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alpineData, rtracklayer, ensembldb, BSgenome.Hsapiens.NCBI.GRCh38, RColorBrewer License: GPL (>= 2) Package: ALPS Version: 1.0.0 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 Package: alsace Version: 1.22.0 Depends: R (>= 2.10), ALS, ptw (>= 1.0.6) Suggests: lattice, knitr License: GPL (>= 2) Package: altcdfenvs Version: 2.48.0 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) Package: AMARETTO Version: 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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 Archs: i386, x64 Package: ANF Version: 1.8.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 Package: animalcules Version: 1.2.1 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 Package: annaffy Version: 1.58.0 Depends: R (>= 2.5.0), methods, Biobase, GO.db, KEGG.db Imports: AnnotationDbi (>= 0.1.15), DBI Suggests: hgu95av2.db, multtest, tcltk License: LGPL Package: annotate Version: 1.64.0 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 Package: AnnotationDbi Version: 1.48.0 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, 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BiocStyle,knitr License: GPL-3 Package: antiProfiles Version: 1.26.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 Package: APAlyzer Version: 1.0.0 Imports: GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq, SummarizedExperiment, Rsubread, stats, methods Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, Rsamtools, ggplot2, testthat License: LGPL-3 Package: apComplex Version: 2.52.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL Package: apeglm Version: 1.8.0 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 Archs: i386, x64 Package: appreci8R Version: 1.4.0 Imports: shiny, shinyjs, DT, VariantAnnotation, BSgenome, BSgenome.Hsapiens.UCSC.hg19, 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simpleaffy, mdqc, affyContam, Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf License: Artistic-2.0 Package: arrayQuality Version: 1.64.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL Package: arrayQualityMetrics Version: 3.42.0 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) Package: ArrayTools Version: 1.46.0 Depends: R (>= 2.7.0), affy (>= 1.23.4), Biobase (>= 2.5.5), methods Imports: affy, Biobase, graphics, grDevices, limma, methods, stats, utils, xtable Suggests: simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy, gcrma, hugene10sttranscriptcluster.db License: LGPL (>= 2.0) Package: ArrayTV Version: 1.24.0 Depends: R (>= 2.14) Imports: methods, foreach, S4Vectors (>= 0.9.25), IRanges (>= 2.13.24), DNAcopy, oligoClasses (>= 1.21.3) Suggests: RColorBrewer, crlmm, ff, BSgenome.Hsapiens.UCSC.hg18,BSgenome.Hsapiens.UCSC.hg19, lattice, latticeExtra, RUnit, BiocGenerics Enhances: doMC, doSNOW, doParallel License: GPL (>= 2) Package: ARRmNormalization Version: 1.26.0 Depends: R (>= 2.15.1), ARRmData License: Artistic-2.0 Package: artMS Version: 1.4.3 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 Package: ASAFE Version: 1.12.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 Package: ASEB Version: 1.30.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) Archs: i386, x64 Package: ASGSCA Version: 1.20.0 Imports: Matrix, MASS Suggests: BiocStyle License: GPL-3 Package: ASICS Version: 2.2.0 Depends: R (>= 3.5) Imports: BiocParallel, ggplot2, grDevices, gridExtra, methods, PepsNMR, plyr, quadprog, ropls, stats, SummarizedExperiment, TSdist, utils, Matrix, zoo Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata License: GPL (>= 2) Package: ASpediaFI Version: 1.0.0 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 Package: ASpli Version: 1.12.0 Depends: methods, grDevices, stats, utils, parallel, edgeR Imports: GenomicRanges, GenomicFeatures, BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, AnnotationDbi, Rsamtools, BiocStyle License: GPL Package: AssessORF Version: 1.4.0 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 Package: ASSET Version: 2.4.0 Depends: MASS, msm, rmeta Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE Package: ASSIGN Version: 1.22.0 Depends: R (>= 3.4) Imports: gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown License: MIT + file LICENSE Package: ATACseqQC Version: 1.10.4 Depends: R (>= 3.4), BiocGenerics, S4Vectors Imports: BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats, motifStack, preseqR, utils, KernSmooth, edgeR Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat License: GPL (>= 2) Package: atSNP Version: 1.2.0 Depends: R (>= 3.6) Imports: BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testit, utils LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-2 Archs: i386, x64 Package: attract Version: 1.38.0 Depends: R (>= 3.4.0), AnnotationDbi Imports: Biobase, limma, cluster, GOstats, graphics, stats, reactome.db, KEGGREST, org.Hs.eg.db, utils, methods Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) Package: AUCell Version: 1.8.0 Imports: data.table, graphics, grDevices, GSEABase, methods, mixtools, R.utils, shiny, stats, SummarizedExperiment, BiocGenerics, S4Vectors, utils Suggests: 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Artistic-2.0 Archs: i386, x64 Package: bacon Version: 1.14.0 Depends: R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 License: GPL (>= 2) Archs: i386, x64 Package: BADER Version: 1.24.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 Archs: i386, x64 Package: BadRegionFinder Version: 1.14.0 Imports: VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 Package: BAGS Version: 2.26.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 Archs: i386, x64 Package: ballgown Version: 2.18.0 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 Package: bamsignals Version: 1.18.0 Depends: R (>= 3.2.0) 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BiocStyle License: GPL (>= 3) Package: BaseSpaceR Version: 1.30.0 Depends: R (>= 2.15.0), RCurl, RJSONIO Imports: methods Suggests: RUnit, IRanges, Rsamtools License: Apache License 2.0 Package: Basic4Cseq Version: 1.22.0 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 Package: BASiCS Version: 1.8.1 Depends: R (>= 3.6), SingleCellExperiment Imports: Biobase, BiocGenerics, coda, cowplot, data.table, ggExtra, ggplot2, graphics, grDevices, KernSmooth, MASS, matrixStats, methods, Rcpp (>= 0.11.3), S4Vectors, scran, stats, stats4, SummarizedExperiment, viridis, utils, Matrix LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) Archs: i386, x64 Package: BasicSTARRseq Version: 1.14.0 Depends: GenomicRanges,GenomicAlignments Imports: S4Vectors,methods,IRanges,GenomeInfoDb,stats 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ChemmineR Suggests: BiocStyle, RCurl, biomaRt, cellHTS2, knitr, knitcitations, knitrBootstrap, testthat, ggplot2, rmarkdown License: Artistic-2.0 Package: Biobase Version: 2.46.0 Depends: R (>= 2.10), BiocGenerics (>= 0.27.1), utils Imports: methods Suggests: tools, tkWidgets, ALL, RUnit, golubEsets License: Artistic-2.0 Archs: i386, x64 Package: biobroom Version: 1.18.0 Depends: R (>= 3.0.0), broom Imports: dplyr, tidyr, Biobase Suggests: limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, SummarizedExperiment License: LGPL Package: bioCancer Version: 1.14.02 Depends: R (>= 3.5.0), radiant.data (>= 1.0.6), cgdsr(>= 1.2.6), XML(>= 3.99) Imports: shiny (>= 1.0.5), AlgDesign (>= 1.1.7.3), import (>= 1.1.0), methods, shinythemes, Biobase, geNetClassifier, AnnotationFuncs, org.Hs.eg.db, DOSE, clusterProfiler, reactome.db, ReactomePA, DiagrammeR(>= 1.0.5), visNetwork, htmlwidgets, plyr, tibble, DT (>= 0.12), dplyr (>= 0.8.5) Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 0.10.0) License: AGPL-3 | file LICENSE Package: BiocCaseStudies Version: 1.48.0 Depends: tools, methods, utils, Biobase Suggests: affy (>= 1.17.3), affyPLM (>= 1.15.1), affyQCReport (>= 1.17.0), ALL (>= 1.4.3), annaffy (>= 1.11.1), annotate (>= 1.17.3), AnnotationDbi (>= 1.1.6), apComplex (>= 2.5.0), Biobase (>= 1.17.5), bioDist (>= 1.11.3), biocGraph (>= 1.1.1), biomaRt (>= 1.13.5), CCl4 (>= 1.0.6), CLL (>= 1.2.4), Category (>= 2.5.0), class (>= 7.2-38), cluster (>= 1.11.9), convert (>= 1.15.0), gcrma (>= 2.11.1), genefilter (>= 1.17.6), geneplotter (>= 1.17.2), GO.db (>= 2.0.2), GOstats (>= 2.5.0), graph (>= 1.17.4), GSEABase (>= 1.1.13), hgu133a.db (>= 2.0.2), hgu95av2.db, hgu95av2cdf (>= 2.0.0), hgu95av2probe (>= 2.0.0), hopach (>= 1.13.0), KEGG.db (>= 2.0.2), kohonen (>= 2.0.2), lattice (>= 0.17.2), latticeExtra (>= 0.3-1), limma (>= 2.13.1), MASS (>= 7.2-38), MLInterfaces (>= 1.13.17), multtest (>= 1.19.0), org.Hs.eg.db (>= 2.0.2), ppiStats (>= 1.5.4), randomForest (>= 4.5-20), RBGL (>= 1.15.6), RColorBrewer (>= 1.0-2), Rgraphviz (>= 1.17.11), vsn (>= 3.4.0), weaver (>= 1.5.0), xtable (>= 1.5-2), yeastExpData (>= 0.9.11) License: Artistic-2.0 Package: BiocCheck Version: 1.22.0 Depends: R (>= 3.5.0) Imports: biocViews (>= 1.33.7), BiocManager, stringdist, graph, httr, tools, optparse, codetools, methods, utils, knitr Suggests: RUnit, BiocGenerics, Biobase, RJSONIO, rmarkdown, devtools (>= 1.4.1), usethis, BiocStyle Enhances: codetoolsBioC License: Artistic-2.0 Package: BiocFileCache Version: 1.10.2 Depends: R (>= 3.4.0), dbplyr (>= 1.0.0) Imports: methods, stats, utils, dplyr, RSQLite, DBI, rappdirs, curl, httr Suggests: testthat, knitr, BiocStyle, rmarkdown, rtracklayer License: Artistic-2.0 Package: BiocGenerics Version: 0.32.0 Depends: R (>= 3.6.0), methods, utils, graphics, stats, parallel Imports: methods, utils, graphics, stats, parallel Suggests: Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray, Biostrings, Rsamtools, AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy, DESeq2, MSnbase, annotate, RUnit License: Artistic-2.0 Package: biocGraph Version: 1.48.0 Depends: Rgraphviz, graph Imports: Rgraphviz, geneplotter, graph, BiocGenerics, methods Suggests: fibroEset, geneplotter, hgu95av2.db License: Artistic-2.0 Package: BiocNeighbors Version: 1.4.2 Imports: Rcpp, S4Vectors, BiocParallel, stats, methods, Matrix LinkingTo: Rcpp, RcppAnnoy, RcppHNSW Suggests: testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy, RcppHNSW License: GPL-3 Archs: i386, x64 Package: BiocOncoTK Version: 1.5.1 Depends: R (>= 3.5.0), methods Imports: ComplexHeatmap, S4Vectors, bigrquery, shiny, stats, httr, rjson, dplyr, magrittr, grid, utils, DT, GenomicRanges, IRanges, ggplot2, SummarizedExperiment, DBI, GenomicFeatures Suggests: knitr, dbplyr, DBI, org.Hs.eg.db, MultiAssayExperiment, BiocStyle, ontoProc, ontologyPlot, pogos, GenomeInfoDb, restfulSE (>= 1.3.7), BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene, Biobase, TxDb.Hsapiens.UCSC.hg18.knownGene, reshape2, testthat, AnnotationDbi, FDb.InfiniumMethylation.hg19, EnsDb.Hsapiens.v75 License: Artistic-2.0 Package: BioCor Version: 1.10.0 Depends: R (>= 3.4.0) Imports: BiocParallel, Matrix, GSEABase Suggests: reactome.db, org.Hs.eg.db, WGCNA, methods, GOSemSim, testthat, knitr, rmarkdown, BiocStyle, airway, DESeq2, boot, targetscan.Hs.eg.db, Hmisc, spelling License: MIT + file LICENSE Package: BiocParallel Version: 1.20.1 Depends: methods Imports: stats, utils, futile.logger, parallel, snow LinkingTo: BH Suggests: BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel, Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit, BiocStyle, knitr, batchtools, data.table License: GPL-2 | GPL-3 Archs: i386, x64 Package: BiocPkgTools Version: 1.4.6 Depends: htmlwidgets Imports: BiocFileCache, BiocManager, biocViews, tibble, methods, rlang, tidyselect, stringr, rvest, rex, dplyr, xml2, rappdirs, readr, httr, htmltools, DT, tools, utils, igraph, tidyr, jsonlite, gh, RBGL, graph, magrittr Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, SnowballC, pdftools, visNetwork, clipr, blastula, kableExtra License: MIT + file LICENSE Package: BiocSet Version: 1.0.1 Depends: R (>= 3.6), dplyr Imports: methods, tibble, utils, rlang, plyr, rtracklayer, AnnotationDbi, KEGGREST Suggests: GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache, GO.db, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 Package: BiocSingular Version: 1.2.2 Imports: BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, irlba, rsvd, Rcpp LinkingTo: Rcpp, beachmat Suggests: testthat, BiocStyle, knitr, rmarkdown, beachmat License: GPL-3 Archs: i386, x64 Package: BiocSklearn Version: 1.7.0 Depends: R (>= 3.5.0), reticulate, methods, SummarizedExperiment, knitr Imports: BBmisc Suggests: testthat, restfulSE, HDF5Array, BiocStyle License: Artistic-2.0 Package: BiocStyle Version: 2.14.4 Imports: bookdown, knitr (>= 1.12), rmarkdown (>= 1.2), stats, utils, yaml, BiocManager Suggests: BiocGenerics, RUnit, htmltools License: Artistic-2.0 Package: BiocVersion Version: 3.10.1 Depends: R (>= 3.6.0) License: Artistic-2.0 Package: biocViews Version: 1.54.0 Depends: R (>= 3.6.0) Imports: Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools, utils, XML, RCurl, RUnit, BiocManager Suggests: BiocGenerics, knitr, commonmark License: Artistic-2.0 Package: BiocWorkflowTools Version: 1.12.1 Depends: R (>= 3.4) Imports: BiocStyle, bookdown, git2r, httr, knitr, rmarkdown, rstudioapi, stringr, tools, utils, usethis License: MIT + file LICENSE Package: bioDist Version: 1.58.0 Depends: R (>= 2.0), methods, Biobase,KernSmooth Suggests: locfit License: Artistic-2.0 Package: biomaRt Version: 2.42.1 Depends: methods Imports: utils, XML, AnnotationDbi, progress, stringr, httr, openssl, BiocFileCache, rappdirs Suggests: annotate, BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 Package: biomformat Version: 1.14.0 Depends: R (>= 3.2), methods Imports: plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5 Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) License: GPL-2 Package: BioMM Version: 1.2.0 Depends: R (>= 3.6) Imports: stats, utils, grDevices, lattice, BiocParallel, glmnet, rms, nsprcomp, ranger, e1071, variancePartition, ggplot2, pROC, vioplot, CMplot Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-3 Package: BioMVCClass Version: 1.54.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz License: LGPL Package: biomvRCNS Version: 1.26.0 Depends: IRanges, GenomicRanges, Gviz Imports: methods, mvtnorm Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) Archs: i386, x64 Package: BioNet Version: 1.46.0 Depends: R (>= 2.10.0), graph, RBGL Imports: igraph (>= 1.0.1), AnnotationDbi, Biobase Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML License: GPL (>= 2) Package: BioNetStat Version: 1.6.0 Depends: R (>= 3.5), shiny, igraph, shinyBS, pathview Imports: BiocParallel, RJSONIO, whisker, yaml, pheatmap, ggplot2, plyr, utils, stats, RColorBrewer, Hmisc, psych, knitr License: GPL (>= 3) Package: BioQC Version: 1.14.0 Depends: Biobase Imports: edgeR, Rcpp, methods, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, ineq, covr License: GPL (>= 3) Archs: i386, x64 Package: BioSeqClass Version: 1.44.0 Depends: R (>= 2.10), scatterplot3d Imports: Biostrings, ipred, e1071, klaR, randomForest, class, tree, nnet, rpart, party, foreign, Biobase, utils, stats, grDevices Suggests: scatterplot3d License: LGPL (>= 2.0) Package: biosigner Version: 1.14.4 Depends: Biobase, ropls Imports: methods, e1071, MultiDataSet, randomForest Suggests: BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, omicade4, rmarkdown, testthat License: CeCILL Package: Biostrings Version: 2.54.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.31.5), S4Vectors (>= 0.21.13), IRanges, XVector (>= 0.23.2) Imports: graphics, methods, stats, utils LinkingTo: S4Vectors, IRanges, XVector Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit Enhances: Rmpi License: Artistic-2.0 Archs: i386, x64 Package: biosvd Version: 2.22.0 Depends: R (>= 3.1.0) Imports: BiocGenerics, Biobase, methods, grid, graphics, NMF License: Artistic-2.0 Package: BioTIP Version: 1.0.0 Depends: R (>= 3.6) Imports: igraph, cluster, psych, stringr, GenomicRanges Suggests: knitr, markdown, base, rmarkdown, ggplot2 License: GPL-2 Package: biotmle Version: 1.10.0 Depends: R (>= 3.4) Imports: stats, methods, dplyr, tibble, ggplot2, ggsci, superheat, assertthat, future, doFuture, tmle (>= 1.4.0.1), S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, limma Suggests: testthat, knitr, rmarkdown, BiocStyle, earth, glmnet, randomForest, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) License: file LICENSE Package: biovizBase Version: 1.34.1 Depends: R (>= 3.5.0), methods Imports: grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors (>= 0.23.19), IRanges (>= 1.99.28), GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21), SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>= 1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4), ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlang Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit License: Artistic-2.0 Archs: i386, x64 Package: BiRewire Version: 3.18.0 Depends: igraph, slam, tsne, Matrix Suggests: RUnit, BiocGenerics License: GPL-3 Archs: i386, x64 Package: birta Version: 1.30.0 Depends: limma, MASS, R(>= 2.10), Biobase, methods License: GPL (>= 2) Archs: i386, x64 Package: birte Version: 1.22.0 Depends: R(>= 3.0.0), RcppArmadillo (>= 0.3.6.1), Rcpp Imports: MASS, limma(>= 3.22.0), glmnet, Biobase, nem, graphics, stats, utils LinkingTo: RcppArmadillo, Rcpp Suggests: knitr Enhances: Rgraphviz License: GPL (>= 2) Archs: i386, x64 Package: biscuiteer Version: 1.0.0 Depends: R (>= 3.6.0), 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 Suggests: DSS, covr, knitr, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10 License: GPL-3 Package: BiSeq Version: 1.26.0 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 Package: BitSeq Version: 1.30.1 Depends: Rsamtools (>= 1.99.3) Imports: S4Vectors, IRanges LinkingTo: Rhtslib (>= 1.15.5) Suggests: edgeR, DESeq, BiocStyle License: Artistic-2.0 + file LICENSE Archs: i386, x64 Package: blacksheepr Version: 1.0.0 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 Package: blima Version: 1.20.0 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 Archs: i386, x64 Package: BLMA Version: 1.10.0 Depends: ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel, Biobase Suggests: RUnit, BiocGenerics License: GPL (>= 2) Package: bnbc Version: 1.8.0 Depends: R (>= 3.4.0), methods, BiocGenerics, SummarizedExperiment, GenomicRanges Imports: Rcpp (>= 0.12.12), IRanges, GenomeInfoDb, S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 Archs: i386, x64 Package: BPRMeth Version: 1.12.0 Depends: R (>= 3.5.0), GenomicRanges Imports: assertthat, methods, MASS, doParallel, parallel, e1071, earth, foreach, randomForest, stats, IRanges, S4Vectors, data.table, graphics, truncnorm, mvtnorm, Rcpp (>= 0.12.14), matrixcalc, magrittr, kernlab, ggplot2, cowplot, BiocStyle LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE Archs: i386, x64 Package: BRAIN Version: 1.32.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 Package: brainflowprobes Version: 1.0.0 Depends: R (>= 3.6.0) Imports: Biostrings (>= 2.52.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), bumphunter (>= 1.26.0), cowplot (>= 1.0.0), derfinder (>= 1.18.1), derfinderPlot (>= 1.18.1), GenomicRanges (>= 1.36.0), ggplot2 (>= 3.1.1), RColorBrewer (>= 1.1), utils, grDevices, GenomicState (>= 0.99.7) Suggests: BiocStyle, knitcitations, knitr, rmarkdown, sessioninfo, testthat (>= 2.1.0) License: Artistic-2.0 Package: BrainStars Version: 1.30.0 Depends: RCurl, Biobase, methods Imports: RJSONIO, Biobase License: Artistic-2.0 Package: branchpointer Version: 1.12.0 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 Package: breakpointR Version: 1.4.0 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 Package: brendaDb Version: 1.0.0 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 Archs: i386, x64 Package: bridge Version: 1.50.0 Depends: R (>= 1.9.0), rama License: GPL (>= 2) Archs: i386, x64 Package: BridgeDbR Version: 1.20.0 Depends: R (>= 3.3.0), rJava Imports: RCurl Suggests: BiocStyle, knitr, rmarkdown, testthat License: AGPL-3 Package: 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Depends: R (>= 3.5), methods, BiocGenerics, GenomicRanges (>= 1.29.14), SummarizedExperiment (>= 1.9.18) Imports: IRanges (>= 2.11.16), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors (>= 0.23.11), 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 Archs: i386, x64 Package: BubbleTree Version: 2.16.0 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) Package: BufferedMatrix Version: 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Depends: R (>= 3.5.0) Imports: gplots, methods, grDevices, stats, SummarizedExperiment Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) Archs: i386, x64 Package: BUSpaRse Version: 1.0.0 Imports: AnnotationDbi, AnnotationFilter, biomaRt, Biostrings, BSgenome, data.table, dplyr, ensembldb, GenomeInfoDb, GenomicFeatures, GenomicRanges, magrittr, Matrix, methods, plyranges, Rcpp, RcppParallel, S4Vectors, stats, stringr, tibble, tidyr, zeallot LinkingTo: Rcpp, RcppArmadillo, RcppProgress, BH, RcppParallel Suggests: knitr, rmarkdown, testthat, BiocStyle, TENxBUSData, DropletUtils, ggplot2, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: BSD_2_clause + file LICENSE Archs: i386, x64 Package: CAFE Version: 1.22.0 Depends: R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio Imports: affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 Package: CAGEfightR Version: 1.6.0 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, Matrix(>= 1.2-12), Matrix.utils(>= 0.9.6), grr(>= 0.9.5), BiocGenerics(>= 0.24.0), S4Vectors(>= 0.16.0), IRanges(>= 2.12.0), GenomeInfoDb(>= 1.14.0), GenomicFeatures(>= 1.29.11), 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 Package: CAGEr Version: 1.28.0 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 Package: CALIB Version: 1.52.0 Depends: R (>= 2.10), limma, methods Imports: limma, methods, graphics, stats, utils License: LGPL Archs: i386, x64 Package: calm Version: 1.0.0 Imports: mgcv, stats, graphics Suggests: knitr, rmarkdown License: GPL (>= 2) Package: CAMERA Version: 1.42.0 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) Archs: i386, x64 Package: CAMTHC Version: 1.4.0 Depends: R (>= 3.5) Imports: methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 Package: canceR Version: 1.20.0 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 Package: cancerclass Version: 1.30.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 Archs: i386, x64 Package: CancerInSilico Version: 2.6.0 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 Archs: i386, x64 Package: CancerMutationAnalysis Version: 1.28.0 Depends: R (>= 2.10.0), qvalue Imports: AnnotationDbi, limma, methods, stats Suggests: KEGG.db License: GPL (>= 2) + file LICENSE Archs: i386, x64 Package: CancerSubtypes Version: 1.12.1 Depends: R (>= 3.4), sigclust, NMF Imports: SNFtool, iCluster, cluster, impute, limma, ConsensusClusterPlus, grDevices, survival Suggests: BiocGenerics, RUnit, knitr, RTCGA.mRNA, RTCGA.clinical License: GPL (>= 2) Package: CAnD Version: 1.18.0 Imports: methods, ggplot2, reshape Suggests: RUnit, BiocGenerics, BiocStyle License: Artistic-2.0 Package: caOmicsV Version: 1.16.0 Depends: R (>= 3.2), igraph (>= 0.7.1), bc3net (>= 1.0.2) License: GPL (>= 2.0) Package: Cardinal Version: 2.4.0 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 Archs: i386, x64 Package: casper Version: 2.20.0 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) Archs: i386, x64 Package: CATALYST Version: 1.10.3 Depends: R (>= 3.6) Imports: Biobase, circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot, data.table, dplyr, drc, DT, flowCore, FlowSOM, ggplot2, ggrepel, ggridges, graphics, grDevices, grid, gridExtra, htmltools, limma, magrittr, Matrix, matrixStats, methods, nnls, plotly, purrr, RColorBrewer, reshape2, Rtsne, SingleCellExperiment, SummarizedExperiment, S4Vectors, scales, scater, shiny, shinydashboard, shinyBS, shinyjs, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, diffcyt License: GPL (>= 2) Package: Category Version: 2.52.1 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 Package: categoryCompare Version: 1.30.0 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 Package: CausalR Version: 1.18.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) Package: cbaf Version: 1.8.1 Imports: BiocFileCache, RColorBrewer, cgdsr, genefilter, gplots, grDevices, stats, utils, xlsx Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 Package: ccfindR Version: 1.6.0 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) Archs: i386, x64 Package: ccmap Version: 1.12.0 Imports: AnnotationDbi (>= 1.36.2), BiocManager (>= 1.24.0), ccdata (>= 1.1.2), doParallel (>= 1.0.10), data.table (>= 1.10.4), foreach (>= 1.4.3), parallel (>= 3.3.3), xgboost (>= 0.6.4), lsa (>= 0.73.1) Suggests: crossmeta, knitr, rmarkdown, testthat, lydata License: MIT + file LICENSE Package: CCPROMISE Version: 1.12.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) Package: ccrepe Version: 1.22.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat License: MIT + file LICENSE Package: celaref Version: 1.4.0 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 Package: celda Version: 1.2.4 Depends: R (>= 3.6) Imports: stats, 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, magrittr LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, corrplot, Matrix, biomaRt, covr, M3DExampleData, BiocManager, BiocStyle License: MIT + file LICENSE Archs: i386, x64 Package: cellbaseR Version: 1.10.0 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) Package: CellBench Version: 1.2.0 Depends: R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils Imports: BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, lubridate Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 License: GPL-3 Package: cellGrowth Version: 1.30.0 Depends: R (>= 2.12.0), locfit (>= 1.5-4) Imports: lattice License: Artistic-2.0 Package: cellHTS2 Version: 2.50.0 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 Package: cellity Version: 1.14.0 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) Package: CellMapper Version: 1.12.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 Package: CellMixS Version: 1.2.6 Depends: kSamples, R (>= 3.6) Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, listarrays, methods, BiocParallel, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat, limma License: GPL (>= 2) Package: CellNOptR Version: 1.32.0 Depends: R (>= 2.15.0), RBGL, graph, methods, hash, RCurl, Rgraphviz, XML, ggplot2 Imports: igraph, stringi, stringr, Suggests: data.table, plyr, dplyr, tidyr, readr, RUnit, BiocGenerics, License: GPL-3 Archs: i386, x64 Package: cellscape Version: 1.10.0 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 Package: CellScore Version: 1.6.0 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 Package: CellTrails Version: 1.4.0 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 Package: cellTree Version: 1.16.0 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 Package: CEMiTool Version: 1.10.2 Depends: R (>= 3.6) 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 Suggests: testthat, BiocManager License: GPL-3 Package: CexoR Version: 1.24.0 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 Package: CFAssay Version: 1.20.0 Depends: R (>= 2.10.0) License: LGPL Package: CGEN Version: 3.22.0 Depends: R (>= 2.10.1), survival, mvtnorm Suggests: cluster License: GPL-2 + file LICENSE Archs: i386, x64 Package: CGHbase Version: 1.46.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL Package: CGHcall Version: 2.48.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall Package: cghMCR Version: 1.44.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL Package: CGHnormaliter Version: 1.40.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) Package: CGHregions Version: 1.44.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase Package: ChAMP Version: 2.16.2 Depends: R (>= 3.3), minfi, ChAMPdata (>= 2.6.0), FEM (>= 3.1),DMRcate, Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest, DT Imports: prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b2.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 Package: CHARGE Version: 1.6.0 Depends: R (>= 3.5), GenomicRanges, methods Imports: SummarizedExperiment, FactoMineR, factoextra, IRanges, graphics, modes, parallel, plyr, cluster, diptest, stats, matrixStats Suggests: roxygen2, EnsDb.Hsapiens.v86 License: GPL-2 Package: ChemmineOB Version: 1.24.0 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 Archs: i386, x64 Package: ChemmineR Version: 3.38.0 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 Archs: i386, x64 Package: CHETAH Version: 1.2.0 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 Package: Chicago Version: 1.14.0 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 Package: chimera Version: 1.27.1 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 Archs: i386, x64 Package: chimeraviz Version: 1.12.3 Depends: Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, AnnotationFilter, data.table Imports: methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, ArgumentCheck, gtools, magick Suggests: testthat, roxygen2, devtools, knitr, lintr License: Artistic-2.0 Package: ChIPanalyser Version: 1.8.0 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 Package: ChIPComp Version: 1.16.0 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 Archs: i386, x64 Package: chipenrich Version: 2.10.0 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 Package: ChIPexoQual Version: 1.10.0 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) Package: ChIPpeakAnno Version: 3.20.1 Depends: R (>= 3.2), methods, grid, IRanges (>= 2.13.12), Biostrings (>= 2.47.6), GenomicRanges (>= 1.31.8), S4Vectors (>= 0.17.25), VennDiagram Imports: BiocGenerics (>= 0.1.0), GO.db, biomaRt, BSgenome, GenomicFeatures, GenomeInfoDb, matrixStats, AnnotationDbi, limma, multtest, RBGL, graph, BiocManager, stats, regioneR, DBI, ensembldb, Biobase, seqinr, idr, GenomicAlignments, DelayedArray, SummarizedExperiment, rtracklayer, Rsamtools Suggests: reactome.db, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, gplots, BiocStyle, knitr, rmarkdown, testthat, trackViewer, motifStack, OrganismDbi License: GPL (>= 2) Package: ChIPQC Version: 1.22.0 Depends: R (>= 3.0.