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org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 MD5sum: 847d056d51f439e6b4aa2a72c8216e26 NeedsCompilation: no Package: AnnotationFilter Version: 1.14.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db License: Artistic-2.0 MD5sum: 9713a855b78fed1a44f2a89227f02033 NeedsCompilation: no Package: AnnotationForge Version: 1.32.0 Depends: R (>= 3.5.0), methods, utils, BiocGenerics (>= 0.15.10), Biobase (>= 1.17.0), AnnotationDbi (>= 1.33.14) Imports: DBI, RSQLite, XML, S4Vectors, RCurl Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, hom.Hs.inp.db, GO.db, BiocStyle, knitr, BiocManager License: Artistic-2.0 MD5sum: 412436fe2c2dfc0929bca1bfeabaee08 NeedsCompilation: no Package: AnnotationFuncs Version: 1.40.0 Depends: R (>= 2.7.0), AnnotationDbi Imports: DBI Suggests: org.Bt.eg.db, GO.db, org.Hs.eg.db, hom.Hs.inp.db License: GPL-2 MD5sum: f63968ee8a66966da0e0a84acf5c2994 NeedsCompilation: no Package: AnnotationHub Version: 2.22.1 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, interactiveDisplayBase, httr, yaml, dplyr Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 999a1c414c84f396c38e17ab5fdafe45 NeedsCompilation: yes Package: AnnotationHubData Version: 1.20.2 Depends: R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges (>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15) Imports: GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocManager, 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TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene License: GPL-3 MD5sum: ae5b221e3e477b331ed97a2bd2b88042 NeedsCompilation: no Package: anota Version: 1.38.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: e8659cc703c94586999656d714cccca9 NeedsCompilation: no Package: anota2seq Version: 1.12.0 Depends: R (>= 3.4.0), methods Imports: multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices, graphics, stats, utils, SummarizedExperiment Suggests: BiocStyle,knitr License: GPL-3 MD5sum: d9eb935903371b9f35a9d6b3e3fa823b NeedsCompilation: no Package: antiProfiles Version: 1.30.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: d865919be4b15669bb59804f99fcbbd7 NeedsCompilation: no 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ComplexHeatmap, corrplot, data.table, dplyr, factoextra, FactoMineR, getopt, ggdendro, ggplot2, gplots, ggrepel, gProfileR, graphics, grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db, org.Mm.eg.db, PerformanceAnalytics, pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 3) + file LICENSE MD5sum: 1cbb891e3c085677edca21fd1f447607 NeedsCompilation: no Package: ASAFE Version: 1.16.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 1145236591d973ea06651fad4434e19b NeedsCompilation: no Package: ASEB Version: 1.34.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) MD5sum: 380e4f496717acdf82a931f9555c4d85 NeedsCompilation: yes Package: ASGSCA Version: 1.24.0 Imports: Matrix, MASS Suggests: BiocStyle License: GPL-3 MD5sum: ad017053e56917850529108d665e7dcb NeedsCompilation: no Package: ASICS Version: 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BiocStyle, igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid, graphics License: GPL MD5sum: f7df37943398c0e259854ae9b4784e26 NeedsCompilation: no Package: AssessORF Version: 1.8.0 Depends: R (>= 3.5.0), DECIPHER (>= 2.10.0) Imports: Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 5d8775a400935a481bf5701aec819e80 NeedsCompilation: no Package: ASSET Version: 2.8.0 Depends: MASS, msm, rmeta Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE MD5sum: 39cae307eebf07e8614010d4f41b8c54 NeedsCompilation: no Package: ASSIGN Version: 1.26.0 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 MD5sum: d0fa1584cd00633d501382bf96632c4c NeedsCompilation: no Package: ATACseqQC Version: 1.14.4 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) MD5sum: 84c22259fa29e28d845fcc5aaae1572f NeedsCompilation: no Package: atSNP Version: 1.6.1 Depends: R (>= 3.6) Imports: BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testthat, utils, lifecycle LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 00cd5fd0c7aadc6e9e327f7eeaa78a69 NeedsCompilation: yes Package: attract Version: 1.42.0 Depends: R (>= 3.4.0), AnnotationDbi Imports: Biobase, limma, cluster, GOstats, graphics, stats, reactome.db, KEGGREST, org.Hs.eg.db, utils, methods Suggests: 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NeedsCompilation: no Package: DAPAR Version: 1.22.9 Depends: R (>= 4.0.3) Imports: Biobase, MSnbase, tibble, 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), forcats, methods, highcharter, DAPARdata (>= 1.18.0), siggenes, graph, lme4, readxl, clusterProfiler, dplyr, tidyr,AnnotationDbi, tidyverse, vsn, FactoMineR, factoextra, multcomp, purrr, visNetwork, foreach, parallel, doParallel, igraph, dendextend, Mfuzz, apcluster, diptest, cluster Suggests: BiocGenerics, testthat, BiocStyle License: Artistic-2.0 MD5sum: 4b045b597e9582f5ded10e732d2dc305 NeedsCompilation: no Package: DART Version: 1.38.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: 37c999b981fc177693e6a2ee94263aed NeedsCompilation: no Package: dasper Version: 1.0.0 Depends: R (>= 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doParallel License: GPL-3 MD5sum: 68dcfdbef97b23156139188eca7ed2ec NeedsCompilation: no Package: dcGSA Version: 1.18.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: c20ff7789a5cff21448da9c1679c47c6 NeedsCompilation: no Package: ddCt Version: 1.46.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: RUnit License: LGPL-3 MD5sum: 2367b6279a1b336056fceae0214690c2 NeedsCompilation: no Package: ddPCRclust Version: 1.10.0 Depends: R (>= 3.5) Imports: plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore, flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks Suggests: BiocStyle License: Artistic-2.0 MD5sum: f44e0b951caccc1efaeed761367ed13d NeedsCompilation: no Package: dearseq Version: 1.2.0 Depends: R (>= 3.6.0) Imports: CompQuadForm, ggplot2, KernSmooth, matrixStats, methods, parallel, pbapply, stats, statmod Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr License: GPL-2 | file LICENSE MD5sum: bd1fc407ae7f45121aed216184bf7862 NeedsCompilation: no Package: debCAM Version: 1.8.0 Depends: R (>= 3.5) Imports: methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 MD5sum: d2974e7fb378be7ff5dafcd34978246f NeedsCompilation: no Package: debrowser Version: 1.18.3 Depends: R (>= 3.5.0), Imports: shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT, ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE, igraph, grDevices, graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker, plotly, heatmaply, Harman, pathview, apeglm, ashr Suggests: testthat, rmarkdown, BiocStyle, knitr, R.rsp License: GPL-3 + file LICENSE MD5sum: 38f85a2a2356f98c43489c298e120599 NeedsCompilation: no Package: DECIPHER Version: 2.18.1 Depends: R (>= 3.5.0), Biostrings (>= 2.35.12), RSQLite (>= 1.1), stats, parallel Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector License: GPL-3 MD5sum: 4cfa154ff5b66988e79b65ed828a922c NeedsCompilation: yes Package: deco Version: 1.6.0 Depends: R (>= 3.5.0), AnnotationDbi, BiocParallel, SummarizedExperiment, limma Imports: stats, methods, ggplot2, foreign, graphics, BiocStyle, Biobase, cluster, gplots, RColorBrewer, locfit, made4, ade4, sfsmisc, scatterplot3d, gdata, grDevices, utils, reshape2, gridExtra Suggests: knitr, curatedTCGAData, MultiAssayExperiment, Homo.sapiens License: GPL (>= 3) MD5sum: 0aa843af87c91e69a96bb4f38ab5e60d NeedsCompilation: no Package: DEComplexDisease Version: 1.10.0 Depends: R (>= 3.3.3) Imports: Rcpp (>= 0.12.7), DESeq2, edgeR, SummarizedExperiment, ComplexHeatmap, grid, parallel, BiocParallel, grDevices, graphics, stats, methods, utils LinkingTo: Rcpp Suggests: knitr License: GPL-3 MD5sum: 4d8a6d31801b6ed09a67a350591bb77b NeedsCompilation: yes Package: decompTumor2Sig Version: 2.6.0 Depends: R(>= 3.6), ggplot2 Imports: methods, Matrix, quadprog(>= 1.5-5), GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table, GenomeInfoDb Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: de216f3ebfae39dd811bcfc3ee242a58 NeedsCompilation: no Package: DeconRNASeq Version: 1.32.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 MD5sum: a284da987315e3ec24fc7b30c3dcd70e NeedsCompilation: no Package: decontam Version: 1.10.0 Depends: R (>= 3.4.1), methods (>= 3.4.1) Imports: ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats Suggests: BiocStyle, knitr, rmarkdown, phyloseq License: Artistic-2.0 MD5sum: 64d6323212294ae77e59acaf4e40cf3e NeedsCompilation: no Package: DeepBlueR Version: 1.16.0 Depends: R (>= 3.3), XML, RCurl Imports: GenomicRanges, data.table, stringr, diffr, dplyr, methods, rjson, utils, R.utils, foreach, withr, rtracklayer, GenomeInfoDb, settings, filehash Suggests: knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr, RColorBrewer, matrixStats License: GPL (>= 2.0) MD5sum: 23f56ef8d0b6085cf7f252578b6af280 NeedsCompilation: no Package: deepSNV Version: 1.36.0 Depends: R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.13.44), Imports: Rhtslib LinkingTo: Rhtslib (>= 1.13.1) Suggests: RColorBrewer, knitr, rmarkdown License: GPL-3 MD5sum: 7c40b8877e8b60b56fbbfd7a33cf7818 NeedsCompilation: yes Package: DEFormats Version: 1.18.0 Imports: checkmate, data.table, DESeq2, edgeR (>= 3.13.4), GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat License: GPL-3 MD5sum: 978cfd2ebf4cc244733bdcf33c202154 NeedsCompilation: no Package: DegNorm Version: 1.0.0 Depends: R (>= 4.0.0), methods Imports: Rcpp (>= 1.0.2),GenomicFeatures, parallel, foreach, S4Vectors, doParallel, Rsamtools (>= 1.31.2), GenomicAlignments, heatmaply, data.table, stats, ggplot2, GenomicRanges, IRanges, plyr, plotly, utils,viridis LinkingTo: Rcpp, RcppArmadillo,S4Vectors,IRanges Suggests: knitr,rmarkdown,formatR License: LGPL (>= 3) MD5sum: 1060c727ca42d4b5baf8270bee2fecce NeedsCompilation: yes Package: DEGraph Version: 1.42.0 Depends: R (>= 2.10.0), R.utils Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph License: GPL-3 MD5sum: 68c52a19f8b515d30d97bbcaee300993 NeedsCompilation: no Package: DEGreport Version: 1.26.0 Depends: R (>= 3.6.0) Imports: utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, lasso2, magrittr, Nozzle.R1, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE MD5sum: f6588a36498425416a61ee994390292c NeedsCompilation: no Package: DEGseq Version: 1.44.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: 1302f87f87a461235a64fce344354f0d NeedsCompilation: yes Package: DelayedArray Version: 0.16.3 Depends: R (>= 3.4), methods, stats4, Matrix, BiocGenerics (>= 0.31.5), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2), IRanges (>= 2.17.3) Imports: stats LinkingTo: S4Vectors Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit License: Artistic-2.0 MD5sum: 24e8e5cf8a88943e7002ef77fc6b1c95 NeedsCompilation: yes Package: DelayedDataFrame Version: 1.6.0 Depends: R (>= 3.6), S4Vectors (>= 0.23.19), DelayedArray (>= 0.7.5) Imports: methods, stats, BiocGenerics Suggests: testthat, knitr, rmarkdown, SeqArray, GDSArray License: GPL-3 MD5sum: bec6c8c8c40396b2de85656e9cf54a1f NeedsCompilation: no Package: DelayedMatrixStats Version: 1.12.3 Depends: MatrixGenerics, DelayedArray (>= 0.15.3) Imports: methods, matrixStats (>= 0.56.0), sparseMatrixStats, Matrix, S4Vectors (>= 0.17.5), IRanges, HDF5Array (>= 1.17.2), BiocParallel Suggests: testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark, profmem License: MIT + file LICENSE MD5sum: 3c50b3baa9f0e4a4f6b40b1e71d852e5 NeedsCompilation: no Package: deltaCaptureC Version: 1.4.0 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2 Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 48814e06e56feff9d7270bd51c3a75ed NeedsCompilation: no Package: deltaGseg Version: 1.30.0 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 MD5sum: 8843bf3cc89ff55a8a025c0fd62dcb3b NeedsCompilation: no Package: DeMAND Version: 1.20.0 Depends: R (>= 2.14.0), KernSmooth, methods License: file LICENSE MD5sum: 95f7f3e0408e9c3d938fc915f116608c NeedsCompilation: no Package: DeMixT Version: 1.6.0 Depends: R (>= 3.6.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment, knitr, KernSmooth, matrixcalc Imports: matrixStats, stats, truncdist, base64enc, ggplot2 LinkingTo: Rcpp License: GPL-3 MD5sum: 3f2c40f85d48d793a7ec29bda407a84f NeedsCompilation: yes Package: densvis Version: 1.00.6 Imports: Rcpp, basilisk, assertthat, reticulate LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, ggplot2, Rtsne, uwot, testthat License: MIT + file LICENSE MD5sum: 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Rcpp, RcppEigen Suggests: uwot, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 3548d14171c9abeec005354a53e4c77c NeedsCompilation: yes Package: DEqMS Version: 1.8.0 Depends: R(>= 3.5),graphics,stats,ggplot2,limma(>= 3.34) Suggests: BiocStyle,knitr,rmarkdown,plyr,matrixStats,reshape2,farms,utils,ggrepel,ExperimentHub,LSD License: LGPL MD5sum: 46716e590039544b253873ce4656cca7 NeedsCompilation: no Package: derfinder Version: 1.24.2 Depends: R (>= 3.5.0) Imports: BiocGenerics (>= 0.25.1), AnnotationDbi (>= 1.27.9), BiocParallel (>= 1.15.15), bumphunter (>= 1.9.2), derfinderHelper (>= 1.1.0), GenomeInfoDb (>= 1.3.3), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges (>= 1.17.40), Hmisc, IRanges (>= 2.3.23), methods, qvalue (>= 1.99.0), Rsamtools (>= 1.25.0), rtracklayer, S4Vectors (>= 0.23.19), stats, utils Suggests: BiocStyle (>= 2.5.19), sessioninfo, derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitr (>= 1.6), limma, RefManageR, 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TxDb.Hsapiens.UCSC.hg19.knownGene, covr License: Artistic-2.0 MD5sum: fd5718d63606669d2bd3362bc2a0ed99 NeedsCompilation: no Package: DEScan2 Version: 1.10.