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(>= 1.17.0), IRanges Imports: DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST Suggests: hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 MD5sum: 9cda13f36cd7223c1bf325c99ac60759 NeedsCompilation: no Package: AnnotationFilter Version: 1.18.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown License: Artistic-2.0 MD5sum: 3bd3d3b7f9f78f3297a0434d7d88afd5 NeedsCompilation: no Package: AnnotationForge Version: 1.36.0 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, GO.db, markdown, BiocStyle, knitr, BiocManager, BiocFileCache License: Artistic-2.0 MD5sum: b888edfb1feaf1c930d0171d5cfb69e9 NeedsCompilation: no Package: AnnotationHub Version: 3.2.2 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, interactiveDisplayBase, httr, yaml, dplyr Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 1504583a31b71617e95c9c1793ed90d6 NeedsCompilation: yes Package: AnnotationHubData Version: 1.24.2 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, biocViews, BiocCheck, graph, AnnotationDbi, Biobase, Biostrings, DBI, GenomeInfoDb (>= 1.15.4), OrganismDbi, RSQLite, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub License: Artistic-2.0 MD5sum: e8c3f8c5c50e5e3fb915c37e03f9f4d0 NeedsCompilation: no Package: annotationTools Version: 1.68.0 Imports: Biobase, stats Suggests: BiocStyle License: GPL MD5sum: d4f77ca026cf1b013298f6495c0d518f NeedsCompilation: no Package: annotatr Version: 1.20.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures, GenomicRanges, GenomeInfoDb (>= 1.10.3), ggplot2, IRanges, methods, readr, regioneR, reshape2, rtracklayer, S4Vectors (>= 0.23.10), stats, utils Suggests: BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene License: GPL-3 MD5sum: d68d24129d9abd101518a8a6095f6c57 NeedsCompilation: no Package: anota Version: 1.42.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: 0de2cfba8335adcb7094c9a62fd01b41 NeedsCompilation: no Package: anota2seq Version: 1.16.0 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: 2cdb2b7795c9fb77f4f4271e9c82918c NeedsCompilation: no Package: antiProfiles Version: 1.34.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: bee9d260201493da5cfce9211adb0083 NeedsCompilation: no 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GenomicAlignments, DESeq2, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, ensembldb, VariantAnnotation, dplyr, tidyr, repmis, Rsamtools Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset License: LGPL-3 MD5sum: de9cc82a61e70ff944f4ab746b0a327e NeedsCompilation: no Package: apComplex Version: 2.60.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: 8b8ffdf3d4310ac5f63259a759a1bd7d NeedsCompilation: no Package: apeglm Version: 1.16.0 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 38f07b23a3c15ae4c6fff24a4084db95 NeedsCompilation: yes Package: appreci8R Version: 1.12.1 Imports: shiny, shinyjs, DT, VariantAnnotation, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, rsnps, Biostrings, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.gnomADex.r2.1.hs37d5, COSMIC.67, rentrez, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137, seqinr, openxlsx, Rsamtools, stringr, utils, stats, GenomicRanges, S4Vectors, GenomicFeatures, IRanges, GenomicScores, SummarizedExperiment Suggests: GO.db, org.Hs.eg.db License: LGPL-3 MD5sum: c106ed2b77f7f1fbe3094f5cb94e61c2 NeedsCompilation: no Package: aroma.light Version: 3.24.0 Depends: R (>= 2.15.2) Imports: stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.23.0), R.utils (>= 2.9.0), matrixStats (>= 0.55.0) Suggests: princurve (>= 2.1.4) License: GPL (>= 2) MD5sum: ffbcd0ceaf8177ce69f11685bda3635a NeedsCompilation: no Package: ArrayExpress Version: 1.54.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: XML, oligo, limma Suggests: affy License: Artistic-2.0 MD5sum: 8ba02029431613cd191826dbc00df0b6 NeedsCompilation: no Package: 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gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat License: GPL (>= 3) + file LICENSE MD5sum: 834fe52996035e500cde130e4734f60d NeedsCompilation: no Package: ASAFE Version: 1.20.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 17e156e533cad0b9d29d2319c13cb7da NeedsCompilation: no Package: ASEB Version: 1.38.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) MD5sum: d1c8fd8bd4e32f278936e21be75aeeff NeedsCompilation: yes Package: ASGSCA Version: 1.28.0 Imports: Matrix, MASS Suggests: BiocStyle License: GPL-3 MD5sum: 854e990a4b8e1e5828c9a26b7ee9dca0 NeedsCompilation: no Package: ASICS Version: 2.10.0 Depends: R (>= 3.5) Imports: BiocParallel, ggplot2, glmnet, grDevices, gridExtra, methods, mvtnorm, PepsNMR, plyr, quadprog, ropls, stats, SummarizedExperiment, utils, Matrix, zoo Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata License: GPL (>= 2) MD5sum: e6864f2b12dfd84ac9307ccd3eda57b8 NeedsCompilation: no Package: ASpediaFI Version: 1.8.0 Depends: R (>= 3.6.0), SummarizedExperiment, ROCR Imports: BiocParallel, GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges, IVAS, Rsamtools, biomaRt, limma, S4Vectors, stats, DRaWR, GenomeInfoDb, Gviz, Matrix, dplyr, fgsea, reshape2, igraph, graphics, e1071, methods, rtracklayer, scales, grid, ggplot2, mGSZ, utils Suggests: knitr License: GPL-3 MD5sum: 20dd8a644b0e5abb3cb8cc3d4c274101 NeedsCompilation: no Package: ASpli Version: 2.4.0 Depends: methods, grDevices, stats, utils, parallel, edgeR, limma, AnnotationDbi Imports: GenomicRanges, GenomicFeatures, BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, Rsamtools, BiocStyle, igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid, graphics, pbmcapply License: GPL MD5sum: fd540f5d6b45fc45cf0ecf5b51124480 NeedsCompilation: no Package: AssessORF Version: 1.12.0 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: e70abdf3cabd99549ed7f493ad8d427e NeedsCompilation: no Package: ASSET Version: 2.12.0 Depends: stats, graphics Imports: MASS, msm, rmeta Suggests: RUnit, BiocGenerics, knitr License: GPL-2 + file LICENSE MD5sum: 5da2760ddf2e864d06c3fc5084cad8ff NeedsCompilation: no Package: ASSIGN Version: 1.30.0 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: 2dce89052b6b6dbc58afca57d751abd8 NeedsCompilation: no Package: ATACseqQC Version: 1.18.1 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, rmarkdown License: GPL (>= 2) MD5sum: 6cdec79cbd6ef0e5dec1098aa19a60e7 NeedsCompilation: no Package: atena Version: 1.0.5 Depends: R (>= 4.1), SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, BiocParallel, S4Vectors, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 38237f016695a41e2f3833b648fa0bcd NeedsCompilation: no Package: atSNP Version: 1.10.0 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: 4eb15dc6592d985d73b4669eeaa37ab4 NeedsCompilation: yes Package: attract Version: 1.46.0 Depends: R (>= 3.4.0), AnnotationDbi Imports: Biobase, limma, cluster, GOstats, graphics, stats, reactome.db, KEGGREST, org.Hs.eg.db, utils, methods Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) MD5sum: 055b93462ff41340d5986d2936760aad NeedsCompilation: no Package: AUCell Version: 1.16.0 Imports: data.table, graphics, grDevices, GSEABase, methods, mixtools, R.utils, shiny, stats, SummarizedExperiment, BiocGenerics, S4Vectors, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, rbokeh, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: e4a79320ae56b828227795ad2b1dcf07 NeedsCompilation: no Package: autonomics Version: 1.2.0 Depends: R (>= 4.0) Imports: abind, assertive, BiocFileCache, BiocGenerics, colorspace, data.table, edgeR, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma, magrittr, matrixStats, methods, MultiAssayExperiment, parallel, pcaMethods, rappdirs, rlang, R.utils, readxl, S4Vectors, scales, stats, stringi, SummarizedExperiment, tidyr, tools, utils Suggests: affy, AnnotationDbi, BiocManager, diagram, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, knitr, lme4, lmerTest, MASS, mixOmics, mpm, nlme, org.Hs.eg.db, org.Mm.eg.db, RCurl, remotes, rmarkdown, ropls, Rsubread, rtracklayer, seqinr, statmod, testthat License: GPL-3 MD5sum: b80d6aeb59f6f01b57785f903fe37fd5 NeedsCompilation: no Package: AWFisher Version: 1.8.0 Depends: R (>= 3.6) Imports: edgeR, limma, stats Suggests: knitr, tightClust License: GPL-3 MD5sum: 41663878babd8d30e84fd3637cf7f010 NeedsCompilation: yes Package: awst Version: 1.2.0 Imports: stats, methods, SummarizedExperiment Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown License: MIT + file LICENSE MD5sum: 906daea0377a7f0715eb401e4e2692b0 NeedsCompilation: no Package: BaalChIP Version: 1.20.0 Depends: R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools, Imports: GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy, reshape2, scales, coda, foreach, ggplot2, methods, utils, graphics, stats Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: b03782deab32260b31c7d8ae21cb51b9 NeedsCompilation: no Package: BAC Version: 1.54.0 Depends: R (>= 2.10) License: Artistic-2.0 MD5sum: 5b81f3b2566b9318d9db02f4cda1ea2d NeedsCompilation: yes Package: bacon Version: 1.22.0 Depends: R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 License: GPL (>= 2) MD5sum: 837eb87e9f3c028d0a76bc3dc7db60f9 NeedsCompilation: yes Package: BADER Version: 1.32.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 MD5sum: f92aeb190355401dda2019511205db5a NeedsCompilation: yes Package: BadRegionFinder Version: 1.22.0 Imports: VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 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ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, apeglm, utils, DEXSeq Enhances: parallel License: GPL-3 + file LICENSE MD5sum: 42b0f0f0bfd6a3d7559b90cb9365d98c NeedsCompilation: yes Package: bamsignals Version: 1.26.0 Depends: R (>= 3.2.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: d66b8af0221a75630a5e1de8e2a283d3 NeedsCompilation: yes Package: BANDITS Version: 1.10.0 Depends: R (>= 3.6.0) Imports: Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings License: GPL (>= 3) MD5sum: 383f816cd3938395e34fd4427985a0b6 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BiocSingular LinkingTo: Rcpp, RcppArmadillo, RcppDist, RcppProgress Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, dplyr, viridis, patchwork, RColorBrewer, Seurat License: MIT + file LICENSE MD5sum: f608fbb4a3c2b8d70d028fdd0a719422 NeedsCompilation: yes Package: bayNorm Version: 1.12.0 Depends: R (>= 3.5), Imports: Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix, parallel, MASS, locfit, fitdistrplus, stats, methods, graphics, grDevices, SingleCellExperiment, SummarizedExperiment, BiocParallel, utils LinkingTo: Rcpp, RcppArmadillo,RcppProgress Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat License: GPL (>= 2) MD5sum: db13998e1ac208d231242e9f1be05468 NeedsCompilation: yes Package: baySeq Version: 2.28.0 Depends: R (>= 2.3.0), methods, GenomicRanges, abind, parallel Imports: edgeR Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: 30cda72226a6cad10ef4fc2e8fc0c58b NeedsCompilation: no Package: BBCAnalyzer Version: 1.24.0 Imports: SummarizedExperiment, 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Suggests: knitr, dbplyr, org.Hs.eg.db, MultiAssayExperiment, BiocStyle, ontoProc, ontologyPlot, pogos, GenomeInfoDb, restfulSE (>= 1.3.7), BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene, Biobase, TxDb.Hsapiens.UCSC.hg18.knownGene, reshape2, testthat, AnnotationDbi, FDb.InfiniumMethylation.hg19, EnsDb.Hsapiens.v75, rmarkdown, rhdf5client License: Artistic-2.0 MD5sum: 2b5abf3ff33b30083010e0d3fd24cb9d NeedsCompilation: no Package: BioCor Version: 1.18.0 Depends: R (>= 3.4.0) Imports: BiocParallel, Matrix, methods, GSEABase Suggests: reactome.db, org.Hs.eg.db, WGCNA, GOSemSim, testthat, knitr, rmarkdown, BiocStyle, airway, DESeq2, boot, targetscan.Hs.eg.db, Hmisc, spelling License: MIT + file LICENSE MD5sum: fff8e729720808b2a6137936f8c9044e NeedsCompilation: no Package: BiocParallel Version: 1.28.3 Depends: methods, R (>= 3.5.0) Imports: stats, utils, futile.logger, parallel, snow LinkingTo: BH Suggests: BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel, Rmpi, GenomicRanges, 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Imports: IRanges (>= 2.23.9), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors (>= 0.27.12), R.utils (>= 2.0.0), DelayedMatrixStats (>= 1.5.2), permute, limma, DelayedArray (>= 0.15.16), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array (>= 1.19.11), rhdf5 LinkingTo: Rcpp, beachmat Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat (>= 1.5.2), BatchJobs License: Artistic-2.0 MD5sum: cf455a0cd18638d3ef9bf2589dbea44f NeedsCompilation: yes Package: BubbleTree Version: 2.24.0 Depends: R (>= 3.5), IRanges, GenomicRanges, plyr, dplyr, magrittr Imports: BiocGenerics (>= 0.31.6), BiocStyle, Biobase, ggplot2, WriteXLS, gtools, RColorBrewer, limma, grid, gtable, gridExtra, biovizBase, e1071, methods, grDevices, stats, utils Suggests: knitr, rmarkdown License: LGPL (>= 3) MD5sum: ff9da2db959959bad4a988a680ac2a76 NeedsCompilation: no Package: BufferedMatrix 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iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats Suggests: testthat, RUnit, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 6d934238a635ddefeb29a2a580a63260 NeedsCompilation: no Package: BumpyMatrix Version: 1.2.0 Imports: utils, methods, Matrix, S4Vectors, IRanges Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: ce955c49321bca85c27120cca052486b NeedsCompilation: no Package: BUS Version: 1.50.0 Depends: R (>= 2.3.0), minet Imports: stats, infotheo License: GPL-3 MD5sum: 01c12102267b23753a256e6ae3e84576 NeedsCompilation: yes Package: BUScorrect Version: 1.12.0 Depends: R (>= 3.5.0) Imports: gplots, methods, grDevices, stats, SummarizedExperiment Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 88e826ca667652c85ab3ac54013c93f4 NeedsCompilation: yes Package: BUSpaRse Version: 1.8.0 Depends: R (>= 3.6) 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Depends: R (>= 4.0), SingleCellExperiment Imports: circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot, data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel, ggridges, graphics, grDevices, grid, gridExtra, magrittr, Matrix, matrixStats, methods, nnls, purrr, RColorBrewer, reshape2, Rtsne, SummarizedExperiment, S4Vectors, scales, scater, stats Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot License: GPL (>= 2) MD5sum: 6f42fd0972ae33e304e1931a8e7a133e NeedsCompilation: no Package: Category Version: 2.60.0 Depends: methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix Imports: utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db License: Artistic-2.0 MD5sum: 056a39817aec1c5affa4548c9c011e89 NeedsCompilation: no Package: categoryCompare Version: 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Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, checkmate, gtools, magick Suggests: testthat, roxygen2, devtools, knitr, lintr License: Artistic-2.0 MD5sum: c626cc86f9ffba337bf2fa3ab573ea43 NeedsCompilation: no Package: ChIPanalyser Version: 1.16.0 Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb Suggests: BSgenome.Dmelanogaster.UCSC.dm3,knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 3accd5257e1b7657ab639ddcafdc292e NeedsCompilation: no Package: ChIPComp Version: 1.24.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,rtracklayer,GenomeInfoDb,S4Vectors Imports: Rsamtools,limma,BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,BiocGenerics Suggests: BiocStyle,RUnit License: GPL MD5sum: b005abf06492fbde95c3169f31739b19 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GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, graphics, grDevices, gtools, methods, plotrix, dplyr, parallel, magrittr, RColorBrewer, rtracklayer, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, tibble License: Artistic-2.0 MD5sum: 648c94b53750f6266289d85bf59b2374 NeedsCompilation: no Package: chipseq Version: 1.44.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), ShortRead Imports: methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges, ShortRead Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene License: Artistic-2.0 MD5sum: 6cc9ca1ff1cb3320f8f0b006a90b9482 NeedsCompilation: yes Package: ChIPseqR Version: 1.48.0 Depends: R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25) Imports: Biostrings, fBasics, GenomicRanges, IRanges (>= 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knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr License: GPL-3 MD5sum: 8117a3c4274babdb0f518290ffe7bb49 NeedsCompilation: no Package: clusterStab Version: 1.66.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 MD5sum: f7b1aa31565d5dc8178e170b93f36dd3 NeedsCompilation: no Package: clustifyr Version: 1.6.0 Depends: R (>= 4.0) Imports: cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, readr, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, matrixStats, S4Vectors, proxy, httr, utils Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr License: MIT + file LICENSE MD5sum: 924341d3517141873632e4a4b68f7182 NeedsCompilation: no Package: CMA Version: 1.52.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, 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knitr, rmarkdown, VGAM License: GPL (>= 2) MD5sum: 2cabd2ed5e09438f4681f8f090a66b13 NeedsCompilation: no Package: cTRAP Version: 1.12.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, binr, cowplot, data.table, dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics, highcharter, htmltools, httr, limma, methods, parallel, pbapply, purrr, qs, R.utils, readxl, reshape2, rhdf5, rlang, scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble, tools, utils Suggests: testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes License: MIT + file LICENSE MD5sum: 7f0865d76c20f2990de4d03aec64321d NeedsCompilation: no Package: ctsGE Version: 1.20.0 Depends: R (>= 3.2) Imports: ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat License: GPL-2 MD5sum: a491a237c857401a3916bdc817e08c0e NeedsCompilation: no Package: cummeRbund Version: 2.36.0 Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, 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MD5sum: 3b1ba76ae2e85d89bd643ae02e13244e NeedsCompilation: no Package: cyanoFilter Version: 1.2.0 Depends: R(>= 4.1.0) Imports: Biobase, flowCore, flowDensity, flowClust, cytometree, ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats, utils Suggests: magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr License: MIT + file LICENSE MD5sum: 1a059c59997fcd7443c1a8214c999210 NeedsCompilation: no Package: cycle Version: 1.48.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 MD5sum: 57fd7f246d005e30ccdb1705f19c4b50 NeedsCompilation: no Package: cydar Version: 1.18.0 Depends: SingleCellExperiment Imports: viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment, flowCore, Biobase, Rcpp, BiocNeighbors LinkingTo: Rcpp Suggests: ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet, BiocStyle, flowStats License: GPL-3 MD5sum: 51bd45a7afc71fca72ebfb0a8695f7bb NeedsCompilation: yes Package: CytoDx Version: 1.14.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: aef71fe5f2ab4a6ed5d5facdca159075 NeedsCompilation: no Package: CyTOFpower Version: 1.0.0 Depends: R (>= 4.1) Imports: CytoGLMM, diffcyt, DT, dplyr, ggplot2, magrittr, methods, rlang, stats, shiny, shinyFeedback, shinyjs, shinyMatrix, SummarizedExperiment, tibble, tidyr Suggests: testthat (>= 3.0.0), BiocStyle, knitr License: LGPL-3 MD5sum: 6643fbde0559d6ae1f9f6d20f755920a NeedsCompilation: no Package: CytoGLMM Version: 1.2.0 Imports: stats, methods, BiocParallel, RColorBrewer, cowplot, doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr, mbest, pheatmap, speedglm, stringr, strucchange, tibble, ggrepel, MASS, logging, Matrix, tidyr, caret, rlang, grDevices Suggests: knitr, rmarkdown, testthat, BiocStyle License: LGPL-3 MD5sum: bbf10148f1b314c63dc4e1e7c925412e NeedsCompilation: no Package: cytoKernel Version: 1.0.0 Depends: R (>= 4.1) Imports: Rcpp, SummarizedExperiment, utils, methods, ComplexHeatmap, circlize, ashr, data.table, BiocParallel, dplyr, stats, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 88a75705d1983ace7b9f6e219d2bf23a NeedsCompilation: yes Package: cytolib Version: 2.6.2 Depends: R (>= 3.4) Imports: RcppParallel, RProtoBufLib LinkingTo: Rcpp, BH(>= 1.75.0.0), RProtoBufLib(>= 2.3.5),Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1) Suggests: knitr, rmarkdown License: file LICENSE License_restricts_use: yes MD5sum: 801be8e95f1eb970ace403d099c08a4b NeedsCompilation: yes Package: cytomapper Version: 1.6.0 Depends: R (>= 4.0), EBImage, SingleCellExperiment, methods Imports: S4Vectors, BiocParallel, HDF5Array, DelayedArray, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5 Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest License: GPL (>= 2) MD5sum: 19818e4f5a480112bc9a9116e6136ed7 NeedsCompilation: no Package: CytoML Version: 2.6.0 Depends: R (>= 3.5.0) Imports: cytolib(>= 2.3.10), flowCore (>= 1.99.10), flowWorkspace (>= 4.1.8), openCyto (>= 1.99.2), XML, data.table, jsonlite, RBGL, Rgraphviz, Biobase, methods, graph, graphics, utils, base64enc, plyr, dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, lattice, stats, corpcor, RUnit, tibble, RcppParallel, xml2 LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1), flowWorkspace Suggests: testthat, flowWorkspaceData , knitr, rmarkdown, parallel License: file LICENSE License_restricts_use: yes MD5sum: 267c8c27024bc2458aeb97c52cf576a4 NeedsCompilation: yes Package: CytoTree Version: 1.4.0 Depends: R (>= 4.0), igraph Imports: FlowSOM, Rtsne, ggplot2, destiny, gmodels, flowUtils, Biobase, Matrix, flowCore, sva, matrixStats, methods, mclust, prettydoc, RANN(>= 2.5), Rcpp (>= 0.12.0), BiocNeighbors, cluster, pheatmap, scatterpie, umap, scatterplot3d, limma, stringr, grDevices, grid, stats LinkingTo: Rcpp Suggests: BiocGenerics, knitr, RColorBrewer, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 37d27f2fec3d3c8c67fa5a30551cef7f NeedsCompilation: yes Package: dada2 Version: 1.22.0 Depends: R (>= 3.4.0), Rcpp (>= 0.12.0), methods (>= 3.4.0) Imports: Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), ShortRead (>= 1.32.