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19) Imports: BiocGenerics (>= 0.11.3), S4Vectors (>= 0.1.0), IRanges (>= 1.99.17), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), chipseq (>= 1.12.0), gtools, BiocParallel, methods, reshape2, Nozzle.R1, Biobase, grDevices, stats, utils, GenomicFeatures, 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) Package: ChIPseeker Version: 1.22.1 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, ggimage, ggplotify, ggupset, ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, tibble License: Artistic-2.0 Package: chipseq Version: 1.36.0 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 Archs: i386, x64 Package: ChIPseqR Version: 1.40.0 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) Archs: i386, x64 Package: ChIPSeqSpike Version: 1.6.0 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 Package: ChIPsim Version: 1.40.0 Depends: Biostrings (>= 2.29.2) Imports: IRanges, XVector, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) Package: chopsticks Version: 1.52.0 Imports: graphics, stats, utils, methods, survival Suggests: hexbin License: GPL-3 Archs: i386, x64 Package: chroGPS Version: 2.4.0 Depends: R (>= 3.2.0), GenomicRanges, IRanges, methods, Biobase, MASS, graphics, stats, changepoint Imports: cluster, DPpackage, ICSNP, ellipse, vegan Enhances: parallel, XML, rgl, gplots, pheatmap, ChIPpeakAnno, org.Dm.eg.db, caTools, plotly License: GPL (>= 2.14) Package: chromDraw Version: 2.16.0 Depends: R (>= 3.0.0) Imports: Rcpp (>= 0.11.1), GenomicRanges (>= 1.17.46) LinkingTo: Rcpp License: GPL-3 Archs: i386, x64 Package: ChromHeatMap Version: 1.40.0 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 Package: chromPlot Version: 1.14.0 Depends: stats, utils, graphics, grDevices, datasets, base, biomaRt, GenomicRanges, R (>= 3.1.0) Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) Package: chromstaR Version: 1.12.0 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 Archs: i386, x64 Package: chromswitch Version: 1.8.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.26.4) Imports: cluster (>= 2.0.6), Biobase (>= 2.36.2), BiocParallel (>= 1.8.2), dplyr (>= 0.5.0), gplots(>= 3.0.1), graphics, grDevices, IRanges (>= 2.4.8), lazyeval (>= 0.2.0), matrixStats (>= 0.52), magrittr (>= 1.5), methods, NMF (>= 0.20.6), rtracklayer (>= 1.36.4), S4Vectors (>= 0.23.19), stats, tidyr (>= 0.6.3) Suggests: BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3), GenomeInfoDb (>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3), testthat License: MIT + file LICENSE Package: chromVAR Version: 1.8.0 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 Archs: i386, x64 Package: CHRONOS Version: 1.14.0 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 Package: cicero Version: 1.4.4 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, 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 Package: CINdex Version: 1.14.0 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) Package: circRNAprofiler Version: 1.0.0 Depends: R(>= 3.6.0), gwascat Imports: dplyr, magrittr, readr, rtracklayer, stringr, Biostrings, BSgenome, stringi, DESeq2, edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors, stats, AnnotationHub, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, Suggests: testthat, knitr, roxygen2, rmarkdown, citr, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, License: GPL-3 Package: cisPath Version: 1.26.0 Depends: R (>= 2.10.0) Imports: methods, utils License: GPL (>= 3) Archs: i386, x64 Package: ClassifyR Version: 2.5.0 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 Package: cleanUpdTSeq Version: 1.24.0 Depends: R (>= 2.15), BiocGenerics (>= 0.1.0), methods, stats Imports: BSgenome, GenomicRanges, seqinr, e1071, GenomeInfoDb, IRanges, utils, BSgenome.Drerio.UCSC.danRer7 Suggests: BiocStyle, knitr, RUnit License: GPL-2 Package: cleaver Version: 1.24.0 Depends: R (>= 3.0.0), methods, Biostrings (>= 1.29.8) Imports: S4Vectors, IRanges Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.1.4) License: GPL (>= 3) Package: clippda Version: 1.36.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>= 2) Package: clipper Version: 1.26.0 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 Package: cliqueMS Version: 1.0.2 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) Archs: i386, x64 Package: Clomial Version: 1.22.0 Depends: R (>= 2.10), matrixStats Imports: methods, permute License: GPL (>= 2) Package: Clonality Version: 1.34.0 Depends: R (>= 2.12.2), DNAcopy Imports: grDevices, graphics, stats, utils Suggests: gdata License: GPL-3 Package: clonotypeR Version: 1.24.0 Imports: methods Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan License: file LICENSE Package: clst Version: 1.34.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 Package: clstutils Version: 1.34.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit, RSVGTipsDevice License: GPL-3 Package: CluMSID Version: 1.2.1 Depends: R (>= 3.6) Imports: mzR, S4Vectors, dbscan, RColorBrewer, ape, network, GGally, ggplot2, plotly, methods, utils, stats, sna, grDevices, graphics, Biobase, gplots, MSnbase Suggests: knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms License: MIT + file LICENSE Package: clustComp Version: 1.14.0 Depends: R (>= 3.3) Imports: sm, stats, graphics, grDevices Suggests: Biobase, colonCA, RUnit, BiocGenerics License: GPL (>= 2) Package: clusterExperiment Version: 2.6.1 Depends: R (>= 3.5.0), SingleCellExperiment, SummarizedExperiment, BiocGenerics Imports: methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, howmany, locfdr, matrixStats, graphics, parallel, RSpectra, kernlab, stringr, S4Vectors, grDevices, DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, scRNAseq, MAST, Rtsne, scran, igraph License: Artistic-2.0 Archs: i386, x64 Package: ClusterJudge Version: 1.8.0 Depends: R (>= 3.4), stats, utils, graphics, infotheo, lattice, latticeExtra, httr, jsonlite Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt License: Artistic-2.0 Package: clusterProfiler Version: 3.14.3 Depends: R (>= 3.4.0) Imports: AnnotationDbi, DOSE (>= 3.5.1), enrichplot (>= 0.99.7), ggplot2, GO.db, GOSemSim, magrittr, methods, plyr, qvalue, rvcheck, stats, tidyr, utils Suggests: AnnotationHub, dplyr, KEGG.db, knitr, org.Hs.eg.db, prettydoc, ReactomePA, testthat License: Artistic-2.0 Package: clusterSeq Version: 1.10.0 Depends: R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats, utils Imports: BiocGenerics Suggests: BiocStyle License: GPL-3 Package: ClusterSignificance Version: 1.14.0 Depends: R (>= 3.3.0) Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr License: GPL-3 Package: clusterStab Version: 1.58.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 Package: CMA Version: 1.44.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm License: GPL (>= 2) Package: cn.farms Version: 1.34.0 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) Archs: i386, x64 Package: cn.mops Version: 1.32.0 Depends: R (>= 2.12), methods, utils, stats, graphics, parallel, GenomicRanges Imports: BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb, S4Vectors, exomeCopy Suggests: DNAcopy License: LGPL (>= 2.0) Archs: i386, x64 Package: CNAnorm Version: 1.32.0 Depends: R (>= 2.10.1), methods Imports: DNAcopy License: GPL-2 Archs: i386, x64 Package: CNEr Version: 1.22.0 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 Archs: i386, x64 Package: CNORdt Version: 1.28.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 Archs: i386, x64 Package: CNORfeeder Version: 1.26.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), graph Suggests: minet, catnet, Rgraphviz, RUnit, BiocGenerics, igraph License: GPL-3 Package: CNORfuzzy Version: 1.28.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 Archs: i386, x64 Package: CNORode Version: 1.28.0 Depends: CellNOptR (>= 1.5.14), genalg Enhances: MEIGOR License: GPL-2 Archs: i386, x64 Package: CNTools Version: 1.42.0 Depends: R (>= 2.10), methods, tools, stats, genefilter License: LGPL Archs: i386, x64 Package: CNVfilteR Version: 1.0.4 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked License: Artistic-2.0 Package: cnvGSA Version: 1.30.0 Depends: brglm, doParallel, foreach, GenomicRanges, methods, splitstackshape Suggests: cnvGSAdata, org.Hs.eg.db License: LGPL Package: CNVPanelizer Version: 1.18.0 Depends: R (>= 3.2.0), GenomicRanges Imports: S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, exomeCopy, foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx Suggests: knitr, RUnit, BiocGenerics License: GPL-3 Package: CNVRanger Version: 1.2.2 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, Gviz, MultiAssayExperiment, TCGAutils, curatedTCGAData, ensembldb, knitr, regioneR, rmarkdown License: Artistic-2.0 Package: CNVrd2 Version: 1.24.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 Package: CNVtools Version: 1.80.0 Depends: R (>= 2.10), survival License: GPL-3 Archs: i386, x64 Package: cobindR Version: 1.24.0 Imports: methods, seqinr, yaml, rtfbs, gplots, mclust, gmp, BiocGenerics (>= 0.13.8), IRanges, Biostrings, BSgenome, biomaRt Suggests: RUnit Enhances: rGADEM, seqLogo, genoPlotR, parallel, VennDiagram, RColorBrewer, vcd, MotifDb, snowfall License: Artistic-2.0 Package: CoCiteStats Version: 1.58.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL Package: COCOA Version: 2.0.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices, simpleCache, fitdistrplus Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 Package: codelink Version: 1.54.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 Package: CODEX Version: 1.18.0 Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors Suggests: WES.1KG.WUGSC License: GPL-2 Package: coexnet Version: 1.8.0 Depends: R (>= 3.4) Imports: affy, siggenes, GEOquery, vsn, igraph, acde, Biobase, limma, graphics, stats, utils, STRINGdb, SummarizedExperiment, minet, rmarkdown Suggests: RUnit, BiocGenerics, knitr License: LGPL Package: CoGAPS Version: 3.6.0 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) Archs: i386, x64 Package: cogena Version: 1.20.0 Depends: R (>= 3.5.0), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, dplyr, devtools Suggests: knitr, rmarkdown License: LGPL-3 Package: coGPS Version: 1.30.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 Package: COHCAP Version: 1.32.0 Depends: WriteXLS, COHCAPanno, RColorBrewer, gplots Imports: Rcpp, RcppArmadillo, BH LinkingTo: Rcpp, BH License: GPL-3 Archs: i386, x64 Package: cola Version: 1.2.1 Depends: R (>= 3.6.0) Imports: grDevices, graphics, grid, stats, utils, ComplexHeatmap (>= 2.0.0), matrixStats, GetoptLong, circlize (>= 0.4.7), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer, cluster, skmeans, png, mclust, crayon, methods, xml2, microbenchmark, httr, knitr, markdown, digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr LinkingTo: Rcpp Suggests: genefilter, mvtnorm, testthat (>= 0.3), data.tree, dendextend, samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db License: MIT + file LICENSE Archs: i386, x64 Package: coMET Version: 1.18.0 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) Package: compartmap Version: 1.4.0 Depends: R (>= 3.5.0), minfi, Homo.sapiens, mixOmics Imports: SummarizedExperiment, GenomicRanges, gtools, parallel Suggests: covr, testthat, knitr License: GPL-3 + file LICENSE Package: COMPASS Version: 1.24.1 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2 License: Artistic-2.0 Archs: i386, x64 Package: compcodeR Version: 1.22.0 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) Enhances: rpanel, DSS License: GPL (>= 2) Package: compEpiTools Version: 1.20.0 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 Package: CompGO Version: 1.22.0 Depends: RDAVIDWebService Imports: rtracklayer, Rgraphviz, ggplot2, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, pcaMethods, reshape2, pathview License: GPL-2 Package: ComplexHeatmap Version: 2.2.0 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.5), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), parallel, png Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, Cairo, jpeg, tiff, fastcluster, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges License: MIT + file LICENSE Package: CONFESS Version: 1.14.0 Depends: R (>= 3.3),grDevices,utils,stats,graphics Imports: methods,changepoint,cluster,contrast,data.table(>= 1.9.7),ecp,EBImage,flexmix,flowCore,flowClust,flowMeans,flowMerge,flowPeaks,foreach,ggplot2,grid,limma,MASS,moments,outliers,parallel,plotrix,raster,readbitmap,reshape2,SamSPECTRAL,waveslim,wavethresh,zoo Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata License: GPL-2 Package: consensus Version: 1.4.0 Depends: R (>= 3.5), RColorBrewer Imports: matrixStats, gplots, grDevices, methods, graphics, stats, utils Suggests: knitr, RUnit, rmarkdown, BiocGenerics License: BSD_3_clause + file LICENSE Package: ConsensusClusterPlus Version: 1.50.0 Imports: Biobase, ALL, graphics, stats, utils, cluster License: GPL-2 Package: consensusDE Version: 1.4.0 Depends: R (>= 3.5), BiocGenerics Imports: airway, AnnotationDbi, BiocParallel, Biobase, Biostrings, data.table, dendextend, DESeq2 (>= 1.20.0), EDASeq, ensembldb, edgeR, EnsDb.Hsapiens.v86, GenomicAlignments, GenomicFeatures, limma, org.Hs.eg.db, pcaMethods, RColorBrewer, Rsamtools, RUVSeq, S4Vectors, stats, SummarizedExperiment, TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils Suggests: knitr, rmarkdown License: GPL-3 Package: consensusOV Version: 1.8.1 Depends: R (>= 3.6) Imports: Biobase, GSVA, gdata, genefu, limma, matrixStats, randomForest, stats, utils, methods Suggests: BiocStyle, ggplot2, knitr, rmarkdown License: Artistic-2.0 Package: consensusSeekeR Version: 1.14.0 Depends: R (>= 2.10), BiocGenerics, IRanges, GenomicRanges, BiocParallel Imports: GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit License: Artistic-2.0 Package: contiBAIT Version: 1.14.0 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, GenomicFiles, gtools, rtracklayer, BiocParallel, DNAcopy, colorspace, reshape2, ggplot2, methods, exomeCopy, GenomicAlignments, diagram LinkingTo: Rcpp, BH Suggests: BiocStyle License: BSD_2_clause + file LICENSE Archs: i386, x64 Package: convert Version: 1.62.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL Package: copa Version: 1.54.0 Depends: Biobase, methods Suggests: colonCA License: Artistic-2.0 Archs: i386, x64 Package: copynumber Version: 1.26.0 Depends: R (>= 2.10), BiocGenerics Imports: S4Vectors, IRanges, GenomicRanges License: Artistic-2.0 Package: CopyNumberPlots Version: 1.2.3 Depends: R (>= 3.6), karyoploteR Imports: regioneR, IRanges, Rsamtools, SummarizedExperiment, VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges, cn.mops, rhdf5, utils Suggests: BiocStyle, knitr, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat License: Artistic-2.0 Package: CopywriteR Version: 2.18.0 Depends: R(>= 3.2), BiocParallel Imports: matrixStats, gtools, data.table, S4Vectors, chipseq, IRanges, Rsamtools, DNAcopy, GenomicAlignments, GenomicRanges, CopyhelpeR, GenomeInfoDb, futile.logger Suggests: BiocStyle, SCLCBam, snow License: GPL-2 Package: coRdon Version: 1.4.0 Depends: R (>= 3.5) Imports: methods, stats, utils, Biostrings, Biobase, dplyr, stringr, purrr, ggplot2, data.table Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 Package: CoRegFlux Version: 1.2.0 Depends: R (>= 3.6) Imports: CoRegNet, sybil Suggests: glpkAPI, testthat, knitr, rmarkdown, digest, R.cache, ggplot2, plyr, igraph, methods, latex2exp, rBayesianOptimization License: GPL-3 Package: CoRegNet Version: 1.24.0 Depends: R (>= 2.14), igraph, shiny, arules, methods Suggests: RColorBrewer, gplots, BiocStyle, knitr License: GPL-3 Archs: i386, x64 Package: Cormotif Version: 1.32.0 Depends: R (>= 2.12.0), affy, limma Imports: affy, graphics, grDevices License: GPL-2 Package: CorMut Version: 1.28.0 Depends: methods,seqinr,igraph License: GPL-2 Package: CORREP Version: 1.52.0 Imports: e1071, stats Suggests: cluster, MASS License: GPL (>= 2) Package: coseq Version: 1.10.0 Depends: R (>= 3.4.0), SummarizedExperiment, S4Vectors Imports: edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2 (>= 2.1.0), scales, HTSFilter, corrplot, HTSCluster (>= 2.0.8), grDevices, graphics, stats, methods, compositions, mvtnorm Suggests: Biobase, knitr, rmarkdown, testthat License: GPL (>= 3) Package: cosmiq Version: 1.20.0 Depends: R (>= 3.6), Rcpp Imports: pracma, xcms, MassSpecWavelet, faahKO Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 Archs: i386, x64 Package: COSNet Version: 1.20.0 Suggests: bionetdata, PerfMeas, RUnit, BiocGenerics License: GPL (>= 2) Archs: i386, x64 Package: CountClust Version: 1.14.0 Depends: R (>= 3.4), ggplot2 (>= 2.1.0) Imports: SQUAREM, slam, maptpx, plyr(>= 1.7.1), cowplot, gtools, flexmix, picante, limma, parallel, reshape2, stats, utils, graphics, grDevices Suggests: knitr, kableExtra, BiocStyle, Biobase, roxygen2, RColorBrewer, devtools, xtable License: GPL (>= 2) Package: countsimQC Version: 1.4.0 Depends: R (>= 3.5) Imports: rmarkdown (>= 0.9.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr, ggplot2, grDevices, tools, SummarizedExperiment, genefilter, DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods Suggests: knitr, testthat License: GPL (>= 2) Package: covEB Version: 1.12.0 Depends: R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats, LaplacesDemon, Matrix Suggests: curatedBladderData License: GPL-3 Package: covRNA Version: 1.12.0 Depends: ade4, Biobase Imports: parallel, genefilter, grDevices, stats, graphics Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) Package: cpvSNP Version: 1.18.0 Depends: R (>= 2.10), GenomicFeatures, GSEABase (>= 1.24.0) Imports: methods, corpcor, BiocParallel, ggplot2, plyr Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle License: Artistic-2.0 Package: cqn Version: 1.32.0 Depends: R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore, splines, quantreg Imports: splines Suggests: scales, edgeR License: Artistic-2.0 Package: CRImage Version: 1.34.0 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach, sgeostat License: Artistic-2.0 Package: CRISPRseek Version: 1.26.0 Depends: R (>= 3.0.1), BiocGenerics, Biostrings Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges, BSgenome, BiocParallel, hash Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL (>= 2) Package: crisprseekplus Version: 1.12.0 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 Package: CrispRVariants Version: 1.14.0 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 Package: crlmm Version: 1.44.0 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, SNPchip, 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 Archs: i386, x64 Package: CrossICC Version: 1.0.0 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 | file LICENSE Package: crossmeta Version: 1.12.0 Depends: R (>= 3.5) Imports: affy (>= 1.52.0), affxparser (>= 1.46.0), AnnotationDbi (>= 1.36.2), Biobase (>= 2.34.0), BiocGenerics (>= 0.20.0), BiocManager (>= 1.30.4), ccmap, DT (>= 0.2), DBI (>= 1.0.0), data.table (>= 1.10.4), doParallel (>= 1.0.10), doRNG (>= 1.6), foreach (>= 1.4.3), fdrtool (>= 1.2.15), ggplot2 (>= 2.2.1), GEOquery (>= 2.40.0), limma (>= 3.30.13), matrixStats (>= 0.51.0), metaMA (>= 3.1.2), metap (>= 0.8), miniUI (>= 0.1.1), oligo (>= 1.38.0), plotly(>= 4.5.6), reshape (>= 0.8.6), reader(>= 1.0.6), RColorBrewer (>= 1.1.2), RCurl (>= 1.95.4.11), RSQLite (>= 2.1.1), rdrop2 (>= 0.7.0), stringr (>= 1.2.0), sva (>= 3.22.0), shiny (>= 1.0.0), stats (>= 3.3.3), XML (>= 3.98.1.17), Suggests: knitr, rmarkdown, lydata, org.Hs.eg.db, testthat, ccdata License: MIT + file LICENSE Package: CSAR Version: 1.38.0 Depends: R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 Archs: i386, x64 Package: csaw Version: 1.20.0 Depends: GenomicRanges, SummarizedExperiment Imports: Rcpp, BiocGenerics, Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, utils LinkingTo: Rhtslib, zlibbioc, Rcpp Suggests: org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager License: GPL-3 Archs: i386, x64 Package: CSSP Version: 1.24.0 Imports: methods, splines, stats, utils Suggests: testthat License: GPL-2 Archs: i386, x64 Package: ctc Version: 1.60.0 Depends: amap License: GPL-2 Package: CTDquerier Version: 1.5.0 Depends: R (>= 3.4.0) Imports: RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils, grid, gridExtra, methods, stats, BiocFileCache, rappdirs Suggests: BiocStyle, knitr License: MIT + file LICENSE Package: cTRAP Version: 1.4.0 Depends: R (>= 3.6.0) Imports: biomaRt, cowplot, data.table, dplyr, fgsea, ggplot2, ggrepel, graphics, httr, limma, methods, pbapply, R.utils, readxl, reshape2, rhdf5, stats, tools, utils Suggests: testthat, knitr, covr, rmarkdown License: MIT + file LICENSE Package: ctsGE Version: 1.12.0 Depends: R (>= 3.2) Imports: ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat License: GPL-2 Package: cummeRbund Version: 2.28.0 Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz Imports: methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson License: Artistic-2.0 Package: customProDB Version: 1.26.1 Depends: R (>= 3.0.1), IRanges, AnnotationDbi, biomaRt(>= 2.17.1) Imports: S4Vectors (>= 0.9.25), DBI, GenomeInfoDb, GenomicRanges, Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>= 2.26.3), GenomicFeatures (>= 1.32.0), stringr, RCurl, plyr, VariantAnnotation (>= 1.13.44), rtracklayer, RSQLite, AhoCorasickTrie, methods Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 Package: CVE Version: 1.11.2 Depends: R (>= 3.4.0), tidyverse, plyr, ggplot2 Imports: shiny, ConsensusClusterPlus, RColorBrewer, gplots, jsonlite, ape, WGCNA, RTCGAToolbox Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 Package: cycle Version: 1.40.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 Package: cydar Version: 1.10.0 Depends: BiocParallel, SingleCellExperiment Imports: viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, flowCore, Biobase, Rcpp, BiocNeighbors, SummarizedExperiment LinkingTo: Rcpp Suggests: ncdfFlow, testthat, knitr, edgeR, limma, glmnet, BiocStyle, flowStats License: GPL-3 Archs: i386, x64 Package: CytoDx Version: 1.6.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr License: GPL-2 Package: cytofast Version: 1.2.0 Depends: R (>= 3.6.0) Imports: flowCore, ggplot2, ggridges, RColorBrewer, reshape2, stats, grDevices, Rdpack, methods, grid, FlowSOM Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 Package: cytolib Version: 1.8.0 Depends: R (>= 3.4) Suggests: knitr License: Artistic-2.0 Package: CytoML Version: 1.12.1 Imports: flowCore (>= 1.43.10), flowWorkspace (>= 3.33.10), openCyto (>= 1.11.3), XML, data.table, jsonlite, RBGL, ncdfFlow, Rgraphviz, Biobase, methods, graph, graphics, utils, base64enc, plyr, dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, lattice, stats, corpcor, RUnit LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.3.7), cytolib(>= 1.3.3), RcppParallel Suggests: testthat, flowWorkspaceData (>= 2.11.1), knitr, parallel License: Artistic-2.0 Archs: i386, x64 Package: dada2 Version: 1.14.1 Depends: R (>= 3.4.0), Rcpp (>= 0.12.0), methods (>= 3.4.0) Imports: Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), ShortRead (>= 1.32.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0), IRanges (>= 2.6.0), XVector (>= 0.16.0), BiocGenerics (>= 0.22.0) LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, knitr, rmarkdown License: LGPL-3 Archs: i386, x64 Package: dagLogo Version: 1.24.0 Depends: R (>= 3.0.1), methods, biomaRt, grImport2, grid, motifStack Imports: pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils Suggests: XML, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) Package: daMA Version: 1.58.0 Imports: MASS, stats License: GPL (>= 2) Package: DaMiRseq Version: 1.10.0 Depends: R (>= 3.4), SummarizedExperiment, ggplot2 Imports: DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap, FactoMineR, corrplot, randomForest, e1071, caret, MASS, lubridate, plsVarSel, kknn, FSelector, methods, stats, utils, graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) Package: DAPAR Version: 1.18.5 Depends: R (>= 3.6.1), foreach, parallel, doParallel, igraph Imports: MSnbase, RColorBrewer,stats,preprocessCore,Cairo,png, lattice,reshape2,gplots,pcaMethods,ggplot2, limma,knitr,tmvtnorm,norm,impute, stringr, grDevices, graphics, openxlsx, utils, cp4p (>= 0.3.5), scales, Matrix, vioplot, imp4p (>= 0.8), highcharter (>= 0.7.0), DAPARdata (>= 1.16.0), siggenes, graph, lme4, readxl, clusterProfiler, dplyr, tidyr,AnnotationDbi, vsn, FactoMineR, factoextra, visNetwork Suggests: BiocGenerics, Biobase, testthat, BiocStyle License: Artistic-2.0 Package: DART Version: 1.34.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 Package: DBChIP Version: 1.30.0 Depends: R (>= 2.15.0), edgeR, DESeq Suggests: ShortRead, BiocGenerics License: GPL (>= 2) Package: dcanr Version: 1.2.0 Depends: R (>= 3.6.0) Imports: igraph, foreach, plyr, stringr, reshape2, methods, Matrix, graphics, stats, RColorBrewer, circlize, doRNG Suggests: EBcoexpress, testthat, EBarrays, GeneNet, COSINE, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 Package: dcGSA Version: 1.14.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 Package: DChIPRep Version: 1.16.0 Depends: R (>= 3.4), DESeq2 Imports: methods, stats, utils, ggplot2, fdrtool, reshape2, GenomicRanges, SummarizedExperiment, smoothmest, plyr, tidyr, assertthat, S4Vectors, purrr, soGGi, ChIPpeakAnno Suggests: mgcv, testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENCE Package: ddCt Version: 1.42.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: RUnit License: LGPL-3 Package: ddPCRclust Version: 1.6.0 Depends: R (>= 3.5) Imports: plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore, flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks Suggests: BiocStyle License: Artistic-2.0 Package: debCAM Version: 1.4.0 Depends: R (>= 3.5) Imports: methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 Package: debrowser Version: 1.14.2 Depends: R (>= 3.5.0), Imports: shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT, ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE, igraph, grDevices, graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, d3heatmap, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker, plotly, heatmaply, Harman, pathview Suggests: testthat, rmarkdown, knitr, R.rsp License: GPL-3 + file LICENSE Package: DECIPHER Version: 2.14.0 Depends: R (>= 3.3.0), Biostrings (>= 2.35.12), RSQLite (>= 1.1), stats, parallel Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector License: GPL-3 Archs: i386, x64 Package: deco Version: 1.2.0 Depends: R (>= 3.5.0), AnnotationDbi, BiocParallel, SummarizedExperiment, limma Imports: stats, methods, ggplot2, foreign, graphics, BiocStyle, Biobase, cluster, gplots, RColorBrewer, locfit, made4, ade4, sfsmisc, scatterplot3d, gdata, grDevices, utils, reshape2, gridExtra Suggests: knitr, curatedTCGAData, MultiAssayExperiment, Homo.sapiens License: GPL (>= 3) Package: DEComplexDisease Version: 1.6.0 Depends: R (>= 3.3.3) Imports: Rcpp (>= 0.12.7), DESeq2, edgeR, SummarizedExperiment, ComplexHeatmap, grid, parallel, BiocParallel, grDevices, graphics, stats, methods, utils LinkingTo: Rcpp Suggests: knitr License: GPL-3 Archs: i386, x64 Package: decompTumor2Sig Version: 2.2.0 Depends: R(>= 3.6), ggplot2 Imports: methods, Matrix, quadprog(>= 1.5-5), vcfR, GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 Package: DeconRNASeq Version: 1.28.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 Package: decontam Version: 1.6.0 Depends: R (>= 3.4.1), methods (>= 3.4.1) Imports: ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats Suggests: BiocStyle, knitr, rmarkdown, phyloseq License: Artistic-2.0 Package: DEDS Version: 1.60.0 Depends: R (>= 1.7.0) License: LGPL Archs: i386, x64 Package: DeepBlueR Version: 1.12.0 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) Package: deepSNV Version: 1.32.0 Depends: R (>= 2.13.0), methods, graphics, parallel, Rhtslib, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.13.44), Imports: Rhtslib LinkingTo: Rhtslib (>= 1.13.1) Suggests: RColorBrewer, knitr, rmarkdown License: GPL-3 Archs: i386, x64 Package: DEFormats Version: 1.14.0 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 Package: DEGreport Version: 1.22.0 Depends: R (>= 3.5.0) Imports: utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, lasso2, magrittr, Nozzle.R1, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE Package: DEGseq Version: 1.40.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) Archs: i386, x64 Package: DelayedArray Version: 0.12.3 Depends: R (>= 3.4), methods, stats4, matrixStats, BiocGenerics (>= 0.31.5), S4Vectors (>= 0.24.4), IRanges (>= 2.17.3), BiocParallel Imports: stats, Matrix LinkingTo: S4Vectors Suggests: HDF5Array, genefilter, SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit License: Artistic-2.0 Archs: i386, x64 Package: DelayedDataFrame Version: 1.2.0 Depends: R (>= 3.6), S4Vectors (>= 0.23.19), DelayedArray (>= 0.7.5) Imports: methods, stats, BiocGenerics Suggests: testthat, knitr, rmarkdown, SeqArray, GDSArray License: GPL-3 Package: DelayedMatrixStats Version: 1.8.0 Depends: DelayedArray (>= 0.11.1) Imports: methods, matrixStats (>= 0.55.0), Matrix, S4Vectors (>= 0.17.5), IRanges, HDF5Array (>= 1.7.10), BiocParallel Suggests: testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark, profmem License: MIT + file LICENSE Package: deltaCaptureC Version: 1.0.0 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2 Suggests: knitr, rmarkdown License: MIT + file LICENSE Package: deltaGseg Version: 1.26.0 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 Package: DeMAND Version: 1.16.0 Depends: R (>= 2.14.0), KernSmooth, methods License: file LICENSE Package: DeMixT Version: 1.2.5 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 Archs: i386, x64 Package: DEP Version: 1.8.0 Depends: R (>= 3.5) Imports: ggplot2, dplyr, purrr, readr, tibble, tidyr, SummarizedExperiment (>= 1.11.5), MSnbase, limma, vsn, fdrtool, ggrepel, ComplexHeatmap, RColorBrewer, circlize, shiny, shinydashboard, DT, 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Depends: BiocGenerics (>= 0.7.5), Biobase (>= 2.21.7), locfit, lattice Imports: genefilter, geneplotter, methods, MASS, RColorBrewer Suggests: pasilla (>= 0.2.10), vsn, gplots License: GPL (>= 3) Archs: i386, x64 Package: DESeq2 Version: 1.26.0 Depends: S4Vectors (>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter, methods, stats4, locfit, geneplotter, ggplot2, Hmisc, Rcpp (>= 0.11.0) LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, IHW, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10) License: LGPL (>= 3) Archs: i386, x64 Package: DEsingle Version: 1.6.0 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 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S4Vectors, SummarizedExperiment, stats, utils Suggests: knitr, rmarkdown, testthat, BiocStyle, IHW License: LGPL (>= 3) Package: DEXSeq Version: 1.32.0 Depends: BiocParallel, Biobase, SummarizedExperiment, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), DESeq2 (>= 1.9.11), AnnotationDbi, RColorBrewer, S4Vectors (>= 0.23.18) Imports: BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter Suggests: GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown License: GPL (>= 3) Package: dexus Version: 1.26.0 Depends: R (>= 2.15), methods, BiocGenerics Imports: stats Suggests: parallel, statmod, DESeq, RColorBrewer License: LGPL (>= 2.0) Archs: i386, x64 Package: DFP Version: 1.44.0 Depends: methods, Biobase (>= 2.5.5) License: GPL-2 Package: DiffBind Version: 2.14.0 Depends: R (>= 3.5), GenomicRanges, SummarizedExperiment Imports: RColorBrewer, amap, edgeR, gplots, grDevices, limma, GenomicAlignments, locfit, stats, 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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 Archs: i386, x64 Package: diggit Version: 1.18.0 Depends: R (>= 3.0.2), Biobase, methods Imports: ks, viper(>= 1.3.1), parallel Suggests: diggitdata License: file LICENSE Package: DirichletMultinomial Version: 1.28.0 Depends: S4Vectors, IRanges Imports: stats4, methods, BiocGenerics Suggests: lattice, parallel, MASS, RColorBrewer, xtable License: LGPL-3 Archs: i386, x64 Package: discordant Version: 1.10.0 Depends: R (>= 3.4) Imports: Biobase, stats, biwt, gtools, MASS, tools Suggests: BiocStyle, knitr License: GPL (>= 2) Archs: i386, x64 Package: DiscoRhythm Version: 1.2.1 Depends: R (>= 3.6.0) Imports: matrixTests, matrixStats, MetaCycle (>= 1.2.0), data.table, ggplot2, ggExtra, dplyr, broom, shiny, shinyBS, shinycssloaders, 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testthat, knitr License: GPL-3 Package: DMRcaller Version: 1.18.0 Depends: R (>= 3.5), GenomicRanges, IRanges, S4Vectors (>= 0.23.10) Imports: parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils Suggests: knitr, RUnit, BiocGenerics License: GPL-3 Package: DMRcate Version: 1.21.0 Depends: R (>= 3.3.0), minfi, DSS, DMRcatedata Imports: limma, missMethyl, GenomicRanges, parallel, methods, graphics, plyr, Gviz, IRanges, stats, utils, S4Vectors Suggests: knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: file LICENSE Package: DMRforPairs Version: 1.22.0 Depends: R (>= 2.15.2), Gviz (>= 1.2.1), R2HTML (>= 2.2.1), GenomicRanges (>= 1.10.7), parallel License: GPL (>= 2) Package: DMRScan Version: 1.11.0 Depends: R (>= 3.4.0) Imports: Matrix, MASS, RcppRoll,GenomicRanges, IRanges, GenomeInfoDb, methods, mvtnorm, stats, parallel Suggests: testthat, knitr, rmarkdown License: GPL-3 Package: 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AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret License: GPL-2 Archs: i386, x64 Package: DominoEffect Version: 1.6.0 Depends: R(>= 3.5) Imports: biomaRt, data.table, utils, stats, Biostrings, SummarizedExperiment, VariantAnnotation, AnnotationDbi, GenomeInfoDb, IRanges, GenomicRanges, methods Suggests: knitr, testthat License: GPL (>= 3) Package: doppelgangR Version: 1.14.0 Depends: R (>= 3.5.0), Biobase, BiocParallel Imports: sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, ROCR, pROC (>= 1.15.0), RUnit, simulatorZ, proxy License: GPL (>= 2.0) Package: Doscheda Version: 1.8.1 Depends: R (>= 3.6) Imports: methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy, limma, stringr, ggplot2, graphics, grDevices, calibrate, corrgram, gridExtra, DT, shiny, shinydashboard, readxl, d3heatmap, prodlim, matrixStats Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 Package: DOSE Version: 3.12.