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocParallel, BiocGenerics, ChIPpeakAnno, data.table, DelayedArray, GenomeInfoDb, GenomicAlignments, glue, IRanges, plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors (>= 0.23.19), SummarizedExperiment, tools, utils LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod License: Artistic-2.0 MD5sum: 6e7bdbfc52668cb7215a9f71fccd489c NeedsCompilation: yes Package: DESeq2 Version: 1.30.1 Depends: S4Vectors (>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter, methods, stats4, locfit, geneplotter, ggplot2, Rcpp (>= 0.11.0) LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10), glmGamPoi, BiocManager License: LGPL (>= 3) MD5sum: 7b22e80a95125b4d377afa854e0edc0a NeedsCompilation: yes Package: DEsingle Version: 1.10.0 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 MD5sum: a01f068379f3bc34f63bf0d823c23cee NeedsCompilation: no Package: destiny Version: 3.4.0 Depends: R (>= 3.4.0) Imports: methods, graphics, grDevices, utils, stats, Matrix, Rcpp (>= 0.10.3), RcppEigen, RSpectra (>= 0.14-0), irlba, pcaMethods, Biobase, BiocGenerics, SummarizedExperiment, SingleCellExperiment, ggplot2, ggplot.multistats, tidyr, tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW, smoother, scales, scatterplot3d LinkingTo: Rcpp, RcppEigen, grDevices Suggests: nbconvertR (>= 1.3.2), igraph, testthat, FNN, tidyr Enhances: rgl, SingleCellExperiment License: GPL MD5sum: 885fa89bd647770e4e44ca84a047916e NeedsCompilation: yes Package: DEsubs Version: 1.16.0 Depends: R (>= 3.3), locfit Imports: graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq, DESeq, stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix, jsonlite, tools, DESeq2, methods Suggests: RUnit, BiocGenerics, knitr License: GPL-3 MD5sum: 57b57e89981a95287f8424ca0ae2fde9 NeedsCompilation: no Package: DEWSeq Version: 1.4.4 Depends: R(>= 4.0.0), R.utils, DESeq2, BiocParallel Imports: BiocGenerics, data.table(>= 1.11.8), GenomeInfoDb, GenomicRanges, methods, S4Vectors, SummarizedExperiment, stats, utils Suggests: knitr, rmarkdown, testthat, BiocStyle, IHW License: LGPL (>= 3) MD5sum: 1511313df222dc308fc120ab69057f96 NeedsCompilation: no Package: DEXSeq Version: 1.36.0 Depends: BiocParallel, Biobase, SummarizedExperiment, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), DESeq2 (>= 1.9.11), AnnotationDbi, 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HDF5Array, matrixStats, methods, OUTRIDER, pcaMethods, pheatmap, plotly, PRROC, RColorBrewer, rhdf5, Rsubread, R.utils, S4Vectors, stats, tibble, tools, utils, VGAM LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, License: MIT + file LICENSE MD5sum: 32b2a81cd139970819354d8597923516 NeedsCompilation: yes Package: frenchFISH Version: 1.2.0 Imports: utils, MCMCpack, NHPoisson Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 2ec382232e7be13a1578d07482ff99db NeedsCompilation: no Package: FRGEpistasis Version: 1.26.0 Depends: R (>= 2.15), MASS, fda, methods, stats Imports: utils License: GPL-2 MD5sum: 6820892ff7d8249f6ff4d8e0b38e8781 NeedsCompilation: no Package: frma Version: 1.42.0 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) 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Depends: R (>= 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene, FunciSNP.data Imports: methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools (>= 1.6.1), rtracklayer (>= 1.14.1), ChIPpeakAnno (>= 2.2.0), VariantAnnotation, plyr, snpStats, ggplot2 (>= 0.9.0), reshape (>= 0.8.4), scales Suggests: org.Hs.eg.db Enhances: parallel License: GPL-3 MD5sum: a92933f233ac7c60c9685c23889803a1 NeedsCompilation: no Package: funtooNorm Version: 1.14.0 Depends: R(>= 3.4) Imports: pls, matrixStats, minfi, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb, grDevices, graphics, stats Suggests: prettydoc, minfiData, knitr, rmarkdown License: GPL-3 MD5sum: 5910f7ed08b524cfe60649838949c8d5 NeedsCompilation: no Package: GA4GHclient Version: 1.14.0 Depends: S4Vectors Imports: BiocGenerics, Biostrings, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, methods, VariantAnnotation Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 740ecf0af30dbf1903d1198e20ee4b63 NeedsCompilation: no Package: GA4GHshiny Version: 1.12.0 Depends: GA4GHclient Imports: AnnotationDbi, BiocGenerics, dplyr, DT, GenomeInfoDb, openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny, shinyjs, tidyr, shinythemes Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 47501914a03a433061a41b755fe42fec NeedsCompilation: no Package: gaga Version: 2.36.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: parallel License: GPL (>= 2) MD5sum: c0b4538abe8abc08a433b7dcab029ef3 NeedsCompilation: yes Package: gage Version: 2.40.2 Depends: R (>= 3.5.0) Imports: graph, KEGGREST, AnnotationDbi, GO.db Suggests: pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma License: GPL (>= 2.0) MD5sum: 0281c966169258b695df8b9678e4af32 NeedsCompilation: no Package: gaggle Version: 1.58.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>= 0.4.17) License: GPL (>= 2) MD5sum: c2e2ed2edbf687c0bdc80eddbbdd4574 NeedsCompilation: no Package: gaia Version: 2.34.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: f378fcd885a35e90aa0afa2674c0ce52 NeedsCompilation: no Package: GAPGOM Version: 1.6.0 Depends: R (>= 4.0) Imports: stats, utils, methods, Matrix, fastmatch, plyr, dplyr, magrittr, data.table, igraph, graph, RBGL, GO.db, org.Hs.eg.db, org.Mm.eg.db, GOSemSim, GEOquery, AnnotationDbi, Biobase, BiocFileCache, matrixStats Suggests: org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Dr.eg.db, org.Ce.eg.db, org.At.tair.db, org.EcK12.eg.db, org.Bt.eg.db, org.Cf.eg.db, org.Ag.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Pt.eg.db, org.Pf.plasmo.db, org.Mmu.eg.db, org.Ss.eg.db, org.Xl.eg.db, testthat, pryr, knitr, rmarkdown, prettydoc, ggplot2, kableExtra, profvis, reshape2 License: 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Biostrings, BSgenome, GenomicRanges, Rsamtools, GenomicAlignments, matrixStats, MASS, splines, grDevices, graphics, stats, methods Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: GPL-3 MD5sum: 0c8372ccd4c8e3c4d259c9345f0e4ab3 NeedsCompilation: no Package: gcatest Version: 1.20.0 Depends: R (>= 3.2) Imports: lfa Suggests: knitr, ggplot2 License: GPL-3 MD5sum: 94680e6cd0cb4483be408cfbac991b87 NeedsCompilation: yes Package: gCrisprTools Version: 1.18.0 Depends: R (>= 3.6) Imports: Biobase, limma, RobustRankAggreg, ggplot2, PANTHER.db, rmarkdown, grDevices, graphics, stats, utils, parallel, SummarizedExperiment Suggests: edgeR, knitr, grid, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 83bf84e056d4806aead6e73fbc01b924 NeedsCompilation: no Package: gcrma Version: 2.62.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 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NeedsCompilation: no Package: GDCRNATools Version: 1.10.1 Depends: R (>= 3.5.0) Imports: shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 64dcc888ddc6ee1db58e8c2ca42224da NeedsCompilation: no Package: GDSArray Version: 1.10.1 Depends: R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>= 0.5.32) Imports: tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray Suggests: testthat, knitr, BiocStyle, BiocManager License: GPL-3 MD5sum: f1a1fae569353157b3353a31d74d8b57 NeedsCompilation: no Package: gdsfmt Version: 1.26.1 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, Matrix, RUnit, knitr, crayon, BiocGenerics License: LGPL-3 MD5sum: 7298b94276856b198364b2817184ba6b NeedsCompilation: yes Package: GEM Version: 1.16.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics License: Artistic-2.0 MD5sum: 4ca6af1b4ecc9c23ef06f03a6c98cb62 NeedsCompilation: no Package: gemini Version: 1.4.0 Depends: R (>= 3.6.0) Imports: dplyr, grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: b4c7f9abf9cf968e0248a5d7bd966c93 NeedsCompilation: no Package: genArise Version: 1.66.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: 158decd3887c2249f288ca113943e780 NeedsCompilation: no Package: genbankr Version: 1.18.0 Depends: methods Imports: BiocGenerics, IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), GenomicFeatures (>= 1.31.5), Biostrings, VariantAnnotation, rtracklayer, S4Vectors (>= 0.17.28), GenomeInfoDb, Biobase Suggests: RUnit, rentrez, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 1c961c48fc499ab946b019fd3e9fa86d NeedsCompilation: no Package: GeneAccord Version: 1.8.0 Depends: R (>= 3.5) Imports: biomaRt, caTools, dplyr, ggplot2, graphics, grDevices, gtools, ggpubr, magrittr, maxLik, RColorBrewer, reshape2, stats, tibble, utils Suggests: assertthat, BiocStyle, devtools, knitr, rmarkdown, testthat License: file LICENSE MD5sum: 17923a6e00f0668a18def047572993dd NeedsCompilation: no Package: GeneAnswers Version: 2.32.0 Depends: R (>= 3.0.0), igraph, RCurl, annotate, Biobase (>= 1.12.0), methods, XML, RSQLite, MASS, Heatplus, RColorBrewer Imports: RBGL, annotate, downloader Suggests: GO.db, KEGG.db, reactome.db, biomaRt, AnnotationDbi, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db, graph License: LGPL (>= 2) MD5sum: 054fbcb91a6dfb49e7860927712fc162 NeedsCompilation: no Package: geneAttribution Version: 1.16.0 Imports: utils, GenomicRanges, org.Hs.eg.db, BiocGenerics, GenomeInfoDb, GenomicFeatures, IRanges, rtracklayer Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: b71e2b9bf302c4ff4cff200971734951 NeedsCompilation: no Package: GeneBreak Version: 1.20.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: 29d73467d2a2796b517f5dee95ce0829 NeedsCompilation: no Package: geneClassifiers Version: 1.14.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: 72f9baa250308b07610b640178cea39e NeedsCompilation: no Package: GeneExpressionSignature Version: 1.36.0 Depends: R (>= 2.13), Biobase, PGSEA Suggests: apcluster,GEOquery License: GPL-2 MD5sum: 361ff3ccd392e771fcabf7976380c3e3 NeedsCompilation: no Package: genefilter Version: 1.72.1 Imports: BiocGenerics (>= 0.31.2), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 MD5sum: ebf02b933c3f4e09ed52cdf46f65cb1e NeedsCompilation: yes Package: genefu Version: 2.22.1 Depends: survcomp, mclust, limma, biomaRt, iC10, AIMS, R (>= 2.10) Imports: amap, impute Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival License: Artistic-2.0 MD5sum: 9872ab9e3aece8c66bb30fb9c5f5a08e NeedsCompilation: no Package: GeneGA Version: 1.40.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: 6074e3f2dff160650a6460b3796a41da NeedsCompilation: no Package: GeneGeneInteR Version: 1.16.0 Depends: R (>= 4.0) Imports: snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods, GGtools License: GPL (>= 2) MD5sum: 4797f4fe092dbbc67deaf57ac40f43b9 NeedsCompilation: yes Package: GeneMeta Version: 1.62.0 Depends: R (>= 2.10), methods, Biobase (>= 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plyr License: GPL (>= 2) MD5sum: f8ce18045c174d1c9dcae71099477a0e NeedsCompilation: no Package: geneplotter Version: 1.68.0 Depends: R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate Imports: AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db License: Artistic-2.0 MD5sum: b56c0040c88b2a934fab8a2959feb587 NeedsCompilation: no Package: geneRecommender Version: 1.62.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: 5a60c9b9990c633938070a7e982f373c NeedsCompilation: no Package: GeneRegionScan Version: 1.46.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) MD5sum: 57c514788d51bd544948a86bdffae2fe NeedsCompilation: no Package: geneRxCluster Version: 1.26.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: f44c83d5838e9785f3c001870d3fbea3 NeedsCompilation: yes Package: GeneSelectMMD Version: 2.34.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: 9ffbbeae12b0e508f030f9a0b137cd0c NeedsCompilation: yes Package: GENESIS Version: 2.20.1 Imports: Biobase, BiocGenerics, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, foreach, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: e3f5272a4c43cfa0334ddaafe3a40cdf NeedsCompilation: yes Package: GeneStructureTools Version: 1.10.0 Imports: Biostrings,GenomicRanges,IRanges,data.table,plyr,stringdist,stringr,S4Vectors,BSgenome.Mmusculus.UCSC.mm10,stats,utils,Gviz,rtracklayer,methods Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 9fd7a37ea74f1b3bb5596c854b00a594 NeedsCompilation: no Package: geNetClassifier Version: 1.30.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics, grDevices Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) MD5sum: 7659433c6d526283048e838b3c0d5974 NeedsCompilation: no Package: GeneticsPed Version: 1.52.