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0), IRanges (>= 2.6.0), XVector (>= 0.16.0), BiocGenerics (>= 0.22.0) LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, knitr, rmarkdown License: LGPL-2 MD5sum: 10a54cf646550ccc540cb9cc75b759aa NeedsCompilation: yes Package: dagLogo Version: 1.32.0 Depends: R (>= 3.0.1), methods, grid Imports: pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils, biomaRt, motifStack Suggests: XML, grImport, grImport2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: a2f1ba6a145f8b0d6a8ee8cfcda1f3e2 NeedsCompilation: no Package: daMA Version: 1.66.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: 0b989aab5b1192a4d5d8937c344757a1 NeedsCompilation: no Package: DAMEfinder Version: 1.6.0 Depends: R (>= 4.0) Imports: stats, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, readr, SummarizedExperiment, GenomicAlignments, stringr, plyr, VariantAnnotation, parallel, ggplot2, Rsamtools, BiocGenerics, methods, limma, bumphunter, Biostrings, reshape2, cowplot, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 4e2678149c3a93c676bc0590d25a4adb NeedsCompilation: no Package: DaMiRseq Version: 2.6.0 Depends: R (>= 3.4), SummarizedExperiment, ggplot2 Imports: DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap, FactoMineR, corrplot, randomForest, e1071, caret, MASS, lubridate, plsVarSel, kknn, FSelector, methods, stats, utils, graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR, plyr Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 67fb209153e399cb013318ef4c031c82 NeedsCompilation: no Package: DAPAR Version: 1.26.1 Depends: R (>= 4.1.0) 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 (>= 1.1), forcats, methods, DAPARdata (>= 1.24.0), siggenes, graph, lme4, readxl, highcharter, 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: 70b7f95161a03febdeff4292930aefd7 NeedsCompilation: no Package: DART Version: 1.42.0 Depends: R (>= 2.10.0), igraph (>= 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BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 MD5sum: e558f772350e75bbec98562763dc08ec NeedsCompilation: no Package: dce Version: 1.2.0 Depends: R (>= 4.1) Imports: stats, methods, assertthat, graph, pcalg, purrr, tidyverse, Matrix, ggraph, tidygraph, ggplot2, rlang, expm, MASS, CombinePValue, edgeR, epiNEM, igraph, metap, mnem, naturalsort, ppcor, glm2, graphite, reshape2, dplyr, glue, Rgraphviz, harmonicmeanp, org.Hs.eg.db, logger Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, cowplot, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment License: GPL-3 MD5sum: c72b92163ee0cef50d78d0a60092d4e0 NeedsCompilation: no Package: dcGSA Version: 1.22.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: 40ff83404ec9af5096b85883823e6476 NeedsCompilation: no Package: ddCt Version: 1.50.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: testthat (>= 3.0.0), RUnit License: LGPL-3 MD5sum: 0e4ea1b3a99a4c9bd727aedb415ece12 NeedsCompilation: no Package: ddPCRclust Version: 1.14.0 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: 47fa8f0f0aeada09dc8d5aad6ed08d94 NeedsCompilation: no Package: dearseq Version: 1.6.0 Depends: R (>= 3.6.0) Imports: ggplot2, KernSmooth, matrixStats, methods, patchwork, parallel, pbapply, stats, statmod, survey, viridisLite Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr License: GPL-2 | file LICENSE MD5sum: 8d6404df4da64272fc9a3d24ee2f1472 NeedsCompilation: no Package: debCAM Version: 1.12.0 Depends: R (>= 3.5) Imports: methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR2, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 MD5sum: abd7cdfb7c7993886e3b3d2fc0aea746 NeedsCompilation: no Package: debrowser Version: 1.22.5 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, knitr License: GPL-3 + file LICENSE MD5sum: 9e868a7ed1728bcd1b561c5f7814d908 NeedsCompilation: no Package: DECIPHER Version: 2.22.0 Depends: R (>= 3.5.0), Biostrings (>= 2.59.1), RSQLite (>= 1.1), stats, parallel Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector License: GPL-3 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GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table, GenomeInfoDb, readxl Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 5e854f609e91719985592947238b29b5 NeedsCompilation: no Package: DeconRNASeq Version: 1.36.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 MD5sum: c70d0f4f6145083827931b36b93563da NeedsCompilation: no Package: decontam Version: 1.14.0 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: 38383c63eba17d6065abf775967870a4 NeedsCompilation: no Package: deconvR Version: 1.0.1 Depends: R (>= 4.1), data.table (>= 1.14.0) Imports: S4Vectors (>= 0.30.0), methylKit (>= 1.18.0), IRanges (>= 2.26.0), GenomicRanges (>= 1.44.0), BiocGenerics (>= 0.38.0), 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76b4fb52aca62b321d4bb69a5442e712 NeedsCompilation: no Package: DEScan2 Version: 1.14.1 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: cacb2211382774935ade540b7df3f9bb NeedsCompilation: yes Package: DESeq2 Version: 1.34.0 Depends: S4Vectors (>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter, methods, stats4, locfit, geneplotter, ggplot2, Rcpp (>= 0.11.0) LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, pasilla (>= 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DBI, ape, phangorn, pracma, RMSNumpress, Rcpp LinkingTo: Rcpp, RcppEigen Suggests: knitr, akima, lattice, scales, gridExtra, latticeExtra, rmarkdown, BiocStyle, BiocParallel, testthat (>= 2.1.0) License: GPL-3 MD5sum: 0e62069bbc3d9cf72e68774501c25d62 NeedsCompilation: yes Package: DiffBind Version: 3.4.11 Depends: R (>= 4.0), GenomicRanges, SummarizedExperiment Imports: RColorBrewer, amap, gplots, grDevices, limma, GenomicAlignments, locfit, stats, utils, IRanges, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools (>= 2.0), DESeq2, methods, graphics, ggrepel, apeglm, ashr, GreyListChIP LinkingTo: Rhtslib (>= 1.15.3), Rcpp Suggests: BiocStyle, testthat, xtable Enhances: rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid License: Artistic-2.0 MD5sum: 9abba38d6ed1dfeaa99fd7c7705e01ea NeedsCompilation: yes Package: diffcoexp Version: 1.14.0 Depends: R (>= 3.5), WGCNA, SummarizedExperiment Imports: stats, 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Suggests: testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter, RColorBrewer License: MIT + file LICENSE MD5sum: b972774d5bf640b5ffafe7de62700be7 NeedsCompilation: yes Package: EnrichmentBrowser Version: 2.24.2 Depends: SummarizedExperiment, graph Imports: AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR, graphite, hwriter, limma, methods, pathview, safe Suggests: ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown License: Artistic-2.0 MD5sum: 31bd3929a8de6e0449b78541d1b811f2 NeedsCompilation: no Package: enrichplot Version: 1.14.2 Depends: R (>= 3.5.0) Imports: aplot, DOSE (>= 3.16.0), ggplot2, ggraph, graphics, grid, igraph, methods, plyr, purrr, RColorBrewer, reshape2, stats, utils, scatterpie, shadowtext, GOSemSim, magrittr, ggtree, yulab.utils (>= 0.0.4) Suggests: clusterProfiler, dplyr, europepmc, ggupset, knitr, rmarkdown, 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ProtGenerics, Biostrings (>= 2.47.9), curl Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), magrittr, rmarkdown, AnnotationHub Enhances: RMariaDB, shiny License: LGPL MD5sum: 63a4974ec0cdf9d6301d26d20fec1a05 NeedsCompilation: no Package: ensemblVEP Version: 1.36.1 Depends: methods, BiocGenerics, GenomicRanges, VariantAnnotation Imports: S4Vectors (>= 0.9.25), Biostrings, SummarizedExperiment, GenomeInfoDb, stats Suggests: RUnit License: Artistic-2.0 MD5sum: 8334f186ea61f0adb503dd20648bd3e9 NeedsCompilation: no Package: epialleleR Version: 1.2.0 Depends: R (>= 4.1) Imports: stats, methods, utils, GenomicRanges, BiocGenerics, GenomeInfoDb, SummarizedExperiment, VariantAnnotation, stringi, data.table LinkingTo: Rcpp, BH, Rhtslib, zlibbioc Suggests: RUnit, knitr, rmarkdown License: Artistic-2.0 MD5sum: 08f6206c96c6ab6a189da9f192f99b44 NeedsCompilation: yes Package: epidecodeR Version: 1.2.0 Depends: R 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MD5sum: f0457772502e95c551f274a16f62753a NeedsCompilation: no Package: epivizr Version: 2.24.0 Depends: R (>= 3.0), methods, Imports: epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4), GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown License: Artistic-2.0 MD5sum: da1e6456d68532232f29617b2eae786c NeedsCompilation: no Package: epivizrChart Version: 1.16.0 Depends: R (>= 3.4.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub License: Artistic-2.0 MD5sum: 4c6c640f6d8fd92ea0ff1007f17f48e0 NeedsCompilation: no Package: epivizrData Version: 1.22.0 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KEGGREST, plyr, stats, graphics, utils Suggests: shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim License: GPL-3 MD5sum: 9517ee6d8aa7a429bb58604d8ea0549b NeedsCompilation: no Package: ffpe Version: 1.38.0 Depends: R (>= 2.10.0), TTR, methods Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc Suggests: genefilter, ffpeExampleData License: GPL (> 2) MD5sum: d0058e7d1ca2337efc32e0e5949d59a6 NeedsCompilation: no Package: fgga Version: 1.2.0 Depends: R (>= 4.1), RBGL Imports: graph, stats, e1071, methods, gRbase, jsonlite, BiocFileCache, curl Suggests: knitr, rmarkdown, GOstats, PerfMeas, GO.db, BiocGenerics License: GPL-3 MD5sum: 19e4e2509f07fcc4981903850e7e891a NeedsCompilation: no Package: FGNet Version: 3.28.0 Depends: R (>= 2.15) Imports: igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2, RColorBrewer, png, methods, stats, utils, graphics, grDevices Suggests: RCurl, gage, topGO, 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SummarizedExperiment Imports: AnnotationDbi, BBmisc, Biobase, BiocGenerics, biomaRt, BSgenome, cowplot, DelayedArray (>= 0.5.11), DelayedMatrixStats, extraDistr, generics, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges, grDevices, ggplot2, ggrepel, 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: cd7bcfcef5e8e541556de70af1747cd4 NeedsCompilation: yes Package: frenchFISH Version: 1.6.0 Imports: utils, MCMCpack, NHPoisson Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 27d0f5065525f269da08a82d7f4a377c NeedsCompilation: no Package: FRGEpistasis Version: 1.30.0 Depends: R (>= 2.15), MASS, fda, methods, stats Imports: utils License: GPL-2 MD5sum: 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GenomicRanges Imports: shiny, fda, doParallel, GenomicAlignments, Rcpp, methods, foreach, parallel, GenomeInfoDb, Rsamtools, grDevices, graphics, stats, RColorBrewer LinkingTo: Rcpp License: Artistic-2.0 MD5sum: 3f00b25c496b04af2f2cdf1011a6763f NeedsCompilation: yes Package: funtooNorm Version: 1.18.0 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: af8a576ba0c6d896136ba1912bfa3c86 NeedsCompilation: no Package: GA4GHclient Version: 1.18.0 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: ea1dd0a6750fd92f9b68552ba3b80ad8 NeedsCompilation: no Package: GA4GHshiny Version: 1.16.0 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: 0d17079b1776b16b29261cd08d1ee5be NeedsCompilation: no Package: gaga Version: 2.40.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: parallel License: GPL (>= 2) MD5sum: ef771d98c880f69b174a05f2915f2bd8 NeedsCompilation: yes Package: gage Version: 2.44.0 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: 5301a405f1f3af85a158b1686d302501 NeedsCompilation: no Package: gaggle Version: 1.62.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>= 0.4.17) License: GPL (>= 2) MD5sum: 80ada9f6e5b68e78167e216581b93232 NeedsCompilation: no Package: gaia Version: 2.38.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: 5fb33f905628e4b2a217b86cec53680b NeedsCompilation: no Package: GAPGOM Version: 1.10.0 Depends: R (>= 4.0) Imports: stats, utils, methods, Matrix, fastmatch, plyr, dplyr, magrittr, data.table, igraph, graph, RBGL, GO.db, org.Hs.eg.db, org.Mm.eg.db, GOSemSim, GEOquery, AnnotationDbi, Biobase, BiocFileCache, matrixStats Suggests: org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Dr.eg.db, org.Ce.eg.db, org.At.tair.db, org.EcK12.eg.db, org.Bt.eg.db, org.Cf.eg.db, org.Ag.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Pt.eg.db, org.Pf.plasmo.db, org.Mmu.eg.db, org.Ss.eg.db, org.Xl.eg.db, testthat, pryr, knitr, rmarkdown, prettydoc, ggplot2, kableExtra, profvis, reshape2 License: MIT + file LICENSE MD5sum: ff14b83caf5a03ab26467f66f58c9bf4 NeedsCompilation: no Package: GAprediction Version: 1.20.0 Depends: R (>= 3.3) Imports: glmnet, stats, utils, Matrix Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 1d115b20094b53afcbd904e564900a5f NeedsCompilation: no Package: garfield Version: 1.22.0 Suggests: knitr License: GPL-3 MD5sum: f21f5251c88717e279581f838e0414b7 NeedsCompilation: yes Package: GARS Version: 1.14.0 Depends: R (>= 3.5), ggplot2, cluster Imports: DaMiRseq, MLSeq, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 87f052b1eaa48ade7a97270f1f753150 NeedsCompilation: no Package: GateFinder Version: 1.14.0 Imports: splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 8e476b9d227b7b1a2d037e85d4b71fab NeedsCompilation: no Package: gcapc Version: 1.18.0 Depends: R (>= 3.4) Imports: BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings, BSgenome, GenomicRanges, Rsamtools, GenomicAlignments, matrixStats, MASS, splines, grDevices, graphics, stats, methods Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: GPL-3 MD5sum: eab63d032c1b9810036aa479ae81fafa NeedsCompilation: no Package: gcatest Version: 1.24.0 Depends: R (>= 3.2) Imports: lfa Suggests: knitr, ggplot2 License: GPL-3 MD5sum: 3cd7c59a7bf757737a29bc5b280bd4b6 NeedsCompilation: yes Package: gCrisprTools Version: 2.0.0 Depends: R (>= 4.1) Imports: Biobase, limma, RobustRankAggreg, ggplot2, SummarizedExperiment, grid, rmarkdown, grDevices, graphics, methods, ComplexHeatmap, stats, utils, parallel Suggests: edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea License: Artistic-2.0 MD5sum: 39a77cdbe61b217fe45354df176d881e NeedsCompilation: no Package: gcrma Version: 2.66.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector, Biostrings (>= 2.11.32), splines, BiocManager Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL MD5sum: 64e4510d3e24882e7c97b2bb6839e992 NeedsCompilation: yes Package: GCSConnection Version: 1.6.0 Depends: R (>= 4.0.0) Imports: Rcpp (>= 1.0.2), httr, googleAuthR, googleCloudStorageR, methods, jsonlite, utils LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: a18bc0103d5e191cccb305a6a33a7544 NeedsCompilation: yes Package: GCSFilesystem Version: 1.4.0 Depends: R (>= 4.0.0) Imports: stats Suggests: testthat, knitr, rmarkdown, BiocStyle, GCSConnection License: GPL (>= 2) MD5sum: 0dc767afb8679cb1292a38b391da0ce3 NeedsCompilation: no Package: GCSscore Version: 1.8.0 Depends: R (>= 3.6) Imports: BiocManager, Biobase, utils, methods, RSQLite, devtools, dplR, stringr, graphics, stats, affxparser, data.table Suggests: siggenes, GEOquery, R.utils License: GPL (>= 3) MD5sum: e87d4db33dc521da16d98730c2dacead NeedsCompilation: no Package: GDCRNATools Version: 1.14.0 Depends: R (>= 3.5.0) Imports: shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel Suggests: knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: 489b72f5e592bcbae5a307a8792ce32c NeedsCompilation: no Package: GDSArray Version: 1.14.1 Depends: R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>= 0.5.32) Imports: tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager License: GPL-3 MD5sum: 3213989c564c4adf78a243cb50aa799e NeedsCompilation: no Package: gdsfmt Version: 1.30.0 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics License: LGPL-3 MD5sum: f7eaeefab308e90d349da01c444d2cf9 NeedsCompilation: yes Package: GEM Version: 1.20.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown License: Artistic-2.0 MD5sum: 07a6a0ac41850a483b458516b60e904b NeedsCompilation: no Package: gemini Version: 1.8.0 Depends: R (>= 4.1.0) Imports: dplyr, grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 4f1baad660f02b55a1897f12ec1ed920 NeedsCompilation: no Package: genArise Version: 1.70.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: 26a8ad19007263a533512f9c6c2fcf79 NeedsCompilation: no Package: genbankr Version: 1.22.0 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: e01037e1aa68e5abc04ae1b23ed06f8c NeedsCompilation: no Package: GeneAccord Version: 1.12.0 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: 968d79f30b0026c8bb2ee8c4af13283e NeedsCompilation: no Package: GeneAnswers Version: 2.36.0 Depends: R (>= 3.0.0), igraph, KEGGREST, RCurl, annotate, Biobase (>= 1.12.0), methods, XML, RSQLite, MASS, Heatplus, RColorBrewer Imports: RBGL, annotate, downloader Suggests: GO.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: 13f5c5631bfa5261624d6763168ef751 NeedsCompilation: no Package: geneAttribution Version: 1.20.0 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: df497c0f2068f221550ed6485661be03 NeedsCompilation: no Package: GeneBreak Version: 1.24.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: f7e0f345954e379ad411c73947d91408 NeedsCompilation: no Package: geneClassifiers Version: 1.18.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: a247ad42fb485b4ca6f45e73e26e6e9b NeedsCompilation: no Package: GeneExpressionSignature Version: 1.40.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: f0cf453c741b8808d4a048dc257db036 NeedsCompilation: no Package: genefilter Version: 1.76.0 Imports: BiocGenerics, AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 MD5sum: 9409aea143843999bbd12e699c5de1c9 NeedsCompilation: yes Package: genefu Version: 2.26.0 Depends: R (>= 4.1), survcomp, biomaRt, iC10, AIMS Imports: amap, impute, mclust, limma, graphics, stats, utils Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown License: Artistic-2.0 MD5sum: 959254a6ac7233eee5c8024700f81518 NeedsCompilation: no Package: GeneGA Version: 1.44.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: 3a842186e12943b6cbafc1dec14eb033 NeedsCompilation: no Package: GeneGeneInteR Version: 1.20.0 Depends: R (>= 4.0) Imports: snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods License: GPL (>= 2) MD5sum: 8506eb632e917f1d6336c4210434687a NeedsCompilation: yes Package: GeneMeta Version: 1.66.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: 1a2fd3ff8d2a6e93fa130765ff21f084 NeedsCompilation: no Package: GeneNetworkBuilder Version: 1.36.1 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick, rmarkdown License: GPL (>= 2) MD5sum: ebb1cd3861cc47006a0162e8fd293ee3 NeedsCompilation: yes Package: GeneOverlap Version: 1.30.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 11dda898cb6231c0cc2172089ef43c1e NeedsCompilation: no Package: geneplast Version: 1.20.1 Depends: R (>= 4.0), methods Imports: igraph, snow, ape, grDevices, graphics, stats, utils, data.table Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: dd0a8f94d5eac5d381de0feb3e6e6786 NeedsCompilation: no Package: geneplotter Version: 1.72.0 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: e48b766452fcf4796fcd6c12d664a31a NeedsCompilation: no Package: geneRecommender Version: 1.66.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: 5862b32fc969f04a1693b32ddf523a7f NeedsCompilation: no Package: GeneRegionScan Version: 1.50.0 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: 11201d1f7d50997bea6d9f3daf75392c NeedsCompilation: no Package: geneRxCluster Version: 1.30.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: c94ed18125954cb030928dd13db42f16 NeedsCompilation: yes Package: GeneSelectMMD Version: 2.38.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: 6d0cb12b555390592e6453311673001b NeedsCompilation: yes Package: GENESIS Version: 2.24.2 Imports: Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, 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: 2cb711a1eb1e0add42b22b6a50b31514 NeedsCompilation: yes Package: GeneStructureTools Version: 1.14.0 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: e3580192af58c1d9cdc1bc77ad0c8c56 NeedsCompilation: no Package: geNetClassifier Version: 1.34.0 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: 9aa475e00ea0ad86cd73b6622d4f70f1 NeedsCompilation: no Package: GeneticsPed Version: 1.56.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: 0db70cc5e43e4c4da752aab195dac293 NeedsCompilation: yes Package: GeneTonic Version: 1.6.4 Depends: R (>= 4.0.0) Imports: AnnotationDbi, backbone, bs4Dash (>= 2.0.0), circlize, colorspace, colourpicker, 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, shinyAce, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tippy, tools, utils, viridis, visNetwork Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 565c4c016cb6cfc6302ad638ca3e2b46 NeedsCompilation: no Package: geneXtendeR Version: 1.20.0 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: 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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: 3df150b6d71b854d5aa97f48628f6ebc NeedsCompilation: no Package: gmapR Version: 1.36.0 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: eabe57475a89bb4c9e6cb6fa58a706b0 NeedsCompilation: yes Package: GmicR Version: 1.8.0 Imports: 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GPL (>= 2) MD5sum: a873a434bd5e48986c6526e7dd983f6d NeedsCompilation: yes Package: GOpro Version: 1.20.0 Depends: R (>= 3.4) Imports: AnnotationDbi, dendextend, doParallel, foreach, parallel, org.Hs.eg.db, GO.db, Rcpp, stats, graphics, MultiAssayExperiment, IRanges, S4Vectors LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat License: GPL-3 MD5sum: 7fa67b56688705097d078b65abb98a3a NeedsCompilation: yes Package: goProfiles Version: 1.56.