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim (>= 2.0.0), methods, qvalue, reshape2, S4Vectors, stats, utils Suggests: prettydoc, clusterProfiler, knitr, org.Hs.eg.db, testthat License: Artistic-2.0 Package: doseR Version: 1.2.0 Depends: R (>= 3.6) Imports: edgeR, methods, stats, graphics, matrixStats, mclust, lme4, RUnit, SummarizedExperiment, digest, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: GPL Package: drawProteins Version: 1.6.0 Depends: R (>= 3.4) Imports: ggplot2, httr, dplyr, readr, stringr, tidyr Suggests: covr, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Package: DRIMSeq Version: 1.14.0 Depends: R (>= 3.4.0) Imports: utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2 Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, 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grDevices, stats, abind, tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils, htmltools, htmlwidgets, RCurl Suggests: BiocStyle, digest, knitr, rmarkdown, shiny License: LGPL Archs: i386, x64 Package: EBSEA Version: 1.14.0 Imports: edgeR, limma, graphics, stats, plyr License: GPL-2 Package: EBSeq Version: 1.26.0 Depends: blockmodeling, gplots, testthat, R (>= 3.0.0) License: Artistic-2.0 Package: EBSeqHMM Version: 1.20.0 Depends: EBSeq License: Artistic-2.0 Package: ecolitk Version: 1.58.0 Depends: R (>= 2.10) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy License: GPL (>= 2) Package: EDASeq Version: 2.20.0 Depends: Biobase (>= 2.15.1), ShortRead (>= 1.11.42) Imports: methods, graphics, BiocGenerics, IRanges (>= 1.13.9), DESeq, aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings, AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager Suggests: BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat License: Artistic-2.0 Package: EDDA Version: 1.24.0 Depends: Rcpp (>= 0.10.4),parallel,methods,ROCR,DESeq,baySeq,snow,edgeR Imports: graphics, stats, utils, parallel, methods, ROCR, DESeq, baySeq, snow, edgeR LinkingTo: Rcpp License: GPL (>= 2) Archs: i386, x64 Package: edge Version: 2.18.0 Depends: R(>= 3.1.0), Biobase Imports: methods, splines, sva, snm, jackstraw, qvalue(>= 1.99.0), MASS Suggests: testthat, knitr, ggplot2, reshape2 License: MIT + file LICENSE Archs: i386, x64 Package: edgeR Version: 3.28.1 Depends: R (>= 3.6.0), limma (>= 3.41.5) Imports: graphics, stats, utils, methods, locfit, Rcpp LinkingTo: Rcpp Suggests: AnnotationDbi, jsonlite, org.Hs.eg.db, readr, rhdf5, splines License: GPL (>= 2) Archs: i386, x64 Package: eegc Version: 1.12.0 Depends: R (>= 3.4.0) Imports: R.utils, gplots, sna, wordcloud, igraph, pheatmap, edgeR, DESeq2, clusterProfiler, S4Vectors, ggplot2, org.Hs.eg.db, org.Mm.eg.db, limma, DOSE, AnnotationDbi Suggests: knitr License: GPL-2 Package: EGAD Version: 1.14.0 Depends: R(>= 3.3) Imports: gplots, Biobase, GEOquery, limma, arrayQualityMetrics, impute, RColorBrewer, zoo, igraph, plyr, Matrix, MASS, RCurl, affy Suggests: knitr, rmarkdown, testthat License: GPL-2 Package: EGSEA Version: 1.14.0 Depends: R (>= 3.5), Biobase, gage (>= 2.14.4), AnnotationDbi, topGO (>= 2.16.0), pathview (>= 1.4.2) Imports: PADOG (>= 1.6.0), GSVA (>= 1.12.0), globaltest (>= 5.18.0), limma (>= 3.20.9), edgeR (>= 3.6.8), HTMLUtils (>= 0.1.5), hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0), safe (>= 3.4.0), stringi (>= 0.5.0), parallel, stats, metap, grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, RColorBrewer, methods, EGSEAdata (>= 1.3.1), Glimma (>= 1.4.0), htmlwidgets, plotly, DT Suggests: BiocStyle, knitr, testthat License: GPL-3 Package: eiR Version: 1.26.0 Depends: R (>= 2.10.0), ChemmineR (>= 2.15.15), methods, DBI Imports: snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl, digest, BiocGenerics, gespeR,RcppAnnoy (>= 0.0.9) Suggests: BiocStyle, knitcitations, knitr, knitrBootstrap License: Artistic-2.0 Archs: x64 Package: eisa Version: 1.38.0 Depends: isa2, Biobase (>= 2.17.8), AnnotationDbi, methods Imports: BiocGenerics, Category, genefilter, DBI Suggests: igraph (>= 0.6), Matrix, GOstats, GO.db, KEGG.db, biclust, MASS, xtable, ALL, hgu95av2.db, targetscan.Hs.eg.db, org.Hs.eg.db License: GPL (>= 2) Package: ELBOW Version: 1.22.0 Depends: R (>= 2.15.0) Imports: graphics, stats, utils Suggests: DESeq, GEOquery, limma, simpleaffy, affyPLM, RColorBrewer, hgu133plus2cdf, hgu133plus2probe License: file LICENSE License_is_FOSS: yes License_restricts_use: no Package: ELMER Version: 2.10.0 Depends: R (>= 3.4.0), ELMER.data (>= 2.9.3) Imports: GenomicRanges, ggplot2, reshape, grid, grDevices, graphics, methods, parallel, stats, utils, IRanges, GenomeInfoDb, S4Vectors, GenomicFeatures, TCGAbiolinks (>= 2.9.2), plyr, Matrix, dplyr, Gviz, ComplexHeatmap, circlize, MultiAssayExperiment, SummarizedExperiment, biomaRt, doParallel, downloader, ggrepel, lattice, magrittr, readr, scales, rvest, xml2, plotly, gridExtra, rmarkdown, stringr, tibble, tidyr, progress, purrr, ggpubr, rtracklayer, DelayedArray Suggests: BiocStyle, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr License: GPL-3 Package: EMDomics Version: 2.16.0 Depends: R (>= 3.2.1) Imports: emdist, BiocParallel, matrixStats, ggplot2, CDFt, preprocessCore Suggests: knitr License: MIT + file LICENSE Package: EmpiricalBrownsMethod Version: 1.14.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE Package: ENCODExplorer Version: 2.12.1 Depends: R (>= 3.6) Imports: methods, tools, jsonlite, RCurl, tidyr, data.table, dplyr, stringr, stringi, utils, AnnotationHub, GenomicRanges, rtracklayer, S4Vectors, GenomeInfoDb Suggests: RUnit,BiocGenerics,knitr, curl, httr, shiny, shinythemes, DT License: Artistic-2.0 Package: EnhancedVolcano Version: 1.4.0 Depends: ggplot2, ggrepel Suggests: RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway, gridExtra, magrittr License: GPL-3 Package: ENmix Version: 1.22.6 Depends: parallel,doParallel,foreach,SummarizedExperiment,stats Imports: grDevices,graphics,preprocessCore,matrixStats,methods,utils,irr, geneplotter,impute,minfi,RPMM,illuminaio,dynamicTreeCut,IRanges, Biobase,ExperimentHub,AnnotationHub,genefilter,gplots,quadprog,S4Vectors Suggests: minfiData, RUnit, BiocGenerics License: Artistic-2.0 Package: EnrichedHeatmap Version: 1.16.0 Depends: R (>= 3.1.2), methods, grid, ComplexHeatmap (>= 1.99.0), GenomicRanges Imports: matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize (>= 0.4.5), IRanges LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, markdown, genefilter, RColorBrewer License: MIT + file LICENSE Archs: i386, x64 Package: EnrichmentBrowser Version: 2.16.1 Depends: SummarizedExperiment, graph Imports: AnnotationDbi, BiocFileCache, BiocManager, ComplexHeatmap, GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, biocGraph, edgeR, geneplotter, graphite, hwriter, limma, methods, pathview, rappdirs, safe, topGO Suggests: ALL, BiocStyle, ReportingTools, airway, hgu95av2.db, knitr License: Artistic-2.0 Package: enrichplot Version: 1.6.1 Depends: R (>= 3.4.0) Imports: AnnotationDbi, cowplot, DOSE (>= 3.5.1), europepmc, ggplot2, ggplotify, ggraph, ggridges, GOSemSim, graphics, grDevices, grid, gridExtra, igraph, methods, purrr, RColorBrewer, reshape2, stats, utils Suggests: clusterProfiler, dplyr, ggupset, knitr, org.Hs.eg.db, prettydoc, tibble License: Artistic-2.0 Package: enrichTF Version: 1.2.3 Depends: pipeFrame Imports: BSgenome, rtracklayer, motifmatchr, TFBSTools, R.utils, methods, JASPAR2018, GenomeInfoDb, GenomicRanges, IRanges, BiocGenerics, S4Vectors, utils, parallel, stats, ggpubr, heatmap3, ggplot2, clusterProfiler, rmarkdown, grDevices, magrittr Suggests: knitr, testthat, webshot License: GPL-3 Package: ensembldb Version: 2.10.2 Depends: BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.31.18), GenomicFeatures (>= 1.29.10), AnnotationFilter (>= 1.5.2) Imports: methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb, AnnotationDbi (>= 1.31.19), rtracklayer, S4Vectors (>= 0.23.10), Rsamtools, IRanges (>= 2.13.24), ProtGenerics, Biostrings (>= 2.47.9), curl Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), magrittr, AnnotationHub Enhances: RMariaDB, shiny License: LGPL Package: ENVISIONQuery Version: 1.34.0 Depends: rJava, XML, utils License: GPL-2 Package: EpiDISH Version: 2.2.2 Depends: R (>= 3.5) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat License: GPL-2 Package: epigenomix Version: 1.26.0 Depends: R (>= 3.2.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment Imports: BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray License: LGPL-3 Package: epihet Version: 1.2.0 Depends: R(>= 3.6), GenomicRanges, IRanges, S4Vectors, ggplot2, foreach, Rtsne, igraph Imports: data.table, doParallel, EntropyExplorer, graphics, stats, grDevices, pheatmap, utils, qvalue, WGCNA, ReactomePA Suggests: knitr, clusterProfiler, ggfortify, org.Hs.eg.db, rmarkdown License: Artistic-2.0 Package: epiNEM Version: 1.10.0 Depends: R (>= 3.4) Imports: BoolNet, e1071, gtools, stats, igraph, nem, utils, lattice, latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db License: GPL-3 Package: epivizr Version: 2.16.0 Depends: R (>= 3.0), methods, Imports: epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4), GenomicRanges, S4Vectors, IRanges Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle License: Artistic-2.0 Package: epivizrChart Version: 1.8.0 Depends: R (>= 3.4.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub License: Artistic-2.0 Package: epivizrData Version: 1.14.0 Depends: R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase Imports: S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0), OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI License: MIT + file LICENSE Package: epivizrServer Version: 1.14.0 Depends: R (>= 3.2.3), methods Imports: httpuv (>= 1.3.0), R6 (>= 2.0.0), rjson, mime (>= 0.2) Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Package: epivizrStandalone Version: 1.14.0 Depends: R (>= 3.2.3), epivizr (>= 2.3.6), methods Imports: git2r, epivizrServer, GenomeInfoDb, BiocGenerics, GenomicFeatures, S4Vectors Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle License: MIT + file LICENSE Package: erccdashboard Version: 1.20.0 Depends: R (>= 3.2), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0) Imports: edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr, qvalue, reshape2, ROCR, scales, stringr License: GPL (>= 2) Package: erma Version: 1.2.0 Depends: R (>= 3.1), methods, Homo.sapiens, GenomicFiles (>= 1.5.2) Imports: rtracklayer (>= 1.38.1), S4Vectors (>= 0.23.18), BiocGenerics, GenomicRanges, SummarizedExperiment, ggplot2, GenomeInfoDb, Biobase, shiny, BiocParallel, IRanges, AnnotationDbi Suggests: rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel License: Artistic-2.0 Package: ERSSA Version: 1.4.0 Depends: R (>= 3.5.0) Imports: edgeR (>= 3.23.3), DESeq2 (>= 1.21.16), ggplot2 (>= 3.0.0), RColorBrewer (>= 1.1-2), plyr (>= 1.8.4), BiocParallel (>= 1.15.8), grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 | file LICENSE Package: esATAC Version: 1.8.0 Depends: R (>= 3.5), Rsamtools, GenomicRanges, ShortRead Imports: Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer, ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph, rJava, DiagrammeR, magrittr, digest, BSgenome, AnnotationDbi, GenomicFeatures, R.utils, GenomeInfoDb, BiocGenerics, S4Vectors, IRanges, rmarkdown, tools, VennDiagram, grid, JASPAR2016, TFBSTools, grDevices, graphics, stats, utils, parallel, corrplot, BiocManager, motifmatchr LinkingTo: Rcpp Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, DiagrammeRsvg, testthat, webshot License: GPL-3 | file LICENSE Archs: x64 Package: esetVis Version: 1.12.0 Imports: mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils, grDevices, methods Suggests: ggplot2, ggvis, rbokeh, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment License: GPL-3 Package: eudysbiome Version: 1.16.0 Depends: R (>= 3.1.0) Imports: plyr, Rsamtools, R.utils, Biostrings License: GPL-2 Package: evaluomeR Version: 1.2.41 Depends: R (>= 3.6), SummarizedExperiment, MultiAssayExperiment, cluster (>= 2.0.7-1), fpc (>= 2.2-3) Imports: corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2, ggdendro, plotrix, stats, matrixStats, Rdpack Suggests: BiocStyle, knitr, rmarkdown, kableExtra, magrittr License: GPL-3 Package: EventPointer Version: 2.4.0 Depends: R (>= 3.4), SGSeq, Matrix, SummarizedExperiment Imports: GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls, limma, matrixStats, RBGL, prodlim, graph, methods, utils, stats, doParallel, foreach, affxparser, GenomicRanges, S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome, BSgenome.Hsapiens.UCSC.hg38, Biostrings Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra License: Artistic-2.0 Package: ExiMiR Version: 2.28.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), affy (>= 1.26.1), limma Imports: affyio(>= 1.13.3), Biobase(>= 2.5.5), preprocessCore(>= 1.10.0) Suggests: mirna10cdf License: GPL-2 Package: exomeCopy Version: 1.32.0 Depends: IRanges (>= 2.5.27), GenomicRanges (>= 1.23.16), Rsamtools Imports: stats4, methods, GenomeInfoDb Suggests: Biostrings License: GPL (>= 2) Archs: i386, x64 Package: ExperimentHub Version: 1.12.0 Depends: methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 2.17.9), BiocFileCache (>= 1.5.1) Imports: utils, S4Vectors, BiocManager, curl, rappdirs Suggests: knitr, BiocStyle Enhances: ExperimentHubData License: Artistic-2.0 Package: ExperimentHubData Version: 1.12.0 Depends: utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData (>= 1.13.11) Imports: methods, ExperimentHub, BiocManager, DBI, BiocCheck, httr, curl, biocViews, graph Suggests: GenomeInfoDb, RUnit, knitr, BiocStyle License: Artistic-2.0 Package: explorase Version: 1.50.0 Depends: R (>= 2.6.2) Imports: limma, rggobi, RGtk2 Suggests: cairoDevice License: GPL-2 Package: ExpressionAtlas Version: 1.14.0 Depends: R (>= 3.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2 Imports: utils, XML, httr Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) Package: ExpressionView Version: 1.38.0 Depends: caTools, bitops, methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi Imports: methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi Suggests: ALL, hgu95av2.db, biclust, affy License: GPL (>= 2) Archs: i386, x64 Package: fabia Version: 2.32.0 Depends: R (>= 3.6.0), Biobase Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) Archs: i386, x64 Package: factDesign Version: 1.62.0 Depends: Biobase (>= 2.5.5) Imports: stats Suggests: affy, genefilter, multtest License: LGPL Package: FamAgg Version: 1.14.0 Depends: methods, kinship2, igraph Imports: gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey Suggests: BiocStyle, knitr, RUnit, rmarkdown License: MIT + file LICENSE Package: farms Version: 1.38.0 Depends: R (>= 2.8), affy (>= 1.20.0), MASS, methods Imports: affy, MASS, Biobase (>= 1.13.41), methods, graphics Suggests: affydata, Biobase, utils License: LGPL (>= 2.1) Package: fastLiquidAssociation Version: 1.22.0 Depends: methods, LiquidAssociation, parallel, doParallel, stats, Hmisc, utils Imports: WGCNA, impute, preprocessCore Suggests: GOstats, yeastCC, org.Sc.sgd.db License: GPL-2 Package: FastqCleaner Version: 1.4.0 Imports: methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, methods, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12) LinkingTo: Rcpp Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL (>= 2) Archs: i386, x64 Package: fastseg Version: 1.32.0 Depends: R (>= 2.13), GenomicRanges, Biobase Imports: methods, graphics, stats, BiocGenerics, S4Vectors, IRanges Suggests: DNAcopy, oligo License: LGPL (>= 2.0) Archs: i386, x64 Package: FCBF Version: 1.4.0 Depends: R (>= 3.6) Imports: ggplot2, gridExtra, pbapply, parallel, SummarizedExperiment, stats, mclust Suggests: caret, mlbench, SingleCellExperiment, knitr, rmarkdown, testthat, BiocManager License: MIT + file LICENSE Package: fCCAC Version: 1.12.0 Depends: R (>= 3.3.0), S4Vectors, IRanges, GenomicRanges, grid Imports: fda, RColorBrewer, genomation, ggplot2, ComplexHeatmap, grDevices, stats, utils Suggests: RUnit, BiocGenerics, BiocStyle License: Artistic-2.0 Package: fCI Version: 1.16.0 Depends: R (>= 3.1),FNN, psych, gtools, zoo, rgl, grid, VennDiagram Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) Package: fcoex Version: 1.0.0 Depends: R (>= 3.6) Imports: FCBF, parallel, progress, dplyr, ggplot2, ggrepel, igraph, grid, intergraph, stringr, clusterProfiler, data.table, grDevices, methods, network, scales, sna, utils, stats, SingleCellExperiment, pathwayPCA Suggests: testthat (>= 2.1.0), devtools, BiocManager, TENxPBMCData, scater, gridExtra, scran, Seurat, knitr License: GPL-3 Package: fcScan Version: 1.0.0 Imports: stats, plyr, VariantAnnotation, SummarizedExperiment, rtracklayer, GenomicRanges, methods, IRanges Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: fdrame Version: 1.58.0 Imports: tcltk, graphics, grDevices, stats, utils License: GPL (>= 2) Archs: i386, x64 Package: FELLA Version: 1.6.0 Depends: R (>= 3.5.0) Imports: methods, igraph, Matrix, KEGGREST, plyr, stats, graphics, utils Suggests: shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim License: GPL-3 Package: FEM Version: 3.14.0 Depends: AnnotationDbi,Matrix,marray,corrplot,igraph,impute,limma,org.Hs.eg.db,graph,BiocGenerics Imports: graph License: GPL (>= 2) Package: ffpe Version: 1.30.0 Depends: R (>= 2.10.0), TTR, methods Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc Suggests: genefilter, ffpeExampleData License: GPL (> 2) Package: FGNet Version: 3.20.0 Depends: R (>= 2.15) Imports: igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2, RColorBrewer, png Suggests: RCurl, RDAVIDWebService, gage, topGO, GO.db, KEGG.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, RGtk2, BiocManager License: GPL (>= 2) Package: fgsea Version: 1.12.0 Depends: R (>= 3.3), Rcpp Imports: 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 Archs: i386, x64 Package: FindMyFriends Version: 1.16.0 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) Archs: i386, x64 Package: FISHalyseR Version: 1.20.0 Depends: EBImage,abind Suggests: knitr License: Artistic-2.0 Package: fishpond Version: 1.2.0 Imports: graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, SummarizedExperiment, matrixStats, svMisc, Rcpp LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm License: GPL-2 Archs: i386, x64 Package: FitHiC Version: 1.12.0 Imports: data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: GPL (>= 2) Archs: i386, x64 Package: flagme Version: 1.42.0 Depends: gcspikelite, xcms, CAMERA Imports: gplots, graphics, MASS, methods, SparseM, stats, utils License: LGPL (>= 2) Archs: i386, x64 Package: flipflop Version: 1.24.0 Depends: R (>= 2.10.0) Imports: methods, Matrix, IRanges, GenomicRanges, parallel Suggests: GenomicFeatures License: GPL-3 Archs: i386, x64 Package: flowAI Version: 1.16.0 Depends: R (>= 3.4) Imports: ggplot2, flowCore, plyr, changepoint, knitr, reshape2, RColorBrewer, scales, methods, graphics, stats, utils, rmarkdown Suggests: testthat, shiny License: GPL (>= 2) Package: flowBeads Version: 1.24.0 Depends: R (>= 2.15.0), methods, Biobase, rrcov, flowCore Imports: flowCore, rrcov, knitr, xtable Suggests: flowViz License: Artistic-2.0 Package: flowBin Version: 1.22.0 Depends: methods, flowCore, flowFP, R (>= 2.10) Imports: class, limma, snow, BiocGenerics Suggests: parallel License: Artistic-2.0 Package: flowcatchR Version: 1.20.0 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 Package: flowCHIC Version: 1.20.0 Depends: R (>= 3.1.0) Imports: methods, flowCore, EBImage, vegan, hexbin, ggplot2, grid License: GPL-2 Package: flowCL Version: 1.24.0 Depends: R (>= 3.4), Rgraphviz, SPARQL Imports: methods, grDevices, utils, graph Suggests: RUnit, BiocGenerics License: Artistic-2.0 Package: flowClean Version: 1.24.0 Depends: R (>= 2.15.0), flowCore Imports: bit, changepoint, sfsmisc Suggests: flowViz, grid, gridExtra License: Artistic-2.0 Package: flowClust Version: 3.24.0 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 Archs: i386, x64 Package: flowCore Version: 1.52.1 Depends: R (>= 3.5.0) Imports: Biobase, BiocGenerics (>= 0.29.2), grDevices, graphics, methods, stats, utils, stats4, Rcpp, matrixStats LinkingTo: Rcpp, BH(>= 1.65.0.1), cytolib(>= 1.7.2) Suggests: Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat, flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto, gridExtra License: Artistic-2.0 Archs: i386, x64 Package: flowCyBar Version: 1.22.0 Depends: R (>= 3.0.0) Imports: gplots, vegan, methods License: GPL-2 Package: flowDensity Version: 1.20.0 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 Package: flowFit Version: 1.24.0 Depends: R (>= 2.12.2) Imports: flowCore, flowViz, graphics, kza, methods, minpack.lm, gplots Suggests: flowFitExampleData License: Artistic-2.0 Package: flowFP Version: 1.44.0 Depends: R (>= 2.10), flowCore, flowViz Imports: Biobase, BiocGenerics (>= 0.1.6), graphics, grDevices, methods, stats, stats4 Suggests: RUnit License: Artistic-2.0 Archs: i386, x64 Package: flowMap Version: 1.24.0 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) Package: flowMatch Version: 1.22.0 Depends: R (>= 3.0.0), Rcpp (>= 0.11.0), methods, flowCore Imports: Biobase LinkingTo: Rcpp Suggests: healthyFlowData License: Artistic-2.0 Archs: i386, x64 Package: flowMeans Version: 1.46.0 Depends: R (>= 2.10.0) Imports: Biobase, graphics, grDevices, methods, rrcov, stats, feature, flowCore License: Artistic-2.0 Package: flowMerge Version: 2.34.0 Depends: graph,feature,flowClust,Rgraphviz,foreach,snow Imports: rrcov,flowCore, graphics, methods, stats, utils Suggests: knitr, rmarkdown Enhances: doMC, multicore License: Artistic-2.0 Package: flowPeaks Version: 1.32.0 Depends: R (>= 2.12.0) Enhances: flowCore License: Artistic-1.0 Archs: i386, x64 Package: flowPloidy Version: 1.12.0 Imports: flowCore, car, caTools, knitr, rmarkdown, minpack.lm, shiny, methods, graphics, stats, utils Suggests: flowPloidyData, testthat License: GPL-3 Package: flowPlots Version: 1.34.0 Depends: R (>= 2.13.0), methods Suggests: vcd License: Artistic-2.0 Package: FlowRepositoryR Version: 1.18.0 Depends: R (>= 3.2) Imports: XML, RCurl, 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LinkingTo: Rcpp Suggests: BiocGenerics, knitr, RColorBrewer, rmarkdown, testthat, BiocStyle License: GPL-3 Archs: i386, x64 Package: flowStats Version: 3.44.0 Imports: BiocGenerics, MASS, flowCore (>= 1.51.6), 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 Package: flowTime Version: 1.10.0 Depends: R (>= 3.4), flowCore, plyr Imports: utils Suggests: knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, moments, stats License: Artistic-2.0 Package: flowTrans Version: 1.38.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 Package: flowType Version: 2.24.0 Depends: R (>= 2.10), Rcpp (>= 0.10.4), BH (>= 1.51.0-3) Imports: Biobase, graphics, grDevices, methods, flowCore, flowMeans, sfsmisc, rrcov, flowClust, flowMerge, stats LinkingTo: Rcpp, BH Suggests: xtable License: Artistic-2.0 Archs: i386, x64 Package: flowUtils Version: 1.50.0 Depends: R (>= 2.2.0) Imports: Biobase, graph, methods, stats, utils, corpcor, RUnit, XML, flowCore (>= 1.32.0) Suggests: gatingMLData License: Artistic-2.0 Package: flowViz Version: 1.50.0 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 Package: flowVS Version: 1.18.0 Depends: R (>= 3.2), methods, flowCore, flowViz, flowStats Suggests: knitr, vsn, License: Artistic-2.0 Package: flowWorkspace Version: 3.34.1 Imports: Biobase, BiocGenerics, graph, graphics, grDevices, lattice, methods, stats, stats4, utils, RBGL, tools, gridExtra, Rgraphviz, data.table, dplyr, latticeExtra, Rcpp, RColorBrewer, stringr, scales, flowViz, matrixStats, digest, RcppParallel, flowCore(>= 1.51.4), ncdfFlow(>= 2.31.1) LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.7.1), cytolib(>= 1.7.4), RcppParallel Suggests: testthat, flowWorkspaceData, knitr, ggcyto, parallel, CytoML, openCyto License: Artistic-2.0 Archs: i386, x64 Package: fmcsR Version: 1.28.0 Depends: R (>= 2.10.0), ChemmineR, methods Imports: RUnit, methods, ChemmineR, BiocGenerics, parallel Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap License: Artistic-2.0 Archs: i386, x64 Package: focalCall Version: 1.20.0 Depends: R(>= 2.10.0), CGHcall Suggests: RUnit, BiocGenerics License: GPL-2 Package: FoldGO Version: 1.4.0 Depends: R (>= 3.5) Imports: topGO (>= 2.30.1), ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), stats, methods Suggests: knitr, rmarkdown, devtools, kableExtra License: GPL-3 Package: FourCSeq Version: 1.20.0 Depends: R (>= 3.0), GenomicRanges, ggplot2, DESeq2 (>= 1.9.11), splines, methods, LSD Imports: DESeq2, Biobase, Biostrings, GenomicRanges, SummarizedExperiment, Rsamtools, ggbio, reshape2, rtracklayer, fda, GenomicAlignments, gtools, Matrix Suggests: BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene License: GPL (>= 3) Package: FRGEpistasis Version: 1.22.0 Depends: R (>= 2.15), MASS, fda, methods, stats Imports: utils License: GPL-2 Package: frma Version: 1.38.0 Depends: R (>= 2.10.0), Biobase (>= 2.6.0) Imports: Biobase, MASS, DBI, affy, methods, oligo, oligoClasses, preprocessCore, utils, BiocGenerics Suggests: hgu133afrmavecs, frmaExampleData License: GPL (>= 2) Package: frmaTools Version: 1.38.0 Depends: R (>= 2.10.0), affy Imports: Biobase, DBI, methods, preprocessCore, stats, utils Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData License: GPL (>= 2) Package: FunChIP Version: 1.12.0 Depends: R (>= 3.2), GenomicRanges Imports: shiny, fda, doParallel, GenomicAlignments, Rcpp, methods, foreach, parallel, GenomeInfoDb, Rsamtools, grDevices, graphics, stats, RColorBrewer LinkingTo: Rcpp License: Artistic-2.0 Archs: i386, x64 Package: FunciSNP Version: 1.30.0 Depends: R (>= 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene, FunciSNP.data Imports: methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools (>= 1.6.1), rtracklayer (>= 1.14.1), ChIPpeakAnno (>= 2.2.0), VariantAnnotation, plyr, snpStats, ggplot2 (>= 0.9.0), reshape (>= 0.8.4), scales Suggests: org.Hs.eg.db Enhances: parallel License: GPL-3 Package: funtooNorm Version: 1.10.0 Depends: R(>= 3.4) Imports: pls, matrixStats, minfi, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb, grDevices, graphics, stats Suggests: prettydoc, minfiData, knitr, rmarkdown License: GPL-3 Package: GA4GHclient Version: 1.10.0 Depends: S4Vectors Imports: BiocGenerics, Biostrings, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, methods, VariantAnnotation Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) Package: GA4GHshiny Version: 1.8.0 Depends: GA4GHclient Imports: AnnotationDbi, BiocGenerics, dplyr, DT, GenomeInfoDb, openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny, shinyjs, tidyr, shinythemes Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 Package: gaga Version: 2.32.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: parallel License: GPL (>= 2) Archs: i386, x64 Package: gage Version: 2.36.0 Depends: R (>= 2.10) Imports: graph, KEGGREST, AnnotationDbi Suggests: pathview, gageData, GO.db, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq, DESeq2, edgeR, limma License: GPL (>= 2.0) Package: gaggle Version: 1.54.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>= 0.4.17) License: GPL (>= 2) Package: gaia Version: 2.30.0 Depends: R (>= 2.10) License: GPL-2 Package: GAPGOM Version: 1.2.0 Depends: R (>= 3.6.0) Imports: stats, utils, methods, Matrix, fastmatch, plyr, dplyr, magrittr, data.table, igraph, graph, RBGL, GO.db, org.Hs.eg.db, org.Mm.eg.db, GOSemSim, GEOquery, AnnotationDbi, Biobase, BiocFileCache, matrixStats Suggests: org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Dr.eg.db, org.Ce.eg.db, org.At.tair.db, org.EcK12.eg.db, org.Bt.eg.db, org.Cf.eg.db, org.Ag.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Pt.eg.db, org.Pf.plasmo.db, org.Mmu.eg.db, org.Ss.eg.db, org.Xl.eg.db, testthat, pryr, knitr, rmarkdown, prettydoc, ggplot2, kableExtra, profvis, reshape2 License: MIT + file LICENSE Package: GAprediction Version: 1.12.0 Depends: R (>= 3.3) Imports: glmnet, stats, utils, Matrix Suggests: knitr, rmarkdown License: GPL (>= 2) Package: garfield Version: 1.14.0 Suggests: knitr License: GPL-3 Archs: i386, x64 Package: GARS Version: 1.6.0 Depends: R (>= 3.5), ggplot2, cluster Imports: DaMiRseq, MLSeq, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) Package: GateFinder Version: 1.6.0 Imports: splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP Suggests: RUnit, BiocGenerics License: Artistic-2.0 Package: gcapc Version: 1.10.0 Depends: R (>= 3.4) Imports: BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings, BSgenome, GenomicRanges, Rsamtools, GenomicAlignments, matrixStats, MASS, splines, grDevices, graphics, stats, methods Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: GPL-3 Package: gcatest Version: 1.16.0 Depends: R (>= 3.2) Imports: lfa Suggests: knitr, ggplot2 License: GPL-3 Archs: i386, x64 Package: gCrisprTools Version: 1.14.0 Depends: R (>= 3.3) Imports: Biobase, limma, RobustRankAggreg, ggplot2, PANTHER.db, rmarkdown, grDevices, graphics, stats, utils, parallel Suggests: edgeR, knitr, grid, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, RUnit, BiocGenerics License: Artistic-2.0 Package: gcrma Version: 2.58.