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: 6372eaac3e2d4e0aadba561d7cb35599 NeedsCompilation: yes Package: GeneTonic Version: 1.2.0 Depends: R (>= 4.0.0) Imports: AnnotationDbi, bs4Dash, colorspace, ComplexHeatmap, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce, ggplot2, ggrepel, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tools, utils, viridis, visNetwork Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 0007edeb2858ab9b078889973d94b9b4 NeedsCompilation: no Package: geneXtendeR Version: 1.16.0 Depends: rtracklayer, GO.db, R (>= 3.5.0) Imports: data.table, dplyr, graphics, networkD3, RColorBrewer, SnowballC, tm, utils, wordcloud, AnnotationDbi, BiocStyle, org.Rn.eg.db Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer License: GPL (>= 3) MD5sum: e04e6be0f4007586b8e99434d1a6bd17 NeedsCompilation: yes Package: GENIE3 Version: 1.12.0 Imports: stats, reshape2 Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods License: GPL (>= 2) MD5sum: 833398ca4048551777471f8c22453cce NeedsCompilation: yes Package: genoCN Version: 1.42.0 Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: d5d0e64e1221fa6296684698b6f00873 NeedsCompilation: yes Package: GenoGAM Version: 2.8.0 Depends: R (>= 3.5), SummarizedExperiment (>= 1.1.19), HDF5Array (>= 1.8.0), rhdf5 (>= 2.21.6), S4Vectors (>= 0.23.18), Matrix (>= 1.2-8), data.table (>= 1.9.4) Imports: Rcpp (>= 0.12.14), sparseinv (>= 0.1.1), Rsamtools (>= 1.18.2), GenomicRanges (>= 1.23.16), BiocParallel (>= 1.5.17), DESeq2 (>= 1.11.23), futile.logger (>= 1.4.1), GenomeInfoDb (>= 1.7.6), GenomicAlignments (>= 1.7.17), IRanges (>= 2.5.30), Biostrings (>= 2.39.14), DelayedArray (>= 0.3.19), methods, stats LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, chipseq (>= 1.21.2), LSD (>= 3.0.0), genefilter (>= 1.54.2), ggplot2 (>= 2.1.0), testthat, knitr, rmarkdown License: GPL-2 MD5sum: 2fac12f4d64fbb6c32c5f1161d70fa15 NeedsCompilation: yes Package: genomation Version: 1.22.0 Depends: R (>= 3.0.0),grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), RUnit, Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown License: Artistic-2.0 MD5sum: c0ecfd2c734ffdb9ae0b22edf51ddad1 NeedsCompilation: yes Package: GenomeInfoDb Version: 1.26.7 Depends: R (>= 3.1), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.25.12), IRanges (>= 2.13.12) Imports: stats, stats4, utils, RCurl, GenomeInfoDbData Suggests: GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 17bb177838890de8702414f7c6f69c85 NeedsCompilation: no Package: genomeIntervals Version: 1.46.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 1.5.8), GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: b7c4556ac74d9f35cf0c64dfd8614688 NeedsCompilation: no Package: genomes Version: 3.20.0 Depends: readr, curl License: GPL-3 MD5sum: 4fcdffd6f6c70603ad8b036f6f36c380 NeedsCompilation: no Package: GenomicAlignments Version: 1.26.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.55.7), Rsamtools (>= 1.31.2) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 3adfdee731d1f065d8e70420abc6e331 NeedsCompilation: yes Package: GenomicDataCommons Version: 1.14.0 Depends: R (>= 3.4.0), magrittr Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, SummarizedExperiment, S4Vectors, tibble Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools License: Artistic-2.0 MD5sum: 9ce9d9241aac4a18a052df4938bd500a NeedsCompilation: no Package: GenomicFeatures Version: 1.42.3 Depends: BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29), IRanges (>= 2.13.23), GenomeInfoDb (>= 1.25.7), 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.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 4b7e53ca9ed7848d8fc7d93d00aa3d50 NeedsCompilation: no Package: GenomicFiles Version: 1.26.0 Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), MatrixGenerics, GenomicRanges (>= 1.31.16), SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3) Imports: GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25), VariantAnnotation (>= 1.27.9), GenomeInfoDb Suggests: BiocStyle, RUnit, genefilter, deepSNV, snpStats, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens License: Artistic-2.0 MD5sum: b05dfa75a2f7548568674dd36c3edeb5 NeedsCompilation: no Package: GenomicInteractions Version: 1.24.0 Depends: R (>= 3.5), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices Suggests: knitr, BiocStyle, testthat License: GPL-3 MD5sum: e6fbd53b07559a44d52a5da81f2455ad NeedsCompilation: no Package: GenomicOZone Version: 1.4.1 Depends: R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2 Imports: grDevices, stats, utils, plyr, gridExtra, lsr, parallel, ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack Suggests: readxl, knitr, rmarkdown License: LGPL (>= 3) MD5sum: cdbac8bb39ff13fe7557c08d01c6bb2e NeedsCompilation: no Package: GenomicRanges Version: 1.42.0 Depends: R (>= 2.10), methods, stats4, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.15.2) Imports: utils, stats, XVector (>= 0.29.2) LinkingTo: S4Vectors, IRanges Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, BiocStyle License: Artistic-2.0 MD5sum: 03bc0867ceaa7a1b2dbee00f9723f230 NeedsCompilation: yes Package: GenomicScores Version: 2.2.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: stats, utils, XML, Biobase, BiocManager, BiocFileCache, IRanges (>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub, rhdf5, DelayedArray, HDF5Array Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5, SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer, shiny, shinythemes, shinyjs, shinycustomloader, data.table, DT License: Artistic-2.0 MD5sum: 109dd61271eaabc81c2bf14e0b429dbd NeedsCompilation: no Package: GenomicTuples Version: 1.24.0 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), GenomeInfoDb (>= 1.15.2), S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: fe49824c537a9ea2ed19392d45a6d6de NeedsCompilation: yes Package: genoset Version: 1.45.1 Depends: R (>= 2.10), BiocGenerics (>= 0.11.3), GenomicRanges (>= 1.17.19), SummarizedExperiment (>= 1.1.6) Imports: S4Vectors (>= 0.27.3), GenomeInfoDb (>= 1.1.3), IRanges (>= 2.5.12), methods, graphics Suggests: testthat, knitr, BiocStyle, rmarkdown, DNAcopy, stats, BSgenome, Biostrings Enhances: parallel License: Artistic-2.0 MD5sum: ad0a5b2587a1c089242fc97f870c14f1 NeedsCompilation: yes Package: genotypeeval Version: 1.22.0 Depends: R (>= 3.4.0), VariantAnnotation Imports: ggplot2, rtracklayer, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, methods, BiocParallel, graphics, stats Suggests: rmarkdown, testthat, SNPlocs.Hsapiens.dbSNP141.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: 1af8b4c3e8096947348caaf4e2247a89 NeedsCompilation: no Package: genphen Version: 1.18.0 Depends: R (>= 3.5.0), Rcpp (>= 0.12.17), methods, stats, graphics Imports: rstan (>= 2.17.3), ranger, parallel, foreach, doParallel, e1071, Biostrings, rPref Suggests: testthat, ggplot2, gridExtra, ape, ggrepel, knitr, reshape, xtable License: GPL (>= 2) MD5sum: 6b3c66592313dcf60fa40c630faa73ed NeedsCompilation: no Package: GenVisR Version: 1.22.1 Depends: R (>= 3.3.0), methods Imports: AnnotationDbi, biomaRt (>= 2.45.8), BiocGenerics, Biostrings, DBI, FField, GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, viridis, data.table, BSgenome, GenomeInfoDb, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 + file LICENSE MD5sum: dbbec931c15071c63c7c8746357c6865 NeedsCompilation: no Package: GEOmetadb Version: 1.52.0 Depends: GEOquery,RSQLite Suggests: knitr, rmarkdown, dplyr, tm, wordcloud License: Artistic-2.0 MD5sum: 1993276ed5110862b2ab6002918f293f NeedsCompilation: no Package: GEOquery Version: 2.58.0 Depends: methods, Biobase Imports: httr, readr (>= 1.3.1), xml2, dplyr, tidyr, magrittr, limma Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr License: GPL-2 MD5sum: 9e041d946e0331210e96b28ecc74c2cb NeedsCompilation: no Package: GEOsubmission Version: 1.42.0 Imports: affy, Biobase, utils License: GPL (>= 2) MD5sum: d5a1748dd91d2d9f99784af998befd6d NeedsCompilation: no Package: gep2pep Version: 1.10.0 Imports: repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators Suggests: WriteXLS, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 8acba2c272a82610ed7491feadedcace NeedsCompilation: no Package: gespeR Version: 1.22.0 Depends: methods, graphics, ggplot2, R(>= 2.10) Imports: Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel, parallel, foreach, reshape2, dplyr Suggests: knitr License: GPL-3 MD5sum: c0709df23a3e6c022d2ffd9d53ab8b11 NeedsCompilation: no Package: getDEE2 Version: 1.0.0 Depends: R (>= 4.0) Imports: stats, utils, SummarizedExperiment, htm2txt Suggests: knitr, testthat License: GPL-3 MD5sum: 4fb7bb9f2596d3f4016641e983fa78d1 NeedsCompilation: no Package: GEWIST Version: 1.34.0 Depends: R (>= 2.10), car License: GPL-2 MD5sum: 82dc3b0caa1383597a2c6a35c29e543b NeedsCompilation: no Package: GGBase Version: 3.52.0 Depends: R (>= 2.14), methods, snpStats Imports: limma, genefilter, Biobase, BiocGenerics (>= 0.35.3), S4Vectors, IRanges, Matrix, AnnotationDbi, digest, GenomicRanges, SummarizedExperiment Suggests: GGtools, illuminaHumanv1.db, knitr License: Artistic-2.0 MD5sum: 6fc62e931457f378d65d503e7734bb02 NeedsCompilation: no Package: ggbio Version: 1.38.0 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.29.14), SummarizedExperiment, Biostrings, Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer (>= 1.25.16), GenomicFeatures (>= 1.29.11), OrganismDbi, GGally, ensembldb (>= 1.99.13), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: 96e6a557917feb186b3ba00ef7b49d47 NeedsCompilation: no Package: ggcyto Version: 1.18.0 Depends: methods, ggplot2(>= 3.3.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 3.33.1) Imports: plyr, scales, hexbin, data.table, RColorBrewer, gridExtra, rlang Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr License: Artistic-2.0 MD5sum: 0c47d99641bcd192a0f0b7081569bfa3 NeedsCompilation: no Package: GGPA Version: 1.2.0 Depends: R (>= 4.0.0), stats, methods, graphics, GGally, network, sna, scales, matrixStats Imports: Rcpp (>= 0.11.3) LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle License: GPL (>= 2) MD5sum: 2f85f7bc1e93b69a9de316eb5344d7be NeedsCompilation: yes Package: GGtools Version: 5.25.3 Depends: R (>= 2.14), GGBase (>= 3.19.7), data.table, parallel, Homo.sapiens Imports: methods, utils, stats, BiocGenerics (>= 0.25.1), snpStats, ff, Rsamtools, AnnotationDbi, Biobase, bit, VariantAnnotation, hexbin, rtracklayer, Gviz, stats4, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges (>= 1.29.6), iterators, Biostrings, ROCR, biglm, ggplot2, reshape2 Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37, multtest, aod, rmeta Enhances: MatrixEQTL, foreach, doParallel, gwascat License: Artistic-2.0 MD5sum: 7fca8396df9e29321d6663c04d51cb04 NeedsCompilation: no Package: ggtree Version: 2.4.2 Depends: R (>= 3.5.0) Imports: ape, aplot (>= 0.0.4), dplyr, ggplot2 (>= 3.0.0), grid, magrittr, methods, purrr, rlang, rvcheck, tidyr, tidytree (>= 0.2.6), treeio (>= 1.8.0), utils, scales Suggests: emojifont, ggimage, ggplotify, grDevices, knitr, prettydoc, rmarkdown, stats, testthat, tibble License: Artistic-2.0 MD5sum: 5a67ec7f12e854b9a12ee842de725195 NeedsCompilation: no Package: ggtreeExtra Version: 1.0.4 Imports: ggplot2, utils, rlang, ggnewscale, stats Suggests: ggtree, treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown License: GPL-3 MD5sum: 7fdf428bc61a50d905c4aa1b4a7bedac NeedsCompilation: no Package: GIGSEA Version: 1.8.0 Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils Suggests: knitr, rmarkdown License: 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Depends: R (>= 3.6.0), data.table (>= 1.9.4) Imports: DBI, RMySQL, RSQLite, numDeriv, RColorBrewer, parallel, stats, methods, graphics, grDevices, xtable, tools, brew, stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: a05ffb29b7a2bdd2dee2fd3ec07a437e NeedsCompilation: no Package: Glimma Version: 2.0.0 Depends: R (>= 4.0.0) Imports: htmlwidgets, edgeR, DESeq2, limma, SummarizedExperiment, stats, jsonlite, methods, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, pryr License: GPL-3 MD5sum: b701109ba91bdfd16edc19bf47d02e51 NeedsCompilation: no Package: glmGamPoi Version: 1.2.0 Imports: Rcpp, DelayedMatrixStats, matrixStats, DelayedArray, HDF5Array, SummarizedExperiment, methods, stats, utils, splines LinkingTo: Rcpp, RcppArmadillo, beachmat Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, scran License: GPL-3 MD5sum: 962cbb19d7fb346c0d2d595e922995c5 NeedsCompilation: yes Package: glmSparseNet Version: 1.8.1 Depends: R (>= 3.5), Matrix, MultiAssayExperiment, glmnet Imports: SummarizedExperiment, STRINGdb, biomaRt, futile.logger, sparsebn, sparsebnUtils, forcats, dplyr, readr, ggplot2, survminer, reshape2, stats, stringr, rlang, parallel, methods, loose.rock (>= 1.0.12) Suggests: testthat, knitr, rmarkdown, survival, survcomp, pROC, VennDiagram, BiocStyle, curatedTCGAData, TCGAutils License: GPL (>= 3) MD5sum: 9c97f462da742afc1cc8189fcf138a8b NeedsCompilation: no Package: GlobalAncova Version: 4.8.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, KEGG.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: 221c300f8d0321b232aa1b96aff4743f NeedsCompilation: yes Package: globalSeq Version: 1.18.0 Depends: R (>= 3.0.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 MD5sum: 554c0aca36bdc355dcca9a905e90e460 NeedsCompilation: no Package: globaltest Version: 5.44.0 Depends: methods, survival Imports: Biobase, AnnotationDbi, annotate, graphics Suggests: vsn, golubEsets, KEGGREST, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart, mstate License: GPL (>= 2) MD5sum: d34f68048d6c10e6a327b72d4f6918df NeedsCompilation: no Package: gmapR Version: 1.32.0 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2) Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome, GenomicAlignments (>= 1.15.6), BiocParallel Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines License: Artistic-2.0 MD5sum: d0c0244da3538780ab07c6b88b431db2 NeedsCompilation: yes Package: GmicR Version: 1.4.0 Imports: AnnotationDbi, ape, bnlearn, Category, DT, doParallel, foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db, org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics, reshape2, stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 + file LICENSE MD5sum: f53948a1de2261760fee7b77229fe85f NeedsCompilation: no Package: gmoviz Version: 1.2.0 Depends: circlize, GenomicRanges, graphics, R (>= 4.0) Imports: grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics, Biostrings, GenomeInfoDb, methods, GenomicAlignments, GenomicFeatures, IRanges, rtracklayer, pracma, colorspace, S4Vectors Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager License: GPL-3 MD5sum: c304746cc76c7d68edee621a5e09a8dd NeedsCompilation: no Package: GMRP Version: 1.18.