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: c8b7ee90384892c1b844c096ae7f6ffc NeedsCompilation: no Package: GOSemSim Version: 2.20.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, GO.db, methods, utils LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, rmarkdown, org.Hs.eg.db, prettydoc, testthat, ROCR License: Artistic-2.0 MD5sum: fd739a102b9e10c132d34323481f7dc4 NeedsCompilation: yes Package: goseq Version: 1.46.0 Depends: R 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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: c85b362ed87be4f15a7003358d63e6a1 NeedsCompilation: no Package: GOsummaries Version: 2.30.0 Depends: R (>= 2.15), Rcpp Imports: plyr, grid, gProfileR, reshape2, limma, ggplot2, gtable LinkingTo: Rcpp Suggests: vegan License: GPL (>= 2) MD5sum: 1f2ee26d6ac40457470c113debed82a8 NeedsCompilation: yes Package: GOTHiC Version: 1.30.0 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: 7b97b1ae757251582b500fed3cd9ceed NeedsCompilation: no Package: goTools Version: 1.68.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 MD5sum: e8e48b255ea93ea4611c44aa175197c0 NeedsCompilation: no Package: GPA Version: 1.6.0 Depends: R (>= 4.0.0), methods, graphics, Rcpp Imports: parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS, stats, utils, grDevices LinkingTo: Rcpp Suggests: gpaExample License: GPL (>= 2) MD5sum: c1236736851efd79db5c6bbae7356762 NeedsCompilation: yes Package: gpart Version: 1.12.0 Depends: R (>= 3.5.0), grid, Homo.sapiens, TxDb.Hsapiens.UCSC.hg38.knownGene, Imports: igraph, biomaRt, Rcpp, data.table, OrganismDbi, AnnotationDbi, grDevices, stats, utils, GenomicRanges, IRanges LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 15612d8c6cbf35ae4f83a69f4786d832 NeedsCompilation: yes Package: gpls Version: 1.66.0 Imports: stats Suggests: MASS License: Artistic-2.0 MD5sum: b85098c1110fe8f537c8a0ac5720417d NeedsCompilation: no Package: gprege Version: 1.38.0 Depends: R (>= 2.10), gptk Suggests: spam License: AGPL-3 MD5sum: 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(>= 0.7.1) Imports: stats, graphics Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle License: GPL (>= 2) MD5sum: 298418f49b341f28ef03de33cb8e3f5a NeedsCompilation: no Package: GSCA Version: 2.24.0 Depends: shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5, R(>= 2.10.0) Imports: graphics Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr License: GPL (>= 2) MD5sum: 84cd53657f56e96e539c3539ccfec073 NeedsCompilation: no Package: gscreend Version: 1.8.0 Depends: R (>= 3.6) Imports: SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics Suggests: knitr, testthat, rmarkdown License: GPL-3 MD5sum: 73e43e08094c4f7cd6d30a2fb028ad9d NeedsCompilation: no Package: GSEABase Version: 1.56.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.13.8), Biobase (>= 2.17.8), annotate (>= 1.45.3), methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: 05918aa9c692fe99a3f6364a98c66f7c NeedsCompilation: no Package: GSEABenchmarkeR Version: 1.14.0 Depends: Biobase, SummarizedExperiment Imports: AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, S4Vectors, stats, utils Suggests: BiocStyle, GSE62944, knitr, rappdirs, rmarkdown License: Artistic-2.0 MD5sum: d43d69e72062fa9ddaf1578f6a77983a NeedsCompilation: no Package: GSEAlm Version: 1.54.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: 5e180933da740b65e82f00a81fc81f77 NeedsCompilation: no Package: GSEAmining Version: 1.4.0 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: 201b2c2b9058077d77dd0de7273cf134 NeedsCompilation: no Package: gsean Version: 1.14.0 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, knitr, plotly, RANKS, WGCNA, rmarkdown License: Artistic-2.0 MD5sum: 43edbe0e932722401e4aeb9c1f98c5a5 NeedsCompilation: no Package: GSgalgoR Version: 1.4.0 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: 29ffc018e292240888a08ba1b761d5ec NeedsCompilation: no Package: GSReg Version: 1.28.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi Suggests: GenomicRanges, GSBenchMark License: GPL-2 MD5sum: f351fed3ce779377769f2eeea2eb9829 NeedsCompilation: yes 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GOexpress, SingleCellExperiment, scater, gplots, pheatmap, airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve (>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks License: MIT + file LICENSE MD5sum: b8042dc6c826b04fbce4b0fa7d56fe26 NeedsCompilation: no Package: interactiveDisplay Version: 1.32.0 Depends: R (>= 2.10), methods, BiocGenerics, grid Imports: interactiveDisplayBase (>= 1.7.3), shiny, RColorBrewer, ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi Suggests: RUnit, hgu95av2.db, knitr, GenomicRanges, SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer, metagenomeSeq, gplots, vegan, Biobase Enhances: rstudio License: Artistic-2.0 MD5sum: d673bd6ea9abe3a506a81f2191ee1a70 NeedsCompilation: no Package: interactiveDisplayBase Version: 1.32.0 Depends: R (>= 2.10), methods, BiocGenerics Imports: shiny, DT Suggests: knitr, markdown Enhances: rstudioapi License: Artistic-2.0 MD5sum: e41b0d679bc35213a096ad9b03e8955e NeedsCompilation: no 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knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: 2fa3a67574fc53d25a1fc67ef91d65f9 NeedsCompilation: yes Package: Mfuzz Version: 2.54.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 MD5sum: b95fffa5f39141120390c7d1c6eb8230 NeedsCompilation: no Package: MGFM Version: 1.28.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 MD5sum: f65f4cd08ee9c806665e37c0a4fb6840 NeedsCompilation: no Package: MGFR Version: 1.20.0 Depends: R (>= 3.5) Imports: biomaRt, annotate License: GPL-3 MD5sum: 04b058edb6118157238de33456a248bf NeedsCompilation: no Package: mgsa Version: 1.42.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: db843f9b593131017e3ef54940c2825c NeedsCompilation: yes Package: mia Version: 1.2.7 Depends: R (>= 4.0), SummarizedExperiment, SingleCellExperiment, TreeSummarizedExperiment (>= 1.99.3), MultiAssayExperiment Imports: methods, stats, utils, MASS, ape, decontam, vegan, BiocGenerics, S4Vectors, IRanges, Biostrings, DECIPHER, BiocParallel, DelayedArray, DelayedMatrixStats, scuttle, scater, DirichletMultinomial, rlang, dplyr, tibble, tidyr Suggests: testthat, knitr, patchwork, BiocStyle, yaml, phyloseq, dada2, stringr, biomformat, reldist, ade4, microbiomeDataSets, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: cfafd49022e571482fa5c03c2cb585ba NeedsCompilation: no Package: miaSim Version: 1.0.0 Depends: SummarizedExperiment Imports: deSolve, stats, poweRlaw Suggests: rmarkdown, knitr, BiocStyle, testthat License: Artistic-2.0 | file LICENSE MD5sum: f66cdd5360f9f497831d3bf127426fb2 NeedsCompilation: no Package: miaViz Version: 1.2.1 Depends: R (>= 4.0), SummarizedExperiment, TreeSummarizedExperiment, mia (>= 0.99), ggplot2, ggraph (>= 2.0) Imports: methods, stats, S4Vectors, BiocGenerics, BiocParallel, DelayedArray, scater, ggtree, ggnewscale, viridis, tibble, tidytree, tidygraph, rlang, purrr, tidyr, dplyr, ape, DirichletMultinomial Suggests: knitr, rmarkdown, BiocStyle, testthat, patchwork, microbiomeDataSets License: Artistic-2.0 | file LICENSE MD5sum: 1f42f284129f32def3683abdd4f478c7 NeedsCompilation: no Package: MiChip Version: 1.48.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: cef58535dec009da9aaf57bccfa1705a NeedsCompilation: no Package: microbiome Version: 1.16.0 Depends: R (>= 3.6.0), phyloseq, ggplot2 Imports: dplyr, reshape2, Rtsne, scales, stats, tibble, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE MD5sum: ae72f754bd35e723747d37cd760b02d7 NeedsCompilation: no Package: microbiomeDASim Version: 1.8.0 Depends: R (>= 3.6.0) Imports: graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase Suggests: testthat (>= 2.1.0), knitr, devtools License: MIT + file LICENSE MD5sum: adbf2c369b9c92b2d16190c48396ab0c NeedsCompilation: no Package: microbiomeExplorer Version: 1.4.0 Depends: shiny, magrittr, metagenomeSeq, Biobase Imports: shinyjs (>= 2.0.0), shinydashboard, shinycssloaders, shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer, dplyr, tidyr, purrr, rlang, knitr, readr, DT (>= 0.12.0), biomformat, tools, stringr, vegan, matrixStats, heatmaply, car, broom, limma, reshape2, tibble, forcats, lubridate, methods, plotly (>= 4.9.1) Suggests: V8, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 988c905b1fa5d189071d9e266bffad4d NeedsCompilation: no Package: microbiomeMarker Version: 1.0.2 Depends: R (>= 4.1.0) Imports: dplyr, phyloseq, magrittr, purrr, MASS, utils, ggplot2, tibble, rlang, stats, coin, ggtree, tidytree, methods, IRanges, tidyr, patchwork, ggsignif, metagenomeSeq, DESeq2, edgeR, BiocGenerics, Biostrings, yaml, biomformat, S4Vectors, Biobase, ComplexHeatmap, ANCOMBC, caret, limma, ALDEx2, multtest, plotROC Suggests: testthat, covr, glmnet, Matrix, kernlab, e1071, ranger, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 03472c75a9eecd0eccc61a019b54ffbc NeedsCompilation: no Package: MicrobiomeProfiler Version: 1.0.0 Depends: R (>= 4.1.0) Imports: clusterProfiler (>= 4.0.2), config, DT, enrichplot, golem, magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader, htmltools, ggplot2, graphics, utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-2 MD5sum: 7bc55f2caff19d088d5dbb6e8e785beb NeedsCompilation: no Package: MicrobiotaProcess Version: 1.6.6 Depends: R (>= 4.0.0) Imports: ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.3.5), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>= 1.17.2), pillar, dtplyr, ggtreeExtra Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, plyr, DECIPHER, randomForest, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, corrr, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, cli, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach License: GPL (>= 3.0) MD5sum: bd1ee524f8a56b97d83dce3fa73312d4 NeedsCompilation: no Package: microRNA Version: 1.52.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: 1e6b5ce6d7122ef4716bf2feec2649fa NeedsCompilation: yes Package: midasHLA Version: 1.2.0 Depends: R (>= 4.1), MultiAssayExperiment (>= 1.8.3) Imports: assertthat (>= 0.2.0), broom (>= 0.5.1), dplyr (>= 0.8.0.1), formattable (>= 0.2.0.1), HardyWeinberg (>= 1.6.3), kableExtra (>= 1.1.0), knitr (>= 1.21), magrittr (>= 1.5), methods, stringi (>= 1.2.4), rlang (>= 0.3.1), S4Vectors (>= 0.20.1), stats, SummarizedExperiment (>= 1.12.0), tibble (>= 2.0.1), utils, qdapTools (>= 1.3.3) Suggests: broom.mixed (>= 0.2.4), cowplot (>= 1.0.0), devtools (>= 2.0.1), ggplot2 (>= 3.1.0), ggpubr (>= 0.2.5), rmarkdown, seqinr (>= 3.4-5), survival (>= 2.43-3), testthat (>= 2.0.1), tidyr (>= 1.1.2) License: MIT + file LICENCE MD5sum: bac08f12461101f522ad4dc1258dc9f1 NeedsCompilation: no Package: MIGSA Version: 1.18.0 Depends: R (>= 3.4), methods, BiocGenerics Imports: AnnotationDbi, Biobase, BiocParallel, compiler, data.table, edgeR, futile.logger, ggdendro, ggplot2, GO.db, GOstats, graph, graphics, grDevices, grid, GSEABase, ismev, 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: b9f4ab48b750981199ae79d894b62c49 NeedsCompilation: no Package: miloR Version: 1.2.0 Depends: R (>= 4.0.0), edgeR Imports: BiocNeighbors, SingleCellExperiment, Matrix (>= 1.3-0), S4Vectors, stats, stringr, methods, igraph, irlba, cowplot, BiocParallel, BiocSingular, limma, ggplot2, tibble, matrixStats, ggraph, gtools, SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices Suggests: testthat, MASS, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, BiocStyle, MouseGastrulationData, magick, RCurl, curl, graphics License: GPL-3 + file LICENSE MD5sum: a7f60672a41a27d56278f108c532f347 NeedsCompilation: no Package: mimager Version: 1.18.0 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: cec44dc71b2d4861d71e6c838076642d NeedsCompilation: no Package: MIMOSA Version: 1.32.0 Depends: R (>= 3.0.2), MASS, plyr, reshape, Biobase, ggplot2 Imports: methods, Formula, data.table, pracma, MCMCpack, coda, modeest, testthat, Rcpp, scales, dplyr, tidyr, rlang LinkingTo: Rcpp, RcppArmadillo Suggests: parallel, knitr License: MIT + file LICENSE MD5sum: 87b6821905011abb6ea9280e1341f72f NeedsCompilation: yes Package: mina Version: 1.2.0 Depends: R (>= 4.0.0) Imports: methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory, foreach, ggplot2, parallel, parallelDist, reshape2, plyr, biganalytics, stringr, Hmisc, utils LinkingTo: Rcpp, RcppParallel, RcppArmadillo Suggests: knitr, rmarkdown Enhances: doMC License: GPL MD5sum: 4f942b670329a50b8953cef874030542 NeedsCompilation: yes Package: MineICA Version: 1.34.0 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: 16d4e430646d64b069b621284455d9d8 NeedsCompilation: no Package: minet Version: 3.52.0 Imports: infotheo License: Artistic-2.0 MD5sum: a3dd882cad47692d5da726627e91c006 NeedsCompilation: yes Package: minfi Version: 1.40.0 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: b1db4aae291caefbdcb1667d718c89d1 NeedsCompilation: no Package: 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MIRA Version: 1.16.0 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: 2a993222a73697b0c5e2229396ab12e0 NeedsCompilation: no Package: MiRaGE Version: 1.36.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: BiocGenerics, S4Vectors, AnnotationDbi, BiocManager Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL MD5sum: e4476391cfc4426d82cc60d033a05fd8 NeedsCompilation: no Package: miRBaseConverter Version: 1.18.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown License: GPL (>= 2) MD5sum: 55e87373fc4ed314c0addd178384b568 NeedsCompilation: no 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dbscan, subspace, mclust, SOMbrero, ppclust, miRspongeR, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, MatrixCorrelation, energy Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 3c5cb038b28988ef8979423e1a0e28cb NeedsCompilation: yes Package: miRspongeR Version: 1.20.1 Depends: R (>= 3.5.0) Imports: corpcor, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, varhandle, linkcomm, utils, Rcpp, org.Hs.eg.db Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 9e1a1774c13bb58166ac3b1e7eee1b6c NeedsCompilation: yes Package: mirTarRnaSeq Version: 1.2.0 Depends: R (>= 4.1.0) Imports: purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap, reshape2, corrplot, grDevices, graphics, stats, utils, data.table, R.utils Suggests: BiocStyle, knitr, rmarkdown, R.cache License: MIT MD5sum: 9c3d5306243576dc4d2eb4c6b4419a70 NeedsCompilation: no Package: missMethyl Version: 1.28.0 Depends: R (>= 3.6.0), 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R.utils, stats, stringr, tibble, tidyr, withr Suggests: BiocStyle, covr, future, igraph, knitr, Matrix, progeny, rmarkdown, sctransform, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, testthat (>= 3.0.0) License: GPL-3 MD5sum: 392fc8ba69045ad123d8c291b1fa35d4 NeedsCompilation: no Package: mitch Version: 1.6.0 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: 8dd6e2240e0ffc5b95d0bba28f9d9dd7 NeedsCompilation: no Package: mitoClone2 Version: 1.0.0 Depends: R (>= 4.1.0) Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2 LinkingTo: Rhtslib (>= 1.13.1) Suggests: knitr, rmarkdown, Biostrings, testthat License: GPL-3 MD5sum: 4e0de5c5c21b464a50b045247c3f1d89 NeedsCompilation: yes Package: mixOmics Version: 6.18.1 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: ad8908fc61599be89e19cc097961e2d1 NeedsCompilation: no Package: MLInterfaces Version: 1.74.0 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, magrittr 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 License: LGPL MD5sum: 7f001925a425a2ef920170971dee96e5 NeedsCompilation: no Package: MLP Version: 1.42.0 Imports: AnnotationDbi, gplots, graphics, stats, utils Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, KEGGREST, annotate, Rgraphviz, GOstats, graph, limma, mouse4302.db, reactome.db License: GPL-3 MD5sum: a9a1a77771f4fac3b6d96a4f48e438a0 NeedsCompilation: no Package: MLSeq Version: 2.12.0 Depends: caret, ggplot2 Imports: testthat, VennDiagram, pamr, methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, e1071, kernlab License: GPL (>= 2) MD5sum: 823bedd9dc669922e8f1ce7678493e75 NeedsCompilation: no Package: MMAPPR2 Version: 1.8.0 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: 7b6f7b944f95641198e603cde1ea2e6a NeedsCompilation: no Package: MMDiff2 Version: 1.22.0 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: 857d6a8877cc65eadcc9fab0e631f561 NeedsCompilation: no Package: MMUPHin Version: 1.8.2 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, genefilter License: MIT + file LICENSE MD5sum: 73191145ffdc92c56cdea3a2d666964c NeedsCompilation: no Package: mnem Version: 1.10.0 Depends: R (>= 4.1) Imports: cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071, ggplot2, wesanderson LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM License: GPL-3 MD5sum: 7a85ef254a56d479c4581b97e7c4a6eb NeedsCompilation: yes Package: moanin Version: 1.2.0 Depends: R (>= 4.0), SummarizedExperiment, topGO, stats Imports: S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics, methods, grDevices, reshape2, NMI, zoo, ClusterR, splines, matrixStats Suggests: testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: 27df5111899bf6d7d440c9abc0516e3f NeedsCompilation: no Package: MODA Version: 1.20.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: abaf53bb514240e860de9bcea1bc771e NeedsCompilation: no Package: ModCon Version: 1.2.0 Depends: data.table, parallel, utils, stats, R (>= 4.1) Suggests: testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny, shinyFiles, shinydashboard, shinyjs License: GPL-3 + file LICENSE MD5sum: 9b4fe5a4fb4117c45564788fd7232495 NeedsCompilation: no Package: Modstrings Version: 1.10.0 Depends: R (>= 3.6), Biostrings (>= 2.51.5) Imports: methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 6c6dc6b91813c1f8f6ba7f39fda101b4 NeedsCompilation: no Package: MOFA2 Version: 1.4.0 Depends: R (>= 4.0) Imports: rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods, RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array, grDevices, stats, magrittr, forcats, utils, corrplot, DelayedArray, Rtsne, uwot, basilisk, stringi Suggests: knitr, testthat, Seurat, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix License: GPL (>= 2) + file LICENSE MD5sum: 15837f8d5907a75e539570318be856da NeedsCompilation: yes Package: MOGAMUN Version: 1.4.0 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: knitr, markdown License: GPL-3 + file LICENSE MD5sum: 088c91391f5fb6d91bc9cb31e6c0eb61 NeedsCompilation: no Package: mogsa Version: 1.28.0 Depends: R (>= 3.4.0) Imports: methods, graphite, genefilter, BiocGenerics, gplots, GSEABase, Biobase, parallel, corpcor, svd, cluster, grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, org.Hs.eg.db License: GPL-2 MD5sum: a7a48b5d9678283f4856ee3e623dce08 NeedsCompilation: no Package: MOMA Version: 1.6.0 Depends: R (>= 4.0) Imports: circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics, grid, grDevices, magrittr, methods, MKmisc, MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr, reshape2, rlang, stats, stringr, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, viper License: GPL-3 MD5sum: c5c41da87f54859dbb4b69ee7eaa9150 NeedsCompilation: no Package: monaLisa Version: 1.0.0 Depends: R (>= 4.1) Imports: methods, stats, utils, grDevices, graphics, BiocGenerics, GenomicRanges, TFBSTools, Biostrings, IRanges, stabs, BSgenome, glmnet, S4Vectors, SummarizedExperiment, BiocParallel, grid, circlize, ComplexHeatmap (>= 2.0.0), XVector, GenomeInfoDb, tools, vioplot Suggests: JASPAR2020, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat, BiocStyle, gridExtra License: GPL-3 MD5sum: 6af2fed04549ebba77bee38e2c458c2a NeedsCompilation: no Package: monocle Version: 2.22.0 Depends: R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-6), DDRTree (>= 0.1.4), Imports: parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, densityClust (>= 0.3), Rtsne, MASS, reshape2, limma, tibble, dplyr, qlcMatrix, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0) LinkingTo: Rcpp Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat License: Artistic-2.0 MD5sum: aaf72312ada737f5ad5dad52c6aa5da9 NeedsCompilation: yes Package: MoonlightR Version: 1.20.0 Depends: R (>= 3.5), doParallel, foreach Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png License: GPL (>= 3) MD5sum: 1bdeb472dd149dd0d4c2724be7f9dc86 NeedsCompilation: no Package: mosaics Version: 2.32.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: 7554c579fb3fb4ef3fd409befdf8518f NeedsCompilation: yes Package: mosbi Version: 1.0.3 Depends: R (>= 4.1) Imports: Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust, isa2, QUBIC, akmbiclust, RColorBrewer LinkingTo: Rcpp, BH, RcppParallel Suggests: knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: e378a334f74231a8746ed03648a1b3d9 NeedsCompilation: yes Package: MOSim Version: 1.8.0 Depends: R (>= 3.6) Imports: HiddenMarkov, zoo, methods, matrixStats, dplyr, stringi, lazyeval, rlang, stats, utils, purrr, scales, stringr, tibble, tidyr, ggplot2, Biobase, IRanges, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 00463cbf735499a4b0ada15b83d90bb7 NeedsCompilation: no Package: motifbreakR Version: 2.8.0 Depends: R (>= 3.5.0), grid, MotifDb Imports: methods, compiler, grDevices, grImport, stringr, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP142.