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector, Biostrings (>= 2.11.32), splines, BiocManager Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL Archs: i386, x64 Package: GCSscore Version: 1.0.0 Depends: R (>= 3.6) Imports: BiocManager, Biobase, utils, methods, RSQLite, AnnotationForge, devtools, dplR, stringr, graphics, stats, affxparser, data.table License: GPL (>= 3) Package: GDCRNATools Version: 1.6.0 Depends: R (>= 3.5.0) Imports: shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel Suggests: knitr, testthat License: Artistic-2.0 Package: GDSArray Version: 1.6.0 Depends: R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>= 0.5.32) Imports: tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray Suggests: testthat, knitr, BiocStyle, BiocManager License: GPL-3 Package: gdsfmt Version: 1.22.0 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, crayon, RUnit, knitr, BiocGenerics License: LGPL-3 Archs: i386, x64 Package: geecc Version: 1.20.0 Depends: R (>= 3.3.0), methods Imports: MASS, hypergea (>= 1.3.0), gplots, Rcpp (>= 0.11.3), graphics, stats, utils LinkingTo: Rcpp Suggests: hgu133plus2.db, GO.db, AnnotationDbi License: GPL (>= 2) Archs: i386, x64 Package: GEM Version: 1.12.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics License: Artistic-2.0 Package: gemini Version: 1.0.0 Depends: R (>= 3.6.0) Imports: dplyr, grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE Package: genArise Version: 1.62.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes Package: genbankr Version: 1.14.0 Depends: methods Imports: BiocGenerics, IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), GenomicFeatures (>= 1.31.5), Biostrings, VariantAnnotation, rtracklayer, S4Vectors (>= 0.17.28), GenomeInfoDb, Biobase Suggests: RUnit, rentrez, knitr, rmarkdown, BiocStyle License: Artistic-2.0 Package: GeneAccord Version: 1.4.0 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 Package: GeneAnswers Version: 2.28.0 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) Package: geneAttribution Version: 1.12.0 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 Package: GeneBreak Version: 1.16.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 Package: geneClassifiers Version: 1.10.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 Package: GeneExpressionSignature Version: 1.32.0 Depends: R (>= 2.13), Biobase, PGSEA Suggests: apcluster,GEOquery License: GPL-2 Package: genefilter Version: 1.68.0 Imports: BiocGenerics (>= 0.31.2), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 Archs: i386, x64 Package: genefu Version: 2.18.1 Depends: survcomp, mclust, limma, biomaRt, iC10, AIMS, R (>= 2.10) Imports: amap, impute Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival License: Artistic-2.0 Package: GeneGeneInteR Version: 1.12.0 Depends: R (>= 3.5) Imports: snpStats, mvtnorm, GGtools, Rsamtools, igraph, kernlab, FactoMineR, plspm, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods License: GPL (>= 2) Archs: i386, x64 Package: GeneMeta Version: 1.58.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 Package: GeneNetworkBuilder Version: 1.28.1 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) Archs: i386, x64 Package: GeneOverlap Version: 1.22.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 Package: geneplast Version: 1.12.2 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) Package: geneplotter Version: 1.64.0 Depends: R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate Imports: AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db License: Artistic-2.0 Package: geneRecommender Version: 1.58.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) Package: GeneRegionScan Version: 1.42.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) Package: geneRxCluster Version: 1.22.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) Archs: i386, x64 Package: GeneSelectMMD Version: 2.30.0 Depends: R (>= 2.13.2), Biobase Imports: Biobase, MASS, graphics, stats, survival, limma Suggests: ALL License: GPL (>= 2) Archs: i386, x64 Package: GENESIS Version: 2.16.1 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 Archs: i386, x64 Package: GeneStructureTools Version: 1.6.0 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 Package: geNetClassifier Version: 1.26.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) Package: GeneticsDesign Version: 1.54.0 Imports: gmodels, graphics, gtools (>= 2.4.0), mvtnorm, stats License: GPL-2 Package: GeneticsPed Version: 1.48.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE Archs: i386, x64 Package: geneXtendeR Version: 1.12.0 Depends: rtracklayer, GO.db, R (>= 3.5.0) Imports: data.table, dplyr, graphics, networkD3, RColorBrewer, SnowballC, tm, utils, wordcloud, AnnotationDbi, BiocStyle, org.Rn.eg.db Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer License: GPL (>= 3) Archs: i386, x64 Package: GENIE3 Version: 1.8.0 Imports: stats, reshape2 Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods License: GPL (>= 2) Archs: i386, x64 Package: genoCN Version: 1.38.0 Imports: graphics, stats, utils License: GPL (>= 2) Archs: i386, x64 Package: GenoGAM Version: 2.4.0 Depends: R (>= 3.5), SummarizedExperiment (>= 1.1.19), HDF5Array (>= 1.8.0), rhdf5 (>= 2.21.6), S4Vectors (>= 0.23.18), Matrix (>= 1.2-8), data.table (>= 1.9.4) Imports: Rcpp (>= 0.12.14), sparseinv (>= 0.1.1), Rsamtools (>= 1.18.2), GenomicRanges (>= 1.23.16), BiocParallel (>= 1.5.17), DESeq2 (>= 1.11.23), futile.logger (>= 1.4.1), GenomeInfoDb (>= 1.7.6), GenomicAlignments (>= 1.7.17), IRanges (>= 2.5.30), Biostrings (>= 2.39.14), DelayedArray (>= 0.3.19), methods, stats LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, chipseq (>= 1.21.2), LSD (>= 3.0.0), genefilter (>= 1.54.2), ggplot2 (>= 2.1.0), testthat, knitr, rmarkdown License: GPL-2 Archs: i386, x64 Package: genomation Version: 1.18.0 Depends: R (>= 3.0.0),grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), RUnit, Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown License: Artistic-2.0 Archs: i386, x64 Package: GenomeGraphs Version: 1.46.0 Depends: R (>= 2.10), methods, biomaRt, grid License: Artistic-2.0 Package: GenomeInfoDb Version: 1.22.1 Depends: R (>= 3.1), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12) Imports: stats, stats4, utils, RCurl, GenomeInfoDbData Suggests: GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr License: Artistic-2.0 Package: genomeIntervals Version: 1.42.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 1.5.8), GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 Package: genomes Version: 3.16.0 Depends: readr, curl License: GPL-3 Package: GenomicAlignments Version: 1.22.1 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.23.19), IRanges (>= 2.15.12), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.37.2), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle License: Artistic-2.0 Archs: i386, x64 Package: GenomicDataCommons Version: 1.10.0 Depends: R (>= 3.4.0), magrittr Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, SummarizedExperiment, S4Vectors, tibble Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools License: Artistic-2.0 Package: GenomicFeatures Version: 1.38.2 Depends: BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29), IRanges (>= 2.13.23), GenomeInfoDb (>= 1.15.4), GenomicRanges (>= 1.31.17), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl, XVector (>= 0.19.7), Biostrings (>= 2.47.6), rtracklayer (>= 1.39.7), biomaRt (>= 2.17.1), Biobase (>= 2.15.1) Suggests: RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, RUnit, BiocStyle, knitr License: Artistic-2.0 Package: GenomicFiles Version: 1.22.0 Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), GenomicRanges (>= 1.31.16), SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>= 1.17.29), rtracklayer (>= 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methods, stats4, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.23.19), IRanges (>= 2.19.9), GenomeInfoDb (>= 1.15.2) Imports: utils, stats, XVector (>= 0.19.8) LinkingTo: S4Vectors, IRanges Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, BiocStyle License: Artistic-2.0 Archs: i386, x64 Package: GenomicScores Version: 1.10.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: utils, XML, Biobase, IRanges (>= 2.3.23), Biostrings, BSgenome, GenomeInfoDb, AnnotationHub Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5, SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer License: Artistic-2.0 Package: GenomicTuples Version: 1.20.0 Depends: R (>= 3.3.0), GenomicRanges (>= 1.37.4), GenomeInfoDb (>= 1.15.2), S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4 LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 Archs: i386, x64 Package: Genominator Version: 1.40.0 Depends: R (>= 2.10), methods, RSQLite, DBI (>= 0.2-5), BiocGenerics (>= 0.1.0), IRanges (>= 2.5.27), GenomeGraphs Imports: graphics, stats, utils Suggests: biomaRt, ShortRead, yeastRNASeq License: Artistic-2.0 Package: genoset Version: 1.42.0 Depends: R (>= 2.10), BiocGenerics (>= 0.11.3), GenomicRanges (>= 1.17.19), SummarizedExperiment (>= 1.1.6) Imports: S4Vectors (>= 0.23.18), GenomeInfoDb (>= 1.1.3), IRanges (>= 2.5.12), methods, graphics Suggests: testthat, knitr, BiocStyle, rmarkdown, DNAcopy, stats, BSgenome, Biostrings Enhances: parallel License: Artistic-2.0 Archs: i386, x64 Package: genotypeeval Version: 1.18.0 Depends: R (>= 3.4.0), VariantAnnotation Imports: ggplot2, rtracklayer, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, methods, BiocParallel, graphics, stats Suggests: rmarkdown, testthat, SNPlocs.Hsapiens.dbSNP141.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE Package: genphen Version: 1.14.0 Depends: R (>= 3.5.0), Rcpp (>= 0.12.17), methods, stats, graphics Imports: rstan (>= 2.17.3), ranger, parallel, foreach, doParallel, e1071, Biostrings, rPref Suggests: testthat, ggplot2, gridExtra, ape, ggrepel, knitr, reshape, xtable License: GPL (>= 2) Package: GenRank Version: 1.14.0 Depends: R (>= 3.2.3) Imports: matrixStats, reshape2, survcomp Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 Package: GenVisR Version: 1.18.1 Depends: R (>= 3.3.0), methods Imports: AnnotationDbi, biomaRt, BiocGenerics, Biostrings, DBI, FField, GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), grid, gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, stats, utils, viridis, data.table, BSgenome, grDevices, GenomeInfoDb, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 + file LICENSE Package: GEOquery Version: 2.54.1 Depends: methods, Biobase Imports: httr, readr (>= 1.3.1), xml2, dplyr, tidyr, magrittr, limma Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr License: GPL-2 Package: GEOsubmission Version: 1.38.0 Imports: affy, Biobase, utils License: GPL (>= 2) Package: gep2pep Version: 1.6.0 Imports: repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators Suggests: WriteXLS, testthat, knitr, rmarkdown License: GPL-3 Package: gespeR Version: 1.18.0 Depends: methods, graphics, ggplot2, R(>= 2.10) Imports: Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel, parallel, foreach, reshape2, dplyr Suggests: knitr License: GPL-3 Package: GEWIST Version: 1.30.0 Depends: R (>= 2.10), car License: GPL-2 Package: GGBase Version: 3.48.0 Depends: R (>= 2.14), methods, snpStats Imports: limma, genefilter, Biobase, BiocGenerics, S4Vectors, IRanges, Matrix, AnnotationDbi, digest, GenomicRanges, SummarizedExperiment Suggests: GGtools, illuminaHumanv1.db, knitr License: Artistic-2.0 Package: ggbio Version: 1.34.0 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.29.14), SummarizedExperiment, Biostrings, Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer (>= 1.25.16), GenomicFeatures (>= 1.29.11), OrganismDbi, GGally, ensembldb (>= 1.99.13), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 Package: ggcyto Version: 1.14.1 Depends: methods, ggplot2(>= 3.3.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 3.33.1) Imports: plyr, scales, data.table, RColorBrewer, gridExtra, rlang Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr License: Artistic-2.0 Package: GGtools Version: 5.22.0 Depends: R (>= 2.14), GGBase (>= 3.19.7), data.table, parallel, Homo.sapiens Imports: methods, utils, stats, BiocGenerics (>= 0.25.1), snpStats, ff, Rsamtools, AnnotationDbi, Biobase, bit, VariantAnnotation, hexbin, rtracklayer, Gviz, stats4, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges (>= 1.29.6), iterators, Biostrings, ROCR, biglm, ggplot2, reshape2 Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37, multtest, aod, rmeta Enhances: MatrixEQTL, foreach, doParallel, gwascat License: Artistic-2.0 Package: ggtree Version: 2.0.4 Depends: R (>= 3.4.0) Imports: ape, dplyr, ggplot2 (>= 3.0.0), grid, magrittr, methods, purrr, rlang, rvcheck, tidyr, tidytree (>= 0.2.6), treeio (>= 1.8.0), utils Suggests: emojifont, ggimage, ggplotify, grDevices, knitr, prettydoc, rmarkdown, scales, stats, testthat, tibble License: Artistic-2.0 Package: GIGSEA Version: 1.4.0 Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils Suggests: knitr, rmarkdown License: LGPL-3 Package: girafe Version: 1.38.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), Rsamtools (>= 1.31.2), intervals (>= 0.13.1), ShortRead (>= 1.37.1), genomeIntervals (>= 1.25.1), grid Imports: methods, Biobase, Biostrings (>= 2.47.6), graphics, grDevices, stats, utils, IRanges (>= 2.13.12) Suggests: MASS, org.Mm.eg.db, RColorBrewer Enhances: genomeIntervals License: Artistic-2.0 Archs: i386, x64 Package: GISPA Version: 1.10.0 Depends: R (>= 3.3.2) Imports: Biobase, changepoint, data.table, genefilter, graphics, GSEABase, HH, lattice, latticeExtra, plyr, scatterplot3d, stats Suggests: knitr License: GPL-2 Package: GLAD Version: 2.50.0 Depends: R (>= 2.10) Imports: aws License: GPL-2 Archs: i386, x64 Package: GladiaTOX Version: 1.2.0 Depends: R (>= 3.6.0), data.table (>= 1.9.4) Imports: DBI, RMySQL, RSQLite, numDeriv, RColorBrewer, parallel, stats, methods, graphics, grDevices, xtable, tools, brew, stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle License: GPL-2 Package: Glimma Version: 1.14.0 Depends: R (>= 3.4.0) Imports: edgeR, grDevices, jsonlite, methods, stats, S4Vectors, utils Suggests: BiocStyle, IRanges, GenomicRanges, SummarizedExperiment, DESeq2, limma, testthat, knitr, rmarkdown, pryr License: GPL-3 | file LICENSE Package: glmSparseNet Version: 1.4.0 Depends: R (>= 3.5), Matrix, MultiAssayExperiment, glmnet Imports: SummarizedExperiment, STRINGdb, biomaRt, futile.logger, sparsebn, sparsebnUtils, forcats, dplyr, readr, ggplot2, survminer, reshape2, stats, stringr, rlang, parallel, methods, loose.rock (>= 1.0.12) Suggests: testthat, knitr, rmarkdown, survival, survcomp, pROC, VennDiagram, BiocStyle, curatedTCGAData, TCGAutils License: GPL (>= 3) Package: GlobalAncova Version: 4.4.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, KEGG.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) Archs: i386, x64 Package: globalSeq Version: 1.14.0 Depends: R (>= 3.5.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 Package: globaltest Version: 5.40.0 Depends: methods, survival Imports: Biobase, AnnotationDbi, annotate, graphics Suggests: vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart, mstate License: GPL (>= 2) Package: GmicR Version: 1.0.6 Imports: AnnotationDbi, ape, bnlearn, Category, DT, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db, org.Mm.eg.db, reshape2, shiny, WGCNA, data.table, grDevices, graphics, stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 + file LICENSE Package: GMRP Version: 1.14.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) Package: GNET2 Version: 1.2.0 Depends: R (>= 3.6) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 Archs: i386, x64 Package: GOexpress Version: 1.20.0 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), randomForest (>= 4.6), RCurl (>= 1.95) Suggests: BiocStyle License: GPL (>= 3) Package: GOfuncR Version: 1.6.1 Depends: R (>= 3.4), vioplot (>= 0.2), Imports: Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils, grDevices, graphics, stats, LinkingTo: Rcpp Suggests: Homo.sapiens, BiocStyle, knitr, testthat License: GPL (>= 2) Archs: i386, x64 Package: GOFunction Version: 1.34.0 Depends: R (>= 2.11.0), methods, Biobase (>= 2.8.0), graph (>= 1.26.0), Rgraphviz (>= 1.26.0), GO.db (>= 2.4.1), AnnotationDbi (>= 1.10.2), SparseM (>= 0.85) Imports: methods, Biobase, graph, Rgraphviz, GO.db, AnnotationDbi, DBI, SparseM License: GPL (>= 2) Package: GOpro Version: 1.12.0 Depends: R (>= 3.4) Imports: AnnotationDbi, dendextend, doParallel, foreach, parallel, org.Hs.eg.db, GO.db, Rcpp, stats, graphics, MultiAssayExperiment, IRanges, S4Vectors LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat License: GPL-3 Archs: i386, x64 Package: goProfiles Version: 1.48.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 Package: GOSemSim Version: 2.12.1 Depends: R (>= 3.4.0) Imports: AnnotationDbi, GO.db, methods, utils LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, testthat License: Artistic-2.0 Archs: i386, x64 Package: goseq Version: 1.38.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2) Imports: mgcv, graphics, stats, utils, AnnotationDbi, GO.db,BiocGenerics Suggests: edgeR, org.Hs.eg.db, rtracklayer License: LGPL (>= 2) Package: GOSim Version: 1.24.0 Depends: GO.db, annotate Imports: org.Hs.eg.db, AnnotationDbi, topGO, cluster, flexmix, RBGL, graph, Matrix, corpcor, Rcpp LinkingTo: Rcpp Enhances: igraph License: GPL (>= 2) Archs: i386, x64 Package: goSTAG Version: 1.10.0 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 Package: GOstats Version: 2.52.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.43.2), graph Imports: methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics License: Artistic-2.0 Package: GOsummaries Version: 2.22.0 Depends: R (>= 2.15), Rcpp Imports: plyr, grid, gProfileR, reshape2, limma, ggplot2, gtable LinkingTo: Rcpp Suggests: vegan License: GPL (>= 2) Archs: i386, x64 Package: GOTHiC Version: 1.22.0 Depends: R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome, data.table Imports: BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils, stats, GenomeInfoDb Suggests: HiCDataLymphoblast Enhances: parallel License: GPL-3 Package: goTools Version: 1.60.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 Package: gpart Version: 1.4.0 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: MIT + file LICENSE Archs: i386, x64 Package: gpls Version: 1.58.0 Imports: stats Suggests: MASS License: Artistic-2.0 Package: gprege Version: 1.30.0 Depends: R (>= 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License: Artistic-2.0 Package: gramm4R Version: 1.0.0 Depends: R (>= 3.6.0) Imports: basicTrendline,investr,minerva,psych,grDevices, graphics, stats,DelayedArray,SummarizedExperiment,DMwR,phyloseq Suggests: knitr, rmarkdown License: GPL-2 Package: graper Version: 1.2.0 Depends: R (>= 3.6) Imports: Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) Archs: i386, x64 Package: graph Version: 1.64.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.11) Imports: stats, stats4, utils Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster Enhances: Rgraphviz License: Artistic-2.0 Archs: i386, x64 Package: GraphAlignment Version: 1.50.0 License: file LICENSE License_restricts_use: yes Archs: i386, x64 Package: GraphAT Version: 1.58.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL Package: graphite Version: 1.32.0 Depends: R (>= 2.10), methods Imports: AnnotationDbi, checkmate, graph, httr, rappdirs, stats, utils Suggests: a4Preproc, ALL, BiocStyle, clipper, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) License: AGPL-3 Package: GraphPAC Version: 1.28.0 Depends: R(>= 2.15),iPAC, igraph, TSP, RMallow Suggests: RUnit, BiocGenerics License: GPL-2 Package: GRENITS Version: 1.38.0 Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) Imports: graphics, grDevices, reshape2, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: network License: GPL (>= 2) Archs: i386, x64 Package: GreyListChIP Version: 1.18.0 Depends: R (>= 3.5), methods, GenomicRanges Imports: GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, RUnit Enhances: BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 Package: GRmetrics Version: 1.12.2 Depends: R (>= 3.6), SummarizedExperiment Imports: drc, plotly, ggplot2, S4Vectors, stats Suggests: knitr, rmarkdown, BiocStyle, tinytex License: GPL-3 Package: groHMM Version: 1.20.0 Depends: R (>= 3.0.2), MASS, parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), rtracklayer (>= 1.39.7) Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 Archs: i386, x64 Package: GRridge Version: 1.10.0 Depends: R (>= 3.2), penalized, Iso, survival, methods, graph,stats,glmnet,mvtnorm Suggests: testthat License: GPL-3 Package: GSALightning Version: 1.14.0 Depends: R (>= 3.3.0) Imports: Matrix, data.table, stats Suggests: knitr, rmarkdown License: GPL (>= 2) Package: GSAR Version: 1.20.0 Depends: R (>= 3.0.1), igraph (>= 0.7.1) Imports: stats, graphics Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle License: GPL (>= 2) Package: GSCA Version: 2.16.0 Depends: shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5, R(>= 2.10.0) Imports: graphics Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr License: GPL (>= 2) Package: gscreend Version: 1.0.0 Depends: R (>= 3.6) Imports: SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics Suggests: knitr, testthat License: GPL-3 Package: GSEABase Version: 1.48.0 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 Package: GSEABenchmarkeR Version: 1.6.4 Depends: Biobase, SummarizedExperiment Imports: AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, rappdirs, S4Vectors, stats, utils Suggests: BiocStyle, GEOquery, knitr, rmarkdown License: Artistic-2.0 Package: GSEAlm Version: 1.46.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 Package: gsean Version: 1.6.0 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, knitr, plotly, RANKS, WGCNA License: Artistic-2.0 Package: GSReg Version: 1.20.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi Suggests: GenomicRanges, GSBenchMark License: GPL-2 Archs: i386, x64 Package: GSRI Version: 2.34.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 Package: GSVA Version: 1.34.0 Depends: R (>= 3.5.0) Imports: methods, BiocGenerics, Biobase, GSEABase (>= 1.17.4), geneplotter, shiny, shinythemes Suggests: limma, RColorBrewer, genefilter, edgeR, snow, parallel, GSVAdata License: GPL (>= 2) Archs: i386, x64 Package: gtrellis Version: 1.18.0 Depends: R (>= 3.1.2), grid, IRanges, GenomicRanges Imports: circlize (>= 0.3.3), GetoptLong, grDevices, utils Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff License: MIT + file LICENSE Package: GUIDEseq Version: 1.16.0 Depends: R (>= 3.2.0), GenomicRanges, BiocGenerics Imports: BiocParallel, Biostrings, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL (>= 2) Package: Guitar Version: 2.2.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges, magrittr, ggplot2, methods, stats,utils 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VariantAnnotation, AnnotationHub, gQTLstats, graph, ggbio, ggplot2, DelayedArray Enhances: SNPlocs.Hsapiens.dbSNP144.GRCh37 License: Artistic-2.0 Package: GWASTools Version: 1.32.0 Depends: Biobase Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation License: Artistic-2.0 Package: gwasurvivr Version: 1.4.0 Depends: R (>= 3.4.0) Imports: GWASTools, survival, VariantAnnotation, parallel, matrixStats, SummarizedExperiment, stats, utils, SNPRelate Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: h5vc Version: 2.20.0 Depends: grid, gridExtra, ggplot2 Imports: rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>= 1.99.1), methods, GenomicRanges, abind, BiocParallel, BatchJobs, h5vcData, GenomeInfoDb LinkingTo: Rhtslib (>= 1.15.3) Suggests: knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics License: GPL (>= 3) Archs: i386, x64 Package: hapFabia Version: 1.28.0 Depends: R (>= 3.6.0), Biobase, fabia (>= 2.3.1) Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) Archs: i386, x64 Package: Harman Version: 1.14.0 Depends: R (>= 3.5) Imports: Rcpp (>= 0.11.2), graphics, stats LinkingTo: Rcpp Suggests: HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva License: GPL-3 + file LICENCE Archs: i386, x64 Package: Harshlight Version: 1.58.0 Depends: R (>= 2.10) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) Archs: i386, x64 Package: HCABrowser Version: 1.2.0 Depends: R (>= 3.6.0), dplyr Imports: BiocFileCache, S4Vectors, curl, googleAuthR, httr, jsonlite, methods, plyr, readr, rlang, stringr, tibble, tidygraph, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 Package: HCAExplorer Version: 1.0.0 Depends: R (>= 3.6.0), dplyr Imports: S4Vectors, vctrs, curl, httr, jsonlite, methods, plyr, rlang, tibble, tidygraph, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0) License: Artistic-2.0 Package: HDF5Array Version: 1.14.4 Depends: R (>= 3.4), methods, DelayedArray (>= 0.12.3), rhdf5 (>= 2.30.1) Imports: utils, tools, Matrix, BiocGenerics (>= 0.32.0), S4Vectors, IRanges LinkingTo: S4Vectors (>= 0.24.4), Rhdf5lib Suggests: h5vcData, SummarizedExperiment (>= 1.15.1), GenomicRanges, ExperimentHub, TENxBrainData, BiocParallel, GenomicFeatures, BiocStyle License: Artistic-2.0 Archs: i386, x64 Package: HDTD Version: 1.20.0 Depends: R (>= 3.6) Imports: stats, Rcpp (>= 1.0.1) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, markdown License: GPL-3 Archs: i386, x64 Package: heatmaps Version: 1.10.0 Depends: R (>= 3.4) Imports: methods, grDevices, graphics, stats, Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage, RColorBrewer, BiocGenerics, GenomeInfoDb Suggests: BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat License: Artistic-2.0 Package: Heatplus Version: 2.32.1 Imports: graphics, grDevices, stats, RColorBrewer Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) Package: HelloRanges Version: 1.12.0 Depends: methods, BiocGenerics, S4Vectors (>= 0.17.39), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.10), Biostrings (>= 2.41.3), BSgenome, GenomicFeatures (>= 1.31.5), VariantAnnotation (>= 1.19.3), Rsamtools, GenomicAlignments (>= 1.15.7), rtracklayer (>= 1.33.8), GenomeInfoDb, SummarizedExperiment Imports: docopt, stats, tools, utils Suggests: HelloRangesData, BiocStyle License: GPL (>= 2) Package: HELP Version: 1.44.0 Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods License: GPL (>= 2) Package: HEM Version: 1.58.0 Depends: R (>= 2.1.0) Imports: Biobase, grDevices, stats, utils License: GPL (>= 2) Archs: i386, x64 Package: 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pheatmap, gtools, rhdf5 Suggests: knitr, rmarkdown, testthat, multiHiCcompare License: MIT + file LICENSE Package: hicrep Version: 1.10.0 Depends: R (>= 3.4) Imports: stats Suggests: knitr, rmarkdown, testthat License: GPL (>= 2.0) Package: hierGWAS Version: 1.16.0 Depends: R (>= 3.2.0) Imports: fastcluster,glmnet, fmsb Suggests: BiocGenerics, RUnit, MASS License: GPL-3 Package: hierinf Version: 1.4.0 Depends: R (>= 3.6.0) Imports: fmsb, glmnet, methods, parallel, stats Suggests: knitr, MASS, testthat License: GPL-3 | file LICENSE Package: HilbertCurve Version: 1.16.0 Depends: R (>= 3.1.2), grid Imports: methods, utils, HilbertVis, png, grDevices, circlize (>= 0.3.3), IRanges, GenomicRanges, polylabelr Suggests: knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0), markdown, RColorBrewer, RCurl, GetoptLong License: MIT + file LICENSE Package: HilbertVis Version: 1.44.0 Depends: R (>= 2.6.0), grid, lattice Suggests: IRanges, EBImage License: GPL (>= 3) Archs: i386, x64 Package: 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RDAVIDWebService, gProfileR, topGO, KEGGprofile, org.Dm.eg.db, rmarkdown, testthat License: GPL-2 Package: inveRsion Version: 1.34.0 Depends: methods, haplo.stats Imports: graphics, methods, utils License: GPL (>= 2) Archs: i386, x64 Package: IONiseR Version: 2.10.0 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 Package: iPAC Version: 1.30.0 Depends: R(>= 2.15),gdata, scatterplot3d, Biostrings, multtest License: GPL-2 Package: ipdDb Version: 1.4.0 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 Package: IPO Version: 1.12.0 Depends: xcms (>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats, utils 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BiocStyle, knitr, rmarkdown, scRNAseq, scater, DelayedArray (>= 0.7.44), Rtsne, irlba, RColorBrewer, viridis, org.Mm.eg.db, htmltools License: MIT + file LICENSE Package: iSeq Version: 1.38.0 Depends: R (>= 2.10.0) License: GPL (>= 2) Archs: i386, x64 Package: isobar Version: 1.32.0 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 Package: IsoCorrectoR Version: 1.4.1 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 Package: IsoCorrectoRGUI Version: 1.2.0 Depends: R (>= 3.6) Imports: IsoCorrectoR, readxl, tcltk2, tcltk, utils Suggests: knitr, rmarkdown, testthat License: GPL-3 Package: IsoformSwitchAnalyzeR Version: 1.8.0 Depends: R (>= 3.5), limma, DEXSeq, ggplot2 Imports: methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>= 2.50.0), IRanges, GenomicRanges, DRIMSeq, RColorBrewer, rtracklayer, VennDiagram, DBI, grDevices, graphics, stats, utils, GenomeInfoDb, grid, tximport (>= 1.7.1), edgeR, futile.logger, stringr, dplyr, magrittr, readr, XVector Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, cummeRbund License: GPL (>= 2) Archs: i386, x64 Package: IsoGeneGUI Version: 2.22.0 Depends: tcltk, xlsx Imports: Rcpp, tkrplot, multtest, relimp, geneplotter, RColorBrewer, Iso, IsoGene, ORCME, ORIClust, orQA, goric, ff, Biobase, jpeg Suggests: RUnit License: GPL-2 Package: ISoLDE Version: 1.14.0 Depends: R (>= 3.3.0),graphics,grDevices,stats,utils License: GPL (>= 2.0) Archs: i386, x64 Package: isomiRs Version: 1.14.0 Depends: R (>= 3.5), DiscriMiner, SummarizedExperiment Imports: AnnotationDbi, assertive.sets, BiocGenerics, 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 Package: ITALICS Version: 2.46.0 Depends: R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser, pd.mapping50k.xba240 Imports: affxparser, DBI, GLAD, oligo, oligoClasses, stats Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp License: GPL-2 Package: iterativeBMA Version: 1.44.