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: 1f4acc214ee4652307add6c125a28557 NeedsCompilation: no Package: GNET2 Version: 1.6.0 Depends: R (>= 3.6) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment,dplyr,igraph, grDevices, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 MD5sum: 9aa2cb5a7bbe98c4cfac2a52feecc3b6 NeedsCompilation: yes Package: GOexpress Version: 1.24.0 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) MD5sum: c22c8894c04227404e32a0afba6b2fdd NeedsCompilation: no Package: GOfuncR Version: 1.10.0 Depends: R (>= 3.4), vioplot (>= 0.2), Imports: Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges (>= 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License: Artistic-2.0 MD5sum: 87cc24c6773fb9b9778a6f4337dfbe7c NeedsCompilation: yes Package: goseq Version: 1.42.0 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) MD5sum: bdc4fb8d47589efbc39cd146901cfee9 NeedsCompilation: no Package: GOSim Version: 1.28.0 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) MD5sum: 8b45d945d771385cd5813804e64ea5c9 NeedsCompilation: yes Package: goSTAG Version: 1.14.2 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 93aa6d282a4a8a907e5d632c3415e73e NeedsCompilation: no Package: GOstats Version: 2.56.0 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 MD5sum: db8a41a811f2f820d3702a4fac45b5f3 NeedsCompilation: no Package: GOsummaries Version: 2.26.0 Depends: R (>= 2.15), Rcpp Imports: plyr, grid, gProfileR, reshape2, limma, ggplot2, gtable LinkingTo: Rcpp Suggests: vegan License: GPL (>= 2) MD5sum: 5bdd6d751c14962407516b1a71324155 NeedsCompilation: yes Package: GOTHiC Version: 1.26.0 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 MD5sum: 58da5756ed06167dd42655eb9383571f NeedsCompilation: no 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parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) License: AGPL-3 MD5sum: 3cb65e6dae93b72547fe770f4cbf96d4 NeedsCompilation: no Package: GraphPAC Version: 1.32.0 Depends: R(>= 2.15),iPAC, igraph, TSP, RMallow Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 0314d922d1ace88be3de2776031d0342 NeedsCompilation: no Package: GRENITS Version: 1.42.0 Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) Imports: graphics, grDevices, reshape2, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: network License: GPL (>= 2) MD5sum: 8257abd52336fad9a9bf8b33228354d9 NeedsCompilation: yes Package: GreyListChIP Version: 1.22.0 Depends: R (>= 4.0), 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 MD5sum: 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Depends: R (>= 4.0) Imports: dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud, stringr, gridExtra, rlang, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat License: GPL-3 | file LICENSE MD5sum: 9b25f392a9b8831159e1138e531f9622 NeedsCompilation: no Package: gsean Version: 1.10.1 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, knitr, plotly, RANKS, WGCNA, rmarkdown License: Artistic-2.0 MD5sum: 87db37bfa1ceb26a48f3afe047d12ce0 NeedsCompilation: no Package: GSgalgoR Version: 1.0.0 Imports: cluster, doParallel, foreach, matchingR, nsga2R, survival, proxy, stats, methods, Suggests: knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp, Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP, iC10TrainingData, pamr, testthat License: MIT + file LICENSE MD5sum: f68cc92e24c76f40e3ac052728dbf4a6 NeedsCompilation: no Package: GSReg Version: 1.24.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, 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RColorBrewer, markdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff License: MIT + file LICENSE MD5sum: 80f43d4832a5e31cadebd0add270b1ce NeedsCompilation: no Package: GUIDEseq Version: 1.20.0 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,dplyr Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL (>= 2) MD5sum: 899007f762b2839cc3319ce5addc5250 NeedsCompilation: no Package: Guitar Version: 2.6.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges, magrittr, ggplot2, methods, stats,utils ,knitr,dplyr License: GPL-2 MD5sum: 9231a0c9c791010b2dd12b276b360160 NeedsCompilation: no Package: Gviz Version: 1.34.1 Depends: R (>= 4.0), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.17.20), grid Imports: XVector (>= 0.5.7), rtracklayer (>= 1.25.13), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.17.22), ensembldb (>= 2.11.3), BSgenome (>= 1.33.1), Biostrings (>= 2.33.11), biovizBase (>= 1.13.8), Rsamtools (>= 1.17.28), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>= 1.1.16), GenomeInfoDb (>= 1.1.3), BiocGenerics (>= 0.11.3), digest(>= 0.6.8), graphics, grDevices, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 36209134e0388df2911da3f772c433e1 NeedsCompilation: no Package: GWAS.BAYES Version: 1.0.0 Depends: R (>= 4.0), Rcpp (>= 1.0.3), RcppEigen (>= 0.3.3.7.0), GA (>= 3.2), caret (>= 6.0-86), ggplot2 (>= 3.3.0), doParallel (>= 1.0.15), memoise (>= 1.1.0), reshape2 (>= 1.4.4), Matrix (>= 1.2-18) LinkingTo: RcppEigen (>= 0.3.3.7.0),Rcpp (>= 1.0.3) Suggests: BiocStyle, knitr, rmarkdown, 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Artistic-2.0 MD5sum: 0ff0c2ad4ba3af9a7434f5271815ba64 NeedsCompilation: no Package: gwasurvivr Version: 1.8.0 Depends: R (>= 3.4.0) Imports: GWASTools, survival, VariantAnnotation, parallel, matrixStats, SummarizedExperiment, stats, utils, SNPRelate Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: a255c21902da8882421c5349fc929abd NeedsCompilation: no Package: GWENA Version: 1.0.1 Depends: R (>= 4.0.0) Imports: WGCNA (>= 1.67), dplyr (>= 0.8.3), dynamicTreeCut (>= 1.63-1), ggplot2 (>= 3.1.1), gprofiler2 (>= 0.1.6), magrittr (>= 1.5), tibble (>= 2.1.1), tidyr (>= 1.0.0), NetRep (>= 1.2.1), igraph (>= 1.2.4.1), RColorBrewer (>= 1.1-2), purrr (>= 0.3.3), rlist (>= 0.4.6.1), matrixStats (>= 0.55.0), SummarizedExperiment (>= 1.14.1), stringr (>= 1.4.0), methods, graphics, stats, utils Suggests: testthat (>= 2.1.0), knitr (>= 1.25), rmarkdown (>= 1.16), prettydoc (>= 0.3.0), httr (>= 1.4.1), S4Vectors (>= 0.22.1), BiocStyle (>= 2.15.8) License: GPL-3 MD5sum: 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Imports: methods, BiocGenerics, httpuv, utils, MotifDb, seqLogo, rtracklayer, VariantAnnotation, RColorBrewer Suggests: RUnit, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: eac58c7e258fe4ef7058ca8b53132ec3 NeedsCompilation: no Package: IHW Version: 1.18.0 Depends: R (>= 3.3.0) Imports: methods, slam, lpsymphony, fdrtool, BiocGenerics Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools License: Artistic-2.0 MD5sum: 17f249a751fda79a7bd2e17c5f350522 NeedsCompilation: no Package: illuminaio Version: 0.32.0 Imports: base64 Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2), BiocStyle License: GPL-2 MD5sum: c05675197148dcbc63991c855659296c NeedsCompilation: yes Package: ILoReg Version: 1.0.0 Depends: R (>= 4.0.0) Imports: Matrix, parallel, foreach, aricode, LiblineaR, SparseM, ggplot2, cowplot, RSpectra, umap, Rtsne, fastcluster, parallelDist, cluster, dendextend, DescTools, plyr, scales, 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SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse Suggests: BiocStyle, knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 17efb11a85c4f7dd7d4cacf51ecd2c7e NeedsCompilation: no Package: infinityFlow Version: 1.0.0 Depends: R (>= 4.0.0), flowCore Imports: stats, grDevices, utils, graphics, pbapply, matlab, png, raster, grid, uwot, gtools, Biobase, generics, parallel, methods, xgboost Suggests: knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071 License: GPL-3 MD5sum: 51bf7c2564d015dcec626d04b9120972 NeedsCompilation: no Package: Informeasure Version: 1.0.0 Depends: R (>= 4.0) Imports: entropy, matrixStats Suggests: knitr, rmarkdown, testthat, SummarizedExperiment License: GPL-3 MD5sum: 80e15daf2a0d9dc0b69eb53c13ca3935 NeedsCompilation: no Package: InPAS Version: 1.22.0 Depends: R (>= 3.1), methods, Biobase, GenomicRanges, GenomicFeatures, S4Vectors Imports: AnnotationDbi, BSgenome, cleanUpdTSeq, Gviz, seqinr, preprocessCore, 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BiocParallel, biomaRt, Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, gplots, graphics, grDevices, harmonicmeanp, heatmaply, htmltools, httr, IRanges, jsonlite, lattice, log4r, magrittr, MASS, Matrix, methods, NBPSeq, pander, parallel, qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite, rtracklayer, S4Vectors, stats, stringr, SummarizedExperiment, survcomp, utils, VennDiagram, vsn, yaml, zoo Suggests: BiocManager, BSgenome, knitr, RMySQL, RUnit Enhances: TCC License: GPL (>= 3) MD5sum: 4d8cbde15c56963cf669abf3266033b9 NeedsCompilation: yes Package: metavizr Version: 1.14.0 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 MD5sum: 613366b7901e6461f2aa14ebacdf452e NeedsCompilation: no Package: MetaVolcanoR Version: 1.4.0 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 MD5sum: 04b2d1efab6d90b2b90e52f2bef6e288 NeedsCompilation: no Package: MetCirc Version: 1.20.0 Depends: R (>= 3.5), amap (>= 0.8), circlize (>= 0.3.9), scales (>= 0.3.0), shiny (>= 1.0.0), MSnbase (>= 2.15.3), Imports: ggplot2 (>= 3.2.1), S4Vectors (>= 0.22.0) Suggests: BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr (>= 1.11), methods (>= 3.5), stats (>= 3.5), testthat (>= 2.2.1) License: GPL (>= 3) MD5sum: 299436809b4c0474c1eaf7064cd9285b NeedsCompilation: no Package: MethCP Version: 1.4.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, S4Vectors, bsseq, DSS, methylKit, DNAcopy, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel Suggests: testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 84bb50535f91db8f7acbabcf0ee5ebb7 NeedsCompilation: no Package: methimpute Version: 1.12.0 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 MD5sum: 17f8d2626db0d775bdef67a1d3afb68c NeedsCompilation: yes Package: methInheritSim Version: 1.12.0 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 MD5sum: 158dd7ee7fdfaac74d07930ecfdfc674 NeedsCompilation: no Package: MethPed Version: 1.18.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 MD5sum: 8cc8d020865af609ce56e307e323b392 NeedsCompilation: no Package: MethReg Version: 1.0.0 Depends: R (>= 4.0) Imports: dplyr, plyr, GenomicRanges, SummarizedExperiment, DelayedArray, ggplot2, ggpubr, tibble, tidyr, S4Vectors, sesameData, stringr, readr, methods, stats, Matrix, MASS, rlang, pscl, IRanges, sfsmisc, progress Suggests: rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, downloader, R.utils, doParallel, reshape2, JASPAR2020, TFBSTools, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr, jpeg License: GPL-3 MD5sum: c6b3bc378c1790c9e5d2281b960dc11f NeedsCompilation: no Package: methrix Version: 1.4.07 Depends: R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment Imports: rtracklayer, DelayedArray, HDF5Array, BSgenome, DelayedMatrixStats, parallel, methods, ggplot2, matrixStats, graphics, stats, utils, GenomicRanges, IRanges Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: a296592e123053f98bd40bf515b4a3ea NeedsCompilation: no Package: MethTargetedNGS Version: 1.22.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings License: Artistic-2.0 MD5sum: 7e626eace2f2306bd1882ab55dde758b NeedsCompilation: no Package: methyAnalysis Version: 1.32.0 Depends: R (>= 2.10), grid, BiocGenerics, IRanges, GenomeInfoDb (>= 1.22.0), GenomicRanges, Biobase (>= 2.34.0), org.Hs.eg.db Imports: grDevices, stats, utils, lumi, methylumi, Gviz, genoset, SummarizedExperiment, IRanges, GenomicRanges, VariantAnnotation, rtracklayer, bigmemoryExtras,GenomicFeatures, annotate, Biobase (>= 2.5.5), AnnotationDbi, genefilter, biomaRt, methods, parallel Suggests: FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 3f3171a32bcc499823cbdf52d675aa90 NeedsCompilation: no Package: MethylAid Version: 1.24.0 Depends: R (>= 3.4) Imports: Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: f00efbf705869cace991575c74f5114b NeedsCompilation: no Package: methylCC Version: 1.4.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: CC BY 4.0 MD5sum: 1d9d48426be88ef5908029395f4ad022 NeedsCompilation: no Package: methylGSA Version: 1.8.0 Depends: R (>= 3.5) Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, shiny, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr, rmarkdown, testthat, enrichplot License: GPL-2 MD5sum: 60c3d0cb9ea866c8019177949857ce74 NeedsCompilation: no Package: methylInheritance Version: 1.14.0 Depends: R (>= 3.5) Imports: methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors, methods, parallel, ggplot2, gridExtra, rebus Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim License: Artistic-2.0 MD5sum: bd56a3e2eab518e9f469c0cf6fd3ec99 NeedsCompilation: no Package: methylKit Version: 1.16.1 Depends: R (>= 3.5.0), GenomicRanges (>= 1.18.1), methods Imports: IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>= 0.13.13), GenomeInfoDb, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager License: Artistic-2.0 MD5sum: bb87f51ebc30d1bdbfaa4d1a0d3ca899 NeedsCompilation: yes Package: MethylMix Version: 2.20.0 Depends: R (>= 3.2.0) Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown License: GPL-2 MD5sum: d94872d61bb43e66e5d7dbe47d54ac34 NeedsCompilation: no Package: methylMnM Version: 1.28.