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle License: GPL-2 MD5sum: a4f36ac86f33efbfc01d17075c7a6f44 NeedsCompilation: no Package: motifcounter Version: 1.18.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: e29b1fa1804ec336fcf23ab632f47b66 NeedsCompilation: yes Package: MotifDb Version: 1.36.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes MD5sum: f520edc4a524c4a2dfeaf3d60b7e4d24 NeedsCompilation: no Package: motifmatchr Version: 1.16.0 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, GenomeInfoDb LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 + file LICENSE MD5sum: 9cf5b760ff3ad1dc2170d5a3c1841e5b NeedsCompilation: yes Package: motifStack Version: 1.38.0 Depends: R (>= 2.15.1), methods, grid Imports: ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets, stats, stats4, utils, XML Suggests: grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown License: GPL (>= 2) MD5sum: a48d439b72fb6f1f0b18d96d51be0594 NeedsCompilation: no Package: MouseFM Version: 1.4.2 Depends: R (>= 4.0.0) Imports: httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales, gtools, tidyr, data.table, jsonlite, rlist, GenomeInfoDb, methods, biomaRt, stats, IRanges Suggests: BiocStyle, testthat, knitr, rmarkdown License: 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e1da309dc723e2c5e5a8f1fc06e7bc73 NeedsCompilation: no Package: msgbsR Version: 1.18.0 Depends: R (>= 3.4), GenomicRanges, methods Imports: BSgenome, easyRNASeq, edgeR, GenomicAlignments, GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges, parallel, plyr, Rsamtools, R.utils, stats, SummarizedExperiment, S4Vectors, utils Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-2 MD5sum: 53a6472027bd8f76c43c248c61e19b72 NeedsCompilation: no Package: MSGFgui Version: 1.28.0 Depends: mzR, xlsx Imports: shiny, mzID (>= 1.2), MSGFplus, shinyFiles (>= 0.4.0), tools Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 8df2c34a02ddedb4d983f75dcdd7f73d NeedsCompilation: no Package: MSGFplus Version: 1.28.0 Depends: methods Imports: mzID, ProtGenerics Suggests: knitr, testthat License: GPL (>= 2) MD5sum: b77ac127aedbead5d4590a3c5872ef3d NeedsCompilation: no Package: msImpute Version: 1.4.0 Depends: R (>= 3.5.0) Imports: softImpute, methods, stats, graphics, pdist, reticulate, scran, 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(>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr, SummarizedExperiment License: Artistic-2.0 MD5sum: 9e84c59bdd2652a3b892e0bad7bed5bc NeedsCompilation: yes Package: MSnID Version: 1.28.0 Depends: R (>= 2.10), Rcpp Imports: MSnbase (>= 1.12.1), mzID (>= 1.3.5), R.cache, foreach, doParallel, parallel, methods, iterators, data.table, Biobase, ProtGenerics, reshape2, dplyr, mzR, BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics, Biostrings, purrr, rlang, stringr, tibble, AnnotationHub, AnnotationDbi, xtable License: Artistic-2.0 MD5sum: 1bcfcb57ac64c37336f8c933bff93398 NeedsCompilation: no Package: MSPrep Version: 1.4.0 Depends: R (>= 4.0) Imports: SummarizedExperiment, S4Vectors, pcaMethods (>= 1.24.0), VIM, crmn, preprocessCore, sva, dplyr (>= 0.7), tidyr, tibble (>= 1.2), magrittr, rlang, stats, stringr, methods, ddpcr, missForest Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 1.0.2) License: GPL-3 MD5sum: b735d462c5f7361d9fb5da253fca0e8b NeedsCompilation: no Package: msPurity Version: 1.20.0 Depends: Rcpp Imports: plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite, uuid, jsonlite Suggests: MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL License: GPL-3 + file LICENSE MD5sum: bbf3bee6663fcf3186bd36c504b063fd NeedsCompilation: no Package: msqrob2 Version: 1.2.0 Depends: R (>= 4.1), QFeatures (>= 1.1.2) Imports: stats, methods, lme4, purrr, BiocParallel, Matrix, MASS, limma, SummarizedExperiment, codetools Suggests: multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata, MSnbase, matrixStats, MsCoreUtils License: Artistic-2.0 MD5sum: 46e78e508a6b456824dac410fc971305 NeedsCompilation: no Package: MSstats Version: 4.2.0 Depends: R (>= 4.0) Imports: MSstatsConvert, data.table, checkmate, MASS, limma, lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel, gplots, marray, stats, grDevices, graphics, methods LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, MSstatsBioData, tinytest, covr, markdown License: Artistic-2.0 MD5sum: 6e52c7584b63b7178b7569f88967ab9b NeedsCompilation: yes Package: MSstatsConvert Version: 1.4.1 Depends: R (>= 4.0) Imports: data.table, log4r, methods, checkmate, utils, stringi Suggests: tinytest, covr, knitr, rmarkdown License: Artistic-2.0 MD5sum: c7683c5fb656fcd5581d07d093498b80 NeedsCompilation: no Package: MSstatsLiP Version: 1.0.0 Depends: R (>= 4.1) Imports: dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats, MSstatsConvert, data.table, Biostrings, MSstatsPTM, Rcpp, checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse, scales, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest License: Artistic-2.0 MD5sum: 6b77d641d8543f360a754e121d549acf NeedsCompilation: yes Package: MSstatsLOBD Version: 1.2.0 Depends: R (>= 4.0) Imports: minpack.lm, ggplot2, utils, stats, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr License: Artistic-2.0 MD5sum: 90ccd3c569b24e12490460bf96487a4e NeedsCompilation: no Package: MSstatsPTM Version: 1.4.2 Depends: R (>= 4.0) Imports: dplyr, gridExtra, stringr, stats, ggplot2, grDevices, MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp, Biostrings, checkmate, ggrepel LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, tinytest, covr License: Artistic-2.0 MD5sum: dd87d78c52143f6df93113a607a8c76a NeedsCompilation: yes Package: MSstatsQC Version: 2.12.0 Depends: R (>= 3.5.0) Imports: dplyr,plotly,ggplot2,ggExtra, stats,grid, MSnbase, qcmetrics Suggests: knitr,rmarkdown, testthat, RforProteomics License: Artistic License 2.0 MD5sum: 8b981391e81b9098b0245da9ee542dd3 NeedsCompilation: no Package: MSstatsQCgui Version: 1.14.0 Imports: shiny, MSstatsQC, ggExtra, 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Depends: R (>= 4.0.0), SummarizedExperiment (>= 1.3.81) Imports: methods, GenomicRanges (>= 1.25.93), BiocGenerics, S4Vectors (>= 0.23.19), IRanges, Biobase, stats, tidyr, utils Suggests: BiocStyle, HDF5Array (>= 1.19.17), knitr, maftools (>= 2.7.10), rmarkdown, R.rsp, RaggedExperiment, UpSetR, survival, survminer, testthat License: Artistic-2.0 MD5sum: bcf7c70f048651ee9011856b885a8d8d NeedsCompilation: no Package: MultiBaC Version: 1.4.0 Imports: Matrix, ggplot2, MultiAssayExperiment, ropls, graphics, methods, plotrix Suggests: knitr, rmarkdown, BiocStyle, devtools License: GPL-3 MD5sum: 1f83caa811dcbe3e73426f5634e21969 NeedsCompilation: no Package: multiClust Version: 1.24.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) MD5sum: 2b1c70da9be0e9d85721efa169b3af7d NeedsCompilation: no Package: multicrispr Version: 1.4.3 Depends: R (>= 4.0) Imports: assertive, BiocGenerics, Biostrings, BSgenome, CRISPRseek, data.table, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, grid, karyoploteR, magrittr, methods, parallel, plyranges, Rbowtie, reticulate, rtracklayer, stats, stringi, tidyr, tidyselect, utils Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, knitr, magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL-2 MD5sum: 46b16252daba4582aec2d8cdc0266c42 NeedsCompilation: no Package: MultiDataSet Version: 1.22.0 Depends: R (>= 4.1), Biobase Imports: BiocGenerics, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman, limma Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment License: file LICENSE MD5sum: 2d24c6668782de7422a89a26f76d89c8 NeedsCompilation: no Package: multiGSEA Version: 1.4.0 Depends: R (>= 4.0.0) Imports: magrittr, graphite, AnnotationDbi, dplyr, fgsea, metap, rappdirs, rlang, methods Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, metaboliteIDmapping, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: GPL-3 MD5sum: a9ad99299928bce92e2fc530b2c3a6b7 NeedsCompilation: no Package: multiHiCcompare Version: 1.12.0 Depends: R (>= 4.0.0) Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 08958919300b97f41d85f36d0f791d95 NeedsCompilation: no Package: MultiMed Version: 2.16.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE MD5sum: d8336578c095ef03b00f5a60f0507690 NeedsCompilation: no Package: multiMiR Version: 1.16.0 Depends: R (>= 3.4) Imports: stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 1.2), methods, BiocGenerics, AnnotationDbi, dplyr, Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) License: MIT + file LICENSE MD5sum: 668e7bd2f2d6c25dd7c8fdd1d30e1523 NeedsCompilation: no Package: multiOmicsViz Version: 1.18.0 Depends: R (>= 3.3.2) Imports: methods, parallel, doParallel, foreach, grDevices, graphics, utils, SummarizedExperiment, stats Suggests: BiocGenerics License: LGPL MD5sum: edd87d1b698f4ee0c186d82f1fdf6af3 NeedsCompilation: no Package: multiscan Version: 1.54.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) MD5sum: e52b64f79e57b190708d634efecc965b NeedsCompilation: yes Package: multiSight Version: 1.2.0 Depends: R (>= 4.1) Imports: golem, config, R6, shiny, shinydashboard, DT, dplyr, stringr, anyLib, caret, biosigner, mixOmics, stats, DESeq2, clusterProfiler, rWikiPathways, ReactomePA, enrichplot, ppcor, metap, infotheo, igraph, networkD3, easyPubMed, utils, htmltools, rmarkdown Suggests: org.Mm.eg.db, rlang, markdown, attempt, processx, testthat, knitr, BiocStyle License: CeCILL + file LICENSE MD5sum: ca168299ee7e72901e34c6c7654ac1cc NeedsCompilation: no Package: multtest Version: 2.50.0 Depends: R (>= 2.10), methods, BiocGenerics, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL MD5sum: 60a8d74fae0081224a69f65d88795d3b NeedsCompilation: yes Package: mumosa Version: 1.2.0 Depends: SingleCellExperiment Imports: stats, utils, methods, igraph, Matrix, BiocGenerics, BiocParallel, IRanges, S4Vectors, DelayedArray, DelayedMatrixStats, SummarizedExperiment, BiocNeighbors, BiocSingular, ScaledMatrix, beachmat, scuttle, metapod, scran, batchelor, uwot Suggests: testthat, knitr, BiocStyle, rmarkdown, scater, bluster, DropletUtils, scRNAseq License: GPL-3 MD5sum: ee887ed457dd5a4e0e76b8f8c17638af NeedsCompilation: no Package: MungeSumstats Version: 1.2.4 Depends: R(>= 4.1) Imports: magrittr, data.table, utils, R.utils, dplyr, stats, GenomicRanges, GenomeInfoDb, BSgenome, Biostrings, VariantAnnotation, stringr, googleAuthR, httr, jsonlite, methods, parallel, rtracklayer, RCurl Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, IRanges, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, seqminer, Rsamtools, MatrixGenerics License: Artistic-2.0 MD5sum: cf73c17c8fabcbef5fa38dc509b7ac71 NeedsCompilation: no Package: muscat Version: 1.8.2 Depends: R (>= 4.1) Imports: BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, S4Vectors, scales, scater, scuttle, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition, viridis Suggests: BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, testthat, UpSetR License: GPL-3 MD5sum: ba17ad452f267d0da54496153c115273 NeedsCompilation: no Package: muscle Version: 3.36.0 Depends: Biostrings License: Unlimited MD5sum: 257784e68aeadb7d2e0e16a7f400e8bd NeedsCompilation: yes Package: musicatk Version: 1.4.0 Depends: R (>= 4.0.0), NMF Imports: SummarizedExperiment, VariantAnnotation, cowplot, Biostrings, base, methods, magrittr, tibble, tidyr, gtools, gridExtra, MCMCprecision, MASS, matrixTests, data.table, dplyr, rlang, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, S4Vectors, uwot, ggplot2, stringr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, deconstructSigs, decompTumor2Sig, topicmodels, ggrepel, withr, plotly, utils, factoextra, cluster, ComplexHeatmap, philentropy, shinydashboard, sortable, maftools, shiny, shinyjs, shinyalert, shinybusy, shinyBS, TCGAbiolinks, shinyjqui, stringi Suggests: testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr License: LGPL-3 MD5sum: 5153ea9a8cc2ee6af15e859db7054ef3 NeedsCompilation: no Package: MutationalPatterns Version: 3.4.1 Depends: R (>= 4.1.0), GenomicRanges (>= 1.24.0), NMF (>= 0.20.6) Imports: stats, S4Vectors, BiocGenerics (>= 0.18.0), BSgenome (>= 1.40.0), VariantAnnotation (>= 1.18.1), dplyr (>= 0.8.3), tibble(>= 2.1.3), purrr (>= 0.3.2), tidyr (>= 1.0.0), stringr (>= 1.4.0), magrittr (>= 1.5), ggplot2 (>= 2.1.0), pracma (>= 1.8.8), IRanges (>= 2.6.0), GenomeInfoDb (>= 1.12.0), Biostrings (>= 2.40.0), ggdendro (>= 0.1-20), cowplot (>= 0.9.2), ggalluvial (>= 0.12.2), RColorBrewer, methods Suggests: BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), ccfindR (>= 1.6.0), GenomicFeatures, AnnotationDbi, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 7e8eebbcb4703ca488ed1da3bb7bc8f7 NeedsCompilation: no Package: MVCClass Version: 1.68.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: 49886a0af1a14c7dbef69ecdd8edc6f0 NeedsCompilation: no Package: MWASTools Version: 1.18.0 Depends: R(>= 3.4) Imports: glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra, igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST, ComplexHeatmap, stats, utils Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: CC BY-NC-ND 4.0 MD5sum: 27d8b0055020910d83d9746640f06a19 NeedsCompilation: no Package: mygene Version: 1.30.0 Depends: R (>= 3.2.1), GenomicFeatures, Imports: httr (>= 0.3), jsonlite (>= 0.9.7), S4Vectors, Hmisc, sqldf, plyr Suggests: BiocStyle License: Artistic-2.0 MD5sum: 129672106ef5a28c1fe3d8d22b12c2d2 NeedsCompilation: no Package: myvariant Version: 1.24.0 Depends: R (>= 3.2.1), VariantAnnotation Imports: httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, GenomeInfoDb Suggests: BiocStyle License: Artistic-2.0 MD5sum: 8aee2c3ca821008a61a2a237d765d497 NeedsCompilation: no Package: mzID Version: 1.32.0 Depends: methods Imports: XML, plyr, parallel, doParallel, foreach, iterators, ProtGenerics Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 96693aca9ed85ab376c958fa164d93e0 NeedsCompilation: no Package: mzR Version: 2.28.0 Depends: Rcpp (>= 0.10.1), methods, utils Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3), ncdf4 LinkingTo: Rcpp, zlibbioc, Rhdf5lib (>= 1.1.4) Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown License: Artistic-2.0 MD5sum: 928b7b2be2752399f55267209932c4e3 NeedsCompilation: yes Package: NADfinder Version: 1.18.0 Depends: R (>= 3.4), BiocGenerics, IRanges, GenomicRanges, S4Vectors, SummarizedExperiment Imports: graphics, methods, baseline, signal, GenomicAlignments, GenomeInfoDb, rtracklayer, limma, trackViewer, stats, utils, Rsamtools, metap, EmpiricalBrownsMethod,ATACseqQC, corrplot, csaw Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager, rmarkdown License: GPL (>= 2) MD5sum: aab662a2f9a0771b756d9351e6b5c545 NeedsCompilation: no Package: NanoMethViz Version: 2.0.0 Depends: R (>= 4.0.0), methods, ggplot2 Imports: cpp11 (>= 0.2.5), readr, S4Vectors, SummarizedExperiment, BiocSingular, bsseq, forcats, assertthat, AnnotationDbi, Rcpp, dplyr, data.table, e1071, fs, GenomicRanges, ggthemes, glue, limma (>= 3.44.0), patchwork, purrr, rlang, RSQLite, Rsamtools, scales, scico, stats, stringr, tibble, tidyr, utils, withr, zlibbioc LinkingTo: Rcpp Suggests: DSS, Mus.musculus, Homo.sapiens, knitr, rmarkdown, testthat (>= 3.0.0), covr License: Apache License (>= 2.0) MD5sum: efbacc715d8f621f45e9c039f7780bf4 NeedsCompilation: yes Package: NanoStringDiff Version: 1.24.0 Depends: Biobase Imports: matrixStats, methods, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle License: GPL 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GenomicRanges, tidyverse, VarfromPDB, org.Hs.eg.db, curl, dplyr, XML, XML2R Suggests: rmarkdown, yaml License: file LICENSE MD5sum: 29fec19ced2b2cf3eaa46f28aa9c0b0c NeedsCompilation: no Package: NanoTube Version: 1.0.0 Depends: R (>= 4.1), Biobase, ggplot2 Imports: fgsea, limma, methods, reshape, stats, utils Suggests: grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly, rlang, rmarkdown, ruv, qusage, shiny, testthat, xlsx License: GPL-3 MD5sum: d690e5ed00f13073a5b543f6913393d8 NeedsCompilation: no Package: NBAMSeq Version: 1.10.0 Depends: R (>= 3.6), SummarizedExperiment, S4Vectors Imports: DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods, stats, Suggests: knitr, rmarkdown, testthat, ggplot2 License: GPL-2 MD5sum: f56bafbce8bff97d2d88f6237385c112 NeedsCompilation: no Package: NBSplice Version: 1.12.0 Depends: R (>= 3.5), methods Imports: edgeR, stats, MASS, car, mppa, BiocParallel, ggplot2, reshape2 Suggests: knitr, RUnit, BiocGenerics, BiocStyle, rmarkdown, markdown License: GPL (>= 2) MD5sum: 0cb32c26d61e05f0392808cab120408d NeedsCompilation: no Package: ncdfFlow Version: 2.40.0 Depends: R (>= 2.14.0), flowCore(>= 1.51.7), RcppArmadillo, methods, BH Imports: Biobase,BiocGenerics,flowCore,zlibbioc LinkingTo: Rcpp,RcppArmadillo,BH, Rhdf5lib Suggests: testthat,parallel,flowStats,knitr License: file LICENSE MD5sum: e75e4b99a5a3c862aa0834fd99bebff3 NeedsCompilation: yes Package: ncGTW Version: 1.8.0 Depends: methods, BiocParallel, xcms Imports: Rcpp, grDevices, graphics, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-2 MD5sum: cd7f96ff657bdcc6d429c76899760d57 NeedsCompilation: yes Package: NCIgraph Version: 1.42.0 Depends: R (>= 2.10.0) Imports: graph, KEGGgraph, methods, RBGL, RCy3, R.methodsS3 Suggests: Rgraphviz Enhances: DEGraph License: GPL-3 MD5sum: 3c9befc042cc964868aba02fc13cc0d6 NeedsCompilation: no Package: ncRNAtools Version: 1.4.0 Imports: httr, xml2, utils, methods, grDevices, ggplot2, IRanges, GenomicRanges, S4Vectors Suggests: knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics License: GPL-3 MD5sum: a42403539b3f068a4cbee694b6c19641 NeedsCompilation: no Package: ndexr Version: 1.16.0 Depends: igraph Imports: httr, jsonlite, plyr, tidyr Suggests: BiocStyle, testthat, knitr, rmarkdown License: BSD MD5sum: 6703a9a7ad9c190bf8c99f29ea6bc4d8 NeedsCompilation: no Package: nearBynding Version: 1.4.0 Depends: R (>= 4.0) Imports: R.utils, matrixStats, plyranges, transport, Rsamtools, S4Vectors, grDevices, graphics, rtracklayer, dplyr, GenomeInfoDb, methods, GenomicRanges, utils, stats, magrittr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, ggplot2, gplots, BiocGenerics, rlang Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: bf23451194dcc70fc7bcd66bab2534b6 NeedsCompilation: no Package: Nebulosa Version: 1.4.0 Depends: R (>= 4.0), ggplot2, patchwork Imports: Seurat, SingleCellExperiment, SummarizedExperiment, ks, Matrix, stats, methods Suggests: testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, SeuratObject License: GPL-3 MD5sum: ca49e649e64eaa6cb279b5baf178465f NeedsCompilation: no Package: NeighborNet Version: 1.12.0 Depends: methods Imports: graph, stats License: CC BY-NC-ND 4.0 MD5sum: d8fb4b447d79d34974da2bbe1ad9dc49 NeedsCompilation: no Package: nempi Version: 1.2.0 Depends: R (>= 4.1), mnem Imports: e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats, epiNEM Suggests: knitr, BiocGenerics, rmarkdown, RUnit License: GPL-3 MD5sum: 562c14a6eea9fb2b24ff9cd29b25d05a NeedsCompilation: no Package: netbiov Version: 1.28.0 Depends: R (>= 3.1.0), igraph (>= 0.7.1) Suggests: BiocStyle,RUnit,BiocGenerics,Matrix License: GPL (>= 2) MD5sum: 6bc7d8c1c6d6db3c2e3e65fa5d40f6eb NeedsCompilation: no Package: netboost Version: 2.2.0 Depends: R (>= 4.0.0) Imports: Rcpp, RcppParallel, parallel, grDevices, graphics, stats, utils, dynamicTreeCut, WGCNA, impute, colorspace, methods, R.utils LinkingTo: Rcpp, RcppParallel Suggests: knitr, markdown, rmarkdown License: GPL-3 OS_type: unix MD5sum: dc7df9af5be8460d2d2ef9ae6c5f1475 NeedsCompilation: yes Package: netboxr Version: 1.6.0 Depends: R (>= 4.0.0), igraph (>= 1.2.4.1), parallel Imports: RColorBrewer, DT, stats, clusterProfiler, data.table, gplots, jsonlite, plyr Suggests: paxtoolsr, BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, cgdsr License: LGPL-3 + file LICENSE MD5sum: e2c923fdf19c3610483fe52d1f695569 NeedsCompilation: no Package: netDx Version: 1.6.0 Depends: R (>= 3.6) Imports: ROCR,pracma,ggplot2,glmnet,igraph,reshape2, parallel,stats,utils,MultiAssayExperiment,graphics,grDevices, methods,BiocFileCache,GenomicRanges, bigmemory,doParallel,foreach, combinat,rappdirs,GenomeInfoDb,S4Vectors, IRanges,RColorBrewer,Rtsne,httr,plotrix Suggests: curatedTCGAData, rmarkdown, testthat, knitr, BiocStyle, RCy3, clusterExperiment, netSmooth, scater License: MIT + file LICENSE MD5sum: 7ce5d48b51c4ee81dac15b789422f258 NeedsCompilation: no Package: nethet Version: 1.26.0 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: 820fdcba70840e9a96b39ce54c4434bd NeedsCompilation: yes Package: netOmics Version: 1.0.0 Depends: R (>= 4.1) Imports: dplyr, ggplot2, igraph, magrittr, minet, purrr, tibble, tidyr, AnnotationDbi, GO.db, RandomWalkRestartMH, gprofiler2, methods, stats Suggests: mixOmics, timeOmics, tidyverse, BiocStyle, testthat, covr, rmarkdown, knitr License: GPL-3 MD5sum: cd6a98a9360c9f60553884d638140aa1 NeedsCompilation: no Package: NetPathMiner Version: 1.30.