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) Package: iterativeBMAsurv Version: 1.44.0 Depends: BMA, leaps, survival, splines Imports: graphics, grDevices, stats, survival, utils License: GPL (>= 2) Package: iterClust Version: 1.8.0 Depends: R (>= 3.4.1) Imports: Biobase, cluster, stats, methods Suggests: tsne, bcellViper License: file LICENSE Package: iteremoval Version: 1.6.0 Depends: R (>= 3.5.0), ggplot2 (>= 2.2.1) Imports: magrittr, graphics, utils, GenomicRanges, SummarizedExperiment Suggests: testthat, knitr License: GPL-2 Package: IVAS Version: 2.6.0 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 Package: ivygapSE Version: 1.8.0 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 Package: IWTomics Version: 1.10.0 Depends: GenomicRanges Imports: parallel,gtable,grid,graphics,methods,IRanges,KernSmooth,fda,S4Vectors,grDevices,stats,utils,tools Suggests: knitr License: GPL (>= 2) Package: joda Version: 1.34.0 Depends: R (>= 2.0), bgmm, RBGL License: GPL (>= 2) Package: JunctionSeq Version: 1.16.0 Depends: R (>= 3.2.2), methods, SummarizedExperiment (>= 0.2.0), Rcpp (>= 0.11.0), RcppArmadillo (>= 0.3.4.4) Imports: DESeq2 (>= 1.10.0), statmod, Hmisc, plotrix, stringr, Biobase (>= 2.30.0), locfit, BiocGenerics (>= 0.7.5), BiocParallel, genefilter, geneplotter, S4Vectors, IRanges, GenomicRanges, LinkingTo: Rcpp, RcppArmadillo Suggests: MASS, knitr, JctSeqData, BiocStyle Enhances: Cairo, pryr License: file LICENSE Archs: i386, x64 Package: karyoploteR Version: 1.12.4 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 Package: KCsmart Version: 2.44.0 Depends: siggenes, multtest, KernSmooth Imports: methods, BiocGenerics Enhances: Biobase, CGHbase License: GPL-3 Package: kebabs Version: 1.20.0 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) Archs: i386, x64 Package: KEGGgraph Version: 1.46.0 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) Package: KEGGlincs Version: 1.12.0 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 Package: keggorthology Version: 2.38.0 Depends: R (>= 2.5.0),stats,graph,hgu95av2.db Imports: AnnotationDbi,graph,DBI, graph, grDevices, methods, stats, tools, utils Suggests: RBGL,ALL License: Artistic-2.0 Package: KEGGprofile Version: 1.28.0 Imports: AnnotationDbi,png,TeachingDemos,XML,KEGG.db,KEGGREST,biomaRt,RCurl,ggplot2,reshape2 License: GPL (>= 2) Package: KEGGREST Version: 1.26.1 Imports: methods, httr, png, Biostrings Suggests: RUnit, BiocGenerics, knitr License: Artistic-2.0 Package: kimod Version: 1.14.0 Depends: R(>= 3.3),methods Imports: cluster, graphics, Biobase License: GPL (>= 2) Package: KinSwingR Version: 1.4.0 Depends: R (>= 3.5) Imports: data.table, BiocParallel, sqldf, stats, grid, grDevices Suggests: knitr, rmarkdown License: GPL-3 Package: kissDE Version: 1.6.0 Imports: aod, Biobase, DESeq2, DSS, ggplot2, gplots, graphics, grDevices, matrixStats, stats, utils, foreach, doParallel, parallel Suggests: BiocStyle, testthat License: GPL (>= 2) 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gplots, grDevices, grid, knitr, Matrix, methods, RColorBrewer, SingleCellExperiment, splines, stats, SummarizedExperiment, utils License: Artistic-2.0 Package: LinkHD Version: 1.0.0 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 Package: Linnorm Version: 2.10.0 Depends: R(>= 3.4) Imports: Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan, mclust, apcluster, ggplot2, ellipse, limma, utils, statmod, MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo, stats, amap, Rtsne, gmodels LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, gplots, RColorBrewer, moments, testthat License: MIT + file LICENSE Archs: i386, x64 Package: lionessR Version: 1.0.0 Depends: R (>= 3.6.0) Imports: stats, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, igraph, reshape2, limma, License: MIT + file LICENSE Package: lipidr Version: 2.0.0 Depends: R (>= 3.6.0), SummarizedExperiment Imports: methods, stats, utils, data.table, S4Vectors, rlang, dplyr, tidyr, forcats, ggplot2, limma, fgsea, ropls, magrittr Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, iheatmapr, spelling, testthat License: MIT + file LICENSE Package: LiquidAssociation Version: 1.40.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>= 3) Package: lmdme Version: 1.28.0 Depends: R (>= 2.14.1), pls, stemHypoxia Imports: stats, methods, limma Enhances: parallel License: GPL (>= 2) Package: LMGene Version: 2.42.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5), multtest, survival, affy Suggests: affydata License: LGPL Package: LOBSTAHS Version: 1.12.0 Depends: R (>= 3.4), xcms, CAMERA, methods Imports: utils Suggests: PtH2O2lipids, knitr, rmarkdown License: GPL (>= 3) + file LICENSE Package: loci2path Version: 1.6.0 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file LICENSE Archs: i386, x64 Package: maser Version: 1.4.0 Depends: R (>= 3.5.0), ggplot2, GenomicRanges Imports: dplyr, rtracklayer, reshape2, Gviz, DT, GenomeInfoDb, stats, utils, IRanges, methods, BiocGenerics, parallel, data.table Suggests: testthat, knitr, rmarkdown, BiocStyle, AnnotationHub License: MIT + file LICENSE Package: maSigPro Version: 1.58.0 Depends: R (>= 2.3.1) Imports: Biobase, graphics, grDevices, venn, mclust, stats, MASS License: GPL (>= 2) Package: maskBAD Version: 1.30.0 Depends: R (>= 2.10), gcrma (>= 2.27.1), affy Suggests: hgu95av2probe, hgu95av2cdf License: GPL (>= 2) Package: MassArray Version: 1.38.0 Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, stats, utils License: GPL (>= 2) Package: massiR Version: 1.22.0 Depends: cluster, gplots, diptest, Biobase, R (>= 3.0.2) Suggests: biomaRt, RUnit, BiocGenerics License: GPL-3 Package: MassSpecWavelet Version: 1.52.0 Depends: waveslim Suggests: xcms, caTools License: LGPL (>= 2) Archs: i386, x64 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irlba, utils Suggests: BiocStyle, testthat License: Artistic-2.0 Archs: i386, x64 Package: MaxContrastProjection Version: 1.10.0 Depends: R (>= 3.4) Imports: EBImage, stats, methods Suggests: knitr, BiocStyle, testthat License: Artistic-2.0 Package: MBAmethyl Version: 1.20.0 Depends: R (>= 2.15) License: Artistic-2.0 Package: MBASED Version: 1.20.0 Depends: RUnit, BiocGenerics, BiocParallel, GenomicRanges, SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 Package: MBCB Version: 1.40.0 Depends: R (>= 2.9.0), tcltk, tcltk2 Imports: preprocessCore, stats, utils License: GPL (>= 2) Package: mbkmeans Version: 1.2.0 Depends: R (>= 3.6) Imports: methods, DelayedArray, Rcpp, SingleCellExperiment, SummarizedExperiment, ClusterR, benchmarkme, Matrix LinkingTo: Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR Suggests: beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData, scater, DelayedMatrixStats, knitr, testthat License: MIT + file LICENSE Archs: i386, x64 Package: 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MASS, dplyr, pander, devtools, testthat, GSVA License: GPL-2 Package: MCRestimate Version: 2.42.0 Depends: R (>= 2.7.2), golubEsets (>= 1.4.6) Imports: e1071 (>= 1.5-12), pamr (>= 1.22), randomForest (>= 3.9-6), RColorBrewer (>= 0.1-3), Biobase (>= 2.5.5), graphics, grDevices, stats, utils Suggests: xtable (>= 1.2-1), ROC (>= 1.8.0), genefilter (>= 1.12.0), gpls (>= 1.6.0) License: GPL (>= 2) Package: mCSEA Version: 1.6.0 Depends: R (>= 3.5), mCSEAdata, Homo.sapiens Imports: biomaRt, fgsea, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, Gviz, IRanges, limma, parallel, S4Vectors, stats, SummarizedExperiment, utils Suggests: Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k, knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit License: GPL-2 Package: mdgsa Version: 1.18.0 Depends: R (>= 2.14) Imports: AnnotationDbi, DBI, GO.db, KEGG.db, cluster, Matrix Suggests: BiocStyle, knitr, rmarkdown, limma, ALL, hgu95av2.db, RUnit, BiocGenerics License: GPL Package: mdp 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1.0.0 Depends: R (>= 3.6.0) Imports: e1071, SummarizedExperiment Suggests: knitr,rmarkdown License: GPL-2 Package: MEDIPS Version: 1.38.0 Depends: R (>= 3.0), BSgenome, Rsamtools Imports: GenomicRanges, Biostrings, graphics, gtools, IRanges, methods, stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer, preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle License: GPL (>= 2) Package: MEDME Version: 1.46.0 Depends: R (>= 2.15), grDevices, graphics, methods, stats, utils Imports: Biostrings, MASS, drc Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 License: GPL (>= 2) Archs: i386, x64 Package: MEIGOR Version: 1.20.0 Depends: Rsolnp, snowfall, CNORode, deSolve Suggests: CellNOptR License: GPL-3 Package: Melissa Version: 1.2.0 Depends: R (>= 3.5.0), BPRMeth, GenomicRanges Imports: data.table, parallel, ROCR, matrixcalc, clues, ggplot2, doParallel, foreach, MCMCpack, cowplot, magrittr, mvtnorm, truncnorm, assertthat, BiocStyle, stats, utils Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE Package: MergeMaid Version: 2.58.0 Depends: R (>= 2.10.0), survival, Biobase, MASS, methods License: GPL (>= 2) Package: Mergeomics Version: 1.14.0 Depends: R (>= 3.0.1) Suggests: RUnit, BiocGenerics License: GPL (>= 2) Package: MeSHDbi Version: 1.22.0 Depends: R (>= 3.0.1), BiocGenerics (>= 0.15.10) Imports: methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase Suggests: RUnit License: Artistic-2.0 Package: meshes Version: 1.12.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, DOSE (>= 3.5.1), enrichplot, GOSemSim (>= 1.99.3), MeSH.db, methods, rvcheck, utils Suggests: knitr, MeSH.Cel.eg.db, MeSH.Hsa.eg.db, prettydoc License: Artistic-2.0 Package: meshr Version: 1.22.0 Depends: R (>= 3.0.1) Imports: methods, stats, utils, fdrtool, MeSH.db, MeSH.AOR.db, MeSH.PCR.db, MeSHDbi, MeSH.Hsa.eg.db, MeSH.Aca.eg.db, MeSH.Bsu.168.eg.db, MeSH.Syn.eg.db, cummeRbund, org.Hs.eg.db, Category, S4Vectors, BiocGenerics, RSQLite License: Artistic-2.0 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RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: GPL-3 Package: metaCCA Version: 1.14.0 Suggests: knitr License: MIT + file LICENSE Package: MetaCyto Version: 1.8.0 Depends: R (>= 3.4) Imports: flowCore (>= 1.4),tidyr (>= 0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices, graphics, stats, utils Suggests: knitr, dplyr License: GPL (>= 2) Package: metagene Version: 2.18.0 Depends: R (>= 3.5.0), R6 (>= 2.0), GenomicRanges, BiocParallel Imports: rtracklayer, gplots, tools, GenomicAlignments, GenomeInfoDb, GenomicFeatures, IRanges, ggplot2, muStat, Rsamtools, DBChIP, matrixStats, purrr, data.table, magrittr, methods, utils, ensembldb, EnsDb.Hsapiens.v86, stringr Suggests: BiocGenerics, similaRpeak, RUnit, knitr, BiocStyle, rmarkdown, similaRpeak License: Artistic-2.0 | file LICENSE Package: metagene2 Version: 1.2.1 Depends: R (>= 3.6), R6 (>= 2.0), GenomicRanges, BiocParallel Imports: rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges, ggplot2, Rsamtools, 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Suggests: BiocGenerics, GenomicRanges, rtracklayer, Rsamtools, survcomp, VennDiagram, knitr, zoo, RUnit, BiocManager, BSgenome, RSQLite Enhances: parallel, TCC, RMySQL License: GPL (>= 3) Package: metavizr Version: 1.10.0 Depends: R (>= 3.4), metagenomeSeq (>= 1.17.1), methods, data.table, Biobase, digest Imports: epivizr, epivizrData, epivizrServer, epivizrStandalone, vegan, GenomeInfoDb, phyloseq, httr Suggests: knitr, BiocStyle, matrixStats, msd16s (>= 0.109.1), etec16s, testthat, gss, curatedMetagenomicData License: MIT + file LICENSE Package: MetaVolcanoR Version: 1.0.1 Depends: R (>= 3.6.0) Imports: methods, data.table, dplyr, tidyr, plotly, ggplot2, cowplot, parallel, metafor, metap, rlang, topconfects, grDevices, graphics, stats, htmlwidgets Suggests: knitr, testthat License: GPL-3 Package: MetCirc Version: 1.16.0 Depends: R (>= 3.5), amap (>= 0.8), circlize (>= 0.3.9), scales (>= 0.3.0), shiny (>= 1.0.0), MSnbase (>= 2.10.1), Imports: ggplot2 (>= 3.2.1), S4Vectors (>= 0.22.0) Suggests: BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr (>= 1.11), methods (>= 3.5), RUnit (>= 0.4.32), stats (>= 3.5) License: GPL (>= 3) Package: MethCP Version: 1.0.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, S4Vectors, parallel, bsseq, DSS, methylKit, DNAcopy, GenomicRanges, IRanges, GenomeInfoDb Suggests: testthat, knitr, rmarkdown License: Artistic-2.0 Package: methimpute Version: 1.8.0 Depends: R (>= 3.4.0), GenomicRanges, ggplot2 Imports: Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats, GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm, data.table LinkingTo: Rcpp Suggests: knitr, BiocStyle License: Artistic-2.0 Archs: i386, x64 Package: methInheritSim Version: 1.8.0 Depends: R (>= 3.4) Imports: methylKit, GenomicRanges, GenomeInfoDb, parallel, BiocGenerics, S4Vectors, methods, stats, IRanges, msm Suggests: BiocStyle, knitr, rmarkdown, RUnit, methylInheritance License: Artistic-2.0 Package: MethPed Version: 1.14.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 Package: methrix Version: 1.0.05 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 Package: MethTargetedNGS Version: 1.18.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings License: Artistic-2.0 Package: methVisual Version: 1.38.0 Depends: R (>= 2.11.0), Biostrings(>= 2.4.8), plotrix,gsubfn, grid,sqldf Imports: Biostrings, ca, graphics, grDevices, grid, gridBase, IRanges, stats, utils License: GPL (>= 2) Package: methyAnalysis Version: 1.28.0 Depends: R (>= 2.10), grid, BiocGenerics, IRanges, GenomeInfoDb, GenomicRanges, Biobase (>= 2.34.0), org.Hs.eg.db Imports: grDevices, stats, utils, lumi, methylumi, Gviz, genoset, SummarizedExperiment, IRanges, GenomicRanges, VariantAnnotation, rtracklayer, GenomicFeatures, annotate, Biobase (>= 2.5.5), AnnotationDbi, genefilter, biomaRt, methods, parallel Suggests: FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 Package: MethylAid Version: 1.20.0 Depends: R (>= 3.4) Imports: Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) Package: methylCC Version: 1.0.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: CC BY 4.0 Package: methylGSA Version: 1.4.9 Depends: R (>= 3.5) Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, shiny, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr, rmarkdown, testthat, enrichplot License: GPL-2 Package: methylInheritance Version: 1.10.0 Depends: R (>= 3.5) Imports: methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors, methods, parallel, ggplot2, gridExtra, rebus Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim License: Artistic-2.0 Package: methylKit Version: 1.12.0 Depends: R (>= 3.3.0), GenomicRanges (>= 1.18.1), methods Imports: IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>= 0.13.13), GenomeInfoDb, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat,knitr, rmarkdown, genomation, BiocManager License: Artistic-2.0 Archs: i386, x64 Package: MethylMix Version: 2.16.0 Depends: R (>= 3.2.0) Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown License: GPL-2 Package: methylMnM Version: 1.24.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 Archs: i386, x64 Package: methylPipe Version: 1.20.0 Depends: R (>= 3.2.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) Archs: i386, x64 Package: MethylSeekR Version: 1.26.0 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), graphics (>= 2.15.2), grDevices (>= 2.15.2), parallel (>= 2.15.2), stats (>= 2.15.2), utils (>= 2.15.2) Suggests: BSgenome.Hsapiens.UCSC.hg18 License: GPL (>= 2) Package: methylumi Version: 2.32.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, methyAnalysis, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 Package: methyvim Version: 1.8.0 Depends: R (>= 3.4.0) Imports: stats, cluster, methods, ggplot2, ggsci, gridExtra, superheat, dplyr, gtools, tmle (>= 1.4.0.1), future, doFuture, S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, GenomeInfoDb, bumphunter, IRanges, limma, minfi Suggests: testthat, knitr, rmarkdown, BiocStyle, SuperLearner, earth, nnet, gam, arm, snow, parallel, BatchJobs, minfiData, methyvimData License: file LICENSE Package: MetID Version: 1.4.0 Depends: R (>= 3.5) Imports: utils (>= 3.3.1), stats (>= 3.4.2), devtools (>= 1.13.0), stringr (>= 1.3.0), Matrix (>= 1.2-12), igraph (>= 1.2.1), ChemmineR (>= 2.30.2) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) License: Artistic-2.0 Package: MetNet Version: 1.4.2 Depends: R (>= 3.5) Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), GENIE3 (>= 1.7.0), methods (>= 3.5), mpmi (>= 0.42), parmigene (>= 1.0.2), ppcor (>= 1.1), sna (>= 2.4), stabs (>= 0.6), stats (>= 3.6) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 2.0-18), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1) License: GPL-2 Package: mfa Version: 1.8.0 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) Archs: i386, x64 Package: Mfuzz Version: 2.46.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 Package: MGFM Version: 1.20.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 Package: MGFR Version: 1.12.0 Depends: R (>= 3.5) Imports: biomaRt, annotate License: GPL-3 Package: mgsa Version: 1.34.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 Archs: i386, x64 Package: MiChip Version: 1.40.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) Package: microbiome Version: 1.8.0 Depends: R (>= 3.3.0), phyloseq, ggplot2 Imports: dplyr, reshape2, Rtsne, scales, stats, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitcitations, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE Package: microbiomeDASim Version: 1.0.0 Depends: R (>= 3.6.0) Imports: graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats Suggests: testthat (>= 2.1.0), knitr, devtools License: MIT + file LICENSE Package: microRNA Version: 1.44.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 Archs: i386, x64 Package: MIGSA Version: 1.10.1 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: breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, mGSZ, MIGSAdata License: GPL (>= 2) Package: mimager Version: 1.10.0 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 Package: MIMOSA Version: 1.24.0 Depends: R (>= 3.0.2), MASS, plyr, reshape, Biobase, ggplot2 Imports: methods, Formula, data.table, pracma, MCMCpack, coda, modeest, testthat, Rcpp, scales, LinkingTo: Rcpp, RcppArmadillo Suggests: parallel, knitr License: Artistic-2.0 Archs: i386, x64 Package: MineICA Version: 1.26.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX Enhances: doMC License: GPL-2 Package: minet Version: 3.44.1 Imports: infotheo License: Artistic-2.0 Archs: i386, x64 Package: minfi Version: 1.32.0 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 Package: MinimumDistance Version: 1.30.0 Depends: R (>= 3.3), 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, SNPchip, RUnit Enhances: snow, doSNOW License: Artistic-2.0 Package: MiPP Version: 1.58.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) Package: MIRA Version: 1.8.0 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 Package: MiRaGE Version: 1.28.0 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 Package: miRBaseConverter Version: 1.10.1 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils License: GPL (>= 2) Package: miRcomp Version: 1.16.0 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 Package: mirIntegrator Version: 1.16.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) Package: miRLAB Version: 1.16.0 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) Package: miRmine Version: 1.8.0 Depends: R (>= 3.4), SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, DESeq2 License: GPL (>= 3) Package: miRNAmeConverter Version: 1.14.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 Package: miRNApath Version: 1.46.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 Package: miRNAtap Version: 1.20.0 Depends: R (>= 3.3.0), AnnotationDbi Imports: DBI, RSQLite, stringr, sqldf, plyr, methods Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat License: GPL-2 Package: miRSM Version: 1.4.1 Depends: R (>= 3.5.0) Imports: WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL, NMF, biclust, runibic, iBBiG, fabia, BicARE, isa2, s4vd, BiBitR, rqubic, Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero, ppclust, miRspongeR, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, MatrixCorrelation, energy Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 Archs: i386, x64 Package: miRspongeR Version: 1.12.0 Depends: R (>= 3.5.0) Imports: corpcor, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, varhandle, linkcomm, utils, Rcpp, org.Hs.eg.db Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 Archs: i386, x64 Package: Mirsynergy Version: 1.22.0 Depends: R (>= 3.0.2), igraph, ggplot2 Imports: graphics, grDevices, gridExtra, Matrix, parallel, RColorBrewer, reshape, scales, utils Suggests: glmnet, RUnit, BiocGenerics, knitr License: GPL-2 Package: missMethyl Version: 1.20.4 Depends: R (>= 2.3.0) Imports: limma, minfi, methylumi, IlluminaHumanMethylation450kmanifest, statmod, ruv, stringr, IlluminaHumanMethylation450kanno.ilmn12.hg19, org.Hs.eg.db, AnnotationDbi, BiasedUrn, GO.db, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: minfiData, BiocStyle, knitr, rmarkdown, edgeR, tweeDEseqCountData License: GPL-2 Package: missRows Version: 1.6.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 Package: mitoODE Version: 1.24.0 Depends: R (>= 2.14.0), minpack.lm, MASS, parallel, mitoODEdata, KernSmooth License: LGPL Archs: i386, x64 Package: mixOmics Version: 6.10.9 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) Package: MLInterfaces Version: 1.66.5 Depends: R (>= 3.5), 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 Enhances: parallel, rda License: LGPL Package: mlm4omics Version: 1.3.0 Depends: R (>= 3.5.0), Rcpp (>= 0.12.17), methods, stats Imports: rstan (>= 2.17.3),rstantools (>= 1.5.0),MASS,Matrix,stats4,ggplot2 LinkingTo: StanHeaders (>= 2.17.2), rstan (>= 2.17.3), BH (>= 1.66.0-1), Rcpp (>= 0.12.17), RcppEigen (>= 0.3.3.4.0) Suggests: testthat, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) License: GPL-3 Archs: i386, x64 Package: MLP Version: 1.34.0 Depends: AnnotationDbi, affy, plotrix, gplots, gmodels, gdata, gtools Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, KEGG.db, annotate, Rgraphviz, GOstats, limma, mouse4302.db, reactome.db License: GPL-3 Package: MLSeq Version: 2.4.0 Depends: caret, ggplot2 Imports: methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, testthat, BiocStyle, VennDiagram, pamr License: GPL (>= 2) Package: MMDiff2 Version: 1.14.0 Depends: R (>= 3.3), Rsamtools, Biobase, Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 Package: MmPalateMiRNA Version: 1.36.0 Depends: R (>= 2.13.0), methods, Biobase, xtable, limma, statmod, lattice, vsn Imports: limma, lattice, Biobase Suggests: GOstats, graph, Category, org.Mm.eg.db, microRNA, targetscan.Mm.eg.db, RSQLite, DBI, AnnotationDbi, clValid, class, cluster, multtest, RColorBrewer, latticeExtra License: GPL-3 Package: MMUPHin Version: 1.0.0 Depends: R (>= 3.6) Imports: Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr, cowplot, utils, stats, grDevices Suggests: testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter License: MIT + file LICENSE Package: mnem Version: 1.2.0 Depends: R (>= 3.6) Imports: cluster, nem, epiNEM, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit License: GPL-3 Archs: i386, x64 Package: MODA Version: 1.12.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) Package: Modstrings Version: 1.2.1 Depends: R (>= 3.6), Biostrings (>= 2.51.5) Imports: methods, assertive, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 Package: MOFA Version: 1.2.0 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 Package: mogsa Version: 1.20.0 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 Package: monocle Version: 2.14.0 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 Archs: i386, x64 Package: MoonlightR Version: 1.12.0 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) Package: MoPS Version: 1.20.0 Imports: Biobase License: GPL-3 Package: mosaics Version: 2.24.0 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) Archs: i386, x64 Package: MOSim Version: 1.0.2 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 Package: motifbreakR Version: 2.0.0 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 Package: motifcounter Version: 1.10.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 Archs: i386, x64 Package: MotifDb Version: 1.28.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes Package: motifmatchr Version: 1.8.0 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 Archs: i386, x64 Package: motifRG Version: 1.30.0 Depends: R (>= 2.15), Biostrings (>= 2.26), IRanges, seqLogo, parallel, methods, grid, graphics, BSgenome, XVector, BSgenome.Hsapiens.UCSC.hg19 Imports: Biostrings,IRanges,seqLogo,parallel,methods,grid,graphics,XVector License: Artistic-2.0 Package: motifStack Version: 1.30.0 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) Package: MotIV Version: 1.42.0 Depends: R (>= 2.10), graphics, BiocGenerics, GenomicRanges Imports: methods, stats, grid, S4Vectors, IRanges (>= 1.13.5), Biostrings, lattice, rGADEM, utils Suggests: rtracklayer License: GPL-2 Archs: i386, x64 Package: MPFE Version: 1.22.0 License: GPL (>= 3) Package: mpra Version: 1.8.0 Depends: R (>= 3.4.0), methods, BiocGenerics, SummarizedExperiment, limma Imports: S4Vectors, scales, stats, graphics, statmod Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 Package: MPRAnalyze Version: 1.4.0 Imports: BiocParallel, methods, progress, stats, SummarizedExperiment Suggests: knitr License: GPL-3 Package: msa Version: 1.18.0 Depends: R (>= 3.1.0), methods, Biostrings (>= 2.40.0) Imports: Rcpp (>= 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edgeR, qvalue License: GPL-2 Package: MSnbase Version: 2.12.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.7.1), Biobase (>= 2.15.2), mzR (>= 2.19.6), S4Vectors, ProtGenerics (>= 1.17.4) Imports: BiocParallel, IRanges (>= 2.13.28), plyr, preprocessCore, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID (>= 1.5.2), digest, lattice, ggplot2, XML, scales, MASS, Rcpp LinkingTo: Rcpp Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, 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 Archs: i386, x64 Package: MSnID Version: 1.20.0 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 Package: msPurity Version: 1.12.2 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) Package: MSstats Version: 3.18.5 Depends: R (>= 3.6) Imports: lme4, marray, limma, gplots, ggplot2, methods, grid, ggrepel, preprocessCore, reshape2, survival, statmod, minpack.lm, utils, grDevices, graphics, stats, doSNOW, snow, foreach, data.table, MASS, dplyr, tidyr, broom, purrr, stringr Suggests: BiocStyle, knitr, rmarkdown, MSstatsBioData License: Artistic-2.0 Package: MSstatsQC Version: 2.4.0 Imports: dplyr,plotly,RecordLinkage,ggplot2,ggExtra, stats,grid, MSnbase, qcmetrics Suggests: knitr,rmarkdown, testthat, RforProteomics License: Artistic License 2.0 Package: MSstatsQCgui Version: 1.6.0 Imports: shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, RecordLinkage, grid Suggests: knitr License: Artistic License 2.0 Package: MSstatsSampleSize Version: 1.0.1 Depends: R (>= 3.6) Imports: ggplot2, BiocParallel, caret, gridExtra, reshape2, stats, utils, grDevices, graphics, MSstats Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 Package: MSstatsTMT Version: 1.4.6 Depends: R (>= 3.6) Imports: limma, lme4, lmerTest, dplyr, tidyr, statmod, methods, reshape2, data.table, matrixStats, stats, utils, ggplot2, grDevices, graphics, MSstats Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 Package: Mulcom Version: 1.36.0 Depends: R (>= 2.10), Biobase Imports: graphics, grDevices, stats, methods, fields License: GPL-2 Archs: i386, x64 Package: MultiAssayExperiment Version: 1.12.6 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 Package: multiClust Version: 1.16.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) Package: MultiDataSet Version: 1.14.0 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 Package: multiHiCcompare Version: 1.4.0 Depends: R (>= 3.5.0) Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, metap, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, BLMA, GenomeInfoDb Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE Package: MultiMed Version: 2.8.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE Package: multiMiR Version: 1.8.0 Depends: R (>= 3.4) Imports: stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 1.2), methods, BiocGenerics, AnnotationDbi, dplyr, Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) License: MIT + file LICENSE Package: multiOmicsViz Version: 1.10.0 Depends: R (>= 3.3.2) Imports: methods, parallel, doParallel, foreach, grDevices, graphics, utils, SummarizedExperiment, stats Suggests: BiocGenerics License: LGPL Package: multiscan Version: 1.46.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) Archs: i386, x64 Package: multtest Version: 2.42.0 Depends: R (>= 2.10), methods, BiocGenerics, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL Archs: i386, x64 Package: muscat Version: 1.0.1 Depends: R (>= 3.6), scater (>= 1.13) Imports: BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, doParallel, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, magrittr, Matrix, matrixStats, methods, parallel, progress, purrr, reshape2, scales, sctransform, stats, SingleCellExperiment, SummarizedExperiment, S4Vectors, tibble, variancePartition, viridis Suggests: BiocStyle, cowplot, ExperimentHub, knitr, RColorBrewer, rmarkdown, testthat, UpSetR License: GPL (>= 2) Package: muscle Version: 3.28.0 Depends: Biostrings License: Unlimited Archs: i386, x64 Package: MutationalPatterns Version: 1.12.0 Depends: R (>= 3.4.0), GenomicRanges (>= 1.24.0), NMF (>= 0.20.6) Imports: stats, parallel, S4Vectors, BiocGenerics (>= 0.18.0), VariantAnnotation (>= 1.18.1), reshape2 (>= 1.4.1), plyr (>= 1.8.3), ggplot2 (>= 2.1.0), pracma (>= 1.8.8), SummarizedExperiment (>= 1.2.2), IRanges (>= 2.6.0), GenomeInfoDb (>= 1.12.0), Biostrings (>= 2.40.0), ggdendro (>= 0.1-20), cowplot (>= 0.9.2) Suggests: BSgenome (>= 1.40.0), BSgenome.Hsapiens.1000genomes.hs37d5 (>= 0.99.1), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), testthat License: MIT + file LICENSE Package: MVCClass Version: 1.60.0 Depends: R (>= 2.1.0), methods License: LGPL Package: MWASTools Version: 1.10.0 Depends: R(>= 3.4) Imports: glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra, igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST, ComplexHeatmap, stats, utils Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: CC BY-NC-ND 4.0 Package: mygene Version: 1.22.0 Depends: R (>= 3.2.1), GenomicFeatures, Imports: httr (>= 0.3), jsonlite (>= 0.9.7), S4Vectors, Hmisc, sqldf, plyr Suggests: BiocStyle License: Artistic-2.0 Package: myvariant Version: 1.16.0 Depends: R (>= 3.2.1), VariantAnnotation Imports: httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, GenomeInfoDb Suggests: BiocStyle License: Artistic-2.0 Package: mzID Version: 1.24.0 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testthat, BiocStyle License: GPL Archs: i386, x64 Package: NanoStringQCPro Version: 1.18.0 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 Package: nanotatoR Version: 1.2.0 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 Package: NarrowPeaks Version: 1.30.0 Depends: R (>= 2.10.0), splines Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, fda, CSAR, ICSNP Suggests: rtracklayer, BiocStyle, GenomicRanges, CSAR License: Artistic-2.0 Archs: i386, x64 Package: NBAMSeq Version: 1.2.1 Depends: R (>= 3.6), SummarizedExperiment, S4Vectors Imports: DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods, stats, Suggests: knitr, rmarkdown, testthat, ggplot2 License: GPL-2 Package: NBSplice Version: 1.4.0 Depends: R (>= 3.5), methods Imports: edgeR, stats, MASS, car, mppa, BiocParallel, ggplot2, reshape2 Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) Package: ncdfFlow Version: 2.32.0 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 License: Artistic-2.0 Archs: i386, x64 Package: ncGTW Version: 1.0.0 Depends: methods, BiocParallel, xcms Imports: Rcpp, grDevices, graphics, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-2 Archs: i386, x64 Package: ndexr Version: 1.8.0 Depends: igraph Imports: httr, jsonlite, plyr, tidyr Suggests: BiocStyle, testthat, knitr, rmarkdown License: BSD Package: NeighborNet Version: 1.4.0 Depends: methods Imports: graph, stats License: CC BY-NC-ND 4.0 Package: nem Version: 2.60.0 Depends: R (>= 3.0) Imports: boot, e1071, graph, graphics, grDevices, methods, RBGL (>= 1.8.1), RColorBrewer, stats, utils, Rgraphviz, statmod, plotrix, limma Suggests: Biobase (>= 1.10) Enhances: doMC, snow, parallel License: GPL (>= 2) Archs: i386, x64 Package: netbenchmark Version: 1.18.0 Depends: grndata (>= 0.99.3) Imports: Rcpp (>= 0.11.0), minet, GENIE3, c3net, PCIT, GeneNet, tools, pracma, Matrix, corpcor, fdrtool LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, knitr, graph License: CC BY-NC-SA 4.0 Archs: i386, x64 Package: netbiov Version: 1.20.0 Depends: R (>= 3.1.0), igraph (>= 0.7.1) Suggests: BiocStyle,RUnit,BiocGenerics,Matrix License: GPL (>= 2) Package: nethet Version: 1.18.0 Imports: glasso, mvtnorm, parcor, 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 Archs: i386, x64 Package: NetPathMiner Version: 1.22.