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: bc66eaa63c8540cf2e387dfb1f823177 NeedsCompilation: yes Package: methylPipe Version: 1.24.0 Depends: R (>= 3.2.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) MD5sum: 0a0a5d4749494616b382d50ab0e740da NeedsCompilation: yes Package: MethylSeekR Version: 1.30.0 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), graphics (>= 2.15.2), grDevices (>= 2.15.2), parallel (>= 2.15.2), stats (>= 2.15.2), utils (>= 2.15.2) Suggests: BSgenome.Hsapiens.UCSC.hg18 License: GPL (>= 2) MD5sum: 1036b75fec464eb2e9ec4bcd6ac7e4bf NeedsCompilation: no Package: methylSig Version: 1.2.0 Depends: R (>= 3.6) Imports: bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, GenomeInfoDb, GenomicRanges, methods, parallel, stats, S4Vectors Suggests: BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr License: GPL-3 MD5sum: 128a3a288242be31b83cfc88c07a4b44 NeedsCompilation: no Package: methylumi Version: 2.36.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, methyAnalysis, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 MD5sum: e5c5cf78b7f6a4611540a297281e7708 NeedsCompilation: no Package: methyvim Version: 1.11.0 Depends: R (>= 3.4.0) Imports: stats, cluster, methods, ggplot2, ggsci, gridExtra, superheat, dplyr, gtools, tmle (>= 1.4.0.1), future, doFuture, S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, GenomeInfoDb, bumphunter, IRanges, limma, minfi Suggests: testthat, knitr, rmarkdown, BiocStyle, SuperLearner, earth, nnet, gam, arm, snow, parallel, BatchJobs, minfiData, methyvimData License: file LICENSE MD5sum: b6b4a5071fcd9defc71b131768425055 NeedsCompilation: no Package: MetID Version: 1.8.0 Depends: R 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ggdendro, ggplot2, GO.db, GOstats, graph, graphics, grDevices, grid, GSEABase, ismev, jsonlite, limma, matrixStats, org.Hs.eg.db, RBGL, reshape2, Rgraphviz, stats, utils, vegan Suggests: BiocStyle, breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, knitr, mGSZ, MIGSAdata, RUnit License: GPL (>= 2) MD5sum: 50e1286b04099e0d2c79d91f1d3ad8cd NeedsCompilation: no Package: mimager Version: 1.14.0 Depends: Biobase Imports: BiocGenerics, S4Vectors, preprocessCore, grDevices, methods, grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 License: MIT + file LICENSE MD5sum: 5376014d2d487c0377a1e994bfeab839 NeedsCompilation: no Package: MIMOSA Version: 1.28.1 Depends: R (>= 3.0.2), MASS, plyr, reshape, Biobase, ggplot2 Imports: methods, Formula, data.table, pracma, MCMCpack, coda, modeest, testthat, Rcpp, scales, dplyr, tidyr, rlang LinkingTo: Rcpp, RcppArmadillo Suggests: parallel, knitr License: MIT + file LICENSE MD5sum: f0f8ccd4d4d5f7590d8471d480ea3ad0 NeedsCompilation: yes Package: MineICA Version: 1.30.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply Enhances: doMC License: GPL-2 MD5sum: f2ab701e9cdf2a3e269d13e1d725b0de NeedsCompilation: no Package: minet Version: 3.48.0 Imports: infotheo License: Artistic-2.0 MD5sum: 4c6cb2b6be2ffec6c7a39a6b5774101d NeedsCompilation: yes Package: minfi Version: 1.36.0 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 (>= 0.15.16), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools License: Artistic-2.0 MD5sum: 7058aab43dbb644a75ad7c5e8489d20d NeedsCompilation: no Package: MinimumDistance Version: 1.34.0 Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1) Imports: methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: 29f7f8d8366c780b855ad72472f07199 NeedsCompilation: no Package: MiPP Version: 1.62.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: 200eec9d3b771676a87f9426ad1362e1 NeedsCompilation: no Package: MIRA Version: 1.12.0 Depends: R (>= 3.5) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 783f43260beeb34056a59296b9a7fcd3 NeedsCompilation: no Package: MiRaGE Version: 1.32.0 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), 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GPL-3 MD5sum: f6a3f16fb111c362e9055fb658e10181 NeedsCompilation: yes Package: missMethyl Version: 1.24.0 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub License: GPL-2 MD5sum: 4ee1a591215a732d4e2ed30dc0cb4efa NeedsCompilation: no Package: missRows Version: 1.10.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 05f24c1eeedf8f4f0e880f99ddf82535 NeedsCompilation: no Package: mitch Version: 1.2.2 Depends: R (>= 4.0) Imports: stats, grDevices, graphics, utils, MASS, plyr, reshape2, parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r Suggests: stringi, testthat (>= 2.1.0) License: CC BY-SA 4.0 + file LICENSE MD5sum: ef7319698705282794483cd04227b249 NeedsCompilation: no Package: mixOmics Version: 6.14.1 Depends: R (>= 3.5.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, ggrepel, BiocParallel, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rgl License: GPL (>= 2) MD5sum: 1558f10fe83332bd26655dd916a18382 NeedsCompilation: no Package: MLInterfaces Version: 1.70.0 Depends: R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4, tools, grDevices, graphics, stats Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, testthat Enhances: parallel, rda License: LGPL MD5sum: 3f35a3c6f426b4b7c0b51ba66930ac43 NeedsCompilation: no Package: MLP Version: 1.38.0 Depends: AnnotationDbi, affy, plotrix, gplots, gmodels, gdata, gtools Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, KEGG.db, annotate, Rgraphviz, GOstats, limma, mouse4302.db, reactome.db License: GPL-3 MD5sum: 1ba06947db5d2d9a73c35836a8c29e0d NeedsCompilation: no Package: MLSeq Version: 2.8.0 Depends: caret, ggplot2 Imports: methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, testthat, BiocStyle, VennDiagram, pamr License: GPL (>= 2) MD5sum: 6dd09cdd31e68e7d8cc82ebbcbb9c8c3 NeedsCompilation: no Package: MMAPPR2 Version: 1.4.0 Depends: R (>= 3.6.0) Imports: ensemblVEP (>= 1.20.0), gmapR, Rsamtools, VariantAnnotation, BiocParallel, Biobase, BiocGenerics, dplyr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, tidyr, VariantTools, magrittr, methods, grDevices, graphics, stats, utils, stringr, data.table Suggests: testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle, MMAPPR2data License: GPL-3 OS_type: unix MD5sum: f834605687a8b50a35df6a0409eac7d2 NeedsCompilation: no Package: MMDiff2 Version: 1.18.0 Depends: R (>= 3.3), Rsamtools, Biobase, Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 MD5sum: 1d0a6eec20256e14d2ebf672fa1e1bd5 NeedsCompilation: no Package: MMUPHin Version: 1.4.2 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, 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License: LGPL-3 + file LICENSE MD5sum: b20d18374937b8cdd5c5268b3a33bb2e NeedsCompilation: no Package: netDx Version: 1.2.2 Depends: R (>= 3.6) Imports: ROCR,pracma,ggplot2,RCy3,glmnet,igraph,reshape2,parallel,stats,utils,MultiAssayExperiment,graphics,grDevices,methods,BiocFileCache,GenomicRanges,bigmemory,doParallel,foreach,combinat,rappdirs,GenomeInfoDb,S4Vectors,IRanges,RColorBrewer, scater, netSmooth, clusterExperiment,Rtsne,httr Suggests: curatedTCGAData, TCGAutils, rmarkdown, testthat, knitr License: MIT + file LICENSE MD5sum: d5b437190914e09145e31b433ab14d09 NeedsCompilation: no Package: nethet Version: 1.22.0 Imports: glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network, ggplot2, grDevices, graphics, stats, utils Suggests: knitr, xtable, BiocStyle, testthat License: GPL-2 MD5sum: 06740fb93d3601c971c324ef4bcbd287 NeedsCompilation: yes Package: NetPathMiner Version: 1.26.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: 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MD5sum: 6fc0f208cfad146dbec94f76f58b0a79 NeedsCompilation: yes Package: NetSAM Version: 1.30.0 Depends: R (>= 2.15.1), methods, igraph (>= 0.6-1), seriation (>= 1.0-6), graph (>= 1.34.0) Imports: methods Suggests: RUnit, BiocGenerics License: LGPL MD5sum: 943c607518a00278a3293bc9ecbda365 NeedsCompilation: no Package: netSmooth Version: 1.10.0 Depends: R (>= 3.5), scater (>= 1.15.11), clusterExperiment (>= 2.1.6) Imports: entropy, SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods, DelayedArray, HDF5Array (>= 1.15.13) Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot License: GPL-3 MD5sum: df87282a913d18a2895310b7375a89b8 NeedsCompilation: no Package: networkBMA Version: 2.30.1 Depends: R (>= 2.15.0), stats, utils, BMA, Rcpp (>= 0.10.3), RcppArmadillo (>= 0.3.810.2), RcppEigen (>= 0.3.1.2.1), leaps LinkingTo: Rcpp, RcppArmadillo, RcppEigen, BH License: GPL (>= 2) MD5sum: 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marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: ea84c0e2af67605e48de3e63ddf1f4d7 NeedsCompilation: no Package: NOISeq Version: 2.34.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 MD5sum: 8cfebb7c3f60dbe0cc29c91ff40f6e67 NeedsCompilation: no Package: nondetects Version: 2.20.0 Depends: R (>= 3.2), Biobase (>= 2.22.0) Imports: limma, mvtnorm, utils, methods, arm, HTqPCR (>= 1.16.0) Suggests: knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics (>= 0.8.0) License: GPL-3 MD5sum: a1fb2efdcdd7a1c866ba4cf0fbe73c18 NeedsCompilation: no Package: NoRCE Version: 1.2.0 Depends: R (>= 4.0) Imports: KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices, S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl, dbplyr,utils,ggplot2,igraph,stats,reshape2,readr, GO.db,zlibbioc, biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi Suggests: knitr, TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene, testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown, TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene, org.Mm.eg.db, org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics, org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, methods, License: MIT + file LICENSE MD5sum: ca45f80d8681fa8e6d7adf322eaae56f NeedsCompilation: no Package: normalize450K Version: 1.18.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 4f3171e982c938f39fc0dff6b32f7746 NeedsCompilation: no Package: NormalyzerDE Version: 1.8.0 Depends: R (>= 3.6) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, Biobase, RcmdrMisc, raster, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 MD5sum: 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Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: 1d301ebeb9a6455a21e37ffe00716dfa NeedsCompilation: no Package: NTW Version: 1.40.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 MD5sum: b3de30ce606bac1cbd046c84696ed8d6 NeedsCompilation: no Package: nucleoSim Version: 1.18.0 Imports: stats, IRanges, S4Vectors, graphics, methods Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: fa44f3e1a63b431ee994578a12745d32 NeedsCompilation: no Package: nucleR Version: 2.22.0 Depends: methods Imports: Biobase, BiocGenerics, Biostrings, GenomeInfoDb, GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr, ggplot2, magrittr, parallel, stats, utils, grDevices Suggests: Starr, BiocStyle, knitr, rmarkdown, testthat License: LGPL (>= 3) MD5sum: c780f966dd1750522172477f602a5dbb NeedsCompilation: no Package: nuCpos Version: 1.8.0 Depends: R 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Imports: affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, zlibbioc LinkingTo: preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl Enhances: doMC, doMPI License: LGPL (>= 2) MD5sum: 49e01715da8ced8d22fbcc59e6b47b6e NeedsCompilation: yes Package: oligoClasses Version: 1.52.0 Depends: R (>= 2.14) Imports: BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods, graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>= 1.23.2), foreach, BiocManager, utils, S4Vectors (>= 0.9.25), RSQLite, DBI, ff Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, VanillaICE, crlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) MD5sum: 8cf6636b898393a44761a3284e4f4322 NeedsCompilation: no Package: OLIN Version: 1.68.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 MD5sum: 37da7af43f40148f802881946d0aa88d NeedsCompilation: no Package: OLINgui Version: 1.64.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 MD5sum: d4bdaa33786327de8eeb59e868f4c02a NeedsCompilation: no Package: OmaDB Version: 2.6.1 Depends: R (>= 3.5), httr (>= 1.2.1), plyr(>= 1.8.4) Imports: utils, ape, Biostrings, GenomicRanges, IRanges, methods, topGO, jsonlite Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 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methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 2) MD5sum: e93e014bcb4d24d0110b58638df6075a NeedsCompilation: no Package: Omixer Version: 1.0.4 Depends: R (>= 3.0.0) Imports: dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr, tidyselect, grid, stats, stringr Suggests: knitr, rmarkdown, BiocStyle, magick, testthat License: MIT + file LICENSE MD5sum: 008fd7cdf24b4b57266448aba8e7becc NeedsCompilation: no Package: OmnipathR Version: 2.0.0 Depends: R(>= 4.0), igraph, graphics, methods, utils, jsonlite Imports: dplyr, stats, rlang, tidyr Suggests: dnet, gprofiler2, BiocStyle, testthat, knitr, rmarkdown, ggplot2, ggraph License: MIT + file LICENSE MD5sum: bd7324b88a510cee63058798fc0884db NeedsCompilation: no Package: Onassis Version: 1.12.0 Depends: R (>= 4.0), rJava, OnassisJavaLibs Imports: GEOmetadb, RSQLite, data.table, methods, tools, utils, AnnotationDbi, RCurl, stats, DT, data.table, knitr, Rtsne, dendextend, clusteval, ggplot2, ggfortify Suggests: BiocStyle, rmarkdown, htmltools, org.Hs.eg.db, gplots, GenomicRanges, kableExtra License: GPL-2 MD5sum: de3fac525a73b557bd02c2a7c130b83f NeedsCompilation: no Package: oncomix Version: 1.12.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: 19d05c9c8f50202d024629383d54518d NeedsCompilation: no Package: OncoScore Version: 1.18.0 Depends: R (>= 4.0.