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 90c6c33a8d7c6976340a16ae254f5af8 NeedsCompilation: yes Package: netprioR Version: 1.20.0 Depends: methods, graphics, R(>= 3.3) Imports: stats, Matrix, dplyr, doParallel, foreach, parallel, sparseMVN, ggplot2, gridExtra, pROC Suggests: knitr, BiocStyle, pander License: GPL-3 MD5sum: 4d190675f943d49f6f8a8df8ccaab6ca NeedsCompilation: no Package: netresponse Version: 1.54.0 Depends: R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods, minet, mclust, reshape2 Imports: dmt, ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer Suggests: knitr License: GPL (>= 2) MD5sum: 89bc70771ac99baf1a3cefc735021846 NeedsCompilation: yes Package: NetSAM Version: 1.34.0 Depends: R (>= 3.0.0), seriation (>= 1.0-6), igraph (>= 0.6-1), tools (>= 3.0.0), WGCNA (>= 1.34.0), biomaRt (>= 2.18.0) Imports: methods, AnnotationDbi (>= 1.28.0), doParallel (>= 1.0.10), foreach (>= 1.4.0), survival (>= 2.37-7), GO.db (>= 2.10.0), R2HTML (>= 2.2.0), DBI (>= 0.5-1) Suggests: RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr, markdown License: LGPL MD5sum: f01c46bd33e2e371db4248d345cc2ae8 NeedsCompilation: no Package: netSmooth Version: 1.14.0 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: 193c465fa25a7eef61fcb5eff52efc3d NeedsCompilation: no Package: networkBMA Version: 2.34.0 Depends: R (>= 2.15.0), stats, utils, BMA, Rcpp (>= 0.10.3), RcppArmadillo (>= 0.3.810.2), RcppEigen (>= 0.3.1.2.1), leaps LinkingTo: Rcpp, RcppArmadillo, RcppEigen, BH License: GPL (>= 2) MD5sum: a57f513948eb7aba9d552088e1db2b1e NeedsCompilation: yes Package: NeuCA Version: 1.0.0 Depends: R(>= 3.5.0), keras, limma, e1071, SingleCellExperiment Suggests: BiocStyle, knitr, rmarkdown, networkD3 License: GPL-2 MD5sum: 8b3c8e0f61fb2797a8bc97d982507007 NeedsCompilation: no Package: NewWave Version: 1.4.0 Depends: R (>= 4.0), SummarizedExperiment Imports: methods, SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, SharedObject, stats Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr License: GPL-3 MD5sum: 39b7492aacf39009809ff9c135fd45e7 NeedsCompilation: no Package: ngsReports Version: 1.10.0 Depends: R (>= 4.1.0), BiocGenerics, ggplot2 (>= 3.3.5), tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 1.0.0), DT, forcats, ggdendro, grDevices (>= 3.6.0), grid, lifecycle, lubridate, methods, pander, plotly (>= 4.9.4), readr, reshape2, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo Suggests: BiocStyle, Cairo, knitr, testthat, truncnorm License: file LICENSE MD5sum: 0fec49efac4ef6352b9aeef7d71498d7 NeedsCompilation: no Package: nnNorm Version: 2.58.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: 249c267cf6fb0cb448c8fb21900a85ab NeedsCompilation: no Package: NOISeq Version: 2.38.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 MD5sum: a2fdcb2c3ba21375b82e91a831a61a4f NeedsCompilation: no Package: nondetects Version: 2.24.0 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: 469e6f33d25971e2fd67c09e5bc2873f NeedsCompilation: no Package: NoRCE Version: 1.6.0 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,markdown License: MIT + file LICENSE MD5sum: 1dcbb2a6d6644c880fc6930c351f2b40 NeedsCompilation: no Package: normalize450K Version: 1.22.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 7c93d6839e720f2b98f5c5926b937d69 NeedsCompilation: no Package: NormalyzerDE Version: 1.12.0 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: 472881055372c992caa16cd92e242c68 NeedsCompilation: no Package: NormqPCR Version: 1.40.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: 28011193f46478922d0fe10f62292737 NeedsCompilation: no Package: normr Version: 1.20.0 Depends: R (>= 3.3.0) Imports: methods, stats, utils, grDevices, parallel, GenomeInfoDb, GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2), bamsignals (>= 1.4), rtracklayer (>= 1.32) LinkingTo: Rcpp Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown Enhances: BiocParallel License: GPL-2 MD5sum: 4ec5af57b4f64337acd17944be0fe875 NeedsCompilation: yes Package: NPARC Version: 1.6.0 Depends: R (>= 4.0.0) Imports: dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr, stats, methods Suggests: testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2, BiocStyle License: GPL-3 MD5sum: f03311f98bdc02a919c2bac7f8ae8060 NeedsCompilation: no Package: npGSEA Version: 1.30.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: ca6552da82d78c9e7a79c8046ccf66dc NeedsCompilation: no Package: NTW Version: 1.44.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 MD5sum: 6592ccbd23c03f0282b6d9b748f4fcf2 NeedsCompilation: no Package: nucleoSim Version: 1.22.0 Imports: stats, IRanges, S4Vectors, graphics, methods Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 27855d6f59ffc816efcc68c40c3b6880 NeedsCompilation: no Package: nucleR Version: 2.26.0 Depends: methods Imports: Biobase, BiocGenerics, Biostrings, GenomeInfoDb, GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr, ggplot2, magrittr, parallel, stats, utils, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat License: LGPL (>= 3) MD5sum: b5485248a17c0b905c8548c0551876ab NeedsCompilation: no Package: nuCpos Version: 1.12.0 Depends: R (>= 3.6) Imports: graphics, methods Suggests: NuPoP, Biostrings, testthat License: file LICENSE MD5sum: f98f0cc2439b6541c93ca873b9d49699 NeedsCompilation: yes Package: nullranges Version: 1.0.1 Imports: stats, IRanges, GenomicRanges, GenomeInfoDb, methods, rlang, S4Vectors, scales, InteractionSet, ggplot2, grDevices, plyranges, ks, speedglm, data.table, progress, ggridges Suggests: testthat, knitr, rmarkdown, DNAcopy, RcppHMM, AnnotationHub, nullrangesData, excluderanges, EnsDb.Hsapiens.v86, microbenchmark, patchwork, plotgardener, magrittr, cobalt License: GPL-3 MD5sum: 22740ff6243b317c995f0774d30076e1 NeedsCompilation: no Package: NuPoP Version: 2.2.0 Depends: R (>= 4.0) Imports: graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 3876925b44123c7ef60ec68f956e7cb3 NeedsCompilation: yes Package: NxtIRFcore Version: 1.0.0 Depends: R (>= 3.5.0), NxtIRFdata Imports: methods, stats, utils, tools, parallel, magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2, AnnotationHub, BiocFileCache, BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray, DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges, HDF5Array, IRanges, plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment, S4Vectors LinkingTo: Rcpp, zlibbioc, RcppProgress Suggests: knitr, rmarkdown, pheatmap, shiny, openssl, crayon, egg, DESeq2, limma, DoubleExpSeq, Rsubread, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: c67eb3df50a96458df68bc18131945b6 NeedsCompilation: yes Package: occugene Version: 1.54.0 Depends: R (>= 2.0.0) License: GPL (>= 2) MD5sum: fe7433a1e536e26ff0824769c46013f7 NeedsCompilation: no Package: OCplus Version: 1.68.0 Depends: R (>= 2.1.0) Imports: multtest (>= 1.7.3), graphics, grDevices, stats, akima License: LGPL MD5sum: 7c39366ea7748e95659940b595b2e23e NeedsCompilation: no Package: ODER Version: 1.0.0 Depends: R (>= 4.1) Imports: BiocGenerics, BiocFileCache, dasper, derfinder, dplyr, IRanges, GenomeInfoDb, GenomicRanges, ggplot2, ggpubr, ggrepel, magrittr, rtracklayer, S4Vectors, stringr, data.table, megadepth, methods, plyr, purrr, tibble, utils Suggests: BiocStyle, covr, knitr, recount, RefManageR, rmarkdown, sessioninfo, SummarizedExperiment, testthat (>= 3.0.0), GenomicFeatures, xfun License: Artistic-2.0 MD5sum: 6fe0110955eb926316b2c7b37a875b53 NeedsCompilation: no Package: odseq Version: 1.22.0 Depends: R (>= 3.2.3) Imports: msa (>= 1.2.1), kebabs (>= 1.4.1), mclust (>= 5.1) Suggests: knitr(>= 1.11) License: MIT + file LICENSE MD5sum: dc206d8f6f3ce49fbc5effa0890df0d9 NeedsCompilation: no Package: oligo Version: 1.58.0 Depends: R (>= 3.2.0), BiocGenerics (>= 0.13.11), oligoClasses (>= 1.29.6), Biobase (>= 2.27.3), Biostrings (>= 2.35.12) Imports: affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, zlibbioc LinkingTo: preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl Enhances: doMC, doMPI License: LGPL (>= 2) MD5sum: 851a184174a24d36b1664fa2e9d50342 NeedsCompilation: yes Package: oligoClasses Version: 1.56.0 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: 1a9e52836c44d47c9af6b39f6d74e708 NeedsCompilation: no Package: OLIN Version: 1.72.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 MD5sum: 00ff48d8419f558610c7d8d10cd741ec NeedsCompilation: no Package: OLINgui Version: 1.68.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 MD5sum: dbd7f505b1f9d08c85fe98e31fd1c768 NeedsCompilation: no Package: OmaDB Version: 2.10.0 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: ff4500554b914c4b7156634a5f12125e NeedsCompilation: no Package: omicade4 Version: 1.34.0 Depends: R (>= 3.0.0), ade4 Imports: made4, Biobase Suggests: BiocStyle License: GPL-2 MD5sum: 500f1e90afb2c3c75b5c7962c83da995 NeedsCompilation: no Package: OmicCircos Version: 1.32.0 Depends: R (>= 2.14.0), methods,GenomicRanges License: GPL-2 MD5sum: d590a207028e8073d2095461fb326e1b NeedsCompilation: no Package: omicplotR Version: 1.14.0 Depends: R (>= 3.6), ALDEx2 (>= 1.18.0) Imports: compositions, DT, grDevices, knitr, jsonlite, matrixStats, rmarkdown, shiny, stats, vegan, zCompositions License: MIT + file LICENSE MD5sum: 0d98519239848e3f26bf933c25fee440 NeedsCompilation: no Package: omicRexposome Version: 1.16.0 Depends: R (>= 3.4), Biobase Imports: stats, utils, grDevices, graphics, methods, rexposome, limma, sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet, SmartSVA, isva, parallel, SummarizedExperiment, stringr Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata License: MIT + file LICENSE MD5sum: f3b5758550e2d3e64d330f3212ab56d6 NeedsCompilation: no Package: OmicsLonDA Version: 1.10.0 Depends: R(>= 3.6) Imports: SummarizedExperiment, gss, plyr, zoo, pracma, ggplot2, BiocParallel, parallel, grDevices, graphics, stats, utils, methods, BiocGenerics Suggests: knitr, rmarkdown, testthat, devtools, BiocManager License: MIT + file LICENSE MD5sum: a40978062e8646603218a681b5ea676f NeedsCompilation: no Package: OMICsPCA Version: 1.12.0 Depends: R (>= 3.5.0), OMICsPCAdata Imports: HelloRanges, fpc, stats, MultiAssayExperiment, pdftools, methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown, kableExtra, rtracklayer, IRanges, GenomeInfoDb, reshape2, ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR, PerformanceAnalytics, tidyr, data.table, cluster, magick Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 608be4bb1d13b8bd15d24da98896bf1d NeedsCompilation: no Package: omicsPrint Version: 1.14.0 Depends: R (>= 3.5), MASS Imports: methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 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rmarkdown License: GPL (>= 3) MD5sum: 644e273215a60bb71f78d0c3219b3ab5 NeedsCompilation: no Package: onlineFDR Version: 2.2.0 Imports: stats, Rcpp, RcppProgress, dplyr, tidyr, ggplot2, progress LinkingTo: Rcpp, RcppProgress Suggests: knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: 7634aa5e45d5d94587d108e87e56f014 NeedsCompilation: yes Package: ontoProc Version: 1.16.0 Depends: R (>= 3.5), ontologyIndex Imports: Biobase, S4Vectors, methods, AnnotationDbi, stats, utils, BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph, AnnotationHub Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown License: Artistic-2.0 MD5sum: da54d0b3056713b1545b8177859aa930 NeedsCompilation: no Package: openCyto Version: 2.6.0 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(>= 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LinkingTo: RcppParallel, Rcpp License: GPL (>= 2) MD5sum: 9afdd78e39f86fe52236b6bb3581c6c0 NeedsCompilation: yes Package: oppar Version: 1.22.0 Depends: R (>= 3.3) Imports: Biobase, methods, GSEABase, GSVA Suggests: knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel License: GPL-2 MD5sum: daae1c21e1a8ec03adf57762a1ac81a8 NeedsCompilation: yes Package: oppti Version: 1.8.0 Depends: R (>= 3.5) Imports: limma, stats, reshape, ggplot2, grDevices, RColorBrewer, pheatmap, knitr, methods, devtools, parallelDist, Suggests: markdown License: MIT MD5sum: 488c6631f70451e47d5163c444c052c8 NeedsCompilation: no Package: optimalFlow Version: 1.6.0 Depends: dplyr, optimalFlowData, rlang (>= 0.4.0) Imports: transport, parallel, Rfast, robustbase, dbscan, randomForest, foreach, graphics, doParallel, stats, flowMeans, rgl, ellipse Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: 53e31b7af573debe1759431498e096b1 NeedsCompilation: no Package: OPWeight Version: 1.16.0 Depends: R (>= 3.4.0), Imports: graphics, qvalue, MASS, tibble, stats, Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat License: Artistic-2.0 MD5sum: 8e0564d96bcd1807b47429174c726e8e NeedsCompilation: no Package: OrderedList Version: 1.66.0 Depends: R (>= 3.6.1), Biobase, twilight Imports: methods License: GPL (>= 2) MD5sum: 9d89b148ae378dd350748b73e9aa258d NeedsCompilation: no Package: ORFhunteR Version: 1.2.0 Depends: Biostrings, rtracklayer, Peptides Imports: Rcpp (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg38, data.table, stringr, randomForest, xfun, stats, utils, parallel, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: dc70cd66638eb368ed1a06d090a050f2 NeedsCompilation: yes Package: ORFik Version: 1.14.7 Depends: R (>= 3.6.0), IRanges (>= 2.17.1), GenomicRanges (>= 1.35.1), GenomicAlignments (>= 1.19.0) Imports: AnnotationDbi (>= 1.45.0), Biostrings (>= 2.51.1), biomartr, BiocGenerics (>= 0.29.1), BiocParallel (>= 1.19.0), BSgenome, cowplot (>= 1.0.0), data.table (>= 1.11.8), DESeq2 (>= 1.24.0), fst (>= 0.9.2), GenomeInfoDb (>= 1.15.5), GenomicFeatures (>= 1.31.10), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), GGally (>= 1.4.0), httr (>= 1.3.0), jsonlite, methods (>= 3.6.0), R.utils, Rcpp (>= 1.0.0), Rsamtools (>= 1.35.0), rtracklayer (>= 1.43.0), stats, SummarizedExperiment (>= 1.14.0), S4Vectors (>= 0.21.3), tools, utils, xml2 (>= 1.2.0) LinkingTo: Rcpp Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 2e54b60ea54df36ab8d5e61a4d284679 NeedsCompilation: yes Package: Organism.dplyr Version: 1.22.1 Depends: R (>= 3.4), dplyr (>= 0.7.0), AnnotationFilter (>= 1.1.3) Imports: RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges, GenomicFeatures, AnnotationDbi, rlang, methods, tools, utils, BiocFileCache, DBI, dbplyr, tibble Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, BiocStyle, ggplot2 License: Artistic-2.0 MD5sum: 26ffe489cc93e9d0acaec61333c1a0ef NeedsCompilation: no Package: OrganismDbi Version: 1.36.0 Depends: R (>= 2.14.0), methods, BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.39.4) Imports: Biobase, BiocManager, GenomicRanges (>= 1.31.13), graph, IRanges, RBGL, DBI, S4Vectors (>= 0.9.25), stats Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB License: Artistic-2.0 MD5sum: 5bda6d1a7ade0d3a4b65aba4cdbf686b NeedsCompilation: no Package: orthogene Version: 1.0.2 Depends: R (>= 4.1) Imports: dplyr, methods, stats, utils, Matrix, jsonlite, homologene, gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr, patchwork, DelayedArray, DelayedMatrixStats, Matrix.utils, grr, repmis, GenomeInfoDbData, tools Suggests: remotes, knitr, BiocStyle, covr, 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matrixStats, plotly, plyr, pcaMethods, PRROC, RColorBrewer, Rcpp, reshape2, S4Vectors, scales, splines, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr License: MIT + file LICENSE MD5sum: 0fa91a3534614ccf856a348e1dcb5369 NeedsCompilation: yes Package: OVESEG Version: 1.10.0 Depends: R (>= 3.6) Imports: stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales License: GPL-2 MD5sum: ae90ae8dfa8e7031fcaa2cfe0dbcc2fd NeedsCompilation: yes Package: PAA Version: 1.28.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.6) Imports: e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR, sva LinkingTo: Rcpp Suggests: BiocStyle, RUnit, BiocGenerics, vsn License: BSD_3_clause + file LICENSE MD5sum: 4317b9ee7912184aefd78d9dda53ad6e 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ComplexHeatmap, plotly, webshot, vegan, shinyjs, glmnet, gmodels, ROCR, RColorBrewer, knitr, devtools, ape Suggests: rmarkdown, testthat License: GPL (>= 2) MD5sum: 598c07d52071cda4100b1be35060c115 NeedsCompilation: no Package: pathRender Version: 1.62.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods, stats4 Suggests: ALL, hgu95av2.db License: LGPL MD5sum: 516c702c762a8fb03172f4e1d3b766a4 NeedsCompilation: no Package: pathVar Version: 1.24.0 Depends: R (>= 3.3.0), methods, ggplot2, gridExtra Imports: EMT, mclust, Matching, data.table, stats, grDevices, graphics, utils License: LGPL (>= 2.0) MD5sum: a7071145fedd85971b559b2b0bdc92ef NeedsCompilation: no Package: pathview Version: 1.34.0 Depends: R (>= 3.5.0) Imports: KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) MD5sum: 50632d6b3003af87bac21ff5866354c3 NeedsCompilation: no Package: pathwayPCA 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rmarkdown, base64enc, tidyr, grDevices, methods Suggests: testthat, BiocStyle, airway, org.Hs.eg.db, htmltools License: MIT + file LICENSE MD5sum: 665e0b7e3b90c495cad939099004f363 NeedsCompilation: no Package: pcaMethods Version: 1.86.0 Depends: Biobase, methods Imports: BiocGenerics, Rcpp (>= 0.11.3), MASS LinkingTo: Rcpp Suggests: matrixStats, lattice, ggplot2 License: GPL (>= 3) MD5sum: 8fb729a4854e146f02f3d5fa7fa6ca6f NeedsCompilation: yes Package: PCAN Version: 1.22.0 Depends: R (>= 3.3), BiocParallel Imports: grDevices, stats Suggests: BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb License: CC BY-NC-ND 4.0 MD5sum: b2fc4793c026fc73c52d94989e9af8dc NeedsCompilation: no Package: PCAtools Version: 2.6.0 Depends: ggplot2, ggrepel Imports: lattice, grDevices, cowplot, methods, reshape2, stats, Matrix, DelayedMatrixStats, DelayedArray, BiocSingular, BiocParallel, Rcpp, dqrng LinkingTo: Rcpp, beachmat, BH, dqrng Suggests: testthat, scran, BiocGenerics, knitr, Biobase, GEOquery, hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2, airway, org.Hs.eg.db, magrittr, rmarkdown License: GPL-3 MD5sum: 8707552e1bbf1b6b001141d53e9ea568 NeedsCompilation: yes Package: pcxn Version: 2.16.0 Depends: R (>= 3.4), pcxnData Imports: methods, grDevices, utils, pheatmap Suggests: igraph, annotate, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 9323495c2ea5d0d89f3763e3b2c50fb2 NeedsCompilation: no Package: PDATK Version: 1.2.0 Depends: R (>= 4.1), SummarizedExperiment Imports: data.table, MultiAssayExperiment, ConsensusClusterPlus, igraph, ggplotify, matrixStats, RColorBrewer, clusterRepro, CoreGx, caret, survminer, methods, S4Vectors, BiocGenerics, survival, stats, plyr, dplyr, MatrixGenerics, BiocParallel, rlang, piano, scales, survcomp, genefu, ggplot2, switchBox, reportROC, pROC, verification, utils Suggests: testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr, HDF5Array License: MIT + file LICENSE MD5sum: 375d774275813b614f0e0e03fca2335b NeedsCompilation: no 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knitr, knitcitations, crayon, testthat, markdown License: Artistic-2.0 MD5sum: c384a6b3cf4f8b10f394078bb286184c NeedsCompilation: no Package: phemd Version: 1.10.0 Depends: R (>= 3.5), monocle, Seurat Imports: SingleCellExperiment, RColorBrewer, igraph, transport, pracma, cluster, Rtsne, destiny, RANN, ggplot2, maptree, pheatmap, scatterplot3d, VGAM, methods, grDevices, graphics, stats, utils, cowplot, S4Vectors, BiocGenerics, SummarizedExperiment, Biobase, phateR, reticulate Suggests: knitr License: GPL-2 MD5sum: 13a6518d2905280ce07e272e083a27b0 NeedsCompilation: no Package: PhenoGeneRanker Version: 1.2.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 International License MD5sum: 5891237ee58652481246b802b2eac67f NeedsCompilation: no Package: phenopath Version: 1.18.0 Imports: Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr, tibble, ggplot2, tidyr LinkingTo: Rcpp Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment License: Apache License (== 2.0) MD5sum: dc33f2c266efce8ab8ce25b91dc66bbc NeedsCompilation: yes Package: phenoTest Version: 1.42.0 Depends: R (>= 3.6.