: GPL-3 | file LICENSE MD5sum: 0cba29dc2bda722db8901b0c4aea2fa9 Package: viper Version: 1.22.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: fdb3bb7efb82f07a3c9a15f8466fbfd6 Package: vsn Version: 3.56.0 Depends: R (>= 3.4.0), Biobase Imports: methods, affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat License: Artistic-2.0 MD5sum: 29cd910bff4c3e0159ee9e00e5fc5b1a Package: vtpnet Version: 0.28.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: 6b4b2e5050efe8981520c8c49c5ebee3 Package: vulcan Version: 1.10.0 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: 266cdfa4cd70a8bd34982b5be6897e20 Package: waddR Version: 1.2.0 Depends: R (>= 3.6.0) Imports: Rcpp (>= 1.0.1), arm (>= 1.10-1), BiocFileCache, BiocParallel, SingleCellExperiment, parallel, methods, stats LinkingTo: Rcpp, RcppArmadillo, Suggests: knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown, scater License: MIT + file LICENSE MD5sum: 31caf171f0c06bca3dc954e5fd4ff3b0 Package: wateRmelon Version: 1.32.0 Depends: R (>= 2.10), Biobase, limma, methods, matrixStats, methylumi, lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19, illuminaio Imports: Biobase Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest, irlba Enhances: minfi License: GPL-3 MD5sum: 5fbb93b95bf1dcdbb895c7e61a5f1faa Package: wavClusteR Version: 2.22.0 Depends: R (>= 3.2), GenomicRanges (>= 1.31.8), Rsamtools Imports: methods, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Biostrings (>= 2.47.6), foreach, GenomicFeatures (>= 1.31.3), ggplot2, Hmisc, mclust, rtracklayer (>= 1.39.7), seqinr, stringr, wmtsa Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 Enhances: doMC License: GPL-2 MD5sum: 9131e01fe483358c8b69aebea6300ee6 Package: weaver Version: 1.54.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 MD5sum: 9c8efbd6fab78851277a32242e5da5b3 Package: webbioc Version: 1.60.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocManager License: GPL (>= 2) MD5sum: bf101b7f2a06115317bfb10b4dd4fa16 Package: weitrix Version: 1.0.0 Depends: R (>= 4.0), SummarizedExperiment Imports: methods, utils, stats, assertthat, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics, limma, dplyr, purrr, ggplot2, scales, reshape2, RhpcBLASctl Suggests: knitr, rmarkdown, tidyverse, airway, edgeR, topconfects, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, testthat (>= 2.1.0) License: LGPL-2.1 | file LICENSE MD5sum: 4456342608c0c57fc566a13204f76f94 Package: widgetTools Version: 1.66.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: 7f2aea6b66db4e661dbd3c98bdf800a1 Package: wiggleplotr Version: 1.12.1 Depends: R (>= 3.6) Imports: dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer, cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter License: Apache License 2.0 MD5sum: 289ee1690d9c11d12b7c7b59d131f94a Package: Wrench Version: 1.6.0 Depends: R (>= 3.5.0) Imports: limma, matrixStats, locfit, stats, graphics Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR License: Artistic-2.0 MD5sum: 4a2b5a66aa0c0a276194ef6d1249b25a Package: XBSeq Version: 1.20.0 Depends: DESeq2, R (>= 3.3) Imports: pracma, matrixStats, locfit, ggplot2, methods, Biobase, dplyr, magrittr, roar Suggests: knitr, DESeq, rmarkdown, BiocStyle, testthat License: GPL (>= 3) MD5sum: 55ae1ceb952b4e42a4987692014297ab Package: XCIR Version: 1.2.0 Depends: methods Imports: stats, utils, data.table, IRanges, VariantAnnotation, seqminer, ggplot2, biomaRt, readxl, S4Vectors Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 51fb893667c89da7ee30e6f5a75837dd Package: XDE Version: 2.34.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5) Imports: BiocGenerics, genefilter, graphics, grDevices, gtools, MergeMaid, methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta, siggenes Suggests: MASS, RUnit Enhances: coda License: LGPL-2 MD5sum: fc742db9e137deec4cfd6c8068f1bce9 Package: Xeva Version: 1.4.0 Depends: R (>= 3.6) Imports: methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2, scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid, nlme, PharmacoGx, downloader Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 67784143683a81631533fed317e6f6fc Package: XINA Version: 1.6.0 Depends: R (>= 3.5) Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 7766b01c2b3d7445bbf3476f14bfbac4 Package: xmapbridge Version: 1.46.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 MD5sum: be775abf52e1e5bc57bd0a4d3859e896 Package: XVector Version: 0.28.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.19.2), S4Vectors (>= 0.25.14), IRanges (>= 2.21.6) Imports: methods, utils, zlibbioc, BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 MD5sum: bd4434a53baa734718738c63df343082 Package: yamss Version: 1.14.0 Depends: R (>= 3.3.0), methods, BiocGenerics (>= 0.15.3), SummarizedExperiment Imports: IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table, grDevices, limma Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat License: Artistic-2.0 MD5sum: 64342b3c3d43f48027eba0821c9d25ae Package: YAPSA Version: 1.14.0 Depends: R (>= 3.6.0), GenomicRanges, ggplot2, grid Imports: lsei, SomaticSignatures, VariantAnnotation, GenomeInfoDb, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, doParallel, PMCMR, ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings, BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 8583c0a18f421b4ee2eceb463d3aa24a Package: yaqcaffy Version: 1.48.0 Depends: simpleaffy (>= 2.19.3), methods Imports: stats4 Suggests: MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk License: Artistic-2.0 MD5sum: 22d9ca79f6d75dc85060780d286a4372 Package: yarn Version: 1.14.0 Depends: Biobase Imports: biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro Suggests: knitr, rmarkdown, testthat (>= 0.8) License: Artistic-2.0 MD5sum: 3ec45dce4636d5ca75d89ba2b98af078 Package: zFPKM Version: 1.10.0 Depends: R (>= 3.4.0) Imports: checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment Suggests: knitr, limma, edgeR, GEOquery, stringr, printr License: GPL-3 | file LICENSE MD5sum: 39aa3aaa8ad66c2c682c2bbfdad7d2c1 Package: zinbwave Version: 1.10.1 Depends: R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment Imports: BiocParallel, softImpute, stats, genefilter, edgeR, Matrix Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, Seurat License: Artistic-2.0 MD5sum: 727d77ab0c7e4ac28bc84ae5f8ee222c Package: zlibbioc Version: 1.34.0 License: Artistic-2.0 + file LICENSE MD5sum: d4fef0fce99d3323632b58c27631ca60