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) Archs: i386, x64 Package: netprioR Version: 1.12.0 Depends: methods, graphics, R(>= 3.3) Imports: stats, Matrix, dplyr, doParallel, foreach, parallel, sparseMVN, ggplot2, gridExtra, pROC Suggests: knitr, BiocStyle, pander License: GPL-3 Package: netReg Version: 1.10.0 Depends: R(>= 3.4) Imports: Rcpp, stats LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BiocStyle, lintr, lassoshooting License: GPL-3 | BSL-1.0 + file LICENSE Archs: i386, x64 Package: netresponse Version: 1.46.0 Depends: R (>= 2.15.1), Rgraphviz, methods, minet, mclust, reshape2 Imports: dmt, ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer License: GPL (>= 2) Archs: i386, x64 Package: NetSAM Version: 1.26.0 Depends: R (>= 2.15.1), methods, igraph (>= 0.6-1), seriation (>= 1.0-6), graph (>= 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stringr, tidyr, tidyselect (>= 0.2.3), truncnorm, utils, viridisLite, XVector, zoo Suggests: BiocStyle, Cairo, knitr, testthat License: file LICENSE Package: nnNorm Version: 2.50.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL Package: NOISeq Version: 2.30.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 Package: nondetects Version: 2.16.0 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 Package: normalize450K Version: 1.14.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE Package: NormalyzerDE Version: 1.4.0 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 Package: NormqPCR Version: 1.32.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 Package: normr Version: 1.12.0 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 Archs: i386, x64 Package: npGSEA Version: 1.22.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 Package: NTW Version: 1.36.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 Package: nucleoSim Version: 1.14.0 Imports: stats, IRanges, S4Vectors, graphics, methods Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit License: Artistic-2.0 Package: nucleR Version: 2.18.4 Depends: methods Imports: Biobase, BiocGenerics, Biostrings, GenomeInfoDb, GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr, ggplot2, magrittr, parallel, stats, utils Suggests: Starr, BiocStyle, knitr, rmarkdown, testthat License: LGPL (>= 3) Package: nuCpos Version: 1.4.0 Depends: R (>= 3.5.1) Imports: graphics, methods Suggests: NuPoP, Biostrings, testthat License: GPL-2 Archs: i386, x64 Package: NuPoP Version: 1.36.0 Depends: R (>= 2.10) License: GPL-2 Archs: i386, x64 Package: occugene Version: 1.46.0 Depends: R (>= 2.0.0) License: GPL (>= 2) Package: OCplus Version: 1.60.0 Depends: R (>= 2.1.0) Imports: multtest (>= 1.7.3), graphics, grDevices, stats, akima License: LGPL Package: odseq Version: 1.14.0 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 Package: OGSA Version: 1.16.0 Depends: R (>= 3.2.0) Imports: gplots(>= 2.8.0), limma(>= 3.18.13), Biobase License: GPL (== 2) Package: oligo Version: 1.50.0 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, GenomeGraphs, RCurl, ACME, biomaRt, AnnotationDbi, GenomeGraphs, RCurl Enhances: ff, doMC, doMPI License: LGPL (>= 2) Archs: i386, x64 Package: oligoClasses Version: 1.48.0 Depends: R (>= 2.14) Imports: BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods, graphics, IRanges (>= 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Suggests: knitr, rmarkdown, testthat License: GPL-3 Package: omicade4 Version: 1.26.0 Depends: R (>= 3.0.0), ade4 Imports: made4 Suggests: BiocStyle License: GPL-2 Package: OmicCircos Version: 1.24.0 Depends: R (>= 2.14.0), methods,GenomicRanges License: GPL-2 Package: omicplotR Version: 1.6.1 Depends: R (>= 3.6), ALDEx2 (>= 1.18.0) Imports: compositions, DT, grDevices, knitr, jsonlite, matrixStats, rmarkdown, shiny, stats, vegan, zCompositions License: MIT + file LICENSE Package: omicRexposome Version: 1.8.0 Depends: R (>= 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 Package: OmicsLonDA Version: 1.2.2 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 Package: OmicsMarkeR Version: 1.18.0 Depends: R (>= 3.2.0) Imports: graphics, stats, utils, plyr (>= 1.8), data.table (>= 1.9.4), caret (>= 6.0-37), DiscriMiner (>= 0.1-29), e1071 (>= 1.6-1), randomForest (>= 4.6-10), gbm (>= 2.1), pamr (>= 1.54.1), glmnet (>= 1.9-5), caTools (>= 1.14), foreach (>= 1.4.1), permute (>= 0.7-0), assertive (>= 0.3-0), assertive.base (>= 0.0-1) Suggests: testthat, BiocStyle, knitr License: GPL-3 Package: OMICsPCA Version: 1.4.0 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 Package: omicsPrint Version: 1.6.0 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) Package: OmnipathR Version: 1.0.1 Depends: igraph, graphics, methods, utils Imports: dplyr, rlang Suggests: tidyr, dnet, gprofiler2, BiocStyle, testthat License: MIT + file LICENSE Package: Onassis Version: 1.8.2 Depends: R (>= 3.4), rJava, OnassisJavaLibs Imports: GEOmetadb, RSQLite, data.table, methods, tools, utils, AnnotationDbi, RCurl, stats, DT, data.table, knitr, Rtsne, dendextend, clusteval, ggplot2, ggfortify Suggests: BiocStyle, rmarkdown, htmltools, org.Hs.eg.db, gplots, GenomicRanges, kableExtra License: GPL-2 Package: oncomix Version: 1.8.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 Package: OncoScore Version: 1.14.0 Depends: R (>= 3.6), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE Package: OncoSimulR Version: 2.16.1 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, nem LinkingTo: Rcpp Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander License: GPL (>= 3) Archs: i386, x64 Package: oneSENSE Version: 1.8.0 Depends: R (>= 3.4), webshot, shiny, shinyFiles, scatterplot3d Imports: Rtsne, plotly, gplots, grDevices, graphics, stats, utils, methods, flowCore Suggests: knitr, rmarkdown License: GPL (>= 3) Package: onlineFDR Version: 1.4.0 Imports: stats Suggests: knitr, rmarkdown, testthat, covr License: GPL-3 Package: ontoProc Version: 1.8.1 Depends: R (>= 3.5), ontologyIndex Imports: 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stats, utils Suggests: ALL, GEOquery, pathprintGEOData, SummarizedExperiment License: GPL Package: pathRender Version: 1.54.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods, stats4 Suggests: ALL, hgu95av2.db License: LGPL Package: pathVar Version: 1.16.0 Depends: R (>= 3.3.0), methods, ggplot2, gridExtra Imports: EMT, mclust, Matching, data.table, stats, grDevices, graphics, utils License: LGPL (>= 2.0) Package: pathview Version: 1.26.0 Depends: R (>= 2.10), org.Hs.eg.db Imports: KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, KEGGREST, methods, utils Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) Package: pathwayPCA Version: 1.2.0 Depends: R (>= 3.6) Imports: lars, methods, parallel, stats, survival, utils Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse License: GPL-3 Package: PathwaySplice Version: 1.10.0 Depends: R (>= 3.5.0) Imports: goseq, Biobase, DOSE, reshape2, igraph, org.Hs.eg.db, org.Mm.eg.db, BiocGenerics, AnnotationDbi, JunctionSeq, BiasedUrn, GO.db,gdata, geneLenDataBase, grDevices, graphics, stats, utils, VennDiagram, RColorBrewer, ensembldb, AnnotationHub, S4Vectors, dplyr, plotly, webshot, htmlwidgets , mgcv ,gridExtra, grid ,gplots, tibble , EnrichmentBrowser, annotate , KEGGREST Suggests: testthat, knitr, rmarkdown License: LGPL (>= 2) Package: paxtoolsr Version: 1.20.0 Depends: R (>= 3.2), rJava (>= 0.9-8), XML Imports: utils, httr, igraph, plyr, rjson, R.utils, jsonlite, readr Suggests: testthat, knitr, BiocStyle, rmarkdown, RColorBrewer, biomaRt, estrogen, affy, hgu95av2, hgu95av2cdf, limma, foreach, doSNOW, parallel, org.Hs.eg.db License: LGPL-3 Package: Pbase Version: 0.26.0 Depends: R (>= 2.10), methods, BiocGenerics, Rcpp, Gviz Imports: cleaver (>= 1.3.6), Biobase, Biostrings (>= 2.47.5), IRanges (>= 2.13.11), S4Vectors (>= 0.17.24), mzID, mzR (>= 1.99.1), MSnbase (>= 1.15.5), Pviz, biomaRt, GenomicRanges (>= 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Version: 1.0.0 Depends: R (>= 3.6.0), sn (>= 1.5.2) Imports: ggplot2 (>= 3.0.0), phyloseq (>= 1.28.0), zoo (>= 1.8.3), psych (>= 1.8.4), stats (>= 3.6.0), Matrix (>= 1.2.14), fitdistrplus (>= 1.0.12), parallel (>= 3.6.0) Suggests: knitr, rmarkdown, kableExtra, ggpubr License: Artistic-2.0 Package: perturbatr Version: 1.6.0 Depends: R (>= 3.5), methods, stats Imports: dplyr, ggplot2, tidyr, assertthat, lme4, 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 Package: PGA Version: 1.16.0 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 Package: pgca Version: 1.10.0 Imports: utils, stats Suggests: knitr, testthat License: GPL (>= 2) Package: PGSEA Version: 1.60.0 Depends: R (>= 2.10), GO.db, KEGG.db, AnnotationDbi, annaffy, methods, Biobase (>= 2.5.5) Suggests: GSEABase, GEOquery, org.Hs.eg.db, hgu95av2.db, limma License: GPL-2 Package: phantasus Version: 1.6.0 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, Matrix.utils, pheatmap, scales, ccaPP, grid, grDevices, AnnotationDbi Suggests: testthat, BiocStyle, knitr, rmarkdown, data.table License: MIT + file LICENSE Package: PharmacoGx Version: 1.17.1 Depends: R (>= 3.6) Imports: Biobase, piano, magicaxis, RColorBrewer, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, lsa, reshape2 Suggests: xtable, testthat License: Artistic-2.0 Package: phemd Version: 1.1.1 Depends: R (>= 3.6), 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 Suggests: knitr License: GPL-2 Package: phenopath Version: 1.10.0 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) Archs: i386, x64 Package: phenoTest Version: 1.34.0 Depends: R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2 Imports: survival, limma, Hmisc, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, SNPchip, hgu133a.db, HTSanalyzeR, ellipse Suggests: GSEABase, KEGG.db, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) Package: PhenStat Version: 2.22.0 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 Package: philr Version: 1.12.0 Imports: ape, phangorn, tidyr, ggplot2, ggtree Suggests: testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet, dplyr License: GPL-3 Package: phosphonormalizer Version: 1.10.0 Depends: R (>= 3.4.0) Imports: plyr, stats, graphics, matrixStats Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) Package: PhyloProfile Version: 1.0.7 Depends: R (>= 3.6.0) 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 Package: phyloseq Version: 1.30.0 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 Package: Pi Version: 1.14.0 Depends: XGR, igraph, dnet, ggplot2, graphics Imports: Matrix, ggbio, GenomicRanges, GenomeInfoDb, supraHex, scales, grDevices, ggrepel, ROCR, randomForest, glmnet, Gviz, lattice, caret, plot3D, stats Suggests: foreach, doParallel, BiocStyle, knitr, rmarkdown, png, GGally, gridExtra, ExpressionAtlas, ggforce, fgsea, pathview, tidyr, dplyr License: GPL-3 Package: piano Version: 2.2.0 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) Package: pickgene Version: 1.58.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) Package: PICS Version: 2.30.0 Depends: R (>= 2.14.0), BiocGenerics (>= 0.1.3) Imports: methods, stats4, IRanges, GenomicRanges, graphics, grDevices, stats, Rsamtools, GenomicAlignments, S4Vectors Suggests: ShortRead, rtracklayer, parallel License: Artistic-2.0 Archs: i386, x64 Package: Pigengene Version: 1.12.0 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) Package: PING Version: 2.30.0 Depends: R(>= 2.15.0), chipseq, IRanges, GenomicRanges Imports: methods, PICS, graphics, grDevices, stats, Gviz, fda, BSgenome, stats4, BiocGenerics, IRanges, S4Vectors Suggests: parallel, ShortRead, rtracklayer License: Artistic-2.0 Archs: i386, x64 Package: pint Version: 1.36.0 Depends: mvtnorm, methods, graphics, Matrix, dmt License: BSD_2_clause + file LICENSE Package: pipeFrame Version: 1.2.2 Imports: BSgenome, digest, visNetwork, magrittr, methods, Biostrings, GenomeInfoDb, parallel, stats, utils Suggests: BiocManager, knitr, rtracklayer, testthat License: GPL-3 Package: pkgDepTools Version: 1.52.0 Depends: methods, graph, RBGL Imports: graph, RBGL Suggests: Biobase, Rgraphviz, RCurl, BiocManager License: GPL-2 Package: plethy Version: 1.24.0 Depends: R (>= 3.1.0), methods, DBI (>= 0.5-1), RSQLite (>= 1.1), BiocGenerics, S4Vectors Imports: Streamer, IRanges, reshape2, plyr, RColorBrewer,ggplot2, Biobase Suggests: RUnit, BiocStyle License: GPL-3 Package: plgem Version: 1.58.0 Depends: R (>= 2.10) Imports: utils, Biobase (>= 2.5.5), MASS License: GPL-2 Package: plier Version: 1.56.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) Archs: i386, x64 Package: plotGrouper Version: 1.4.0 Depends: R (>= 3.5) Imports: ggplot2 (>= 3.0.0), dplyr (>= 0.7.6), tidyr (>= 0.2.0), tibble (>= 1.4.2), stringr (>= 1.3.1), readr (>= 1.1.1), readxl (>= 1.1.0), scales (>= 1.0.0), stats, grid, gridExtra (>= 2.3), egg (>= 0.4.0), gtable (>= 0.2.0), ggpubr (>= 0.1.8), shiny (>= 1.1.0), shinythemes (>= 1.1.1), colourpicker (>= 1.0), magrittr (>= 1.5), Hmisc (>= 4.1.1), rlang (>= 0.2.2) Suggests: knitr, htmltools, BiocStyle, rmarkdown, testthat License: GPL-3 Package: PLPE Version: 1.46.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) Package: plrs Version: 1.26.0 Depends: R (>= 2.10), Biobase Imports: BiocGenerics, CGHbase, graphics, grDevices, ic.infer, marray, methods, quadprog, Rcsdp, stats, stats4, utils Suggests: mvtnorm, methods License: GPL (>= 2.0) Package: plw Version: 1.46.0 Depends: R (>= 2.10), affy (>= 1.23.4) Imports: MASS, affy, graphics, splines, stats Suggests: limma License: GPL-2 Archs: i386, x64 Package: plyranges Version: 1.6.10 Depends: R (>= 3.5), BiocGenerics, IRanges (>= 2.12.0), GenomicRanges (>= 1.28.4) Imports: methods, dplyr, rlang (>= 0.2.0), magrittr, tidyselect (>= 1.0.0), rtracklayer, GenomicAlignments, GenomeInfoDb, Rsamtools, S4Vectors (>= 0.23.10), utils Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 2.1.0), HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, covr, ggplot2 License: Artistic-2.0 Package: pmm Version: 1.18.0 Depends: R (>= 2.10) Imports: lme4, splines License: GPL-3 Package: podkat Version: 1.18.0 Depends: R (>= 3.2.0), methods, Rsamtools (>= 1.99.1), GenomicRanges Imports: Rcpp (>= 0.11.1), parallel, stats, graphics, grDevices, utils, Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges, Biostrings, BSgenome (>= 1.32.0) LinkingTo: Rcpp, Rhtslib (>= 1.15.3) Suggests: 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) Archs: i386, x64 Package: pogos Version: 1.6.0 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 Package: polyester Version: 1.22.0 Depends: R (>= 3.0.0) Imports: Biostrings (>= 2.32.0), IRanges, S4Vectors, logspline, limma, zlibbioc Suggests: knitr, ballgown License: Artistic-2.0 Package: Polyfit Version: 1.20.0 Depends: DESeq Suggests: BiocStyle License: GPL (>= 3) Package: POST Version: 1.10.0 Depends: R (>= 3.4.0) Imports: stats, CompQuadForm, Matrix, survival, Biobase, GSEABase License: GPL (>= 2) Package: PoTRA Version: 1.2.0 Depends: R (>= 3.6.0), stats, BiocGenerics, org.Hs.eg.db, igraph, graph, graphite Suggests: BiocStyle, knitr, rmarkdown, colr, metap, repmis License: LGPL Package: PowerExplorer Version: 1.6.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: DESeq2, ROTS, vsn, stats, utils, methods, gridExtra, MASS, data.table, ggplot2, Biobase, S4Vectors, BiocParallel Suggests: knitr, rmarkdown License: Artistic-2.0 Package: powerTCR Version: 1.6.0 Imports: cubature, doParallel, evmix, foreach, magrittr, methods, parallel, purrr, stats, tcR, truncdist, vegan, VGAM Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: Artistic-2.0 Package: PPInfer Version: 1.12.0 Depends: biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb, yeastExpData License: Artistic-2.0 Package: ppiStats Version: 1.52.0 Depends: ScISI (>= 1.13.2), lattice, ppiData (>= 0.1.19) Imports: Biobase, Category, graph, graphics, grDevices, lattice, methods, RColorBrewer, stats Suggests: yeastExpData, xtable License: Artistic-2.0 Package: pqsfinder Version: 2.2.0 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 Archs: i386, x64 Package: prada Version: 1.62.0 Depends: R (>= 2.10), Biobase, RColorBrewer, grid, methods, rrcov Imports: Biobase, BiocGenerics, graphics, grDevices, grid, MASS, methods, RColorBrewer, rrcov, stats4, utils Suggests: cellHTS2, tcltk License: LGPL Archs: i386, x64 Package: pram Version: 1.2.0 Depends: R (>= 3.6) Imports: methods, BiocParallel, tools, utils, data.table (>= 1.11.8), GenomicAlignments (>= 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lokern (>= 1.0.9), multtest, stats, methods, annotate Suggests: quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata Enhances: Rmpi, rsprng License: GPL-2 Package: preprocessCore Version: 1.48.0 Imports: stats License: LGPL (>= 2) Archs: i386, x64 Package: primirTSS Version: 1.4.0 Depends: R (>= 3.5.0) Imports: GenomicRanges (>= 1.32.2), S4Vectors (>= 0.18.2), rtracklayer (>= 1.40.3), dplyr (>= 0.7.6), stringr (>= 1.3.1), tidyr (>= 0.8.1), Biostrings (>= 2.48.0), purrr (>= 0.2.5), BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.1), phastCons100way.UCSC.hg38 (>= 3.7.1), GenomicScores (>= 1.4.1), shiny (>= 1.0.5), Gviz (>= 1.24.0), BiocGenerics (>= 0.26.0), IRanges (>= 2.14.10), TFBSTools (>= 1.18.0), JASPAR2018 (>= 1.1.1), tibble (>= 1.4.2), R.utils (>= 2.6.0), stats, utils Suggests: knitr, rmarkdown License: GPL-2 Package: PrInCE Version: 1.2.0 Depends: R (>= 3.6.0) Imports: purrr (>= 0.2.4), dplyr (>= 0.7.4), tidyr (>= 0.8.99), forecast (>= 8.2), progress (>= 1.1.2), Hmisc (>= 4.0), 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Suggests: knitr, rmarkdown, devtools, ggpubr, gtable, gridExtra, roxygen2, testthat (>= 2.1.0), spelling License: GPL-3 Package: PROcess Version: 1.62.0 Depends: Icens Imports: graphics, grDevices, Icens, stats, utils License: Artistic-2.0 Package: procoil Version: 2.14.0 Depends: R (>= 3.3.0), kebabs Imports: methods, stats, graphics, S4Vectors, Biostrings, utils Suggests: knitr License: GPL (>= 2) Package: proDA Version: 1.0.0 Imports: stats, utils, methods, BiocGenerics, SummarizedExperiment, S4Vectors, extraDistr Suggests: testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr, tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown License: GPL-3 Package: proFIA Version: 1.12.0 Depends: R (>= 2.5.0), xcms Imports: stats, graphics, utils, grDevices, methods, pracma, Biobase, minpack.lm, BiocParallel, missForest, ropls Suggests: BiocGenerics, plasFIA, knitr, License: CeCILL Archs: i386, x64 Package: profileplyr Version: 1.2.0 Depends: R (>= 3.6), BiocGenerics, SummarizedExperiment Imports: GenomicRanges, stats, soGGi, methods, utils, S4Vectors, R.utils, dplyr, magrittr, tidyr, IRanges, rjson, ChIPseeker,GenomicFeatures,TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene,org.Hs.eg.db,org.Mm.eg.db,rGREAT, pheatmap, EnrichedHeatmap, ComplexHeatmap, grid, circlize, BiocParallel, rtracklayer, GenomeInfoDb Suggests: BiocStyle, testthat, knitr, rmarkdown, png, Rsamtools, ggplot2 License: GPL (>= 3) Package: profileScoreDist Version: 1.14.0 Depends: R(>= 3.3) Imports: Rcpp, BiocGenerics, methods, graphics LinkingTo: Rcpp Suggests: BiocStyle, knitr, MotifDb License: MIT + file LICENSE Archs: i386, x64 Package: progeny Version: 1.8.0 Depends: R (>= 3.4.0) Imports: Biobase Suggests: airway, biomaRt, BiocFileCache, broom, DESeq2, dplyr, knitr, readr, readxl License: Apache License (== 2.0) | file LICENSE Package: projectR Version: 1.2.0 Imports: methods, cluster, stats, limma, CoGAPS, NMF, ROCR Suggests: BiocStyle, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap, viridis, ggplot2 License: GPL (== 2) Package: pRoloc Version: 1.26.0 Depends: R (>= 2.15), MSnbase (>= 1.19.20), MLInterfaces (>= 1.37.1), methods, Rcpp (>= 0.10.3), BiocParallel Imports: 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 (>= 2.5.19), hpar (>= 1.15.3), dplyr, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape License: GPL-2 Archs: i386, x64 Package: pRolocGUI Version: 1.20.0 Depends: methods, R (>= 3.1.0), pRoloc (>= 1.11.1), Biobase, MSnbase (>= 2.1.11) Imports: shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics, utils, ggplot2 Suggests: pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown License: GPL-2 Package: PROMISE Version: 1.38.0 Depends: R (>= 3.1.0), Biobase, GSEABase Imports: Biobase, GSEABase, stats License: GPL (>= 2) Package: PROPER Version: 1.18.0 Depends: R (>= 3.3) Imports: edgeR Suggests: BiocStyle,DESeq,DSS,knitr License: GPL Package: PROPS Version: 1.8.0 Imports: bnlearn, reshape2, sva, stats, utils, Biobase Suggests: knitr, rmarkdown License: GPL-2 Package: Prostar Version: 1.18.6 Depends: R (>= 3.6.1) Imports: DAPAR (>= 1.18.1), DAPARdata (>= 1.16.0), rhandsontable, data.table, shinyjs, DT, shiny, shinyBS, shinyAce, highcharter (>= 0.7.0), htmlwidgets, webshot, R.utils, shinythemes, XML,later, rclipboard, shinycssloaders, future, promises, colourpicker, BiocManager, shinyTree, shinyWidgets, sass, tibble Suggests: BiocStyle, testthat License: Artistic-2.0 Package: proteinProfiles Version: 1.26.0 Depends: R (>= 2.15.2) Imports: graphics, stats Suggests: testthat License: GPL-3 Package: ProteomicsAnnotationHubData Version: 1.16.0 Depends: AnnotationHub (>= 2.1.45), AnnotationHubData, Imports: mzR (>= 2.3.2), MSnbase, Biostrings, GenomeInfoDb, utils, Biobase, BiocManager, RCurl Suggests: knitr, BiocStyle, rmarkdown, testthat License: Artistic-2.0 Package: ProteoMM Version: 1.4.0 Depends: R (>= 3.5) Imports: gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats, graphics Suggests: BiocStyle, knitr, rmarkdown License: MIT Package: proteoQC Version: 1.21.0 Depends: R (>= 3.0.0), XML, VennDiagram, MSnbase Imports: rTANDEM, plyr, seqinr, Nozzle.R1, ggplot2, reshape2, parallel, rpx, tidyr, dplyr, plotly, rmarkdown, Suggests: RforProteomics, knitr, BiocStyle, R.utils, RUnit,BiocGenerics License: LGPL-2 Package: ProtGenerics Version: 1.18.0 Depends: methods License: Artistic-2.0 Package: PSEA Version: 1.20.0 Imports: Biobase, MASS Suggests: BiocStyle License: Artistic-2.0 Package: psichomics Version: 1.12.1 Depends: R (>= 3.6), shiny (>= 1.0.3), shinyBS Imports: AnnotationDbi, AnnotationHub, BiocFileCache, cluster, colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR, fastICA, fastmatch, ggplot2, ggrepel, graphics, grDevices, highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma, miscTools, pairsD3, plyr, Rcpp (>= 0.12.14), recount, R.utils, reshape2, shinyjs, stringr, stats, SummarizedExperiment, survival, tools, utils, XML, xtable, methods, org.Hs.eg.db LinkingTo: Rcpp Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling License: MIT + file LICENSE Archs: i386, x64 Package: PSICQUIC Version: 1.24.0 Depends: R (>= 3.2.2), methods, IRanges, biomaRt (>= 2.34.1), BiocGenerics, httr, plyr Imports: RCurl Suggests: org.Hs.eg.db License: Apache License 2.0 Package: psygenet2r Version: 1.18.0 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 Package: pulsedSilac Version: 1.0.1 Depends: R (>= 3.6.0) Imports: robustbase, methods, R.utils, taRifx, S4Vectors, SummarizedExperiment, ggplot2, ggridges, stats, utils, UpSetR, cowplot, grid, MuMIn Suggests: testthat (>= 2.1.0), knitr, rmarkdown, gridExtra License: GPL-3 Package: puma Version: 3.28.0 Depends: R (>= 3.2.0), oligo (>= 1.32.0),graphics,grDevices, methods, stats, utils, mclust, oligoClasses Imports: Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses Suggests: pumadata, affydata, snow, limma, ROCR,annotate License: LGPL Archs: i386, x64 Package: PureCN Version: 1.16.0 Depends: R (>= 3.3), DNAcopy, VariantAnnotation (>= 1.14.1) Imports: GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer, S4Vectors, data.table, grDevices, graphics, stats, utils, SummarizedExperiment, GenomeInfoDb, GenomicFeatures, Rsamtools, Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra, futile.logger, VGAM, tools, methods, rhdf5, Matrix Suggests: BiocParallel, BiocStyle, PSCBS, TxDb.Hsapiens.UCSC.hg19.knownGene, copynumber, covr, knitr, optparse, org.Hs.eg.db, rmarkdown, testthat License: Artistic-2.0 Package: pvac Version: 1.34.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) Package: pvca Version: 1.26.0 Depends: R (>= 2.15.1) Imports: Matrix, Biobase, vsn, stats, lme4 Suggests: golubEsets License: LGPL (>= 2.0) Package: Pviz Version: 1.20.0 Depends: R(>= 3.0.0), Gviz(>= 1.7.10) Imports: biovizBase, Biostrings, GenomicRanges, IRanges, data.table, methods Suggests: knitr, pepDat License: Artistic-2.0 Package: PWMEnrich Version: 4.22.0 Depends: methods, grid, BiocGenerics, Biostrings, Imports: seqLogo, gdata, evd Suggests: MotifDb, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr License: LGPL (>= 2) Package: pwOmics Version: 1.18.0 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) Package: pwrEWAS Version: 1.0.0 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 Package: qckitfastq Version: 1.2.0 Imports: magrittr, ggplot2, dplyr, seqTools, zlibbioc, data.table, reshape2, grDevices, graphics, stats, utils, Rcpp, rlang LinkingTo: Rcpp Suggests: knitr, rmarkdown, kableExtra, testthat License: Artistic-2.0 Archs: i386, x64 Package: qcmetrics Version: 1.24.0 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 Package: QDNAseq Version: 1.22.0 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 License: GPL Package: qpcrNorm Version: 1.44.0 Depends: methods, Biobase, limma, affy License: LGPL (>= 2) Package: qpgraph Version: 2.20.0 Depends: R (>= 3.4) Imports: methods, parallel, Matrix (>= 1.0), grid, annotate, graph (>= 1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm, qtl, Rgraphviz Suggests: RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats License: GPL (>= 2) Archs: i386, x64 Package: qPLEXanalyzer Version: 1.4.0 Depends: R (>= 3.6), Biobase, statmod, MSnbase Imports: tidyr, preprocessCore, limma, ggplot2, RColorBrewer, stats, utils, Biostrings, GenomicRanges, IRanges, graphics, BiocGenerics, stringr, purrr, tibble, ggdendro, grDevices, dplyr, magrittr, assertthat Suggests: UniProt.ws, knitr, qPLEXdata License: GPL-2 Package: qrqc Version: 1.40.0 Depends: reshape, ggplot2, Biostrings, biovizBase, brew, xtable, testthat Imports: reshape, ggplot2, Biostrings, biovizBase, graphics, methods, plyr, stats LinkingTo: Rhtslib (>= 1.15.3) License: GPL (>= 2) Archs: i386, x64 Package: qsea Version: 1.12.0 Depends: R (>= 3.5) Imports: Biostrings, graphics, gtools, methods, stats, utils, HMMcopy, rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges, limma, GenomeInfoDb, BiocGenerics, grDevices, zoo, BiocParallel Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager License: GPL (>= 2) Archs: i386, x64 Package: qsmooth Version: 1.2.0 Depends: R (>= 3.6.0) Imports: SummarizedExperiment, utils, sva, stats, methods, graphics Suggests: bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat License: CC BY 4.0 Package: QSutils Version: 1.4.0 Depends: R (>= 3.5), Biostrings, BiocGenerics,methods Imports: ape, stats, psych Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: file LICENSE Package: Qtlizer Version: 1.0.0 Depends: R (>= 3.6.0) Imports: httr, curl, GenomicRanges, stringi Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 Package: QUALIFIER Version: 1.29.1 Depends: R (>= 2.14.0),flowCore,flowViz,ncdfFlow,flowWorkspace, data.table,reshape Imports: MASS,hwriter,lattice,stats4,flowCore,flowViz,methods,flowWorkspace,latticeExtra,grDevices,tools, Biobase,XML,grid Suggests: RSVGTipsDevice, knitr License: Artistic-2.0 Package: quantro Version: 1.20.0 Depends: R (>= 3.1.3) Imports: Biobase, minfi, doParallel, foreach, iterators, ggplot2, methods, RColorBrewer Suggests: knitr, RUnit, BiocGenerics, BiocStyle License: GPL (>= 3) Package: quantsmooth Version: 1.52.0 Depends: R(>= 2.10.0), quantreg, grid License: GPL-2 Package: QuartPAC Version: 1.18.0 Depends: iPAC, GraphPAC, SpacePAC, data.table Suggests: RUnit, BiocGenerics, rgl License: GPL-2 Package: QuasR Version: 1.26.0 Depends: R (>= 3.6), parallel, GenomicRanges (>= 1.13.3), Rbowtie Imports: methods, grDevices, graphics, utils, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, BiocManager, Biobase, Biostrings, BSgenome, Rsamtools (>= 1.99.1), GenomicFeatures (>= 1.17.13), ShortRead (>= 1.19.1), GenomicAlignments, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, Rhisat2, AnnotationDbi LinkingTo: Rhtslib (>= 1.15.3) Suggests: Gviz, BiocStyle, knitr, rmarkdown, covr, testthat License: GPL-2 Archs: x64 Package: QuaternaryProd Version: 1.20.0 Depends: R (>= 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TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny, ChIPpeakAnno License: GPL (>= 2) Archs: i386, x64 Package: r3Cseq Version: 1.32.0 Depends: GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue Imports: methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf, RColorBrewer Suggests: BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Rnorvegicus.UCSC.rn5.masked License: GPL-3 Package: R453Plus1Toolbox Version: 1.36.0 Depends: R (>= 2.12.0), methods, VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6), Biobase Imports: utils, grDevices, graphics, stats, tools, xtable, R2HTML, TeachingDemos, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector, GenomicRanges (>= 1.31.8), SummarizedExperiment, biomaRt, BSgenome (>= 1.47.3), Rsamtools, ShortRead (>= 1.37.1) Suggests: rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2 License: LGPL-3 Archs: i386, x64 Package: R4RNA Version: 1.14.0 Depends: R (>= 3.2.0), Biostrings (>= 2.38.0) License: GPL-3 Package: RaggedExperiment Version: 1.10.0 Depends: R (>= 3.6.0), GenomicRanges (>= 1.37.17) Imports: BiocGenerics, GenomeInfoDb, IRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle, knitr, testthat, MultiAssayExperiment License: Artistic-2.0 Package: rain Version: 1.20.0 Depends: R (>= 2.10), gmp, multtest Suggests: lattice, BiocStyle License: GPL-2 Package: rama Version: 1.60.0 Depends: R(>= 2.5.0) License: GPL (>= 2) Archs: i386, x64 Package: ramwas Version: 1.10.5 Depends: R (>= 3.3.0), methods, filematrix Imports: graphics, stats, utils, digest, glmnet, KernSmooth, grDevices, GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings, BiocGenerics Suggests: knitr, rmarkdown, pander, BiocStyle, BSgenome.Ecoli.NCBI.20080805 License: LGPL-3 Archs: i386, x64 Package: RandomWalkRestartMH Version: 1.6.0 Depends: R(>= 3.5.0) Imports: igraph, Matrix, dnet, methods Suggests: BiocStyle, testthat License: GPL (>= 2) Package: randPack Version: 1.32.0 Depends: methods Imports: Biobase License: Artistic-2.0 Package: RankProd Version: 3.12.0 Depends: R (>= 3.2.1), stats, methods, Rmpfr, gmp Imports: graphics License: file LICENSE License_restricts_use: yes Package: RareVariantVis Version: 2.14.0 Depends: BiocGenerics, VariantAnnotation, googleVis, GenomicFeatures Imports: S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, SummarizedExperiment, GenomicScores Suggests: knitr License: Artistic-2.0 Package: Rariant Version: 1.22.0 Depends: R (>= 3.0.2), GenomicRanges, VariantAnnotation Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, ggbio, ggplot2, exomeCopy, SomaticSignatures, Rsamtools, shiny, VGAM, dplyr, reshape2 Suggests: h5vcData, testthat, knitr, optparse, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 Package: RbcBook1 Version: 1.54.0 Depends: R (>= 2.10), Biobase, graph, rpart License: Artistic-2.0 Package: RBGL Version: 1.62.1 Depends: graph, methods Imports: methods LinkingTo: BH Suggests: Rgraphviz, XML, RUnit, BiocGenerics License: Artistic-2.0 Archs: i386, x64 Package: RBioinf Version: 1.46.0 Depends: graph, methods Suggests: Rgraphviz License: Artistic-2.0 Archs: i386, x64 Package: rBiopaxParser Version: 2.26.0 Depends: R (>= 3.0.0), data.table Imports: XML Suggests: Rgraphviz, RCurl, graph, RUnit, BiocGenerics, nem, RBGL, igraph License: GPL (>= 2) Package: RBM Version: 1.18.0 Depends: R (>= 3.2.0), limma, marray License: GPL (>= 2) Package: Rbowtie Version: 1.26.0 Suggests: parallel, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | file LICENSE Archs: x64 Package: Rbowtie2 Version: 1.8.0 Depends: R (>= 3.5) Suggests: knitr License: GPL (>= 3) Archs: x64 Package: rbsurv Version: 2.44.