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2, Hmisc Imports: survival, limma, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, hgu133a.db, ellipse Suggests: GSEABase, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) MD5sum: d08617a2a8d591e2f0debdaa53c6bc71 NeedsCompilation: no Package: PhenStat Version: 2.30.0 Depends: R (>= 3.5.0) Imports: SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf, knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4, graphics, grDevices, utils, stats Suggests: RUnit, BiocGenerics License: file LICENSE MD5sum: 2e3c460aef24aa2799b03f9a1eee621a NeedsCompilation: no Package: philr Version: 1.20.1 Imports: ape, phangorn, tidyr, ggplot2, ggtree, methods Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia License: GPL-3 MD5sum: 0907d36b669e42771d3e39b0f416dd16 NeedsCompilation: no Package: PhIPData Version: 1.2.0 Depends: R (>= 4.1.0), SummarizedExperiment (>= 1.3.81) Imports: BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors, edgeR, cli, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr License: MIT + file LICENSE MD5sum: efe66eb73514b07e43ade528a5d8e804 NeedsCompilation: no Package: phosphonormalizer Version: 1.18.0 Depends: R (>= 4.0) Imports: plyr, stats, graphics, matrixStats, methods Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) MD5sum: 610a75c2a3a0ece34fc01bba15eacf03 NeedsCompilation: no Package: PhosR Version: 1.4.0 Depends: R (>= 4.1.0) Imports: ruv, e1071, dendextend, limma, pcaMethods, stats, RColorBrewer, circlize, dplyr, igraph, pheatmap, preprocessCore, tidyr, rlang, graphics, grDevices, utils, SummarizedExperiment, methods, S4Vectors, BiocGenerics, ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate License: GPL-3 + file LICENSE MD5sum: c74e51b729a48422c65d52b18a9dbcb4 NeedsCompilation: no Package: PhyloProfile Version: 1.8.6 Depends: R (>= 4.1.0) Imports: ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, DT, energy, ExperimentHub, ggplot2, gridExtra, pbapply, RColorBrewer, RCurl, shiny, shinyBS, shinyFiles, shinyjs, OmaDB, plyr, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 949c6ca989e2a309553a5b44d81c1e9b NeedsCompilation: no Package: phyloseq Version: 1.38.0 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 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data.table, dplyr, grDevices, grid, ggplotify, IRanges, methods, plyranges, purrr, Rcpp, RColorBrewer, rlang, stats, strawr, tools, utils LinkingTo: Rcpp Suggests: AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, GenomeInfoDb, GenomicRanges, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene License: MIT + file LICENSE MD5sum: 28634f0a2b8b3172a2dd1000f87e58be NeedsCompilation: yes Package: plotGrouper Version: 1.12.0 Depends: R (>= 3.5) Imports: ggplot2 (>= 3.0.0), dplyr (>= 0.7.6), tidyr (>= 0.2.0), tibble (>= 1.4.2), stringr (>= 1.3.1), readr (>= 1.1.1), readxl (>= 1.1.0), scales (>= 1.0.0), stats, grid, gridExtra (>= 2.3), egg (>= 0.4.0), gtable (>= 0.2.0), ggpubr (>= 0.1.8), shiny (>= 1.1.0), shinythemes (>= 1.1.1), colourpicker (>= 1.0), magrittr (>= 1.5), Hmisc (>= 4.1.1), rlang (>= 0.2.2) Suggests: knitr, 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GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, IRanges, plotly, rlang Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: ef9ebc3cf7404f7a5bd62317aa1b3a93 NeedsCompilation: no Package: RiboDiPA Version: 1.2.0 Depends: R (>= 4.1), Rsamtools, GenomicFeatures, GenomicAlignments Imports: Rcpp (>= 1.0.2), graphics, stats, data.table, elitism, methods, S4Vectors, IRanges, GenomicRanges, matrixStats, reldist, doParallel, foreach, parallel, qvalue, DESeq2, ggplot2, BiocFileCache LinkingTo: Rcpp Suggests: knitr, rmarkdown License: LGPL (>= 3) MD5sum: 13ea3d71df8902b824574ec0bfec6df3 NeedsCompilation: yes Package: RiboProfiling Version: 1.24.0 Depends: R (>= 3.2.2), Biostrings Imports: BiocGenerics, GenomeInfoDb, GenomicRanges, IRanges, reshape2, GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments, ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment License: GPL-3 MD5sum: 272215ea0193a23b30e09a0a229622a3 NeedsCompilation: no Package: ribor Version: 1.6.0 Depends: R (>= 3.6.0) Imports: dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors, tidyr, tools, yaml Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: b5148cb12431481e0b88e76775011cd2 NeedsCompilation: no Package: riboSeqR Version: 1.28.0 Depends: R (>= 3.0.2), methods, GenomicRanges, abind Imports: Rsamtools, IRanges, baySeq, GenomeInfoDb, seqLogo Suggests: BiocStyle, RUnit, BiocGenerics License: GPL-3 MD5sum: 172ff636ba2093c33f1b178c155cd922 NeedsCompilation: no Package: ribosomeProfilingQC Version: 1.6.1 Depends: R (>= 4.0), GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq, GenomicAlignments, GenomicFeatures, GenomeInfoDb, IRanges, methods, motifStack, rtracklayer, Rsamtools, RUVSeq, Rsubread, S4Vectors, XVector, ggplot2, ggfittext, scales, ggrepel, utils, cluster, stats, graphics, grid Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, limma, testthat, rmarkdown License: GPL (>= 3) + file LICENSE MD5sum: f7cd5ef7fffa6b4757175bdd8f3c1d35 NeedsCompilation: no Package: RImmPort Version: 1.22.0 Imports: plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools, utils, RSQLite Suggests: knitr License: GPL-3 MD5sum: 10de63aab41d112e3ef68952eeebc451 NeedsCompilation: no Package: Ringo Version: 1.58.0 Depends: methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix, grid, lattice Imports: BiocGenerics (>= 0.1.11), genefilter, limma, vsn, stats4 Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0) License: Artistic-2.0 MD5sum: e1aeb43596449e7430c87ec8fbd473e7 NeedsCompilation: yes Package: RIPAT Version: 1.4.0 Depends: R (>= 4.0) Imports: biomaRt (>= 2.38.0), GenomicRanges (>= 1.34.0), ggplot2 (>= 3.1.0), grDevices (>= 3.5.3), IRanges (>= 2.16.0), karyoploteR (>= 1.6.3), 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GPL-3 MD5sum: d9a81e336d48168cee7839e457f2641a NeedsCompilation: no Package: Rsamtools Version: 2.10.0 Depends: methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Biostrings (>= 2.47.6), R (>= 3.5.0) Imports: utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops, BiocParallel, stats LinkingTo: Rhtslib (>= 1.17.7), S4Vectors, IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle License: Artistic-2.0 | file LICENSE MD5sum: d53af0a206a0e7e56b4e56bb752d7758 NeedsCompilation: yes Package: rsbml Version: 2.52.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils Imports: BiocGenerics, graph, utils License: Artistic-2.0 MD5sum: c3905e11077cebbc29c7a6c33d4ef8d0 NeedsCompilation: yes Package: rScudo Version: 1.10.0 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ShortRead Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer License: LGPL-3 MD5sum: c53db838dc4d4da7b0de3a8b9a82a2c2 NeedsCompilation: no Package: rSWeeP Version: 1.6.0 Depends: R (>= 4.0) Imports: pracma, stats Suggests: Biostrings, methods, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: a85e2cd77da4b357ac99018e66ae4c07 NeedsCompilation: no Package: RTCA Version: 1.46.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 MD5sum: 69c4c7c0cf831b48f72ce9afa612cc0a NeedsCompilation: no Package: RTCGA Version: 1.24.0 Depends: R (>= 3.3.0) Imports: XML, assertthat, stringi, rvest, data.table, xml2, dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr, scales Suggests: devtools, testthat, pander, rmarkdown, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, RTCGA.PANCAN12, magrittr, tidyr License: GPL-2 MD5sum: 33b9026b513ee3ce614295e41a43a5a3 NeedsCompilation: no Package: RTCGAToolbox Version: 2.24.0 Depends: R (>= 3.5.0) Imports: BiocGenerics, data.table, DelayedArray, GenomicRanges, GenomeInfoDb, httr, limma, methods, RaggedExperiment, RCircos, RCurl, RJSONIO, S4Vectors (>= 0.23.10), stats, stringr, SummarizedExperiment, survival, TCGAutils (>= 1.9.4), XML Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown License: file LICENSE MD5sum: f6cd40a0e8f1a1f8fbdd2f3b2c6b9f36 NeedsCompilation: no Package: RTN Version: 2.18.0 Depends: R (>= 3.6.3), methods, Imports: RedeR, minet, viper, mixtools, snow, stats, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr, pheatmap, grDevices, graphics, utils Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: af78cde30aa9afb4f332f95deb6d4ada NeedsCompilation: no Package: RTNduals Version: 1.18.0 Depends: R(>= 3.6.3), RTN(>= 2.14.1), methods Imports: 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Version: 1.32.0 Depends: R (>= 2.10), igraph (>= 1.0) Imports: methods, AnnotationDbi, DBI, RSQLite Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 9ce856c97670c9d0c022d11ffbb6c463 NeedsCompilation: no Package: rTRMui Version: 1.32.0 Imports: shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 1d7b1ea1de2ff08079986423c75ab1f6 NeedsCompilation: no Package: runibic Version: 1.16.0 Depends: R (>= 3.4.0), biclust, SummarizedExperiment Imports: Rcpp (>= 0.12.12), testthat, methods LinkingTo: Rcpp Suggests: knitr, rmarkdown, GEOquery, affy, airway, QUBIC License: MIT + file LICENSE MD5sum: d788faee08d89e448b4df58d7d1db3a3 NeedsCompilation: yes Package: RUVcorr Version: 1.26.0 Imports: corrplot, MASS, stats, lattice, grDevices, gridExtra, snowfall, psych, BiocParallel, grid, bladderbatch, reshape2, graphics 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RcppParallel, SPAtest (>= 3.0.0) LinkingTo: Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0) Suggests: parallel, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics, SNPRelate License: GPL-3 MD5sum: 2f33ad35f227490c300e9933dafb4c7d NeedsCompilation: yes Package: sampleClassifier Version: 1.18.0 Depends: R (>= 4.0), MGFM, MGFR, annotate Imports: e1071, ggplot2, stats, utils Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db License: Artistic-2.0 MD5sum: 72b38f3e26092838571e4ec32f87fbda NeedsCompilation: no Package: SamSPECTRAL Version: 1.48.0 Depends: R (>= 3.3.3) Imports: methods License: GPL (>= 2) MD5sum: 909b5f72f976415ba24faba437cc1161 NeedsCompilation: yes Package: sangeranalyseR Version: 1.4.0 Depends: R (>= 4.0.0), stringr, ape, Biostrings, DECIPHER, parallel, reshape2, phangorn, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown (>= 2.9), knitr (>= 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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: 6fcee18b932a6cf29b91eea3ecb79000 NeedsCompilation: yes Package: Scale4C Version: 1.16.0 Depends: R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: 01193890d242d06733e09da863952eea NeedsCompilation: no Package: ScaledMatrix Version: 1.2.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular License: GPL-3 MD5sum: 289ef8390a6046db37740fad9581049f NeedsCompilation: no Package: scAlign Version: 1.8.0 Depends: R (>= 3.6), SingleCellExperiment (>= 1.4), Seurat (>= 2.3.4), tensorflow, purrr, 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GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs, rtracklayer, S4Vectors, scanMiR, scanMiRData, shiny, shinycssloaders, shinydashboard, stats, utils, waiter Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-3 MD5sum: 413aac0b622bedafc4e7f6063aee3be9 NeedsCompilation: no Package: scAnnotatR Version: 1.0.0 Depends: R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment Imports: dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, AnnotationHub, utils Suggests: knitr, rmarkdown, scRNAseq, testthat License: MIT + file LICENSE MD5sum: 81365789f2d5ac77067b779a4212df96 NeedsCompilation: no Package: SCANVIS Version: 1.8.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file LICENSE MD5sum: 0ccd31b00b44497e8a102d0ad830612c NeedsCompilation: no Package: SCArray Version: 1.2.1 Depends: R (>= 3.5.0), gdsfmt (>= 1.27.4), methods, DelayedArray (>= 0.16.0) Imports: BiocGenerics, S4Vectors, IRanges, utils, SummarizedExperiment, SingleCellExperiment, DelayedMatrixStats Suggests: Matrix, scater, uwot, RUnit, knitr, markdown, rmarkdown License: GPL-3 MD5sum: d795328e767d3f63109a10bdbafbeefd NeedsCompilation: yes Package: SCATE Version: 1.4.0 Depends: parallel, preprocessCore, splines, splines2, xgboost, SCATEData, Rtsne, mclust Imports: utils, stats, GenomicAlignments, GenomicRanges Suggests: rmarkdown, ggplot2, knitr License: MIT + file LICENSE MD5sum: 553d6318f46ca3b6224a6c3e48851b21 NeedsCompilation: no Package: scater Version: 1.22.0 Depends: SingleCellExperiment, scuttle, ggplot2 Imports: stats, utils, methods, grid, gridExtra, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, 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1.4.0 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: d79488ccf4ca93488a0c8834e82ca272 NeedsCompilation: yes Package: scClassifR Version: 1.2.0 Depends: R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment Imports: dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, utils Suggests: knitr, rmarkdown, scRNAseq, testthat License: MIT + file LICENSE MD5sum: 28c53a271241896486f9e1db55ba55bc NeedsCompilation: no Package: scClassify Version: 1.6.0 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, Cepo Suggests: knitr, rmarkdown, BiocStyle, pkgdown License: GPL-3 MD5sum: 3b10efb802b0c15a9463034c67553ebd NeedsCompilation: no Package: scDataviz Version: 1.4.0 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, RUnit, knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: 7632608d2981747452576158680a3722 NeedsCompilation: no Package: scDblFinder Version: 1.8.0 Depends: R (>= 4.0) Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, SingleCellExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost, stats, utils, MASS Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, MASS, viridisLite, mbkmeans License: GPL-3 MD5sum: c187da33a96da60c33e90da8464ce31d NeedsCompilation: no Package: scDD Version: 1.18.0 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: 02ed08f59d375bf5d745bff37e60a851 NeedsCompilation: yes Package: scde Version: 2.22.0 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: 466449f23604948adaef7b4b67afd70d NeedsCompilation: yes Package: scds Version: 1.10.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown License: MIT + file LICENSE MD5sum: 6a1a61339d91295f7c84adaf86bdc543 NeedsCompilation: no Package: SCFA Version: 1.4.0 Depends: R (>= 4.0) Imports: matrixStats, keras, tensorflow, BiocParallel, igraph, Matrix, cluster, clusterCrit, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival Suggests: knitr, rmarkdown License: LGPL MD5sum: bc7fa31370195b5235f54ba85c6a114c NeedsCompilation: no Package: scFeatureFilter Version: 1.14.0 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: 69e4982380c319784c63591781c5c810 NeedsCompilation: no Package: scGPS Version: 1.8.0 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, DESeq2, 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: 9b10bd21abba9bcdc62094ecb83041af NeedsCompilation: yes Package: schex Version: 1.8.0 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: 8a64f77cdac0ec73b6882dbddd0e1c42 NeedsCompilation: no Package: scHOT Version: 1.6.0 Depends: R (>= 4.0) Imports: S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix, SummarizedExperiment, IRanges, methods, stats, BiocParallel, reshape, ggplot2, igraph, grDevices, ggforce, graphics Suggests: knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir License: GPL-3 MD5sum: 6c4b442624340e163c754f8a67d93238 NeedsCompilation: no Package: scMAGeCK Version: 1.6.0 Imports: Seurat, ggplot2, stats, utils Suggests: knitr, rmarkdown License: BSD_2_clause MD5sum: 3b611c2b3fcd30e0a72b3fc251d03a49 NeedsCompilation: yes Package: scmap Version: 1.16.0 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: 563891a0e4aee602dee6159ad82038ea NeedsCompilation: yes Package: scMerge Version: 1.10.0 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: 293c020b72bbdb5a1eb22531846e4c97 NeedsCompilation: no Package: scmeth Version: 1.14.0 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: d59379bd2c0effd3f815cee16e0466ec NeedsCompilation: no Package: SCnorm Version: 1.16.0 Depends: R (>= 3.4.0), Imports: SingleCellExperiment, SummarizedExperiment, stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, S4Vectors, ggplot2, forcats, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) MD5sum: 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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: af5df50265d6c77966406cc5d3748208 NeedsCompilation: no Package: scoreInvHap Version: 1.16.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: 7d55701199ecb5e2f7790d2b55de7123 NeedsCompilation: no Package: scp Version: 1.4.0 Depends: R (>= 4.0), QFeatures (>= 1.3.5) Imports: methods, stats, utils, SingleCellExperiment, SummarizedExperiment, MultiAssayExperiment, MsCoreUtils, matrixStats, S4Vectors, dplyr, magrittr, rlang Suggests: testthat, knitr, BiocStyle, rmarkdown, patchwork, ggplot2, impute, scater, sva, preprocessCore, vsn, uwot License: Artistic-2.0 MD5sum: 123124a7bd5af87564b2e29051a81690 NeedsCompilation: no Package: scPCA Version: 1.8.0 Depends: R (>= 4.0.0) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca, cluster, kernlab, origami, RSpectra, coop, Matrix, DelayedArray, ScaledMatrix, MatrixGenerics Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark License: MIT + file LICENSE MD5sum: 28b53a09773f1edd4f5e9617825713e7 NeedsCompilation: no Package: scPipe Version: 1.16.1 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: a27a1ae1e442778b4b2244df51ed86dd NeedsCompilation: yes Package: scran Version: 1.22.1 Depends: SingleCellExperiment, scuttle Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, bluster, metapod, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, monocle, Biobase, pheatmap, scater License: GPL-3 MD5sum: 8195a851d0102ddaddbd7866dd5579be NeedsCompilation: yes Package: scReClassify Version: 1.0.0 Depends: R (>= 4.1) Imports: randomForest, e1071, stats, SummarizedExperiment, SingleCellExperiment, methods Suggests: testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr License: GPL-3 + file LICENSE MD5sum: 9c4987240d8885e5034dfe6d868a2002 NeedsCompilation: no Package: scRecover Version: 1.10.0 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: ccdd015cc66b9ee962923cecb7436039 NeedsCompilation: no Package: scRepertoire Version: 1.4.0 Depends: ggplot2, R (>= 4.0) Imports: stringdist, dplyr, reshape2, ggalluvial, stringr, vegan, powerTCR, SummarizedExperiment, plyr, parallel, doParallel, methods, utils, rlang, igraph, SeuratObject Suggests: knitr, rmarkdown, BiocStyle, scater, circlize, scales, Seurat License: Apache License 2.0 MD5sum: 17bba436e8c46b3e335ade10115f1a95 NeedsCompilation: no Package: scruff Version: 1.12.1 Depends: R (>= 4.0) 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: 750156ae4cf3f643aec52714db4a9da3 NeedsCompilation: no Package: scry Version: 1.6.0 Depends: R (>= 4.0), stats, methods Imports: DelayedArray, glmpca (>= 0.2.0), HDF5Array, Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular Suggests: markdown, BiocGenerics, covr, DuoClustering2018, ggplot2, knitr, rmarkdown, TENxPBMCData, testthat License: Artistic-2.0 MD5sum: 42a7d46cdfa17c94ab769febe93ab5da NeedsCompilation: no Package: scShapes Version: 1.0.0 Depends: R (>= 4.1) Imports: Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS, emdbook, magrittr, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: b7ccddb179711559c280dd64996663fc NeedsCompilation: yes Package: scTensor Version: 2.4.1 Depends: R (>= 4.1.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8), abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics, stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2 Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens License: Artistic-2.0 MD5sum: 31b009acf7e8f2629bdfd00b2472cd6a NeedsCompilation: no Package: scTGIF Version: 1.8.0 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: ee8a8f183c422b3458ac3a878ebf6e9a NeedsCompilation: no Package: scTHI Version: 1.6.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown License: GPL-2 MD5sum: 1c845ad6fa3c6b73f5b3665e01cb74f5 NeedsCompilation: no Package: scTreeViz Version: 1.0.0 Depends: R (>= 4.0), methods, epivizr, SummarizedExperiment Imports: data.table, S4Vectors, digest, Matrix, Rtsne, httr, igraph, clustree, scran, sys, epivizrData, epivizrServer, ggraph, scater, Seurat, SingleCellExperiment, ggplot2, stats, utils Suggests: knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb License: Artistic-2.0 MD5sum: 16c73264fdb6d0ce65ef70025ff40710 NeedsCompilation: no Package: scuttle Version: 1.4.0 Depends: SingleCellExperiment 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graphics, stats, utils, methods, chromhmmData Suggests: testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz License: GPL-3 MD5sum: e47f98ae10b59d3f804a9011571a08ea NeedsCompilation: no Package: segmentSeq Version: 2.28.0 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: 791c60cb9794dfec848e475f6a4bd0ed NeedsCompilation: no Package: selectKSigs Version: 1.6.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: b3af0a9766e9a04f881d802a973f7be3 NeedsCompilation: yes Package: SELEX Version: 1.26.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: f3d76194a5148509a851ee70eebc1fc0 NeedsCompilation: no Package: SemDist 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Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation License: GPL-3 MD5sum: ed091a84e3c600d651f41aa145ae82d8 NeedsCompilation: yes Package: seqbias Version: 1.42.0 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: 19a01de5a8bfb8319e972eb3bced66a4 NeedsCompilation: yes Package: seqCAT Version: 1.16.1 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE MD5sum: afe6f23e8ce3f07e2f931968f19e6748 NeedsCompilation: no Package: seqCNA Version: 1.40.0 Depends: R (>= 3.0), GLAD (>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot (>= 0.99), methods License: GPL-3 MD5sum: 52f1be8e6b892c428682edd642b30d61 NeedsCompilation: yes Package: seqcombo Version: 1.16.1 Depends: R (>= 3.4.0) Imports: Biostrings, cowplot, dplyr, ggplot2, grid, igraph, magrittr, methods, utils, yulab.utils Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble License: Artistic-2.0 MD5sum: 39a3e01b8e327501690e15f91622a673 NeedsCompilation: no Package: SeqGate Version: 1.4.0 Depends: S4Vectors, SummarizedExperiment, GenomicRanges Imports: stats, methods, BiocManager Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown License: GPL (>= 2.0) MD5sum: a322df25d60bbebedc64da8090e5b361 NeedsCompilation: no Package: SeqGSEA Version: 1.34.0 Depends: Biobase, doParallel, DESeq2 Imports: methods, biomaRt Suggests: GenomicRanges License: GPL (>= 3) MD5sum: 167b355cf9ee29885554f5e977ae5638 NeedsCompilation: no Package: seqLogo Version: 1.60.0 Depends: methods, grid Imports: stats4, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: LGPL (>= 2) MD5sum: 25c7614f4a3b61b23b4532e4cd7ced83 NeedsCompilation: no Package: seqPattern Version: 1.26.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 MD5sum: a34ad790ca84b23f88c3086ef1322f13 NeedsCompilation: no Package: seqsetvis Version: 1.14.4 Depends: R (>= 3.6), ggplot2 Imports: data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, ggplotify, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, stats, UpSetR Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, cowplot, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: b3970759a13568aab3d51f07e6b6e30b NeedsCompilation: no Package: SeqSQC Version: 1.16.0 Depends: R (>= 3.4), ExperimentHub (>= 1.3.7), SNPRelate (>= 1.10.2) Imports: e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, rbokeh, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: 77ac2581d9aa186429b52d62b77c6e70 NeedsCompilation: no Package: seqTools Version: 1.28.