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: a33848eb8100f4bf218b93f8c503694e NeedsCompilation: no Package: OncoSimulR Version: 2.20.0 Depends: R (>= 3.3.0) Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel LinkingTo: Rcpp Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander License: GPL (>= 3) MD5sum: 2790589220d2d8fac081c713f386675f NeedsCompilation: yes Package: oneSENSE Version: 1.12.0 Depends: R (>= 3.4), webshot, shiny, shinyFiles, scatterplot3d Imports: Rtsne, plotly, gplots, grDevices, graphics, stats, utils, methods, flowCore Suggests: knitr, rmarkdown License: GPL (>= 3) MD5sum: f4d90d29d23a94680ca338fb1709458f NeedsCompilation: no Package: onlineFDR Version: 1.8.0 Imports: stats Suggests: knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: 2a536f0c90efaa32d749675703827cc8 NeedsCompilation: no Package: ontoProc Version: 1.12.0 Depends: R (>= 3.5), ontologyIndex Imports: Biobase, S4Vectors, methods, AnnotationDbi, stats, utils, BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex License: Artistic-2.0 MD5sum: 5954d402b55c16041c70952bac6a651f NeedsCompilation: no Package: openCyto Version: 2.2.0 Depends: R (>= 3.5.0) Imports: methods,Biobase,BiocGenerics,gtools,flowCore(>= 1.99.17),flowViz,ncdfFlow(>= 2.11.34),flowWorkspace(>= 3.99.1),flowStats(>= 3.99.1),flowClust(>= 3.11.4),MASS,clue,plyr,RBGL,graph,data.table,ks,RColorBrewer,lattice,rrcov,R.utils LinkingTo: Rcpp Suggests: flowWorkspaceData, knitr, testthat, utils, tools, parallel, ggcyto, CytoML License: Artistic-2.0 MD5sum: ea991d8f53811caae5a761cfd911a306 NeedsCompilation: yes Package: openPrimeR Version: 1.12.1 Depends: R (>= 4.0.0) Imports: Biostrings (>= 2.38.4), XML (>= 3.98-1.4), scales (>= 0.4.0), reshape2 (>= 1.4.1), seqinr (>= 3.3-3), IRanges (>= 2.4.8), GenomicRanges (>= 1.22.4), ggplot2 (>= 2.1.0), plyr (>= 1.8.4), dplyr (>= 0.5.0), stringdist (>= 0.9.4.1), stringr (>= 1.0.0), RColorBrewer (>= 1.1-2), DECIPHER (>= 1.16.1), lpSolveAPI (>= 5.5.2.0-17), digest (>= 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stats, Matrix, pheatmap, scales, ccaPP, grid, grDevices, AnnotationDbi, DESeq2, curl Suggests: testthat, BiocStyle, knitr, rmarkdown, data.table License: MIT + file LICENSE MD5sum: b268e715c5b8945110589701f45fb77d NeedsCompilation: no Package: PharmacoGx Version: 2.2.4 Depends: R (>= 3.6), CoreGx Imports: Biobase, S4Vectors, SummarizedExperiment, BiocParallel, ggplot2, magicaxis, RColorBrewer, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, BiocGenerics License: Artistic-2.0 MD5sum: d17ee6d5628a4a5ea7a86e0a3776a35e NeedsCompilation: no Package: phemd Version: 1.6.0 Depends: R (>= 3.5), monocle Imports: SingleCellExperiment, RColorBrewer, igraph, transport, pracma, cluster, Rtsne, destiny, Seurat, RANN, ggplot2, maptree, pheatmap, scatterplot3d, VGAM, methods, grDevices, graphics, stats, utils, cowplot, S4Vectors, BiocGenerics, SummarizedExperiment, Biobase, 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nortest, MASS, msgps, logistf, knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4, graphics, grDevices, utils, stats Suggests: RUnit, BiocGenerics License: file LICENSE MD5sum: dbcdd74ac948507dd599a18785dd3af4 NeedsCompilation: no Package: philr Version: 1.16.0 Imports: ape, phangorn, tidyr, ggplot2, ggtree Suggests: testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet, dplyr License: GPL-3 MD5sum: de943446828a9935f5eeada443c3c3bb NeedsCompilation: no Package: phosphonormalizer Version: 1.14.3 Depends: R (>= 4.0) Imports: plyr, stats, graphics, matrixStats, methods Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) MD5sum: 40d8d3e2d938b4b16e469976a9f7f53b NeedsCompilation: no Package: PhosR Version: 1.0.0 Depends: R (>= 4.0.0) Imports: ruv, e1071, calibrate, dendextend, limma, pcaMethods, stats, RColorBrewer, circlize, dplyr, igraph, pheatmap, preprocessCore, tidyr, rlang, graphics, grDevices, utils Suggests: testthat, knitr, GGally, network, reshape2, ClueR, directPA, ggplot2, ggpubr License: GPL-3 + file LICENSE MD5sum: a730450acacb48e1e9975bc42f3b15bb NeedsCompilation: no Package: PhyloProfile Version: 1.4.11 Depends: R (>= 4.0.0) Imports: ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, DT, energy, ExperimentHub, ggplot2, gridExtra, pbapply, RColorBrewer, shiny, shinyBS, shinyjs, OmaDB, plyr, xml2, zoo Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 36aeadf79a2571110b12e11cc2696288 NeedsCompilation: no Package: phyloseq Version: 1.34.0 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 (>= 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plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 2afe6447e92a40849b561d442019d31f NeedsCompilation: no Package: pickgene Version: 1.62.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: b503af602af8a13dc46869eb9dd9d166 NeedsCompilation: no Package: PICS Version: 2.34.0 Depends: R (>= 3.0.0) Imports: utils, stats, graphics, grDevices, methods, IRanges, GenomicRanges, Rsamtools, GenomicAlignments Suggests: rtracklayer, parallel, knitr License: Artistic-2.0 MD5sum: ef140114e4a6713f55d9c8ccf2dd3bfa NeedsCompilation: yes Package: Pigengene Version: 1.16.0 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, 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glmnet, gridExtra, grid, Hmisc, gplots, gtools, scales, lme4, grDevices, graphics, ggrepel, mice Suggests: mclust, flexmix, testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 66e9ba38bf482f3ea6abf5bdfa489452 NeedsCompilation: no Package: rfaRm Version: 1.2.1 Imports: httr, stringi, rsvg, magick, data.table, Biostrings, utils, rvest, xml2, IRanges, S4Vectors Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics License: GPL-3 MD5sum: a88e30882d5f9af960eeb8a9d22c145d NeedsCompilation: no Package: Rfastp Version: 1.0.0 Imports: Rcpp, rjson, ggplot2, reshape2 LinkingTo: Rcpp, Rhtslib, zlibbioc Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 18ca256b458754d0a32acc3f548e8e30 NeedsCompilation: yes Package: rfPred Version: 1.28.0 Depends: Rsamtools, GenomicRanges, IRanges, data.table, methods, parallel Suggests: BiocStyle License: GPL (>= 2) MD5sum: cb9d820ee3937ddb8819c1312b2b20bb NeedsCompilation: yes Package: rGADEM 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IRanges, utils, stats, cluster, binom Suggests: RUnit, BiocGenerics, ggplot2 License: BSD_3_clause + file LICENSE MD5sum: 1df1293567a9a6bfaff6550d943e9fe1 NeedsCompilation: no Package: savR Version: 1.28.0 Depends: ggplot2 Imports: methods, reshape2, scales, gridExtra, XML Suggests: Cairo, testthat License: AGPL-3 MD5sum: 7bde190036722dc4de229ab11560f6b1 NeedsCompilation: no Package: SBGNview Version: 1.4.1 Depends: R (>= 3.6), pathview, SBGNview.data Imports: Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi, httr, KEGGREST, bookdown Suggests: testthat, gage License: AGPL-3 MD5sum: bc6e25c3d34ce30768f7ead8d823166f NeedsCompilation: no Package: SBMLR Version: 1.86.0 Depends: XML, deSolve Suggests: rsbml License: GPL-2 MD5sum: b64751edd010e079263aea8110837005 NeedsCompilation: no Package: SC3 Version: 1.18.0 Depends: R(>= 3.3) Imports: graphics, stats, utils, methods, e1071, parallel, foreach, doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR, robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1), SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, mclust, scater License: GPL-3 MD5sum: acc43d2595516022da5aa719a63d7409 NeedsCompilation: yes Package: Scale4C Version: 1.12.0 Depends: R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: 0932064fd3fda1303a3b55003fc52d4a NeedsCompilation: no Package: scAlign Version: 1.4.0 Depends: R (>= 3.5), SingleCellExperiment (>= 1.4), Seurat (>= 2.3.4), tensorflow, purrr, irlba, Rtsne, ggplot2, methods, utils, FNN Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 4c28d2b3f84c0f35f7eb6efb750cf0f6 NeedsCompilation: no Package: SCAN.UPC Version: 2.32.0 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva Imports: utils, methods, MASS, tools, IRanges Suggests: pd.hg.u95a License: MIT MD5sum: eb1828be7f93dd88cd962d0edfb4a92e NeedsCompilation: no Package: SCANVIS Version: 1.4.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file LICENSE MD5sum: 2d5fbade5cfa8c29811a6543af0372cb NeedsCompilation: no Package: SCATE Version: 1.0.0 Depends: parallel, preprocessCore, splines, splines2, xgboost, SCATEData, Rtsne, mclust Imports: utils, stats, GenomicAlignments, GenomicRanges Suggests: rmarkdown, ggplot2, knitr License: MIT + file LICENSE MD5sum: d2749ebe898e83a8a06c2bcf8151a23f NeedsCompilation: no Package: scater Version: 1.18.6 Depends: SingleCellExperiment, ggplot2 Imports: stats, utils, methods, grid, gridExtra, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, DelayedArray, DelayedMatrixStats, BiocNeighbors, BiocSingular, BiocParallel, scuttle, rlang, ggbeeswarm, viridis Suggests: BiocStyle, biomaRt, cowplot, destiny, knitr, scRNAseq, robustbase, rmarkdown, Rtsne, uwot, NMF, testthat, pheatmap, Biobase License: GPL-3 MD5sum: 24edeb577da40121460438717f283e98 NeedsCompilation: no Package: scBFA Version: 1.4.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods, Matrix Suggests: knitr, rmarkdown, testthat, Rtsne License: GPL-3 + file LICENSE MD5sum: 897bf642e9c90421ec5c99e570fa75d0 NeedsCompilation: no Package: SCBN Version: 1.8.0 Depends: R (>= 3.5.0) Imports: stats Suggests: knitr,rmarkdown License: GPL-2 MD5sum: a3ce76b14bbe53acc0a33752b98652d8 NeedsCompilation: no Package: scCB2 Version: 1.0.0 Depends: R (>= 3.6.0) Imports: SingleCellExperiment, SummarizedExperiment, Matrix, methods, utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel, iterators, foreach, Seurat Suggests: testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: a8310eed9bc53d4044927605bd5349f7 NeedsCompilation: yes Package: scClassify Version: 1.2.0 Depends: R (>= 4.0) Imports: S4Vectors, limma, ggraph, igraph, methods, cluster, minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix, ggplot2, hopach, diptest, mgcv, stats, graphics, statmod Suggests: knitr, rmarkdown, BiocStyle, pkgdown License: GPL-3 MD5sum: 20c2eeb2b40e896427eca5de552ce7b9 NeedsCompilation: no Package: scDataviz Version: 1.0.0 Depends: R (>= 4.0), S4Vectors, SingleCellExperiment, Imports: ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales, RColorBrewer, corrplot, stats, grDevices, graphics, utils, MASS, matrixStats, methods Suggests: PCAtools, cowplot, BiocGenerics, knitr, kableExtra License: GPL-3 MD5sum: c1acebf791f7b1edf81fe15a7bff94cb NeedsCompilation: no Package: scDblFinder Version: 1.4.0 Depends: R (>= 4.0) Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, SingleCellExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, bluster License: GPL-3 MD5sum: 6a323e13629a59af2dbe164d99dcec44 NeedsCompilation: no Package: scDD Version: 1.14.0 Depends: R (>= 3.4) Imports: fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm, SingleCellExperiment, SummarizedExperiment, grDevices, graphics, stats, S4Vectors, scran Suggests: BiocStyle, knitr, gridExtra License: GPL-2 MD5sum: 053c63c32a58a93f6bcdc535b5d3378b NeedsCompilation: yes Package: scde Version: 2.18.0 Depends: R (>= 3.0.0), flexmix Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown License: GPL-2 MD5sum: cd7aed0ff63008fd309d67f05e29d587 NeedsCompilation: yes Package: scds Version: 1.6.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot License: MIT + file LICENSE MD5sum: a12e5054ddf18e96270abb6a6243528b NeedsCompilation: no Package: SCFA Version: 1.0.0 Depends: R (>= 4.0) Imports: matrixStats, keras, tensorflow, BiocParallel, igraph, Matrix, cluster, clusterCrit, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival Suggests: knitr License: LGPL MD5sum: 791789515f445542eda9cf1ac0f6f9fc NeedsCompilation: no Package: scFeatureFilter Version: 1.10.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods Suggests: testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE MD5sum: a4ddd8b398e4d665342387fd480a45fb NeedsCompilation: no Package: scGPS Version: 1.4.0 Depends: R (>= 3.6), SummarizedExperiment, dynamicTreeCut, SingleCellExperiment Imports: glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1), fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel, grDevices, graphics, stats, utils, DESeq, locfit LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE License: GPL-3 MD5sum: 099ebb979b8757da6f09ad65ead809b2 NeedsCompilation: yes Package: schex Version: 1.4.0 Depends: SingleCellExperiment (>= 1.7.4), Seurat, ggplot2 (>= 3.2.1), shiny Imports: hexbin, stats, methods, cluster, dplyr, entropy, ggforce, scales, grid, concaveman Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran License: GPL-3 MD5sum: 76dcb9af0922299bcc7863340bbb656c NeedsCompilation: no Package: scHOT Version: 1.2.0 Depends: R (>= 4.0) Imports: S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix, SummarizedExperiment, IRanges, methods, stats, BiocParallel, reshape, ggplot2, igraph, grDevices, ggforce, graphics Suggests: knitr, rmarkdown, scater, scattermore, scales, matrixStats, deldir License: GPL-3 MD5sum: 5199f93313fca0e9b0f0548ebbcca880 NeedsCompilation: no Package: ScISI Version: 1.62.0 Depends: R (>= 2.10), GO.db, RpsiXML, annotate, apComplex Imports: AnnotationDbi, GO.db, RpsiXML, annotate, methods, org.Sc.sgd.db, utils Suggests: ppiData, xtable License: LGPL MD5sum: 744c66609ecc3f32861749660c782c3f NeedsCompilation: no Package: scMAGeCK Version: 1.2.0 Imports: Seurat, stats, utils Suggests: knitr, rmarkdown License: BSD_2_clause MD5sum: 2ea9f9ffe71231886b5f45d8aa78efb6 NeedsCompilation: yes Package: scmap Version: 1.12.0 Depends: R(>= 3.4) Imports: Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 219e2e094873e2eadaeea41d2da903db NeedsCompilation: yes Package: scMerge Version: 1.6.