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), survival License: GPL (>= 2) Package: Rcade Version: 1.28.0 Depends: R (>= 3.5.0), methods, GenomicRanges, Rsamtools, baySeq Imports: utils, grDevices, stats, graphics, rgl, plotrix, S4Vectors (>= 0.23.19), IRanges, GenomeInfoDb, GenomicAlignments Suggests: limma, biomaRt, RUnit, BiocGenerics, BiocStyle License: GPL-2 Package: RCAS Version: 1.12.0 Depends: R (>= 3.3.0), plotly (>= 4.5.2), DT (>= 0.2), data.table, topGO, motifRG Imports: biomaRt, AnnotationDbi, GenomicRanges, BSgenome.Hsapiens.UCSC.hg19, GenomeInfoDb (>= 1.12.0), Biostrings, rtracklayer, org.Hs.eg.db, GenomicFeatures, rmarkdown (>= 0.9.5), genomation (>= 1.5.5), knitr (>= 1.12.3), BiocGenerics, S4Vectors, stats, plotrix, pbapply, RSQLite, proxy, DBI, pheatmap, ggplot2, cowplot, ggseqlogo, methods, utils Suggests: BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Celegans.UCSC.ce10, BSgenome.Dmelanogaster.UCSC.dm3, org.Mm.eg.db, org.Ce.eg.db, org.Dm.eg.db, testthat, covr License: Artistic-2.0 Package: RCASPAR Version: 1.32.0 License: GPL (>= 3) Package: rcellminer Version: 2.8.0 Depends: R (>= 3.2), Biobase, rcdk, fingerprint, rcellminerData Imports: stringr, gplots, ggplot2, methods, stats, utils, shiny Suggests: knitr, RColorBrewer, sqldf, BiocGenerics, testthat, BiocStyle, jsonlite, d3heatmap, glmnet, foreach, doSNOW, parallel License: LGPL-3 + file LICENSE Package: rCGH Version: 1.16.0 Depends: R (>= 3.4),methods,stats,utils,graphics Imports: plyr,DNAcopy,lattice,ggplot2,grid,shiny (>= 0.11.1), limma,affy,mclust,TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db,GenomicFeatures,GenomeInfoDb,GenomicRanges,AnnotationDbi, parallel,IRanges,grDevices,aCGH Suggests: BiocStyle, knitr, BiocGenerics, RUnit License: Artistic-2.0 Package: Rchemcpp Version: 2.24.0 Depends: R (>= 2.15.0) Imports: Rcpp (>= 0.11.1), methods, ChemmineR LinkingTo: Rcpp Suggests: apcluster, kernlab License: GPL (>= 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GOSemSim, ChemmineR, fmcsR, rcdk (>= 3.3.8) Suggests: knitr, rmarkdown, RUnit, BiocGenerics Enhances: ChemmineOB License: Artistic-2.0 | file LICENSE Package: RCy3 Version: 2.6.3 Imports: httr, methods, RJSONIO, XML, utils, BiocGenerics, igraph, stats, graph, R.utils Suggests: RUnit, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE Package: RCyjs Version: 2.8.0 Depends: R (>= 3.5.0), BrowserViz (>= 2.7.18), graph (>= 1.56.0) Imports: methods, httpuv (>= 1.5.0), BiocGenerics, base64enc, utils Suggests: RUnit, BiocStyle, RefNet, knitr, rmarkdown License: MIT + file LICENSE Package: RDAVIDWebService Version: 1.24.0 Depends: R (>= 2.14.1), methods, graph, GOstats, ggplot2 Imports: Category, GO.db, RBGL, rJava Suggests: Rgraphviz License: GPL (>= 2) Package: rDGIdb Version: 1.12.0 Imports: jsonlite,httr,methods,graphics Suggests: BiocStyle,knitr,testthat License: MIT + file LICENSE Package: Rdisop Version: 1.46.0 Depends: R (>= 2.0.0), Rcpp LinkingTo: Rcpp Suggests: RUnit License: GPL-2 Archs: i386, x64 Package: RDRToolbox Version: 1.36.0 Depends: R (>= 2.9.0) Imports: graphics, grDevices, methods, stats, MASS, rgl Suggests: golubEsets License: GPL (>= 2) Package: ReactomeGSA Version: 1.0.0 Imports: jsonlite, httr, progress, ggplot2, methods Suggests: testthat, knitr, rmarkdown, ReactomeGSA.data, Biobase, devtools Enhances: limma, edgeR License: MIT + file LICENSE Package: ReactomePA Version: 1.30.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, DOSE (>= 3.5.1), enrichplot, ggplot2, ggraph, reactome.db, igraph, graphite Suggests: BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, prettydoc, testthat License: GPL-2 Package: readat Version: 1.11.0 Depends: R (>= 3.4.0) Imports: assertive.base (>= 0.0-7), assertive.files (>= 0.0-2), assertive.numbers (>= 0.0-2), assertive.properties (>= 0.0-4), assertive.sets (>= 0.0-3), assertive.types (>= 0.0-3), Biobase (>= 2.34.0), data.table (>= 1.10.4), dplyr (>= 0.5.0), magrittr (>= 1.5), openxlsx (>= 4.0.17), pathological (>= 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gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker License: Artistic-2.0 Package: regsplice Version: 1.12.6 Imports: glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats, pbapply, utils, methods Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE Package: REMP Version: 1.10.1 Depends: R (>= 3.6), SummarizedExperiment(>= 1.1.6), minfi (>= 1.22.0) Imports: readr, rtracklayer, graphics, stats, utils, methods, settings, BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel, doParallel, parallel, foreach, caret, kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db, impute, iterators Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC License: GPL-3 Package: Repitools Version: 1.32.0 Depends: R (>= 3.0.0), methods, BiocGenerics (>= 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parallel Suggests: BiocStyle License: GPL (>= 2) Archs: i386, x64 Package: rGADEM Version: 2.34.1 Depends: R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo Imports: Biostrings, GenomicRanges, methods, graphics, seqLogo Suggests: BSgenome.Hsapiens.UCSC.hg19, rtracklayer License: Artistic-2.0 Archs: i386, x64 Package: RGalaxy Version: 1.30.0 Depends: XML, methods, tools, optparse Imports: BiocGenerics, Biobase, roxygen2 Suggests: RUnit, hgu95av2.db, AnnotationDbi, knitr, formatR, Rserve Enhances: RSclient License: Artistic-2.0 Package: Rgin Version: 1.6.0 Depends: R (>= 3.5) LinkingTo: RcppEigen (>= 0.3.3.5.0) Suggests: knitr, rmarkdown License: MIT + file LICENSE Archs: i386, x64 Package: RGMQL Version: 1.6.0 Depends: R(>= 3.4.2), RGMQLlib Imports: httr, rJava, GenomicRanges, rtracklayer, data.table, utils, plyr, xml2, methods, S4Vectors, dplyr, stats, glue, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: RGraph2js Version: 1.14.0 Imports: 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ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment License: GPL-3 Package: riboSeqR Version: 1.20.0 Depends: R (>= 3.0.2), methods, GenomicRanges, abind Imports: Rsamtools, IRanges, baySeq, GenomeInfoDb, seqLogo Suggests: BiocStyle, RUnit, BiocGenerics License: GPL-3 Package: RImmPort Version: 1.14.0 Imports: plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools, utils, RSQLite Suggests: knitr License: GPL-3 Package: Ringo Version: 1.50.0 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 Archs: i386, x64 Package: RIPSeeker Version: 1.26.0 Depends: R (>= 2.15), methods, S4Vectors (>= 0.9.25), IRanges, GenomicRanges, SummarizedExperiment, Rsamtools, GenomicAlignments, rtracklayer Suggests: biomaRt, ChIPpeakAnno, parallel, GenomicFeatures License: GPL-2 Package: Risa Version: 1.28.0 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 Package: RITAN Version: 1.10.0 Depends: R (>= 3.4), Imports: graphics, stats, utils, grid, gridExtra, reshape2, gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL, linkcomm, dynamicTreeCut, sqldf, gsubfn, hash, png, sqldf, igraph, BgeeDB, knitr, RITANdata Suggests: rmarkdown License: file LICENSE Package: RIVER Version: 1.10.0 Depends: R (>= 3.3.2) Imports: glmnet, pROC, ggplot2, graphics, stats, Biobase, methods, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools License: GPL (>= 2) Package: RJMCMCNucleosomes Version: 1.10.0 Depends: R (>= 3.4), IRanges, GenomicRanges Imports: Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb, S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit License: Artistic-2.0 Archs: i386, x64 Package: RLMM Version: 1.48.0 Depends: R (>= 2.1.0) Imports: graphics, grDevices, MASS, stats, utils License: LGPL (>= 2) Package: Rmagpie Version: 1.42.0 Depends: R (>= 2.6.1), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab, methods, pamr, stats, utils Suggests: xtable License: GPL (>= 3) Package: RMassBank Version: 2.14.1 Depends: Rcpp Imports: XML,RCurl,rjson,S4Vectors,digest, rcdk,yaml,mzR,methods,Biobase,MSnbase,httr Suggests: gplots,RMassBankData, xcms (>= 1.37.1), CAMERA, RUnit, enviPat License: Artistic-2.0 Package: rmelting Version: 1.2.0 Depends: R (>= 3.6) Imports: Rdpack, rJava (>= 0.5-0) Suggests: readxl, knitr, rmarkdown, reshape2, pander, testthat License: GPL-2 | GPL-3 Package: Rmmquant Version: 1.4.0 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 Archs: i386, x64 Package: RNAinteract Version: 1.34.0 Depends: R (>= 2.12.0), abind, locfit, Biobase Imports: RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid, hwriter, lattice, latticeExtra, limma, methods, splots (>= 1.13.12) License: Artistic-2.0 Package: RNAither Version: 2.34.0 Depends: R (>= 2.10), topGO, RankProd, prada Imports: geneplotter, limma, biomaRt, car, splots, methods License: Artistic-2.0 Package: RNAmodR Version: 1.0.2 Depends: R (>= 3.6), IRanges (>= 2.19.7), S4Vectors (>= 0.23.18), GenomicRanges, Modstrings Imports: methods, stats, graphics, grDevices, grid, matrixStats, assertive, BiocGenerics, XVector, Biostrings, BiocParallel, GenomicFeatures, GenomicAlignments, GenomeInfoDb, rtracklayer, Rsamtools, BSgenome, RColorBrewer, colorRamps, biovizBase, ggplot2, Gviz, reshape2, stringi, stringr, ROCR Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data License: Artistic-2.0 Package: RNAmodR.AlkAnilineSeq Version: 1.0.0 Depends: R (>= 3.6), RNAmodR Imports: methods, S4Vectors, IRanges, BiocGenerics, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, Biostrings, RNAmodR.Data License: Artistic-2.0 Package: RNAmodR.ML Version: 1.0.0 Depends: R (>= 3.6), RNAmodR Imports: methods, assertive, BiocGenerics, S4Vectors, IRanges, GenomicRanges, stats, ranger Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data, RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer, keras License: Artistic-2.0 Package: RNAmodR.RiboMethSeq Version: 1.0.0 Depends: R (>= 3.6), RNAmodR Imports: methods, S4Vectors, BiocGenerics, IRanges, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, RNAmodR.Data License: Artistic-2.0 Package: RNAprobR Version: 1.18.0 Depends: R (>= 3.1.1), GenomicFeatures(>= 1.16.3), plyr(>= 1.8.1), BiocGenerics(>= 0.10.0) Imports: Biostrings(>= 2.32.1), GenomicRanges(>= 1.16.4), IRanges(>= 2.10.5), Rsamtools(>= 1.16.1), rtracklayer(>= 1.24.2), GenomicAlignments(>= 1.5.12), S4Vectors(>= 0.14.7), graphics, stats, utils Suggests: BiocStyle License: GPL (>= 2) Package: RNAsense Version: 1.0.0 Depends: R (>= 3.6) Imports: ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment, stats, utils, methods Suggests: knitr, rmarkdown License: GPL-3 Package: rnaseqcomp Version: 1.16.0 Depends: R (>= 3.2.0) Imports: RColorBrewer, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 Package: rnaSeqMap Version: 2.44.0 Depends: R (>= 2.11.0), methods, Biobase, Rsamtools, GenomicAlignments Imports: GenomicRanges , IRanges, edgeR, DESeq, DBI License: GPL-2 Archs: i386, x64 Package: RNASeqPower Version: 1.26.0 License: LGPL (>= 2) Package: RnaSeqSampleSize Version: 1.17.0 Depends: R (>= 2.10), RnaSeqSampleSizeData Imports: biomaRt,edgeR,heatmap3,matlab,KEGGREST,Rcpp (>= 0.11.2) LinkingTo: Rcpp Suggests: BiocStyle, knitr License: GPL (>= 2) Archs: i386, x64 Package: RnBeads Version: 2.4.0 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 Package: Rnits Version: 1.20.0 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 Package: roar Version: 1.22.0 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 Package: ROC Version: 1.62.0 Depends: R (>= 1.9.0), utils, methods Imports: knitr Suggests: Biobase License: Artistic-2.0 Archs: i386, x64 Package: Roleswitch Version: 1.24.0 Depends: R (>= 2.10), pracma, reshape, plotrix, microRNA, biomaRt, Biostrings, Biobase, DBI Suggests: ggplot2 License: GPL-2 Package: rols Version: 2.14.0 Depends: methods Imports: httr, progress, jsonlite, utils, Biobase, BiocGenerics (>= 0.23.1) Suggests: GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat, lubridate, DT, rmarkdown, License: GPL-2 Package: ROntoTools Version: 2.14.0 Depends: methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz Suggests: RUnit, BiocGenerics License: CC BY-NC-ND 4.0 + file LICENSE Package: ropls Version: 1.18.8 Depends: Biobase Imports: graphics, grDevices, methods, MultiDataSet, stats Suggests: BiocGenerics, BiocStyle, knitr, multtest, omicade4, rmarkdown, testthat License: CeCILL Package: ROTS Version: 1.14.0 Depends: R (>= 3.3) Imports: Rcpp, stats, Biobase, methods LinkingTo: Rcpp Suggests: testthat License: GPL (>= 2) Archs: i386, x64 Package: RPA Version: 1.42.0 Depends: R (>= 3.1.1), affy, BiocGenerics, methods Imports: phyloseq Suggests: affydata, knitr, parallel License: BSD_2_clause + file LICENSE Package: RProtoBufLib Version: 1.8.0 License: BSD_3_clause Archs: i386, x64 Package: RpsiXML Version: 2.28.0 Depends: methods, annotate (>= 1.21.0), graph (>= 1.21.0), Biobase, RBGL (>= 1.17.0), XML (>= 2.4.0), hypergraph (>= 1.15.2), AnnotationDbi Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db,hom.Hs.inp.db, hom.Mm.inp.db, hom.Dm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db,Rgraphviz, ppiStats, ScISI License: LGPL-3 Package: rpx Version: 1.22.0 Depends: methods Imports: xml2, RCurl, utils Suggests: MSnbase, Biostrings, BiocStyle, testthat, knitr License: GPL-2 Package: Rqc Version: 1.20.0 Depends: BiocParallel, ShortRead, ggplot2 Imports: BiocGenerics (>= 0.25.1), Biostrings, IRanges, methods, S4Vectors, knitr (>= 1.7), BiocStyle, plyr, markdown, grid, reshape2, Rcpp (>= 0.11.6), biovizBase, shiny, Rsamtools, GenomicAlignments, GenomicFiles LinkingTo: Rcpp Suggests: testthat License: GPL (>= 2) Archs: i386, x64 Package: rqt Version: 1.12.0 Depends: R (>= 3.4), SummarizedExperiment Imports: stats,Matrix,ropls,methods,car,RUnit,metap,CompQuadForm,glmnet,utils,pls Suggests: BiocStyle, knitr, rmarkdown License: GPL Package: rqubic Version: 1.32.0 Imports: methods, Biobase, BiocGenerics, biclust Suggests: RColorBrewer License: GPL-2 Archs: i386, x64 Package: rRDP Version: 1.20.0 Depends: Biostrings (>= 2.26.2) Suggests: rRDPData License: GPL-2 | file LICENSE Package: RRHO Version: 1.26.0 Depends: R (>= 2.10), grid Imports: VennDiagram Suggests: lattice License: GPL-2 Package: Rsamtools Version: 2.2.3 Depends: methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Biostrings (>= 2.47.6) Imports: utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops, BiocParallel 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 Archs: i386, x64 Package: rsbml Version: 2.44.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils Imports: BiocGenerics, graph, utils License: Artistic-2.0 Archs: i386, x64 Package: rScudo Version: 1.2.0 Depends: R (>= 3.6) Imports: methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, SummarizedExperiment, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel License: GPL-3 Package: RSeqAn Version: 1.6.0 License: BSD_3_clause + file LICENSE Package: Rsubread Version: 2.0.1 Imports: grDevices, stats, utils License: GPL-3 Archs: i386, x64 Package: RSVSim Version: 1.26.0 Depends: R (>= 3.0.0), Biostrings, GenomicRanges Imports: methods, IRanges, ShortRead Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer License: LGPL-3 Package: rTANDEM Version: 1.26.0 Depends: XML, Rcpp, data.table (>= 1.8.8) Imports: methods LinkingTo: Rcpp Suggests: biomaRt License: Artistic-1.0 | file LICENSE Archs: i386, x64 Package: RTCA Version: 1.38.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 Package: RTCGA Version: 1.16.0 Depends: R (>= 3.3.0) Imports: XML, assertthat, stringi, rvest, data.table, xml2, dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr, scales Suggests: devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, RTCGA.PANCAN12, magrittr, tidyr License: GPL-2 Package: RTCGAToolbox Version: 2.16.3 Depends: R (>= 3.5.0) Imports: BiocGenerics, data.table, DelayedArray, GenomicRanges, GenomeInfoDb, httr, IRanges, 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 Package: RTN Version: 2.10.1 Depends: R (>= 3.5.0), methods Imports: RedeR, minet, viper, mixtools, snow, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: RTNduals Version: 1.10.0 Depends: R(>= 3.5), RTN(>= 2.6.3), methods Imports: graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 Package: RTNsurvival Version: 1.10.0 Depends: R(>= 3.5), RTN(>= 2.6.3), RTNduals(>= 1.6.1), methods Imports: survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test Suggests: Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 Package: RTopper Version: 1.32.0 Depends: R (>= 2.11.0), Biobase Imports: limma, multtest Suggests: limma, org.Hs.eg.db, KEGG.db, GO.db License: GPL (>= 3) Package: rtracklayer Version: 1.46.0 Depends: R (>= 3.3), methods, GenomicRanges (>= 1.37.2) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.25.1), S4Vectors (>= 0.23.18), IRanges (>= 2.13.13), XVector (>= 0.19.7), GenomeInfoDb (>= 1.15.2), Biostrings (>= 2.47.6), zlibbioc, RCurl (>= 1.4-2), 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 Archs: i386, x64 Package: Rtreemix Version: 1.48.0 Depends: R (>= 2.5.0) Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz License: LGPL Archs: i386, x64 Package: rTRM Version: 1.24.0 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 Package: rTRMui Version: 1.24.0 Imports: shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 Package: runibic Version: 1.8.0 Depends: R (>= 3.4.0), biclust, SummarizedExperiment Imports: Rcpp (>= 0.12.12), testthat, methods LinkingTo: Rcpp Suggests: knitr, rmarkdown, GEOquery, affy, airway, QUBIC License: MIT + file LICENSE Archs: i386, x64 Package: RUVcorr Version: 1.18.0 Imports: corrplot, MASS, stats, lattice, grDevices, gridExtra, snowfall, psych, BiocParallel, grid, bladderbatch, reshape2 Suggests: knitr, BiocStyle, hgu133a2.db License: GPL-2 Package: RUVnormalize Version: 1.20.1 Depends: R (>= 2.10.0) Imports: RUVnormalizeData, Biobase Enhances: spams License: GPL-3 Package: RUVSeq Version: 1.20.0 Depends: Biobase, EDASeq (>= 1.99.1), edgeR Imports: methods, MASS Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 License: Artistic-2.0 Package: RVS Version: 1.8.0 Depends: R (>= 3.5.0) Imports: GENLIB, gRain, snpStats, kinship2, methods, stats, utils Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation License: GPL-2 Package: rWikiPathways Version: 1.6.1 Imports: caTools, httr, rjson, utils, XML Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE Package: S4Vectors Version: 0.24.4 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 Archs: i386, x64 Package: safe Version: 3.26.0 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) Package: sagenhaft Version: 1.56.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, methods, SparseM, stats, utils License: GPL (>= 2) Package: SAGx Version: 1.60.0 Depends: R (>= 2.5.0), stats, multtest, methods Imports: Biobase, stats4 Suggests: KEGG.db, hu6800.db, MASS License: GPL-3 Archs: i386, x64 Package: SAIGEgds Version: 1.0.2 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 Archs: i386, x64 Package: sampleClassifier Version: 1.10.0 Depends: R (>= 3.4), MGFM, MGFR, annotate Imports: e1071, ggplot2, stats, utils Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db License: Artistic-2.0 Package: SamSPECTRAL Version: 1.40.0 Depends: R (>= 3.3.3) Imports: methods License: GPL (>= 2) Archs: i386, x64 Package: sangerseqR Version: 1.22.0 Depends: R (>= 3.0.2), Biostrings Imports: methods, shiny Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 Package: SANTA Version: 2.24.0 Depends: R (>= 2.14), igraph Imports: Matrix, snow Suggests: RUnit, BiocGenerics, knitr, knitcitations, formatR, org.Sc.sgd.db, BioNet, DLBCL, msm License: GPL (>= 2) Archs: i386, x64 Package: sapFinder Version: 1.24.0 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 Archs: i386, x64 Package: savR Version: 1.24.0 Depends: ggplot2 Imports: methods, reshape2, scales, gridExtra, XML Suggests: Cairo, testthat License: AGPL-3 Package: SBGNview Version: 1.0.0 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 Package: SBMLR Version: 1.82.0 Depends: XML, deSolve Suggests: rsbml License: GPL-2 Package: SC3 Version: 1.14.0 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 Archs: i386, x64 Package: Scale4C Version: 1.8.0 Depends: R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 Package: SCAN.UPC Version: 2.28.0 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 Package: SCANVIS Version: 1.0.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file LICENSE Package: scater Version: 1.14.0 Depends: SingleCellExperiment, ggplot2 Imports: BiocGenerics, SummarizedExperiment, Matrix, ggbeeswarm, grid, DelayedArray, DelayedMatrixStats, methods, S4Vectors, stats, utils, viridis, Rcpp, BiocNeighbors, BiocSingular, BiocParallel LinkingTo: Rcpp, beachmat Suggests: BiocStyle, BiocFileCache, biomaRt, beachmat, cowplot, destiny, knitr, robustbase, rmarkdown, Rtsne, uwot, testthat, pheatmap, Biobase, limma, DropletUtils License: GPL-3 Archs: i386, x64 Package: scBFA Version: 1.0.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods Suggests: knitr, rmarkdown, testthat, Rtsne License: GPL-3 Package: SCBN Version: 1.4.0 Depends: R (>= 3.5.0) Imports: stats Suggests: knitr,rmarkdown License: GPL-2 Package: scDblFinder Version: 1.1.8 Depends: R (>= 3.6) Imports: igraph, Matrix, matrixStats, BiocParallel, BiocNeighbors, SummarizedExperiment, SingleCellExperiment, scran, scater, data.table, dplyr, ggplot2, randomForest, graphics, methods, stats, DelayedArray Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 Package: scDD Version: 1.10.0 Depends: R (>= 3.4) Imports: fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm, SingleCellExperiment, SummarizedExperiment, grDevices, graphics, stats, S4Vectors, scran Suggests: BiocStyle, knitr, gridExtra License: GPL-2 Package: scde Version: 2.14.0 Depends: R (>= 3.0.0), flexmix Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown License: GPL-2 Archs: i386, x64 Package: scds Version: 1.2.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot License: MIT + file LICENSE Package: scFeatureFilter Version: 1.6.0 Depends: R (>= 3.5) Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods Suggests: testthat, knitr, rmarkdown, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE Package: scfind Version: 1.8.0 Depends: R(>= 3.4) Imports: SingleCellExperiment, SummarizedExperiment, methods, stats, bit, dplyr, hash, reshape2, Rcpp(>= 0.12.12) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 Archs: i386, x64 Package: scGPS Version: 1.0.0 Depends: R (>= 3.6), SummarizedExperiment, dynamicTreeCut, SingleCellExperiment Imports: glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1), fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel, grDevices, graphics, stats, utils, DESeq, locfit LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE License: GPL-3 Archs: i386, x64 Package: schex Version: 1.0.55 Depends: SingleCellExperiment (>= 1.7.4), Seurat, ggplot2 Imports: hexbin, stats, methods, cluster, dplyr, entropy Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran License: GPL-3 Package: ScISI Version: 1.58.0 Depends: R (>= 2.10), GO.db, RpsiXML, annotate, apComplex Imports: AnnotationDbi, GO.db, RpsiXML, annotate, methods, org.Sc.sgd.db, utils Suggests: ppiData, xtable License: LGPL Package: scmap Version: 1.8.0 Depends: R(>= 3.4) Imports: Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown License: GPL-3 Archs: i386, x64 Package: scMerge Version: 1.2.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), parallel, pdist, proxy, Rcpp (>= 0.12.18), RcppEigen (>= 0.3.3.4.0), ruv, S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3), SummarizedExperiment LinkingTo: Rcpp (>= 0.12.18), RcppEigen, testthat Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, scater, testthat, badger License: GPL-3 Archs: i386, x64 Package: scmeth Version: 1.6.0 Depends: R (>= 3.5.0) Imports: knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes License: GPL-2 Package: SCnorm Version: 1.8.2 Depends: R (>= 3.4.0), Imports: SingleCellExperiment, SummarizedExperiment, stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, S4Vectors, ggplot2, forcats, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) Package: scone Version: 1.10.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, BatchJobs License: Artistic-2.0 Package: Sconify Version: 1.6.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 Package: scoreInvHap Version: 1.8.0 Depends: R (>= 3.4.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE Package: scPCA Version: 1.0.0 Depends: R (>= 3.6) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, BiocParallel, elasticnet, cluster, kernlab, origami Suggests: testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, Matrix, ggplot2, ggpubr, splatter, SingleCellExperiment License: MIT + file LICENSE Package: scPipe Version: 1.8.0 Depends: R (>= 3.4), ggplot2, methods, SingleCellExperiment Imports: Rhtslib, biomaRt, GGally, MASS, mclust, Rcpp (>= 0.11.3), reshape, BiocGenerics, robustbase, scales, utils, stats, S4Vectors, SummarizedExperiment, AnnotationDbi, org.Hs.eg.db, org.Mm.eg.db, stringr, rtracklayer, hashmap, dplyr, GenomicRanges, magrittr, glue LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat Suggests: Rsubread, knitr, rmarkdown, testthat License: GPL (>= 2) Archs: i386, x64 Package: scran Version: 1.14.6 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, scater, edgeR, limma, BiocNeighbors, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, dqrng LinkingTo: Rcpp, beachmat, BH, dqrng Suggests: testthat, BiocStyle, knitr, beachmat, HDF5Array, scRNAseq, dynamicTreeCut, DESeq2, monocle, Biobase, aroma.light, pheatmap License: GPL-3 Archs: i386, x64 Package: scRecover Version: 1.2.0 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), Rmagic (>= 1.3.0), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL Package: scsR Version: 1.22.0 Depends: R (>= 2.14.0), STRINGdb, methods, BiocGenerics, Biostrings, IRanges, plyr, tcltk Imports: sqldf, hash, ggplot2, graphics,grDevices, RColorBrewer Suggests: RUnit License: GPL-2 Package: scTensor Version: 1.2.1 Depends: R (>= 3.5.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor, rTensor, abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi, grDevices, graphics, stats, utils, outliers, Category, meshr, GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork Suggests: testthat, LRBase.Hsa.eg.db, MeSH.Hsa.eg.db, LRBase.Mmu.eg.db, MeSH.Mmu.eg.db, LRBaseDbi, Seurat, Homo.sapiens License: Artistic-2.0 Package: scTGIF Version: 1.0.0 Depends: R (>= 3.6.0) Imports: GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly, tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr, S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor, methods, scales, msigdbr Suggests: testthat License: Artistic-2.0 Package: SDAMS Version: 1.6.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL Package: segmentSeq Version: 2.20.0 Depends: R (>= 3.0.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics License: GPL-3 Package: SELEX Version: 1.18.0 Depends: R (>= 2.7.0), rJava (>= 0.5-0), Biostrings (>= 2.26.0) License: GPL (>= 2) Package: SemDist Version: 1.20.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) Package: semisup Version: 1.10.0 Depends: R (>= 3.5.0) Imports: VGAM Suggests: knitr, testthat, SummarizedExperiment License: GPL-3 Package: SEPIRA Version: 1.6.0 Depends: R (>= 3.5.0) Imports: limma (>= 3.32.5), corpcor (>= 1.6.9), parallel (>= 3.3.1), stats Suggests: knitr, rmarkdown, testthat, igraph License: GPL-3 Package: seq2pathway Version: 1.18.0 Depends: R (>= 2.10.0) Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data License: GPL-2 Package: SeqArray Version: 1.26.2 Depends: R (>= 3.5.0), gdsfmt (>= 1.18.0) Imports: methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors LinkingTo: gdsfmt Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, Rsamtools, VariantAnnotation License: GPL-3 Archs: i386, x64 Package: seqbias Version: 1.33.0 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 Archs: i386, x64 Package: seqCAT Version: 1.8.1 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE Package: seqCNA Version: 1.32.0 Depends: R (>= 3.0), GLAD (>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot (>= 0.99), methods License: GPL-3 Archs: i386, x64 Package: seqcombo Version: 1.8.0 Depends: R (>= 3.4.0) Imports: Biostrings, cowplot, dplyr, ggplot2, grid, igraph, magrittr, methods, rvcheck, utils Suggests: emojifont, knitr, prettydoc, tibble License: Artistic-2.0 Package: SeqGSEA Version: 1.26.0 Depends: Biobase, doParallel, DESeq Imports: methods, biomaRt Suggests: easyRNASeq, GenomicRanges License: GPL (>= 3) Package: seqLogo Version: 1.52.0 Depends: methods, grid Imports: stats4 License: LGPL (>= 2) Package: seqPattern Version: 1.18.