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: dfc4766dfdcbf65bfe548510c06975ee NeedsCompilation: yes Package: SeqVarTools Version: 1.32.0 Depends: SeqArray Imports: grDevices, graphics, stats, methods, Biobase, BiocGenerics, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, data.table, Suggests: BiocStyle, RUnit, stringr License: GPL-3 MD5sum: 847feec215c6d1450e2ff30b861fe31a NeedsCompilation: no Package: sesame Version: 1.12.9 Depends: R (>= 4.1), sesameData, methods Imports: BiocParallel, grDevices, utils, stringr, tibble, illuminaio, MASS, GenomicRanges, IRanges, grid, preprocessCore, S4Vectors, randomForest, wheatmap, ggplot2, graphics, KernSmooth, parallel, matrixStats, DNAcopy, stats, SummarizedExperiment, e1071, fgsea, ggrepel, reshape2 Suggests: scales, knitr, rmarkdown, testthat, dplyr, tidyr, BiocStyle, IlluminaHumanMethylation450kmanifest, minfi, FlowSorted.CordBloodNorway.450k, FlowSorted.Blood.450k, HDF5Array License: MIT + file LICENSE MD5sum: 3a4a496baffa106f3355394c81d06ecf NeedsCompilation: no Package: SEtools Version: 1.8.0 Depends: R (>= 4.0) Imports: S4Vectors, SummarizedExperiment, data.table, seriation, ComplexHeatmap, circlize, methods, BiocParallel, randomcoloR, edgeR, openxlsx, sva, stats, DESeq2, Matrix, grid Suggests: BiocStyle, knitr, rmarkdown, ggplot2, pheatmap License: GPL MD5sum: 51c560559fc1a590d91667b6dcb6ddea NeedsCompilation: no Package: sevenbridges Version: 1.24.0 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: 0b0e3969ed12b62ea2ca69a8489fafd4 NeedsCompilation: no Package: sevenC Version: 1.14.0 Depends: R (>= 3.5), InteractionSet (>= 1.2.0) Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), GenomeInfoDb (>= 1.12.2), GenomicRanges (>= 1.28.5), IRanges (>= 2.10.3), S4Vectors (>= 0.14.4), readr (>= 1.1.0), purrr (>= 0.2.2), data.table (>= 1.10.4), boot (>= 1.3-20), methods (>= 3.4.1) Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr License: GPL-3 MD5sum: 051397dd6f287ac6aa042fa471ef0a3e NeedsCompilation: no Package: SGSeq Version: 1.28.0 Depends: R (>= 4.0), IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), Rsamtools (>= 1.31.2), SummarizedExperiment, methods Imports: AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>= 2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>= 1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19), grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7), stats Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown License: Artistic-2.0 MD5sum: 11aad89860c57ef8aa5a921a41a1fa7c NeedsCompilation: no Package: SharedObject Version: 1.8.0 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, Rcpp Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 015f1a42130d955ce058b206a2e49bb1 NeedsCompilation: yes Package: shinyepico Version: 1.2.0 Depends: R (>= 4.0.0) Imports: DT (>= 0.15.0), data.table (>= 1.13.0), doParallel (>= 1.0.0), dplyr (>= 1.0.0), foreach (>= 1.5.0), GenomicRanges (>= 1.38.0), ggplot2 (>= 3.3.0), gplots (>= 3.0.0), heatmaply (>= 1.1.0), limma (>= 3.42.0), minfi (>= 1.32.0), plotly (>= 4.9.2), reshape2 (>= 1.4.0), rlang (>= 0.4.0), rmarkdown (>= 2.3.0), rtracklayer (>= 1.46.0), shiny (>= 1.5.0), shinyWidgets (>= 0.5.0), shinycssloaders (>= 0.3.0), shinyjs (>= 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GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), hwriter, methods, zlibbioc, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi License: Artistic-2.0 MD5sum: 798355d1af39f3ba320f517069ec8cb2 NeedsCompilation: yes Package: SIAMCAT Version: 1.14.0 Depends: R (>= 3.6.0), mlr, phyloseq Imports: beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, ParamHelpers, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot Suggests: BiocStyle, optparse, testthat, knitr, rmarkdown, tidyverse, ggpubr License: GPL-3 MD5sum: c82fb1a1c5b639f3585e2a5c361963b6 NeedsCompilation: no Package: SICtools Version: 1.24.0 Depends: R (>= 3.0.0), methods, Rsamtools (>= 1.18.1), doParallel (>= 1.0.8), Biostrings (>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges (>= 1.22.4), IRanges (>= 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f7017ec4683da2731fdede88e8cc41b1 NeedsCompilation: no Package: siggenes Version: 1.68.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: f9629d7071c0d78f3b970198cc9375dd NeedsCompilation: no Package: sights Version: 1.20.0 Depends: R(>= 3.3) Imports: MASS(>= 7.3), qvalue(>= 2.2), ggplot2(>= 2.0), reshape2(>= 1.4), lattice(>= 0.2), stats(>= 3.3) Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx License: GPL-3 | file LICENSE MD5sum: 7ac8a5d058b3c9e611efbaa9edd197c7 NeedsCompilation: no Package: signatureSearch Version: 1.8.2 Depends: R(>= 3.6.0), Rcpp, SummarizedExperiment Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, utils, reshape2, visNetwork, BiocParallel, fastmatch, reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray, BiocGenerics, tools LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, org.Hs.eg.db, signatureSearchData, DT License: Artistic-2.0 MD5sum: 66c729f89fcb736cce5a617c98ae24f0 NeedsCompilation: yes Package: signeR Version: 1.20.0 Depends: VariantAnnotation, NMF Imports: BiocGenerics, Biostrings, class, graphics, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: e53dedfacc2ebfd2db8f39048b0bcbee NeedsCompilation: yes Package: sigPathway Version: 1.62.0 Depends: R (>= 2.10) Suggests: hgu133a.db (>= 1.10.0), XML (>= 1.6-3), AnnotationDbi (>= 1.3.12) License: GPL-2 MD5sum: 35d9e8abaec9ea31009b5f33636f27a6 NeedsCompilation: yes Package: SigsPack Version: 1.8.0 Depends: R (>= 3.6) Imports: quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0), VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb, GenomicRanges, rtracklayer, SummarizedExperiment, graphics, stats, utils Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: dc8b6bca8c75c5849abbab8387f22314 NeedsCompilation: no Package: sigsquared Version: 1.26.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 37695c75f9fac3b9e005319f1899fa52 NeedsCompilation: no Package: SIM Version: 1.64.0 Depends: R (>= 3.5), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) MD5sum: c051410b2eada2a5fc0ae6d80ad80bdd NeedsCompilation: yes Package: SIMAT Version: 1.26.0 Depends: R (>= 3.5.0), Rcpp (>= 0.11.3) Imports: mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 139ba55a7156e3d1704bd2bd995d4459 NeedsCompilation: no Package: SimBindProfiles Version: 1.32.0 Depends: R (>= 2.10), methods, Ringo Imports: limma, mclust, Biobase License: 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testthat, knitr, igraph License: file LICENSE MD5sum: 0201cc71732514fa54570d047946e44f NeedsCompilation: yes Package: simplifyEnrichment Version: 1.4.0 Depends: R (>= 3.6.0), BiocGenerics, grid Imports: GOSemSim, ComplexHeatmap (>= 2.7.4), circlize, GetoptLong, digest, tm, GO.db, org.Hs.eg.db, AnnotationDbi, slam, methods, clue, grDevices, graphics, stats, utils, proxyC, Matrix, cluster (>= 1.14.2) Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, clusterProfiler, msigdbr, DOSE, DO.db, reactome.db, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown License: MIT + file LICENSE MD5sum: 508a0deee9dfc206a4f57697adb7d877 NeedsCompilation: no Package: sincell Version: 1.26.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: GPL (>= 2) MD5sum: a04c31bb8204f290b8435fc91ac90111 NeedsCompilation: yes Package: SingleCellExperiment Version: 1.16.0 Depends: SummarizedExperiment Imports: methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq, Rtsne License: GPL-3 MD5sum: 934e33067b6a88b5c210f52d067b0e7e NeedsCompilation: no Package: SingleCellSignalR Version: 1.6.0 Depends: R (>= 4.0) Imports: BiocManager, circlize, limma, igraph, gplots, grDevices, edgeR, SIMLR, data.table, pheatmap, stats, Rtsne, graphics, stringr, foreach, multtest, scran, utils, Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 3a75c75c26a8cebcef4321af68c27e82 NeedsCompilation: no Package: singleCellTK Version: 2.4.0 Depends: R (>= 4.0), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase Imports: ape, batchelor, BiocParallel, celldex, colourpicker, colorspace, cowplot, cluster, ComplexHeatmap, data.table, DelayedMatrixStats, DESeq2, dplyr, DT, ExperimentHub, fields, ggplot2, ggplotify, ggrepel, ggtree, gridExtra, GSVA (>= 1.26.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix, matrixStats, methods, msigdbr, multtest, plotly, RColorBrewer, ROCR, Rtsne, S4Vectors, scater, scMerge (>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, sva, reshape2, AnnotationDbi, shinyalert, circlize, enrichR, celda, shinycssloaders, DropletUtils, scds (>= 1.2.0), reticulate (>= 1.14), tools, tximport, fishpond, withr, GSEABase, R.utils, zinbwave, scRNAseq (>= 2.0.2), TENxPBMCData, yaml, rmarkdown, magrittr, scDblFinder, metap, VAM (>= 0.5.3), tibble, rlang, stats Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, xtable, spelling, org.Mm.eg.db, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics License: MIT + file LICENSE MD5sum: a6d0ac53cc587f5a469cde5596e62379 NeedsCompilation: no Package: SingleMoleculeFootprinting Version: 1.2.0 Depends: R (>= 4.1.0) Imports: BiocGenerics, Biostrings, BSgenome, GenomeInfoDb, GenomicRanges, data.table, grDevices, plyr, IRanges, RColorBrewer, stats, QuasR Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, parallel, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0) License: GPL-3 MD5sum: 26bb4c6f7e3656541a8dffe248b0075b NeedsCompilation: no Package: SingleR Version: 1.8.1 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocNeighbors, BiocParallel, BiocSingular, stats, utils, Rcpp, beachmat, parallel LinkingTo: Rcpp, beachmat Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scater, scran, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 + file LICENSE MD5sum: 73a881b154d99eabe554f215fefc1fe0 NeedsCompilation: yes Package: singscore Version: 1.14.0 Depends: R (>= 3.6) Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, reshape2, S4Vectors Suggests: hexbin, knitr, rmarkdown, testthat License: GPL-3 MD5sum: abaebdd4666b6462710917d552713498 NeedsCompilation: no Package: SISPA Version: 1.24.0 Depends: R (>= 3.5),genefilter,GSVA,changepoint Imports: data.table, plyr, ggplot2 Suggests: knitr License: GPL-2 MD5sum: 1f865f71097be13c79a45472d6b2b0d9 NeedsCompilation: no Package: sitadela Version: 1.2.0 Depends: R (>= 4.1.0) Imports: Biobase, BiocGenerics, biomaRt, Biostrings, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, methods, parallel, Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, utils Suggests: BSgenome, knitr, rmarkdown, RMySQL, RUnit License: Artistic-2.0 MD5sum: e5208be5adaddd4cf70932219794b32b NeedsCompilation: no Package: sitePath Version: 1.10.2 Depends: R (>= 4.1) Imports: RColorBrewer, Rcpp, 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ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer, BiocStyle License: MIT + file LICENSE MD5sum: a3800a8db0096873197209a9c024d871 NeedsCompilation: no Package: target Version: 1.8.0 Depends: R (>= 3.6) Imports: BiocGenerics, GenomicRanges, IRanges, matrixStats, methods, stats, graphics, shiny Suggests: testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS, covr License: GPL-3 MD5sum: 2b8bf6ba7eb8fb9aec80007f66da169f NeedsCompilation: no Package: TargetDecoy Version: 1.0.0 Depends: R (>= 4.1) Imports: ggplot2, ggpubr, methods, mzID, mzR, stats Suggests: BiocStyle, knitr, msdata, sessioninfo, rmarkdown, gridExtra, testthat (>= 3.0.0), covr License: Artistic-2.0 MD5sum: 86b385d98460b2a9f0f047f0c632a664 NeedsCompilation: no Package: TargetScore Version: 1.32.0 Depends: pracma, Matrix Suggests: TargetScoreData, gplots, Biobase, GEOquery License: GPL-2 MD5sum: 58df9482694da8fc8ec8e3936c514d26 NeedsCompilation: no Package: TargetSearch Version: 1.50.1 Imports: graphics, grDevices, methods, ncdf4, stats, utils, assertthat Suggests: TargetSearchData, BiocStyle, knitr, tinytest License: GPL (>= 2) MD5sum: 3a3f005a8bfadccc6ae16111007f921d NeedsCompilation: yes Package: TarSeqQC Version: 1.24.0 Depends: R (>= 3.5.1), methods, GenomicRanges, Rsamtools (>= 1.9.2), ggplot2, plyr, openxlsx Imports: grDevices, stats, utils, S4Vectors, IRanges, BiocGenerics, reshape2, GenomeInfoDb, BiocParallel, Biostrings, cowplot, graphics, GenomicAlignments, Hmisc Suggests: BiocManager, RUnit License: GPL (>= 2) MD5sum: 0565982a1fc5e152bec53ab249a7adb0 NeedsCompilation: no Package: TBSignatureProfiler Version: 1.6.0 Depends: R (>= 4.1) Imports: ASSIGN (>= 1.23.1), GSVA, singscore, methods, ComplexHeatmap, RColorBrewer, ggplot2, S4Vectors, reshape2, ROCit, DESeq2, DT, edgeR, gdata, SummarizedExperiment, magrittr, stats, rlang, BiocParallel, BiocGenerics Suggests: testthat, spelling, lintr, covr, knitr, rmarkdown, BiocStyle, shiny, circlize, caret, dplyr, plyr, impute, sva, glmnet, randomForest, MASS, class, e1071, pROC, HGNChelper License: MIT + file LICENSE MD5sum: f0ced58e565fa5df60bf0abf048d1331 NeedsCompilation: no Package: TCC Version: 1.34.0 Depends: R (>= 3.0), methods, DESeq2, edgeR, baySeq, ROC Suggests: RUnit, BiocGenerics Enhances: snow License: GPL-2 MD5sum: d336f8be41579aa601b43ed6b9b55c94 NeedsCompilation: no Package: TCGAbiolinks Version: 2.22.4 Depends: R (>= 4.0) 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: aba45477e900a891c93d9040d863f964 NeedsCompilation: no Package: TCGAbiolinksGUI Version: 1.20.0 Depends: R (>= 3.3.1), shinydashboard (>= 0.5.3), TCGAbiolinksGUI.data Imports: shiny (>= 0.14.1), downloader (>= 0.4), grid, DT, plotly, readr, maftools, stringr (>= 1.1.0), SummarizedExperiment, ggrepel, data.table, caret, shinyFiles (>= 0.6.2), ggplot2 (>= 2.1.0), pathview, ELMER (>= 2.0.0), clusterProfiler, parallel, TCGAbiolinks (>= 2.5.5), shinyjs (>= 0.7), colourpicker, sesame, shinyBS (>= 0.61) Suggests: testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2, BiocStyle, animation, rmarkdown, pander License: GPL (>= 3) MD5sum: 7ebd2b9771d6e42445efe8ddc941a881 NeedsCompilation: no Package: TCGAutils Version: 1.14.1 Depends: R (>= 4.0.0) Imports: AnnotationDbi, BiocGenerics, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment (>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2 Suggests: BiocFileCache, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: a246361848a4cfec8d10bf3856f63f15 NeedsCompilation: no Package: TCseq Version: 1.18.0 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: a5f7c518ca7d5d1efea83bd6bfa095e2 NeedsCompilation: no Package: TDARACNE Version: 1.44.0 Depends: GenKern, Rgraphviz, Biobase License: GPL-2 MD5sum: 8b6930680f39376f1e3873369f8e094a NeedsCompilation: no Package: tenXplore Version: 1.16.0 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, rmarkdown License: Artistic-2.0 MD5sum: 05345fe761d168c7b5e407558cb27978 NeedsCompilation: no Package: TEQC Version: 4.16.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Rsamtools, hwriter Imports: Biobase (>= 2.15.1) License: GPL (>= 2) MD5sum: da11f78e56130ec50d684b5dc87c121d NeedsCompilation: no Package: ternarynet Version: 1.38.0 Depends: R (>= 4.0) Imports: utils, igraph, methods, graphics, stats, BiocParallel Suggests: testthat Enhances: Rmpi, snow License: GPL (>= 2) MD5sum: f4d8d99a7032d91364cc8c580dc311a8 NeedsCompilation: yes Package: TFARM Version: 1.16.0 Depends: R (>= 3.4) Imports: arules, fields, GenomicRanges, graphics, stringr, methods, stats, gplots Suggests: BiocStyle, knitr, plyr License: Artistic-2.0 MD5sum: 1468adbf75ccc7cdf9170468e315d026 NeedsCompilation: no Package: TFBSTools Version: 1.32.0 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), rmarkdown License: GPL-2 MD5sum: 668957d41cea76909fd1abe824fc76e4 NeedsCompilation: yes Package: TFEA.ChIP Version: 1.14.0 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: 7a389ab22c64bdfe6fb70129df69c122 NeedsCompilation: no Package: TFHAZ Version: 1.16.0 Depends: R(>= 3.4) Imports: GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 9511c4a1391b09937dd74dfb7744c02b NeedsCompilation: no Package: TFutils Version: 1.14.0 Depends: R (>= 4.1.0) Imports: methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase, rjson, BiocFileCache, DT, httr, readxl, AnnotationDbi, org.Hs.eg.db, utils Suggests: knitr, data.table, testthat, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer, rmarkdown License: Artistic-2.0 MD5sum: bbce1e63abdff3e677236d83c5d75922 NeedsCompilation: no Package: tidybulk Version: 1.6.1 Depends: R (>= 4.1.0) Imports: tibble, readr, dplyr, magrittr, tidyr, stringi, stringr, rlang, purrr, tidyselect, preprocessCore, stats, parallel, utils, lifecycle, scales, SummarizedExperiment, GenomicRanges, 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, survminer, tidySummarizedExperiment, markdown, uwot License: GPL-3 MD5sum: 1f36d23f809ca86eca4d1b5fd012fa34 NeedsCompilation: no Package: tidySingleCellExperiment Version: 1.4.0 Depends: R (>= 4.0.0), SingleCellExperiment Imports: SummarizedExperiment, 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, EnsDb.Hsapiens.v86 License: GPL-3 MD5sum: 08e6ed77371413af3417b3071e91cbd2 NeedsCompilation: no Package: tidySummarizedExperiment Version: 1.4.1 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: 6238615733c837fe8f0378fbc1318d8a NeedsCompilation: no Package: tigre Version: 1.48.0 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: 7043effb25195defb2e8f0ca8c161c8e NeedsCompilation: yes Package: TileDBArray Version: 1.4.0 Depends: DelayedArray (>= 0.15.16) Imports: methods, Rcpp, tiledb, S4Vectors LinkingTo: Rcpp Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat License: MIT + file LICENSE MD5sum: 70813a765c2f493028ae9fa2cbf4b809 NeedsCompilation: yes Package: tilingArray Version: 1.72.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 MD5sum: b2de6efcef37b7e834a9fbe0e102e4ef NeedsCompilation: yes Package: timecourse Version: 1.66.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL MD5sum: 3d0382f25c0650b9814a6e53891a0b0d NeedsCompilation: no Package: timeOmics Version: 1.6.0 Depends: mixOmics, R (>= 4.0) Imports: dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, propr, lmtest, plyr Suggests: BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots License: GPL-3 MD5sum: 0ea9f516c23b3f1022b02ca3f101d199 NeedsCompilation: no Package: timescape Version: 1.18.0 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: f71b67194ac3de33911b42e74ea9159a NeedsCompilation: no Package: TimeSeriesExperiment Version: 1.12.0 Depends: R (>= 4.1), 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: MIT + file LICENSE MD5sum: 3d80350179d3cf02a0b1aafc83c291ad NeedsCompilation: no Package: TimiRGeN Version: 1.4.0 Depends: R (>= 4.0), 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MD5sum: 3d6ffe030efe1582305224a7eab46854 NeedsCompilation: no Package: TitanCNA Version: 1.32.0 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: 87b90e944e3ffd6a3e32bfb83d33150f NeedsCompilation: yes Package: tkWidgets Version: 1.72.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 MD5sum: 6291d5791d3aaedb0317c89a08616c36 NeedsCompilation: no Package: tLOH Version: 1.2.0 Depends: R (>= 4.0) Imports: scales, stats, utils, ggplot2, data.table, purrr, dplyr, VariantAnnotation, GenomicRanges, MatrixGenerics Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: cec67fe98997cce9870ee00aece1c06f NeedsCompilation: no Package: TMixClust Version: 1.16.0 Depends: R (>= 3.4) Imports: gss, mvtnorm, stats, zoo, 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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: 2eb77fa2bee0c8470faa0e20b8e32d84 NeedsCompilation: no Package: topdownr Version: 1.16.0 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, rmarkdown, ranger, testthat, BiocStyle, xml2 License: GPL (>= 3) MD5sum: b469ae2463fef4272c078825f64d5e7f NeedsCompilation: no Package: topGO Version: 2.46.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.6), graph (>= 1.14.0), Biobase (>= 2.0.0), GO.db (>= 2.3.0), AnnotationDbi (>= 1.7.19), SparseM (>= 0.73) Imports: lattice, matrixStats, DBI Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest License: LGPL MD5sum: 126e8d4ffbfe2c0e10772ed48bce2c50 NeedsCompilation: no Package: ToxicoGx Version: 1.4.0 Depends: R (>= 4.1), CoreGx Imports: SummarizedExperiment, S4Vectors, Biobase, BiocParallel, ggplot2, tibble, dplyr, caTools, downloader, magrittr, methods, reshape2, tidyr, data.table, assertthat, scales, graphics, grDevices, parallel, stats, utils, limma, jsonlite Suggests: rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools, PharmacoGx, xtable, markdown License: MIT + file LICENSE MD5sum: 642be1371d67b21115abab38a789fb1a NeedsCompilation: no Package: TPP Version: 3.22.1 Depends: R (>= 3.4), Biobase, dplyr, magrittr, tidyr Imports: biobroom, broom, data.table, doParallel, foreach, futile.logger, ggplot2, grDevices, gridExtra, grid, knitr, limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr, purrr, RColorBrewer, RCurl, reshape2, rmarkdown, splines, stats, stringr, tibble, utils, VennDiagram, VGAM Suggests: BiocStyle, testthat License: Artistic-2.0 MD5sum: d61b1a3571446c31cd11af71e4c8179e NeedsCompilation: no Package: TPP2D Version: 1.10.0 Depends: R (>= 3.6.0), stats, utils, dplyr, methods Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl, parallel, MASS, BiocParallel, limma Suggests: knitr, testthat, rmarkdown License: GPL-3 MD5sum: 9b722d55a27b1b2e84313e66a72f1ec3 NeedsCompilation: no Package: tracktables Version: 1.28.0 Depends: R (>= 3.0.0) Imports: IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base, stringr, RColorBrewer, methods Suggests: knitr, BiocStyle License: GPL (>= 3) MD5sum: a11e30715fd40bd625fed9cfb8294808 NeedsCompilation: no Package: trackViewer Version: 1.30.0 Depends: R (>= 3.5.0), grDevices, methods, GenomicRanges, grid, Rcpp Imports: GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, plotrix, Rgraphviz, InteractionSet, graph, utils, rhdf5 LinkingTo: Rcpp Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown License: GPL (>= 2) MD5sum: 50316e46c6e645c1b4a6bfd58cf529c7 NeedsCompilation: yes Package: tradeSeq Version: 1.8.0 Depends: R (>= 3.6) Imports: mgcv, edgeR, SingleCellExperiment, SummarizedExperiment, slingshot, magrittr, RColorBrewer, BiocParallel, Biobase, pbapply, igraph, ggplot2, princurve, methods, S4Vectors, tibble, Matrix, TrajectoryUtils, viridis, matrixStats, MASS Suggests: knitr, rmarkdown, testthat, covr, clusterExperiment License: MIT + file LICENSE MD5sum: 1ce3cba0a1a2f58ee9e3f62e869d7301 NeedsCompilation: no Package: TrajectoryGeometry Version: 1.2.0 Depends: R (>= 4.1) Imports: pracma, rgl, ggplot2, stats, methods Suggests: dplyr, knitr, RColorBrewer, rmarkdown License: MIT + file LICENSE MD5sum: e2c1a8e68899cfc4ab11d12c8c938904 NeedsCompilation: no Package: TrajectoryUtils Version: 1.2.0 Depends: SingleCellExperiment Imports: methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: ec5b57db6fbee2f715c5cab4380cc851 NeedsCompilation: no Package: transcriptogramer Version: 1.16.0 Depends: R (>= 3.4), methods Imports: biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 901d1104835f70487249594949f8efbd NeedsCompilation: no Package: transcriptR Version: 1.22.0 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: f10773424f5bad04ff1567a99f4994b4 NeedsCompilation: no Package: transformGamPoi Version: 1.0.0 Imports: glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown License: GPL-3 MD5sum: 3a67b1af075b9b80a1fa2ed0fcb158d3 NeedsCompilation: no Package: transite Version: 1.12.1 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: 731ce321d745a29a8db48d52bbdc2821 NeedsCompilation: yes Package: tRanslatome Version: 1.32.0 Depends: R (>= 2.15.0), methods, limma, sigPathway, anota, DESeq2, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 MD5sum: 11249dc10007789ec5e057e6fce5a338 NeedsCompilation: no Package: transomics2cytoscape Version: 1.4.0 Imports: RCy3, KEGGREST, dplyr Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 00904f3c08cd80570381964761ed2d99 NeedsCompilation: no Package: TransView Version: 1.38.0 Depends: methods, GenomicRanges Imports: BiocGenerics, S4Vectors (>= 0.9.25), IRanges, zlibbioc, gplots LinkingTo: Rhtslib (>= 1.15.3) Suggests: RUnit, pasillaBamSubset, BiocManager License: GPL-3 MD5sum: c0bace8480b1e373aee778cefc39cb40 NeedsCompilation: yes Package: TraRe Version: 1.2.0 Depends: R (>= 4.1) Imports: hash, ggplot2, stats, methods, igraph, utils, glmnet, vbsr, grDevices, gplots, gtools, pvclust, R.utils, dqrng, SummarizedExperiment, BiocParallel, matrixStats Suggests: knitr, rmarkdown, BiocGenerics, RUnit, BiocStyle License: MIT + file LICENSE MD5sum: e44d6365bf9f6cb1b483852a568d1a6b NeedsCompilation: no Package: traseR Version: 1.24.