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), parallel, pdist, proxy, ruv, S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3), SummarizedExperiment Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, scater, testthat, badger License: GPL-3 MD5sum: bd79355234f34cd5bff402d4677a95f7 NeedsCompilation: no Package: scmeth Version: 1.10.0 Depends: R (>= 3.5.0) Imports: knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes License: GPL-2 MD5sum: aa2647b8c41b672011df49b5137dd65e NeedsCompilation: no Package: SCnorm Version: 1.12.1 Depends: R (>= 3.4.0), Imports: SingleCellExperiment, SummarizedExperiment, stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, S4Vectors, ggplot2, forcats, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) MD5sum: 75d3026b56e643fae323176194bdfb89 NeedsCompilation: no Package: scone Version: 1.14.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, BatchJobs License: Artistic-2.0 MD5sum: bbeecc9f72669c64af81737f9afa36ba NeedsCompilation: no Package: Sconify Version: 1.10.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 19e99a8fe6112746ef9204c5272bbff4 NeedsCompilation: no Package: SCOPE Version: 1.2.0 Depends: R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19 Imports: stats, grDevices, graphics, utils, DescTools, RColorBrewer, gplots, foreach, parallel, doParallel, DNAcopy, BSgenome, Biostrings, BiocGenerics, S4Vectors Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) License: GPL-2 MD5sum: daac9fdc5645eb3f90ed0721c67aa2ac NeedsCompilation: no Package: scoreInvHap Version: 1.12.1 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: ff5a3bdae7f9b58e1ba4abf15b46bb50 NeedsCompilation: no Package: scp Version: 1.0.0 Depends: R (>= 4.0), QFeatures Imports: methods, stats, utils, SingleCellExperiment, SummarizedExperiment, MultiAssayExperiment, S4Vectors, dplyr, magrittr, rlang Suggests: testthat, knitr, BiocStyle, rmarkdown, patchwork, ggplot2, matrixStats, impute, scater, sva, uwot License: Artistic-2.0 MD5sum: 87549a1b622e4a38095bed0b787021dd NeedsCompilation: no Package: scPCA Version: 1.4.0 Depends: R (>= 3.6) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca, cluster, kernlab, origami, RSpectra, coop, Matrix, DelayedArray Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark License: MIT + file LICENSE MD5sum: 5d87d19f018a0ae1757a00a206a9f0b1 NeedsCompilation: no Package: scPipe Version: 1.12.0 Depends: R (>= 3.4), ggplot2, methods, SingleCellExperiment Imports: Rhtslib, biomaRt, GGally, MASS, mclust, Rcpp (>= 0.11.3), reshape, BiocGenerics, robustbase, scales, utils, stats, S4Vectors, SummarizedExperiment, AnnotationDbi, org.Hs.eg.db, org.Mm.eg.db, stringr, rtracklayer, hash, dplyr, GenomicRanges, magrittr, glue (>= 1.3.0), rlang, scater (>= 1.11.0) LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat Suggests: Rsubread, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: c1c909da8ac4381a966cb545f110dbb1 NeedsCompilation: yes Package: scran Version: 1.18.7 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, scuttle, edgeR, limma, BiocNeighbors, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, bluster, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, DESeq2, monocle, Biobase, pheatmap, scater License: GPL-3 MD5sum: 4e892927c7aa941d1c3161ce1894883c NeedsCompilation: yes Package: scRecover Version: 1.6.0 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), Rmagic (>= 1.3.0), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL MD5sum: f321eeed61df40f2696ab16874f5347e NeedsCompilation: no Package: scRepertoire Version: 1.0.0 Depends: dplyr, ggalluvial, ggplot2, reshape2, R (>= 4.0) Imports: Biostrings, RColorBrewer, colorRamps, ggdendro, ggfittext, stringr, vegan, powerTCR, SummarizedExperiment, SingleCellExperiment, Seurat Suggests: knitr, rmarkdown, BiocStyle, scater, circlize, scales License: Apache License 2.0 MD5sum: c641917f3bc0f2f915dc8d3b93dfb99d NeedsCompilation: no Package: scruff Version: 1.8.3 Depends: R (>= 3.5.0) Imports: data.table, GenomicAlignments, GenomicFeatures, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 0e1ab404db3efb4555974052cda710d3 NeedsCompilation: no Package: scry Version: 1.2.0 Depends: R (>= 4.0), stats, methods Imports: DelayedArray, glmpca (>= 0.2.0), HDF5Array, Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, knitr, rmarkdown, TENxPBMCData, testthat License: Artistic-2.0 MD5sum: 6b2ac0461d310a3a9900b7e6af7a9f35 NeedsCompilation: no Package: scTensor Version: 2.0.0 Depends: R (>= 3.5.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor, rTensor, abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi, grDevices, graphics, stats, utils, outliers, Category, meshr, GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2 Suggests: testthat, LRBase.Hsa.eg.db, LRBase.Mmu.eg.db, LRBaseDbi, Seurat, scTGIF, Homo.sapiens License: Artistic-2.0 MD5sum: 759efab6569d55d6d1a071f5c3bd39d9 NeedsCompilation: no Package: scTGIF Version: 1.4.0 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, schex, tibble, ggplot2, igraph Suggests: testthat License: Artistic-2.0 MD5sum: 3f2a2789a1c1c7c81d7f78d3ce9633ae NeedsCompilation: no Package: scTHI Version: 1.2.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown License: GPL-2 MD5sum: e61f7f17b44a36974bbe60bd0fe093c4 NeedsCompilation: no Package: scuttle Version: 1.0.4 Depends: SingleCellExperiment Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat License: GPL-3 MD5sum: bf36544154a929f50351799e0fa8dc6a NeedsCompilation: yes Package: SDAMS Version: 1.10.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: dfa0209377474068ca31c17580159022 NeedsCompilation: no Package: segmentSeq Version: 2.24.0 Depends: R (>= 3.0.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: dec10829a978abae8f9117ed59250485 NeedsCompilation: no Package: selectKSigs Version: 1.2.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: 47a4ee8fc9433c801020413a9d815e79 NeedsCompilation: yes Package: SELEX Version: 1.22.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: cab90a66001dffea6f38ed73804fd207 NeedsCompilation: no Package: SemDist Version: 1.24.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) MD5sum: 363752b1bd1b9a14ca0c23f2f2a8c6f8 NeedsCompilation: no Package: semisup Version: 1.14.0 Depends: R (>= 3.0.0) Imports: VGAM Suggests: knitr, testthat, SummarizedExperiment License: GPL-3 MD5sum: 55a57a14314e7da258964bde4eb46ca2 NeedsCompilation: no Package: SEPIRA Version: 1.10.0 Depends: R (>= 3.5.0) Imports: limma (>= 3.32.5), corpcor (>= 1.6.9), parallel (>= 3.3.1), stats Suggests: knitr, rmarkdown, testthat, igraph License: GPL-3 MD5sum: ec98d04385bc0f7e5c301c42ac96b189 NeedsCompilation: no Package: seq2pathway Version: 1.22.0 Depends: R (>= 3.5.0) Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data License: GPL-2 MD5sum: 74f4ed6e8561fff1591b997e6d2fe5e6 NeedsCompilation: no Package: SeqArray Version: 1.30.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.23.5) Imports: methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors LinkingTo: gdsfmt Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, Rsamtools, VariantAnnotation License: GPL-3 MD5sum: ae0099d34540967262d94ccafbd2b8c6 NeedsCompilation: yes Package: seqbias Version: 1.38.0 Depends: R (>= 3.0.2), GenomicRanges (>= 0.1.0), Biostrings (>= 2.15.0), methods LinkingTo: Rhtslib (>= 1.15.3) Suggests: Rsamtools, ggplot2 License: LGPL-3 MD5sum: ca03bfd9ae6dc3a221e5c2d84a9934ba NeedsCompilation: yes Package: seqCAT Version: 1.12.0 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE MD5sum: a8a350096d61741e86ef7451e92b235d NeedsCompilation: no Package: seqCNA Version: 1.36.0 Depends: R (>= 3.0), GLAD (>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot (>= 0.99), methods License: GPL-3 MD5sum: 1220c2d42392f924c77545ab9dd7ece3 NeedsCompilation: yes Package: seqcombo Version: 1.12.0 Depends: R (>= 3.4.0) Imports: Biostrings, cowplot, dplyr, ggplot2, grid, igraph, magrittr, methods, rvcheck, utils Suggests: emojifont, knitr, prettydoc, tibble License: Artistic-2.0 MD5sum: 4dc624d339de360bd278ce443c4e4418 NeedsCompilation: no Package: SeqGate Version: 1.0.1 Depends: S4Vectors, 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wheatmap, ggplot2, parallel, matrixStats, DNAcopy, stats, SummarizedExperiment Suggests: scales, knitr, rmarkdown, testthat, dplyr, tidyr, BiocStyle, IlluminaHumanMethylation450kmanifest, minfi, FlowSorted.CordBloodNorway.450k, FlowSorted.Blood.450k, HDF5Array License: MIT + file LICENSE MD5sum: f7a7747c60793c8da4bab7a65338a93f NeedsCompilation: no Package: SEtools Version: 1.4.0 Depends: R (>= 4.0) Imports: S4Vectors, SummarizedExperiment, data.table, pheatmap, seriation, ComplexHeatmap, circlize, methods, BiocParallel, randomcoloR, edgeR, openxlsx Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL MD5sum: ebbe69d3fbf38e0c5a38c2071bf71e87 NeedsCompilation: no Package: sevenbridges Version: 1.20.1 Depends: methods, utils, stats Imports: httr, jsonlite, yaml, objectProperties, stringr, S4Vectors, docopt, curl, uuid, data.table Suggests: knitr, rmarkdown, testthat, readr License: Apache License 2.0 | file LICENSE MD5sum: 5739f1e52f46c8aaffc0ba01ea23c895 NeedsCompilation: no 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Imports: downloader (>= 0.4), grDevices, biomaRt, dplyr, graphics, tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite (>= 1.0.0), plyr, knitr, methods, ggplot2, stringr (>= 1.0.0), IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils, SummarizedExperiment (>= 1.4.0), TCGAbiolinksGUI.data, readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1) Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame, pathview, clusterProfiler, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid License: GPL (>= 3) MD5sum: fe386cee73e48b931a72e47edf3f0608 NeedsCompilation: no Package: TCGAbiolinksGUI Version: 1.16.0 Depends: R (>= 3.3.1), shinydashboard (>= 0.5.3), TCGAbiolinksGUI.data Imports: shiny (>= 0.14.1), downloader (>= 0.4), grid, DT, plotly, readr, maftools, stringr (>= 1.1.0), 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TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: b32a47801fded6742d49583d387afd0e NeedsCompilation: no Package: TCseq Version: 1.14.0 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) MD5sum: b820e36cd770a6c2898920f3b35a0930 NeedsCompilation: no Package: TDARACNE Version: 1.40.0 Depends: GenKern, Rgraphviz, Biobase License: GPL-2 MD5sum: 172d68bedbb727a40eb3d399f829e803 NeedsCompilation: no Package: tenXplore Version: 1.12.0 Depends: R (>= 3.4), shiny, restfulSE (>= 0.99.12) Imports: methods, ontoProc (>= 0.99.7), SummarizedExperiment, AnnotationDbi, matrixStats, org.Mm.eg.db, stats, utils Suggests: org.Hs.eg.db, testthat, knitr License: Artistic-2.0 MD5sum: 14ceb7f4ad3906f3045d95e1c4cadc04 NeedsCompilation: no Package: TEQC Version: 4.12.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Rsamtools, hwriter Imports: Biobase (>= 2.15.1) License: GPL (>= 2) MD5sum: 8c7a1a73706ce4881a133dda2ad719cb NeedsCompilation: no Package: ternarynet Version: 1.34.0 Depends: R (>= 2.10.0), methods Imports: utils, igraph License: GPL (>= 2) MD5sum: c23a7709a46449a66610027e649795ff NeedsCompilation: yes Package: TFARM Version: 1.12.0 Depends: R (>= 3.4) Imports: arules, fields, GenomicRanges, graphics, stringr, methods, stats, gplots Suggests: BiocStyle, knitr, plyr License: Artistic-2.0 MD5sum: 90ba2fdeb960c3e63d6155215a93a091 NeedsCompilation: no Package: TFBSTools Version: 1.28.0 Depends: R (>= 3.2.2) Imports: Biobase(>= 2.28), Biostrings(>= 2.36.4), BiocGenerics(>= 0.14.0), BiocParallel(>= 1.2.21), BSgenome(>= 1.36.3), caTools(>= 1.17.1), CNEr(>= 1.4.0), DirichletMultinomial(>= 1.10.0), GenomeInfoDb(>= 1.6.1), GenomicRanges(>= 1.20.6), gtools(>= 3.5.0), grid, IRanges(>= 2.2.7), methods, DBI (>= 0.6), RSQLite(>= 1.0.0), rtracklayer(>= 1.28.10), seqLogo(>= 1.34.0), S4Vectors(>= 0.9.25), TFMPvalue(>= 0.0.5), XML(>= 3.98-1.3), XVector(>= 0.8.0), parallel Suggests: BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr(>= 1.11), testthat, JASPAR2016(>= 1.0.0), JASPAR2018(>= 1.0.0) License: GPL-2 MD5sum: e84a0debde9f458174967613bfd20b2d NeedsCompilation: yes Package: TFEA.ChIP Version: 1.10.0 Depends: R (>= 3.3) Imports: GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices, dplyr, stats, utils, R.utils, methods, org.Hs.eg.db Suggests: knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, GSEABase, DESeq2, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: d297905e8a6cbb11daeb75ebb16464d4 NeedsCompilation: no Package: TFHAZ Version: 1.12.0 Depends: R(>= 3.4) Imports: GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 934cc164d4bffc9b3d270f8a31c94af3 NeedsCompilation: no Package: TFutils Version: 1.10.1 Depends: R (>= 3.5.0) Imports: methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase, rjson, BiocFileCache, DT, httr, readxl Suggests: knitr, data.table, testthat, AnnotationDbi, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, Rsamtools, S4Vectors, org.Hs.eg.db, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer License: Artistic-2.0 MD5sum: bf8ce31ea43efba6c4054e4dca877126 NeedsCompilation: no Package: tidybulk Version: 1.2.1 Depends: R (>= 4.0.0) Imports: tibble, readr, dplyr, magrittr, tidyr, stringr, rlang, purrr, preprocessCore, stats, parallel, utils, lifecycle, scales, SummarizedExperiment, methods Suggests: BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, S4Vectors, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional License: GPL-3 MD5sum: 603c286bea273c1fd8763e68ef4367a3 NeedsCompilation: no Package: tidySingleCellExperiment Version: 1.0.0 Depends: R (>= 4.0.0), SingleCellExperiment Imports: dplyr, tibble, tidyr, ggplot2, plotly, magrittr, rlang, purrr, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, pillar, stringr, cli, fansi Suggests: BiocStyle, testthat, knitr, markdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, Matrix, uwot, celldex, dittoSeq License: GPL-3 MD5sum: b65d48e906c19806480fac94bc743bbb NeedsCompilation: no Package: tidySummarizedExperiment Version: 1.0.0 Depends: R (>= 4.0.0), SummarizedExperiment Imports: tibble (>= 3.0.4), dplyr, magrittr, tidyr, ggplot2, rlang, purrr, lifecycle, methods, plotly, utils, S4Vectors, tidyselect, ellipsis, pillar, stringr, cli, fansi Suggests: BiocStyle, testthat, knitr, markdown License: GPL-3 MD5sum: 93675dd010fbfca824c5225c4b3262cd NeedsCompilation: no Package: tigre Version: 1.44.0 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, AnnotationDbi, gplots, graphics, grDevices, stats, utils, annotate, DBI, RSQLite Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager License: AGPL-3 MD5sum: c6279febcd7963c1ed505acb5ee72b92 NeedsCompilation: yes Package: TileDBArray Version: 1.0.0 Depends: DelayedArray (>= 0.15.16) Imports: methods, Rcpp, tiledb, S4Vectors LinkingTo: Rcpp Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat License: MIT + file LICENSE MD5sum: 617b4e36d186c6eac146bc44f746353b NeedsCompilation: yes Package: tilingArray Version: 1.68.