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 Package: seqplots Version: 1.24.0 Depends: R (>= 3.2.0) Imports: methods, IRanges, BSgenome, digest, rtracklayer, GenomicRanges, Biostrings, shiny (>= 0.13.0), DBI, RSQLite, plotrix, fields, grid, kohonen, parallel, GenomeInfoDb, class, S4Vectors, ggplot2, reshape2, gridExtra, jsonlite, DT (>= 0.1.0), RColorBrewer, Rsamtools, GenomicAlignments, BiocManager Suggests: testthat, BiocStyle, knitr, rmarkdown, covr License: GPL-3 Package: seqsetvis Version: 1.6.0 Depends: R (>= 3.5), ggplot2 Imports: data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, IRanges, limma, methods, parallel, pbapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, stats Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, cowplot, knitr, rmarkdown, testthat License: MIT + file LICENSE Package: SeqSQC Version: 1.8.1 Depends: R (>= 3.4), ExperimentHub (>= 1.3.7), SNPRelate (>= 1.10.2) Imports: e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, rbokeh, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils Suggests: BiocStyle, knitr, testthat License: GPL-3 Package: seqTools Version: 1.20.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 Archs: i386, x64 Package: SeqVarTools Version: 1.24.1 Depends: SeqArray Imports: grDevices, graphics, stats, methods, Biobase, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, dplyr, rlang, tidyr Suggests: BiocGenerics, BiocStyle, RUnit, stringr License: GPL-3 Package: sesame Version: 1.4.0 Depends: R (>= 3.6), sesameData, methods Imports: BiocParallel, R6, grDevices, utils, illuminaio, MASS, GenomicRanges, IRanges, grid, preprocessCore, stats, S4Vectors, randomForest, wheatmap, ggplot2, parallel, matrixStats, DNAcopy Suggests: scales, knitr, rmarkdown, testthat, minfi, SummarizedExperiment, FlowSorted.CordBloodNorway.450k, FlowSorted.Blood.450k, dplyr, tidyr, BiocStyle License: MIT + file LICENSE Package: SEtools Version: 1.0.0 Depends: R (>= 3.6) Imports: SummarizedExperiment, data.table, pheatmap, seriation, ComplexHeatmap, circlize, methods Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL Package: sevenbridges Version: 1.16.1 Depends: methods, utils, stats Imports: httr, jsonlite, yaml, objectProperties, stringr, S4Vectors, docopt, curl, uuid, dplyr Suggests: knitr, rmarkdown, testthat, readr License: Apache License 2.0 | file LICENSE Package: sevenC Version: 1.6.0 Depends: R (>= 3.5), InteractionSet (>= 1.2.0) Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), GenomeInfoDb (>= 1.12.2), GenomicRanges (>= 1.28.5), IRanges (>= 2.10.3), S4Vectors (>= 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BiocGenerics (>= 0.3.2), shiny (>= 0.13.2), minfi (>= 1.18.2), IlluminaHumanMethylation450kmanifest, matrixStats, R (>= 3.0.0) Imports: RColorBrewer Suggests: shinyMethylData, minfiData, BiocStyle, RUnit, digest, knitr License: Artistic-2.0 Package: shinyTANDEM Version: 1.24.0 Depends: rTANDEM (>= 1.3.5), shiny, mixtools, methods, xtable License: GPL-3 Package: ShortRead Version: 1.44.3 Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), hwriter, methods, zlibbioc, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi License: Artistic-2.0 Archs: i386, x64 Package: SIAMCAT Version: 1.6.0 Depends: R (>= 3.5.0), 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 Package: sigaR Version: 1.34.0 Depends: Biobase, CGHbase, methods, mvtnorm, Imports: corpcor (>= 1.6.2), graphics, igraph, limma, marray, MASS, penalized, quadprog, snowfall, stats Suggests: CGHcall License: GPL (>= 2) Package: SigCheck Version: 2.18.0 Depends: R (>= 3.2.0), MLInterfaces, Biobase, e1071, BiocParallel, survival Imports: graphics, stats, utils, methods Suggests: BiocStyle, breastCancerNKI, qusage License: Artistic-2.0 Package: sigFeature Version: 1.4.0 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 Package: SigFuge Version: 1.24.0 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 Package: siggenes Version: 1.60.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) Package: sights Version: 1.12.0 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 Package: signatureSearch Version: 1.0.4 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 Archs: i386, x64 Package: signeR Version: 1.12.0 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 Archs: i386, x64 Package: signet Version: 1.6.0 Depends: R (>= 3.4.0) Imports: graph, igraph, RBGL, graphics, utils, stats, methods Suggests: graphite, BiocStyle, knitr, rmarkdown License: GPL-2 Package: sigPathway Version: 1.54.0 Depends: R (>= 2.10) Suggests: hgu133a.db (>= 1.10.0), XML (>= 1.6-3), AnnotationDbi (>= 1.3.12) License: GPL-2 Archs: i386, x64 Package: SigsPack Version: 1.0.0 Depends: R (>= 3.6) Imports: quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0), VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb, GenomicRanges, rtracklayer, SummarizedExperiment, graphics, stats, utils Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown License: GPL-3 Package: sigsquared Version: 1.18.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 Package: SIM Version: 1.56.0 Depends: R (>= 2.4), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) Archs: i386, x64 Package: SIMAT Version: 1.18.0 Depends: R (>= 3.5.0), Rcpp (>= 0.11.3) Imports: mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 Package: SimBindProfiles Version: 1.24.0 Depends: R (>= 2.10), methods, Ringo Imports: limma, mclust, Biobase License: GPL-3 Package: SIMD Version: 1.4.0 Depends: R (>= 3.5.0) Imports: edgeR, statmod, methylMnM, stats, utils Suggests: BiocStyle, knitr,rmarkdown License: GPL-3 Archs: i386, x64 Package: similaRpeak Version: 1.18.0 Depends: R6 (>= 2.0) Imports: stats Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle License: Artistic-2.0 Package: SIMLR Version: 1.12.0 Depends: R (>= 3.6), Imports: parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra LinkingTo: Rcpp Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph License: file LICENSE Archs: i386, x64 Package: simpleaffy Version: 2.62.0 Depends: R (>= 2.0.0), methods, utils, grDevices, graphics, stats, BiocGenerics (>= 0.1.12), Biobase, affy (>= 1.33.6), genefilter, gcrma Imports: methods, utils, grDevices, graphics, stats, BiocGenerics, Biobase, affy, genefilter, gcrma License: GPL (>= 2) Archs: i386, x64 Package: simulatorZ Version: 1.20.0 Depends: R (>= 3.5), Biobase, SummarizedExperiment, survival, CoxBoost, BiocGenerics Imports: graphics, stats, gbm, Hmisc, GenomicRanges, methods Suggests: RUnit, BiocStyle, curatedOvarianData, parathyroidSE, superpc License: Artistic-2.0 Archs: i386, x64 Package: sincell Version: 1.18.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: GPL (>= 2) Archs: i386, x64 Package: SingleCellExperiment Version: 1.8.0 Depends: SummarizedExperiment Imports: S4Vectors (>= 0.23.19), methods, BiocGenerics, utils, stats Suggests: testthat, BiocStyle, knitr, rmarkdown, scRNAseq, Rtsne, Matrix License: GPL-3 Package: singleCellTK Version: 1.6.0 Depends: R (>= 3.5), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase Imports: ape, colourpicker, cluster, ComplexHeatmap, data.table, DESeq2, DT, ggplot2, ggtree, gridExtra, GSVA (>= 1.26.0), GSVAdata, limma, MAST, matrixStats, methods, multtest, plotly, RColorBrewer, Rtsne, S4Vectors, shiny, shinyjs, shinyBS, sva, reshape2, AnnotationDbi, shinyalert, circlize, enrichR, celda, shinycssloaders, shinythemes, umap Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, bladderbatch, rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable, spelling, GSEABase License: MIT + file LICENSE Package: SingleR Version: 1.0.6 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocNeighbors, BiocParallel, stats, utils, Rcpp, ExperimentHub LinkingTo: Rcpp, beachmat Suggests: testthat, knitr, rmarkdown, BiocStyle, beachmat, SingleCellExperiment, scater, scRNAseq, scran, BiocGenerics, ggplot2, pheatmap, grDevices, viridis, AnnotationHub, AnnotationDbi License: GPL-3 + file LICENSE Archs: i386, x64 Package: singscore Version: 1.6.0 Depends: R (>= 3.5),GSEABase Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, reshape2, S4Vectors Suggests: knitr, rmarkdown, testthat License: GPL-3 Package: SISPA Version: 1.16.0 Depends: R (>= 3.2),genefilter,GSVA,changepoint Imports: data.table, plyr, ggplot2 Suggests: knitr License: GPL-2 Package: sitePath Version: 1.2.3 Depends: R (>= 3.6.0) Imports: ape, seqinr, Rcpp, methods, graphics, utils, stats LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE Archs: i386, x64 Package: sizepower Version: 1.56.0 Depends: stats License: LGPL Package: skewr Version: 1.18.0 Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports: minfi, S4Vectors (>= 0.19.1), RColorBrewer Suggests: GEOquery, knitr, minfiData License: GPL-2 Package: slalom Version: 1.8.0 Depends: R (>= 3.4) Imports: Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase, methods, rsvd, SingleCellExperiment, SummarizedExperiment, stats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: knitr, rhdf5, scater, testthat License: GPL-2 Archs: i386, x64 Package: SLGI Version: 1.46.0 Depends: R (>= 2.10), ScISI, lattice Imports: AnnotationDbi, Biobase, GO.db, ScISI, graphics, lattice, methods, stats, BiocGenerics Suggests: GO.db, org.Sc.sgd.db License: Artistic-2.0 Package: slingshot Version: 1.4.0 Depends: R (>= 3.5), princurve (>= 2.0.4), stats Imports: ape, graphics, grDevices, igraph, matrixStats, methods, SingleCellExperiment, SummarizedExperiment Suggests: BiocGenerics, BiocStyle, clusterExperiment, destiny, gam, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, covr License: Artistic-2.0 Package: slinky Version: 1.4.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment, curl, dplyr, foreach, httr, stats, utils, methods, readr, rhdf5, jsonlite, tidyr Suggests: GeoDE, doParallel, testthat, knitr, rmarkdown, ggplot2, Rtsne, Biobase, BiocStyle License: MIT + file LICENSE Package: SLqPCR Version: 1.52.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) Package: SMAD Version: 1.2.0 Depends: R (>= 3.6.0) Imports: magrittr (>= 1.5), matrixStats, dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE Archs: i386, x64 Package: SMAP Version: 1.50.0 Depends: R (>= 2.10), methods License: GPL-2 Archs: i386, x64 Package: SMITE Version: 1.14.0 Depends: R (>= 3.3), GenomicRanges Imports: scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2, reactome.db, KEGG.db, BioNet, goseq, methods, IRanges, igraph, Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics, stats, utils Suggests: knitr License: GPL (>= 2) Package: SNAGEE Version: 1.26.0 Depends: R (>= 2.6.0), SNAGEEdata Suggests: ALL, hgu95av2.db Enhances: parallel License: Artistic-2.0 Package: snapCGH Version: 1.56.0 Depends: R (>= 3.5.0) Imports: aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma, methods, stats, tilingArray, utils License: GPL Archs: i386, x64 Package: snm Version: 1.34.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL Package: SNPchip Version: 2.32.0 Depends: R (>= 2.14.0) Imports: methods, graphics, lattice, grid, foreach, utils, Biobase, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, oligoClasses (>= 1.31.1) Suggests: crlmm (>= 1.17.14), RUnit Enhances: doSNOW, VanillaICE (>= 1.21.24), RColorBrewer License: LGPL (>= 2) Package: SNPhood Version: 1.16.0 Depends: R (>= 3.1), GenomicRanges, Rsamtools, data.table, checkmate Imports: DESeq2, cluster, ggplot2, lattice, GenomeInfoDb, BiocParallel, VariantAnnotation, BiocGenerics, IRanges, methods, SummarizedExperiment, RColorBrewer, Biostrings, grDevices, gridExtra, stats, grid, utils, reshape2, scales, S4Vectors Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot License: LGPL (>= 3) Package: SNPRelate Version: 1.20.1 Depends: R (>= 2.15), gdsfmt (>= 1.8.3) Imports: methods LinkingTo: gdsfmt Suggests: parallel, Matrix, RUnit, knitr, MASS, BiocGenerics Enhances: SeqArray (>= 1.12.0) License: GPL-3 Archs: i386, x64 Package: snpStats Version: 1.36.0 Depends: R(>= 2.10.0), survival, Matrix, methods Imports: graphics, grDevices, stats, utils, BiocGenerics, zlibbioc Suggests: hexbin License: GPL-3 Archs: i386, x64 Package: soGGi Version: 1.18.0 Depends: R (>= 3.2.0), BiocGenerics, SummarizedExperiment Imports: methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, preprocessCore, chipseq, BiocParallel Suggests: testthat, BiocStyle, knitr License: GPL (>= 3) Package: sojourner Version: 1.0.2 Imports: ggplot2,dplyr,reshape2,gridExtra,EBImage,MASS,R.matlab,Rcpp,boot,fitdistrplus,mclust,minpack.lm,mixtools,mltools,nls2,plyr,rtiff,sampSurf,scales,shiny,shinyjs,sp,truncnorm,utils,stats,pixmap,rlang,graphics,grDevices,grid,compiler,lattice Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: Artistic-2.0 Package: SomaticSignatures Version: 2.22.0 Depends: R (>= 3.1.0), VariantAnnotation, GenomicRanges, NMF Imports: S4Vectors, IRanges, GenomeInfoDb, Biostrings, ggplot2, ggbio, reshape2, NMF, pcaMethods, Biobase, methods, proxy Suggests: testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva License: MIT + file LICENSE Package: SpacePAC Version: 1.24.0 Depends: R(>= 2.15),iPAC Suggests: RUnit, BiocGenerics, rgl License: GPL-2 Package: Spaniel Version: 1.0.0 Depends: R (>= 3.6), Seurat, SingleCellExperiment, SummarizedExperiment, dplyr Imports: methods, ggplot2, scater (>= 1.13.27), shiny, jpeg, magrittr, utils, S4Vectors Suggests: knitr, rmarkdown, testthat, devtools License: MIT + file LICENSE Package: sparseDOSSA Version: 1.10.0 Imports: stats, utils, optparse, MASS, tmvtnorm (>= 1.4.10), MCMCpack Suggests: knitr, BiocStyle, BiocGenerics, rmarkdown License: MIT + file LICENSE Package: sparsenetgls Version: 1.4.0 Depends: R (>= 3.5.0), Matrix, MASS Imports: methods, glmnet, parcor, huge, stats, graphics, utils Suggests: testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) License: GPL-3 Package: SparseSignatures Version: 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file LICENSE Package: specL Version: 1.20.0 Depends: R (>= 3.6), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.4), RSQLite (>= 1.1), seqinr (>= 3.3) Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) License: GPL-3 Package: SpeCond Version: 1.40.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) Package: SpectralTAD Version: 1.2.0 Depends: R (>= 3.6) Imports: dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr License: MIT + file LICENSE Package: SPEM Version: 1.26.0 Depends: R (>= 2.15.1), Rsolnp, Biobase, methods License: GPL-2 Package: SPIA Version: 2.38.0 Depends: R (>= 2.14.0), graphics, KEGGgraph Imports: graphics Suggests: graph, Rgraphviz, hgu133plus2.db License: file LICENSE License_restricts_use: yes Package: SpidermiR 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testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2, BiocStyle, animation, pander License: GPL (>= 3) Package: TCGAutils Version: 1.6.2 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 (>= 2.7.5), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 Package: TCseq Version: 1.10.0 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) Package: TDARACNE Version: 1.36.0 Depends: GenKern, Rgraphviz, Biobase License: GPL-2 Package: tenXplore Version: 1.8.0 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 Package: TEQC Version: 4.8.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Rsamtools, hwriter Imports: Biobase (>= 2.15.1) License: GPL (>= 2) Package: ternarynet Version: 1.30.0 Depends: R (>= 2.10.0), methods Imports: utils, igraph License: GPL (>= 2) Archs: i386, x64 Package: TFARM Version: 1.8.0 Depends: R (>= 3.4) Imports: arules, fields, GenomicRanges, graphics, stringr, methods, stats, gplots Suggests: BiocStyle, knitr, plyr License: Artistic-2.0 Package: TFBSTools Version: 1.24.0 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 Archs: i386, x64 Package: TFEA.ChIP Version: 1.6.0 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 Package: TFHAZ Version: 1.8.0 Depends: R(>= 3.4) Imports: GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 Package: TFutils Version: 1.5.7 Depends: R (>= 3.5.0) Imports: methods, dplyr, magrittr, miniUI, shiny, Rsamtools Suggests: knitr, data.table, GSEABase, 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 Package: tigre Version: 1.40.0 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 Archs: i386, x64 Package: tilingArray Version: 1.64.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 Archs: i386, x64 Package: timecourse Version: 1.58.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL Package: timescape Version: 1.10.0 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 Package: TimeSeriesExperiment Version: 1.4.0 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) Package: TIN Version: 1.18.0 Depends: R (>= 2.12.0), data.table, impute, aroma.affymetrix Imports: WGCNA, squash, stringr Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics License: Artistic-2.0 Package: TissueEnrich Version: 1.6.0 Depends: R (>= 3.5), ensurer (>= 1.1.0), ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), SummarizedExperiment (>= 1.6.5), GSEABase (>= 1.38.2) Imports: dplyr (>= 0.7.3), stats Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE Package: TitanCNA Version: 1.24.0 Depends: R (>= 3.5.1) Imports: BiocGenerics (>= 0.31.6), IRanges (>= 2.6.1), GenomicRanges (>= 1.24.3), VariantAnnotation (>= 1.18.7), foreach (>= 1.4.3), GenomeInfoDb (>= 1.8.7), data.table (>= 1.10.4), dplyr (>= 0.5.0), License: GPL-3 Archs: i386, x64 Package: tkWidgets Version: 1.64.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 Package: TMixClust Version: 1.8.0 Depends: R (>= 3.4) Imports: gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel, flexclust, grDevices, graphics, Biobase, SPEM Suggests: rmarkdown, knitr, BiocStyle, testthat License: GPL (>= 2) Package: TNBC.CMS Version: 1.2.0 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 Package: TnT Version: 1.8.1 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 Package: TOAST Version: 1.0.0 Depends: R (>= 3.6), RefFreeEWAS, EpiDISH Imports: stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, csSAM, gplots, matrixStats, Matrix License: GPL-2 Package: tofsims Version: 1.14.0 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 Archs: i386, x64 Package: ToPASeq Version: 1.20.0 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 Archs: i386, x64 Package: topconfects Version: 1.2.0 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 Package: topdownr Version: 1.8.0 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.20.0), ProtGenerics (>= 1.10.0), Biostrings (>= 2.42.1), S4Vectors (>= 0.12.2) Imports: grDevices, stats, tools, utils, Biobase, Matrix (>= 1.2.10), MSnbase (>= 2.3.10), ggplot2 (>= 2.2.1), mzR (>= 2.11.4) Suggests: topdownrdata (>= 0.2), knitr, ranger, testthat, BiocStyle, xml2 License: GPL (>= 3) Package: topGO Version: 2.38.1 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.6), graph (>= 1.14.0), Biobase (>= 2.0.0), GO.db (>= 2.3.0), AnnotationDbi (>= 1.7.19), SparseM (>= 0.73) Imports: lattice, matrixStats, DBI Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest License: LGPL Package: TPP Version: 3.14.1 Depends: R (>= 3.4), Biobase, dplyr, magrittr, tidyr Imports: biobroom, broom, data.table, doParallel, foreach, futile.logger, ggplot2, grDevices, gridExtra, grid, knitr, limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr, purrr, RColorBrewer, RCurl, reshape2, rmarkdown, splines, stats, stringr, utils, VennDiagram, VGAM Suggests: BiocStyle, testthat License: Artistic-2.0 Package: TPP2D Version: 1.2.3 Depends: R (>= 3.6.0), stats, utils, dplyr, methods Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl, parallel, MASS Suggests: knitr, testthat License: GPL-3 Package: tracktables Version: 1.20.0 Depends: R (>= 3.0.0) Imports: IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base, stringr, RColorBrewer, methods Suggests: knitr, BiocStyle License: GPL (>= 3) Package: trackViewer Version: 1.22.1 Depends: R (>= 3.1.0), 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) Package: tradeSeq Version: 1.0.1 Depends: R (>= 3.6) Imports: mgcv, edgeR, SingleCellExperiment, SummarizedExperiment, slingshot, magrittr, RColorBrewer, clusterExperiment, BiocParallel, pbapply, ggplot2, princurve, methods, S4Vectors Suggests: knitr, rmarkdown, cowplot, dplyr, tidyr, testthat License: MIT + file LICENSE Package: transcriptogramer Version: 1.8.0 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) Package: transcriptR Version: 1.14.0 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 Package: transite Version: 1.4.0 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), gridExtra (>= 2.3), methods, parallel, Rcpp (>= 0.12.18), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils LinkingTo: Rcpp (>= 0.12.18) Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0) License: MIT + file LICENSE Archs: i386, x64 Package: tRanslatome Version: 1.24.0 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 Package: TransView Version: 1.30.0 Depends: methods, GenomicRanges Imports: BiocGenerics, S4Vectors (>= 0.9.25), IRanges, zlibbioc, gplots LinkingTo: Rhtslib (>= 1.15.3) Suggests: RUnit, pasillaBamSubset, BiocManager License: GPL-3 Archs: i386, x64 Package: traseR Version: 1.16.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL Package: treeio Version: 1.10.0 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 License: Artistic-2.0 Package: TreeSummarizedExperiment Version: 1.2.0 Depends: R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18) Imports: methods, utils, ape, dplyr, SummarizedExperiment Suggests: ggtree, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) Package: Trendy Version: 1.8.2 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 Package: triform Version: 1.28.0 Depends: R (>= 2.11.0), IRanges, yaml Imports: BiocGenerics, IRanges (>= 2.5.27), yaml Suggests: RUnit License: GPL-2 Package: trigger Version: 1.32.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 Archs: i386, x64 Package: trio Version: 3.24.3 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1) Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 Package: triplex Version: 1.26.0 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 Archs: i386, x64 Package: tRNA Version: 1.4.0 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, assertive, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE Package: tRNAdbImport Version: 1.4.0 Depends: R (>= 3.5), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, BiocGenerics, stringr, xml2, S4Vectors, assertive, methods, httr, IRanges, utils Suggests: knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE Package: tRNAscanImport Version: 1.6.0 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, assertive, 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 Package: TRONCO Version: 2.18.0 Depends: R (>= 3.6), 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 Package: TSCAN Version: 1.24.0 Depends: R(>= 2.10.0) Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots Suggests: knitr License: GPL (>= 2) Package: tspair Version: 1.44.0 Depends: R (>= 2.10), Biobase (>= 2.4.0) License: GPL-2 Archs: i386, x64 Package: TSRchitect Version: 1.12.4 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 Package: TTMap Version: 1.8.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 Package: TurboNorm Version: 1.34.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata License: LGPL Archs: i386, x64 Package: tweeDEseq Version: 1.32.0 Depends: R (>= 2.12.0) Imports: MASS, limma, edgeR, parallel, cqn Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) Archs: i386, x64 Package: twilight Version: 1.62.0 Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, grDevices, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) Archs: i386, x64 Package: twoddpcr Version: 1.10.0 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 Package: tximeta Version: 1.4.5 Imports: SummarizedExperiment, tximport, jsonlite, S4Vectors, GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb, Biostrings, BiocFileCache, tibble, GenomeInfoDb, rappdirs, utils, methods Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, edgeR, limma, devtools License: GPL-2 Package: tximport Version: 1.14.2 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) Package: TxRegInfra Version: 1.6.0 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 Package: TypeInfo Version: 1.52.0 Depends: methods Suggests: Biobase License: BSD Package: Ularcirc Version: 1.4.0 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 Package: UNDO Version: 1.28.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 Package: unifiedWMWqPCR Version: 1.22.0 Depends: methods Imports: BiocGenerics, stats, graphics, HTqPCR License: GPL (>= 2) Package: UniProt.ws Version: 2.26.0 Depends: methods, utils, RSQLite, RCurl, BiocGenerics (>= 0.13.8) Imports: AnnotationDbi, BiocFileCache, rappdirs Suggests: RUnit, BiocStyle, knitr License: Artistic License 2.0 Package: Uniquorn Version: 2.6.0 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 Package: universalmotif Version: 1.4.10 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 Archs: i386, x64 Package: uSORT Version: 1.12.0 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 Package: VanillaICE Version: 1.48.0 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, SNPchip, human610quadv1bCrlmm, ArrayTV Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 Archs: i386, x64 Package: variancePartition Version: 1.16.1 Depends: R (>= 3.5.0), 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) Package: VariantAnnotation Version: 1.32.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.15.3), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.37.4), SummarizedExperiment (>= 1.9.9), Rsamtools (>= 1.99.0) Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.17.24), IRanges (>= 2.13.13), XVector (>= 0.19.7), Biostrings (>= 2.47.6), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome (>= 1.47.3), GenomicFeatures (>= 1.31.3) LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle License: Artistic-2.0 Archs: i386, x64 Package: VariantExperiment Version: 1.0.0 Depends: R (>= 3.6.0), S4Vectors (>= 0.21.24), SummarizedExperiment (>= 1.13.0), GenomicRanges, GDSArray (>= 1.3.0), DelayedDataFrame (>= 1.0.0) Imports: tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray, SeqVarTools, DelayedArray, Biostrings, IRanges Suggests: testthat, knitr License: GPL-3 Package: VariantFiltering Version: 1.22.0 Depends: R (>= 3.0.0), methods, BiocGenerics (>= 0.25.1), VariantAnnotation (>= 1.13.29) Imports: utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Biostrings (>= 2.33.11), GenomeInfoDb (>= 1.3.6), GenomicRanges (>= 1.19.13), SummarizedExperiment, GenomicFeatures, 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 Archs: i386, x64 Package: VariantTools Version: 1.28.1 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 Package: vbmp Version: 1.54.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) Package: VCFArray Version: 1.2.0 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 Package: Vega Version: 1.34.0 Depends: R (>= 2.10) License: GPL-2 Archs: i386, x64 Package: VegaMC Version: 3.24.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods, genoset License: GPL-2 Archs: i386, x64 Package: VennDetail Version: 1.2.0 Imports: utils, grDevices, stats, methods, dplyr, purrr, tibble, magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger Suggests: knitr, rmarkdown, testthat License: GPL-2 Package: vidger Version: 1.6.0 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 Package: viper Version: 1.20.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE Package: ViSEAGO Version: 1.0.0 Depends: R (>= 3.6) Imports: data.table, AnnotationDbi, AnnotationForge, biomaRt, dendextend, DiagrammeR, DT, dynamicTreeCut, GOSemSim, ggplot2, GO.db, grDevices, heatmaply, htmlwidgets, igraph, methods, plotly, topGO, RColorBrewer, R.utils, scales, stats, UpSetR, utils, webshot Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager License: GPL-3 Package: vsn Version: 3.54.0 Depends: R (>= 3.4.0), Biobase Imports: methods, affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat License: Artistic-2.0 Archs: i386, x64 Package: vtpnet Version: 0.26.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 Package: vulcan Version: 1.8.0 Depends: R (>= 3.4), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene, zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit Imports: wordcloud, csaw, gplots, stats, utils, caTools, graphics, DESeq, Biobase Suggests: vulcandata License: LGPL-3 Package: waddR Version: 1.0.1 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 Archs: i386, x64 Package: wateRmelon Version: 1.30.0 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 Package: wavClusteR Version: 2.20.0 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 Package: waveTiling Version: 1.28.0 Depends: oligo, oligoClasses, Biobase, Biostrings, GenomeGraphs Imports: methods, affy, preprocessCore, GenomicRanges, waveslim, IRanges Suggests: BSgenome, BSgenome.Athaliana.TAIR.TAIR9, waveTilingData, pd.atdschip.tiling, TxDb.Athaliana.BioMart.plantsmart22 License: GPL (>= 2) Archs: i386, x64 Package: weaver Version: 1.52.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 Package: webbioc Version: 1.58.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocManager License: GPL (>= 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VariantAnnotation, seqminer, ggplot2, biomaRt, readxl, S4Vectors Suggests: knitr, rmarkdown License: GPL-2 Package: xcms Version: 3.8.2 Depends: R (>= 2.14.0), methods, Biobase, BiocParallel (>= 1.8.0), MSnbase (>= 2.9.3) Imports: mzR (>= 2.19.5), BiocGenerics, ProtGenerics (>= 1.17.2), lattice, RColorBrewer, plyr, RANN, multtest, MassSpecWavelet (>= 1.5.2), S4Vectors, robustbase, IRanges Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>= 0.25.1), ncdf4, rgl, microbenchmark, testthat, pander, magrittr, MALDIquant, pheatmap Enhances: Rgraphviz, Rmpi, XML License: GPL (>= 2) + file LICENSE Archs: i386, x64 Package: XDE Version: 2.32.0 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 Archs: i386, x64 Package: Xeva Version: 1.2.0 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 Package: XINA Version: 1.4.0 Depends: R (>= 3.5), Biobase Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb Suggests: knitr, rmarkdown License: GPL-3 Package: xmapbridge Version: 1.44.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 Package: XVector Version: 0.26.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.19.2), S4Vectors (>= 0.21.13), IRanges (>= 2.15.12) Imports: methods, utils, zlibbioc, BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 Archs: i386, x64 Package: yamss Version: 1.12.1 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 Package: YAPSA Version: 1.12.0 Depends: R (>= 3.3.0), GenomicRanges, ggplot2, grid Imports: lsei, SomaticSignatures, VariantAnnotation, GenomeInfoDb, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, PMCMR, ComplexHeatmap, KEGGREST, grDevices Suggests: BSgenome.Hsapiens.UCSC.hg19, testthat, BiocStyle, knitr, rmarkdown License: GPL-3 Package: yaqcaffy Version: 1.46.0 Depends: simpleaffy (>= 2.19.3), methods Imports: stats4 Suggests: MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk License: Artistic-2.0 Package: yarn Version: 1.12.0 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 Package: zFPKM Version: 1.8.0 Depends: R (>= 3.4.0) Imports: checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment Suggests: knitr, limma, edgeR, GEOquery, stringr, printr License: GPL-3 | file LICENSE Package: zinbwave Version: 1.8.0 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 Package: zlibbioc Version: 1.32.0 License: Artistic-2.0 + file LICENSE Archs: i386, x64