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL MD5sum: 83e280371d4c1437cee91ff9f2b4e307 NeedsCompilation: no Package: Travel Version: 1.2.0 Imports: Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, inline, parallel License: GPL-3 MD5sum: f67a36b5df7db2da6df4ad58c32fcbfa NeedsCompilation: yes Package: traviz Version: 1.0.0 Depends: R (>= 4.0) Imports: ggplot2, viridis, mgcv, SingleCellExperiment, slingshot, princurve, Biobase, methods, RColorBrewer, SummarizedExperiment, grDevices, graphics, rgl Suggests: scater, dplyr, testthat (>= 3.0.0), covr, S4Vectors, rmarkdown, knitr License: MIT + file LICENSE MD5sum: 2e26680ea086aeb17bc6c7d2a984ae1c NeedsCompilation: no Package: TreeAndLeaf Version: 1.6.1 Depends: R(>= 4.0) Imports: RedeR(>= 1.40.4), igraph, ape Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer License: Artistic-2.0 MD5sum: 4c099f333822b9b04f2948d362560b5b NeedsCompilation: no Package: treeio Version: 1.18.1 Depends: R (>= 3.6.0) Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, tibble, tidytree (>= 0.3.0), utils Suggests: Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml License: Artistic-2.0 MD5sum: 91c82ed0c2a4b8bdbe16a293e0f81260 NeedsCompilation: no Package: treekoR Version: 1.2.1 Depends: R (>= 4.1) Imports: stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2, hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt, edgeR, lme4, multcomp Suggests: knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0) License: GPL-3 MD5sum: 075b212ee8d8f0d59989a205236c5bba NeedsCompilation: no Package: TreeSummarizedExperiment Version: 2.2.0 Depends: R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18), Biostrings Imports: methods, BiocGenerics, utils, ape, rlang, dplyr, SummarizedExperiment, BiocParallel, IRanges, treeio Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 2d39c20eb5e2cf50173bac3b737b05b3 NeedsCompilation: no Package: trena Version: 1.16.0 Depends: R (>= 3.5.0), utils, glmnet (>= 2.0.3), MotifDb (>= 1.19.17) Imports: RSQLite, RMySQL, lassopv, randomForest, vbsr, xgboost, RPostgreSQL, methods, DBI, BSgenome, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, SNPlocs.Hsapiens.dbSNP150.GRCh38, org.Hs.eg.db, Biostrings, GenomicRanges, biomaRt, AnnotationDbi, WGCNA Suggests: RUnit, plyr, knitr, BiocGenerics, rmarkdown, formatR, markdown, BiocParallel, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Athaliana.TAIR.TAIR9 License: GPL-3 MD5sum: 4d6e73f9d66e50cc2fb0d52f6a51410e NeedsCompilation: no Package: Trendy Version: 1.16.0 Depends: R (>= 3.4) Imports: stats, utils, graphics, grDevices, segmented, gplots, parallel, magrittr, BiocParallel, DT, S4Vectors, SummarizedExperiment, methods, shiny, shinyFiles Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL-3 MD5sum: 4ed6dea781d4e41992ed91991ada7fa7 NeedsCompilation: no Package: TRESS Version: 1.0.0 Depends: R (>= 4.1.0), parallel, S4Vectors Imports: utils, rtracklayer, Matrix, matrixStats, stats, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi Suggests: knitr, rmarkdown,BiocStyle License: GPL-3 + file LICENSE MD5sum: da1cc6546ed84a3a04cdc77f0182ade8 NeedsCompilation: no Package: tricycle Version: 1.2.1 Depends: R (>= 4.0), SingleCellExperiment Imports: methods, circular, ggplot2, AnnotationDbi, scater, GenomicRanges, IRanges, S4Vectors, scattermore, dplyr, RColorBrewer, grDevices, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 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Depends: shiny (>= 1.6.0), shinyBS Imports: shinyjs, shinyFiles, plyr, data.table, DT, stringr, stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr, pryr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices, graphics, stats, utils Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis Enhances: parallel License: MIT + file LICENSE MD5sum: 5f1a581c0be90b78ff6d5f8aad534eac NeedsCompilation: no Package: tRNA Version: 1.12.0 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: 91aee9028479d8eb4950936dd55ed287 NeedsCompilation: no Package: tRNAdbImport Version: 1.12.0 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: 30f0171397f840263f2781347d37154f NeedsCompilation: no Package: tRNAscanImport Version: 1.14.0 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: 0abda612f29f57aeb69fee03e8d738e2 NeedsCompilation: no Package: TRONCO Version: 2.26.0 Depends: R (>= 4.1.0), 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: 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NeedsCompilation: no Package: tximeta Version: 1.12.4 Imports: SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, tools, utils, methods, Matrix Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, edgeR, limma, devtools License: GPL-2 MD5sum: f0561894dbad7cdd72237b289e32dbdf NeedsCompilation: no Package: tximport Version: 1.22.0 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, fishpond License: GPL (>= 2) MD5sum: 570127c29d79d3d2b3e07910f72158f8 NeedsCompilation: no Package: TypeInfo Version: 1.60.0 Depends: methods Suggests: Biobase License: BSD MD5sum: 77201e33c7a343af0e964679c0038189 NeedsCompilation: no Package: Ularcirc Version: 1.12.0 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: 1ba593da6d107a6bac661a94296e80ab NeedsCompilation: no Package: UMI4Cats Version: 1.4.0 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, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat License: Artistic-2.0 MD5sum: 7fa82646d4b58953f6848eff6098c990 NeedsCompilation: no Package: uncoverappLib Version: 1.4.0 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: fa75abcbee0f5a868d8a55ccf9423b89 NeedsCompilation: no Package: UNDO Version: 1.36.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 512a571412dad10f3ee6432f3ac4af3f NeedsCompilation: no Package: unifiedWMWqPCR Version: 1.30.0 Depends: methods Imports: BiocGenerics, stats, graphics, HTqPCR License: GPL (>= 2) MD5sum: 38aeb8026ffd92f8c902be5d774a554d NeedsCompilation: no Package: UniProt.ws Version: 2.34.0 Depends: methods, utils, RSQLite, RCurl, BiocGenerics (>= 0.13.8) Imports: AnnotationDbi, BiocFileCache, rappdirs Suggests: RUnit, BiocStyle, knitr License: Artistic License 2.0 MD5sum: 3aef68eb5e2afac0809638739b484ef2 NeedsCompilation: no Package: Uniquorn Version: 2.14.0 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: 08b3aa896f07743fe80d0a8affb15d02 NeedsCompilation: no Package: universalmotif Version: 1.12.4 Depends: R (>= 3.5.0) Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid LinkingTo: Rcpp, RcppThread Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio Enhances: PWMEnrich, rGADEM License: GPL-3 MD5sum: 3baabf63fb0d1119fd6cc6c97cb42b42 NeedsCompilation: yes Package: uSORT Version: 1.20.0 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: 52219b1541e964482fee57d151b76c11 NeedsCompilation: no Package: VAExprs Version: 1.0.1 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, gradDescent, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: cc773583e9e4489c377938a7be66dad7 NeedsCompilation: no Package: VanillaICE Version: 1.56.3 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 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methods, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr License: GPL-2 MD5sum: 922a5518ac302be34b1e416772190db5 NeedsCompilation: no Package: VariantAnnotation Version: 1.40.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5), Rsamtools (>= 1.99.0) Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.57.2), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome (>= 1.47.3), GenomicFeatures (>= 1.31.3) LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle License: Artistic-2.0 MD5sum: 6f150cac9c1797e5b11500c9830bd570 NeedsCompilation: yes Package: VariantExperiment Version: 1.8.0 Depends: R (>= 3.6.0), S4Vectors (>= 0.21.24), SummarizedExperiment (>= 1.13.0), GenomicRanges, Imports: GDSArray (>= 1.11.1), DelayedDataFrame (>= 1.6.0), tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray, SeqVarTools, DelayedArray, Biostrings, IRanges Suggests: testthat, knitr, rmarkdown, markdown License: GPL-3 MD5sum: 527a22b0d2e9eb37ae7d0e4918f5b12a NeedsCompilation: no Package: VariantFiltering Version: 1.30.0 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, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 License: Artistic-2.0 MD5sum: d83409a07079fafbe076cc5f5ab8eb1e NeedsCompilation: yes Package: VariantTools Version: 1.36.0 Depends: S4Vectors (>= 0.17.33), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), VariantAnnotation (>= 1.11.16), methods Imports: Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel, GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7), BiocParallel, GenomeInfoDb, BSgenome, Biobase Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3) License: Artistic-2.0 MD5sum: 48c85fbfebb35a94117f1dcd3e1d969f NeedsCompilation: no Package: VaSP Version: 1.6.0 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, Sushi, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 32360b7af859bcaf96dc90b96b3b76bd NeedsCompilation: no Package: vbmp Version: 1.62.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: 5e1c38504956a8d824eb45ca5029ffdf NeedsCompilation: no Package: VCFArray Version: 1.10.0 Depends: R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28) Imports: tools, GenomicRanges, VariantAnnotation (>= 1.29.3), GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown License: GPL-3 MD5sum: b3c9cdde27f9480b981d856c54859e36 NeedsCompilation: no Package: VegaMC Version: 3.32.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods License: GPL-2 MD5sum: d7c44adbfaee606e2f94b1f88597a00f NeedsCompilation: yes Package: velociraptor Version: 1.4.0 Depends: SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors, DelayedArray, basilisk, zellkonverter, scuttle, SingleCellExperiment, BiocParallel, BiocSingular Suggests: BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran, scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot, GGally, patchwork, metR License: MIT + file LICENSE MD5sum: 04414fdd42363c724129a63b212b0fd5 NeedsCompilation: no Package: veloviz Version: 1.0.0 Depends: R (>= 4.1) Imports: Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 7ddc94961ab377cf7b360d8973a74731 NeedsCompilation: yes Package: VennDetail Version: 1.10.0 Imports: utils, grDevices, stats, methods, dplyr, purrr, tibble, magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger Suggests: knitr, rmarkdown, testthat, markdown License: GPL-2 MD5sum: 70d25b00db989cb6b6fb39b52a28d3ac NeedsCompilation: no Package: VERSO Version: 1.4.0 Depends: R (>= 4.1.0) Imports: ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: cab61bcb67cd6a697dca8b75369e819c NeedsCompilation: no Package: vidger Version: 1.14.0 Depends: R (>= 3.5) Imports: Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr, RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, testthat License: GPL-3 | file LICENSE MD5sum: e528e47fc132a016ff9573ed0007251e NeedsCompilation: no Package: viper Version: 1.28.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: b41027a67e0097b1e80b0e0ee38e5660 NeedsCompilation: no Package: ViSEAGO Version: 1.8.0 Depends: R (>= 3.6) Imports: data.table, AnnotationDbi, AnnotationForge, biomaRt, dendextend, DiagrammeR, DT, dynamicTreeCut, fgsea, GOSemSim, ggplot2, GO.db, grDevices, heatmaply, htmlwidgets, igraph, methods, plotly, processx, topGO, RColorBrewer, R.utils, scales, stats, UpSetR, utils Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager License: GPL-3 MD5sum: a429b0e4a8ead0caf774fa3335ed8e78 NeedsCompilation: no Package: vissE Version: 1.2.2 Depends: R (>= 4.1) Imports: igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm, ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb, ggrepel, textstem, tidygraph, stats, scales, ggraph Suggests: testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr License: GPL-3 MD5sum: 9700ae26b8e0563d806e1ea3badbbfef NeedsCompilation: no Package: VplotR Version: 1.4.0 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown License: GPL-3 MD5sum: e116b1e5930bd102e296cf35a45bb190 NeedsCompilation: no Package: vsn Version: 3.62.0 Depends: R (>= 4.0.0), methods, Biobase Imports: affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat License: Artistic-2.0 MD5sum: 1b9030239dd822c114a31456a441fa2c NeedsCompilation: yes Package: vtpnet Version: 0.34.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: e31d045178198f95c04329b6322e2aee NeedsCompilation: no Package: vulcan Version: 1.16.0 Depends: R (>= 4.0), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene, zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit Imports: wordcloud, csaw, gplots, stats, utils, caTools, graphics, DESeq2, Biobase Suggests: vulcandata License: LGPL-3 MD5sum: 5fe26aca22b3f4d63cbbc39817b23df1 NeedsCompilation: no Package: waddR Version: 1.8.0 Depends: R (>= 3.6.0) Imports: Rcpp (>= 1.0.1), arm (>= 1.10-1), eva, BiocFileCache, BiocParallel, SingleCellExperiment, parallel, methods, stats LinkingTo: Rcpp, RcppArmadillo, Suggests: knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown, scater License: MIT + file LICENSE MD5sum: af9b21f538b15e500b80049c298c5b91 NeedsCompilation: yes Package: wateRmelon Version: 2.0.0 Depends: R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi, lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19, illuminaio Imports: Biobase Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore Enhances: minfi License: GPL-3 MD5sum: c9d4485c55aa79bd2c8c880f815bfd95 NeedsCompilation: no Package: wavClusteR Version: 2.28.0 Depends: R (>= 3.2), GenomicRanges (>= 1.31.8), Rsamtools Imports: methods, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Biostrings (>= 2.47.6), foreach, GenomicFeatures (>= 1.31.3), ggplot2, Hmisc, mclust, rtracklayer (>= 1.39.7), seqinr, stringr Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 Enhances: doMC License: GPL-2 MD5sum: 4046f9106efb35f5155b9687aaad24d1 NeedsCompilation: no Package: weaver Version: 1.60.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 MD5sum: 232531f1f3567303a0e44177241dec75 NeedsCompilation: no Package: webbioc Version: 1.66.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocManager License: GPL (>= 2) MD5sum: 7bc92ae3495ec30fa86d5b13cf228fc6 NeedsCompilation: no Package: weitrix Version: 1.6.0 Depends: R (>= 3.6), SummarizedExperiment Imports: methods, utils, stats, grDevices, assertthat, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics, limma, topconfects, dplyr, purrr, ggplot2, rlang, scales, reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl Suggests: knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0) License: LGPL-2.1 | file LICENSE MD5sum: 980ae21056a49246d2c1d8e96be376f3 NeedsCompilation: no Package: widgetTools Version: 1.72.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: b5923ca9255d410e3ddd88bb5a212e06 NeedsCompilation: no Package: wiggleplotr Version: 1.18.0 Depends: R (>= 3.6) Imports: dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer, cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter License: Apache License 2.0 MD5sum: f6c2256bf0b294f9da1b148f6b4e168b NeedsCompilation: no Package: wpm Version: 1.4.0 Depends: R (>= 4.1.0) Imports: utils, methods, cli, Biobase, SummarizedExperiment, config, golem, shiny, DT, ggplot2, dplyr, rlang, stringr, shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer, logging Suggests: MSnbase, testthat, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 141be6037e13eed570ee89dcec7c28dd NeedsCompilation: no Package: wppi Version: 1.2.0 Depends: R(>= 4.1) Imports: dplyr, igraph, logger, methods, magrittr, Matrix, OmnipathR(>= 2.99.8), progress, purrr, rlang, RCurl, stats, tibble, tidyr Suggests: knitr, testthat, rmarkdown License: MIT + file LICENSE MD5sum: fa7e8f002f59219506c0d94e9ec6fdfe NeedsCompilation: no Package: Wrench Version: 1.12.0 Depends: R (>= 3.5.0) Imports: limma, matrixStats, locfit, stats, graphics Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR License: Artistic-2.0 MD5sum: 51467b040e3a72f2203785b577c1c878 NeedsCompilation: no Package: xcms Version: 3.16.1 Depends: R (>= 4.0.0), BiocParallel (>= 1.8.0), MSnbase (>= 2.19.1) Imports: mzR (>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics (>= 1.25.1), lattice, RColorBrewer, plyr, RANN, MassSpecWavelet (>= 1.5.2), S4Vectors, robustbase, IRanges, SummarizedExperiment, MsCoreUtils, MsFeatures Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>= 0.25.1), ncdf4, testthat, pander, magrittr, rmarkdown, multtest, MALDIquant, pheatmap, Spectra (>= 1.1.17), MsBackendMgf, progress Enhances: Rgraphviz, rgl, XML License: GPL (>= 2) + file LICENSE MD5sum: c9e87528867ee0acf4ca84c3086001a0 NeedsCompilation: yes Package: XDE Version: 2.40.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5) Imports: BiocGenerics, genefilter, graphics, grDevices, gtools, methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta, siggenes Suggests: MASS, RUnit Enhances: coda License: LGPL-2 MD5sum: b1db04370776951d52178e467017df73 NeedsCompilation: yes Package: Xeva Version: 1.10.0 Depends: R (>= 3.6) Imports: methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2, scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid, nlme, PharmacoGx, downloader Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: f2db8b9d37d1e192423d61be18e077a3 NeedsCompilation: no Package: XINA Version: 1.12.0 Depends: R (>= 3.5) Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb Suggests: knitr, rmarkdown License: GPL-3 MD5sum: d6c7f08a8606cee588508a0d03da8834 NeedsCompilation: no Package: xmapbridge Version: 1.52.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 MD5sum: 6575158536ffcd8dc42cb5481a397789 NeedsCompilation: no Package: XNAString Version: 1.2.2 Depends: R (>= 4.1) Imports: utils, Biostrings, BSgenome, data.table, GenomicRanges, IRanges, methods, Rcpp, stringi, S4Vectors, future.apply, stringr, formattable, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, BSgenome.Hsapiens.UCSC.hg38, pander License: GPL-2 MD5sum: b479157d68c0ad67dc6d08a60f0d330a NeedsCompilation: yes Package: XVector Version: 0.34.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 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utils Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: f6b15750450f910df2c3d3efd659e69f NeedsCompilation: no Package: yarn Version: 1.20.0 Depends: Biobase Imports: biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro Suggests: knitr, rmarkdown, testthat (>= 0.8) License: Artistic-2.0 MD5sum: ee144ef85f49d08f2c26a4e611466b25 NeedsCompilation: no Package: zellkonverter Version: 1.4.0 Imports: Matrix, basilisk, reticulate, SingleCellExperiment (>= 1.11.6), SummarizedExperiment, DelayedArray, methods, S4Vectors, utils, cli Suggests: covr, spelling, testthat, knitr, rmarkdown, BiocStyle, scRNAseq, HDF5Array, rhdf5, BiocFileCache License: MIT + file LICENSE MD5sum: fdf72d7f1606811939ba211058579537 NeedsCompilation: no Package: zFPKM Version: 1.16.0 Depends: R (>= 3.4.0) Imports: checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment Suggests: knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown License: GPL-3 | file LICENSE MD5sum: eb6d1b394afb4c5afbb4a991b3a88aac NeedsCompilation: no Package: zinbwave Version: 1.16.0 Depends: R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment Imports: BiocParallel, softImpute, stats, genefilter, edgeR, Matrix Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2 License: Artistic-2.0 MD5sum: 169db34940de5634addf1be86efb2d94 NeedsCompilation: no Package: zlibbioc Version: 1.40.0 License: Artistic-2.0 + file LICENSE MD5sum: 33b033a0149ad5f89340b20cc000847a NeedsCompilation: yes