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 MD5sum: d5694e101b2f1b72ac08d9a6d85cf327 NeedsCompilation: yes Package: timecourse Version: 1.62.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL MD5sum: 40a89b2331ebaa80166ddbe72ac7a2eb NeedsCompilation: no Package: timeOmics Version: 1.2.0 Depends: mixOmics, R (>= 4.0) Imports: dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, propr, lmtest Suggests: BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots License: GPL-3 MD5sum: 7d300ffccc391f178126230eb26f50b1 NeedsCompilation: no Package: timescape Version: 1.14.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), stringr (>= 1.0.0), dplyr (>= 0.4.3), gtools (>= 3.5.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: a4d4d4ebaf375225413153d15285f197 NeedsCompilation: no Package: TimeSeriesExperiment Version: 1.8.0 Depends: R (>= 3.5.0), S4Vectors (>= 0.19.23), SummarizedExperiment (>= 1.11.6) Imports: dynamicTreeCut, dplyr, edgeR, DESeq2, ggplot2 (>= 3.0.0), graphics, Hmisc, limma, methods, magrittr, proxy, stats, tibble, tidyr, vegan, viridis, utils Suggests: Biobase, BiocFileCache (>= 1.5.8), circlize, ComplexHeatmap, GO.db, grDevices, grid, knitr, org.Mm.eg.db, org.Hs.eg.db, MASS, RColorBrewer, rmarkdown, UpSetR, License: LGPL (>= 3) MD5sum: c48af5118f35866d8dfda385aa8bd39f NeedsCompilation: no Package: TimiRGeN Version: 1.0.6 Depends: R (>= 4.0), Mfuzz, MultiAssayExperiment Imports: biomaRt, clusterProfiler, dplyr (>= 0.8.4), FreqProf, gtools (>= 3.8.1), gplots, ggdendro, gghighlight, ggplot2, graphics, grDevices, igraph (>= 1.2.4.2), RCy3, readxl, reshape2, rWikiPathways, scales, stats, tidyr (>= 1.0.2), stringr (>= 1.4.0) Suggests: BiocManager, kableExtra, knitr (>= 1.27), org.Hs.eg.db, org.Mm.eg.db, testthat, rmarkdown License: GPL-3 MD5sum: 6f335d4e7c1b51221c35d4b2506480de NeedsCompilation: no Package: TIN Version: 1.22.0 Depends: R (>= 2.12.0), data.table, impute, aroma.affymetrix Imports: WGCNA, squash, stringr Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 46a0d583e1912fe13de9b18662262331 NeedsCompilation: no Package: TissueEnrich Version: 1.10.1 Depends: R (>= 3.5), ensurer (>= 1.1.0), ggplot2 (>= 2.2.1), SummarizedExperiment (>= 1.6.5), GSEABase (>= 1.38.2) Imports: dplyr (>= 0.7.3), tidyr (>= 0.8.0), stats Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 96c73969d2cf54fbff615fcd992ec512 NeedsCompilation: no Package: TitanCNA Version: 1.28.0 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 MD5sum: 6da18640c59f3d807291779c5ab63dc0 NeedsCompilation: yes Package: tkWidgets Version: 1.68.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 MD5sum: a174b3b1466447777024b0144c29280d NeedsCompilation: no Package: TMixClust Version: 1.12.0 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) MD5sum: 851d6d25eae12151a914ee76473d7030 NeedsCompilation: no Package: TNBC.CMS Version: 1.6.0 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 MD5sum: 037ed90407b5923a23e5769ce6d05fda NeedsCompilation: no Package: TnT Version: 1.12.0 Depends: R (>= 3.4), GenomicRanges Imports: methods, stats, utils, grDevices, htmlwidgets, jsonlite, data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr Suggests: GenomicFeatures, shiny, BiocManager, rmarkdown, testthat License: AGPL-3 MD5sum: e316957a86ee48bbd92b5af34cfb7b34 NeedsCompilation: no Package: TOAST Version: 1.4.0 Depends: R (>= 3.6), RefFreeEWAS, EpiDISH, limma, 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Biobase, RBGL, SummarizedExperiment, gRbase, limma, corpcor LinkingTo: Rcpp Suggests: BiocStyle, airway, knitr, rmarkdown, DESeq2, DESeq, edgeR, plotrix, breastCancerVDX, EnrichmentBrowser License: AGPL-3 MD5sum: eadf605fa6d6bc1b1cf35cf24eee7a8a NeedsCompilation: yes Package: topconfects Version: 1.6.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, assertthat, ggplot2 Suggests: limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle License: LGPL-2.1 | file LICENSE MD5sum: 83f787ffe6f248ec6f2a80bdbd5fa1f2 NeedsCompilation: no Package: topdownr Version: 1.12.0 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: 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Depends: R (>= 3.4), methods Imports: biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 062c2080d93603a5e2a5d59d583dfd20 NeedsCompilation: no Package: transcriptR Version: 1.18.0 Depends: methods, R (>= 3.3) Imports: BiocGenerics, caret, chipseq, e1071, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2, Rsamtools, rtracklayer, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat License: GPL-3 MD5sum: 852db2a664395d361fdc39a2db6606f7 NeedsCompilation: no Package: transite Version: 1.8.0 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), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils LinkingTo: Rcpp (>= 1.0.4.8) Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 6e8830d4874924cdb4245eaade39de90 NeedsCompilation: yes Package: tRanslatome Version: 1.28.0 Depends: R (>= 2.15.0), methods, limma, sigPathway, anota, DESeq, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 MD5sum: 84211cd3b5b3a15191751f9febb23a77 NeedsCompilation: no Package: transomics2cytoscape Version: 1.0.0 Imports: RCy3, KEGGREST, dplyr Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 683d8bffb3b58849fdc3ade7280d371c NeedsCompilation: no Package: TransView Version: 1.34.0 Depends: methods, GenomicRanges Imports: BiocGenerics, S4Vectors (>= 0.9.25), IRanges, zlibbioc, gplots LinkingTo: Rhtslib (>= 1.15.3) Suggests: RUnit, pasillaBamSubset, BiocManager 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BSgenome.Celegans.UCSC.ce10, rtracklayer License: BSD_2_clause + file LICENSE MD5sum: f9c9d862a6f8f5e7c2e26c0720cd1313 NeedsCompilation: yes Package: tRNA Version: 1.8.0 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE MD5sum: 684750a4d3f7b2a5a89469d672c6c4fe NeedsCompilation: no Package: tRNAdbImport Version: 1.8.0 Depends: R (>= 3.5), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, BiocGenerics, stringr, xml2, S4Vectors, methods, httr, IRanges, utils Suggests: knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE MD5sum: d75d1b527b5599de64cf66995228b697 NeedsCompilation: no Package: tRNAscanImport Version: 1.10.0 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, stringr, BiocGenerics, Biostrings, Structstrings, S4Vectors, IRanges, XVector, GenomeInfoDb, rtracklayer, BSgenome, Rsamtools Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 + file LICENSE MD5sum: 1349b6d20318d1496ab69884494fe0e3 NeedsCompilation: no Package: TRONCO Version: 2.22.0 Depends: R (>= 4.0.0), Imports: bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, cgdsr, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways License: GPL-3 MD5sum: e735fe41b8e11dc7b4c29379ff2954f1 NeedsCompilation: no Package: TSCAN Version: 1.28.0 Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, SingleCellExperiment, DelayedArray, S4Vectors Suggests: knitr, testthat, beachmat, scuttle, scran, BiocParallel, BiocNeighbors, batchelor License: GPL (>= 2) MD5sum: 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AnnotationDbi, GenomicFeatures, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, rappdirs, utils, methods, Matrix Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, edgeR, limma, devtools License: GPL-2 MD5sum: f592d0b2b20b5dbe958001cc870db778 NeedsCompilation: no Package: tximport Version: 1.18.0 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, csaw, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, fishpond License: GPL (>= 2) MD5sum: 2d19640a8769386ff6116b7e50415be0 NeedsCompilation: no Package: TxRegInfra Version: 1.10.0 Depends: R (>= 3.5), RaggedExperiment (>= 1.3.11), mongolite Imports: methods, rjson, GenomicRanges, IRanges, BiocParallel, GenomeInfoDb, S4Vectors, SummarizedExperiment, utils Suggests: knitr, GenomicFiles, EnsDb.Hsapiens.v75, testthat, shiny, biovizBase (>= 1.27.2), Gviz, AnnotationFilter, ensembldb, ontoProc, rjson, graph, TFutils (>= 1.5.4) License: Artistic-2.0 MD5sum: 7610d7effab88ee8340c34f8deebccbd NeedsCompilation: no Package: TypeInfo Version: 1.56.0 Depends: methods Suggests: Biobase License: BSD MD5sum: 5fe08d628f8c1f46a12ee7f663a520ff NeedsCompilation: no Package: Ularcirc Version: 1.8.0 Depends: R (>= 3.4.0) Imports: AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments, Organism.dplyr, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, Sushi, yaml Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: df6fe8536f173152aef0d0006decba73 NeedsCompilation: no Package: UMI4Cats Version: 1.0.1 Depends: R (>= 4.0.0), SummarizedExperiment Imports: magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, magrittr, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats, org.Hs.eg.db, annotate, TxDb.Hsapiens.UCSC.hg19.knownGene, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda Suggests: knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat License: Artistic-2.0 MD5sum: c645163c70ce554335d8b618a88639c7 NeedsCompilation: no Package: uncoverappLib Version: 1.0.0 Imports: markdown, shiny, shinyjs, shinyBS, shinyWidgets,shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx, condformat, stringr, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache,rappdirs, TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, BSgenome.Hsapiens.UCSC.hg19, processx, Rsamtools, GenomicRanges Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: 8b669167014897a092ef31ee19ad73f3 NeedsCompilation: no Package: UNDO Version: 1.32.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 76e07fb8c93c1cb95665826dca97652c NeedsCompilation: no Package: unifiedWMWqPCR Version: 1.26.0 Depends: methods Imports: BiocGenerics, stats, graphics, HTqPCR License: GPL (>= 2) MD5sum: 683d520dcfaeb1fb196808498364450b NeedsCompilation: no Package: UniProt.ws Version: 2.30.0 Depends: methods, utils, RSQLite, RCurl, BiocGenerics (>= 0.13.8) Imports: AnnotationDbi, BiocFileCache, rappdirs Suggests: RUnit, BiocStyle, knitr License: Artistic License 2.0 MD5sum: 5eb0af3e2ee8fb308d73aed1c7fe4aa4 NeedsCompilation: no Package: Uniquorn Version: 2.10.0 Depends: R (>= 3.5) Imports: stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation Suggests: testthat, knitr, rmarkdown, BiocGenerics, RUnit License: Artistic-2.0 MD5sum: 0ca90493cbb8293089c09f38be969d37 NeedsCompilation: no Package: universalmotif Version: 1.8.5 Depends: R (>= 3.5.0) Imports: methods, stats, utils, MASS, ggplot2, ggseqlogo, yaml, IRanges, Rcpp, Rdpack (>= 0.7), Biostrings, BiocGenerics, S4Vectors, rlang, grid LinkingTo: Rcpp, RcppThread Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, Logolas, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx Enhances: MotIV, PWMEnrich, rGADEM, motifRG License: GPL-3 MD5sum: 5bb0460f7fd19e7cca6c90d5ea06580a NeedsCompilation: yes Package: uSORT Version: 1.16.0 Depends: R (>= 3.3.0), tcltk Imports: igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 MD5sum: c2a9b9400c93aa952578b174ec27b8ca NeedsCompilation: no Package: VanillaICE Version: 1.52.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, human610quadv1bCrlmm, ArrayTV Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 MD5sum: f6a982ebd8b134f269413f39364d7fa6 NeedsCompilation: yes Package: variancePartition Version: 1.20.0 Depends: R (>= 3.6.0), ggplot2, limma, BiocParallel, scales, Biobase, methods Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, iterators, splines, foreach, doParallel, colorRamps, gplots, progress, reshape2, lme4 (>= 1.1-10), grDevices, graphics, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr License: GPL (>= 2) MD5sum: 1d1fa2cab04eed88dd36836f6778d543 NeedsCompilation: no Package: 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DelayedDataFrame (>= 1.0.0) Imports: tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray, SeqVarTools, DelayedArray, Biostrings, IRanges Suggests: testthat, knitr License: GPL-3 MD5sum: c8f3d7304c0f6a2a84b63bd1c27b6be3 NeedsCompilation: no Package: VariantFiltering Version: 1.26.0 Depends: R (>= 3.5.0), 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, 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