Package: a4 Version: 1.58.0 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats, hgu95av2.db License: GPL-3 MD5sum: 9dd41feae83ffe1ce3b2fd1ddaa32448 Package: a4Base Version: 1.58.0 Depends: a4Preproc, a4Core Imports: methods, graphics, grid, Biobase, annaffy, mpm, genefilter, limma, multtest, glmnet, gplots Suggests: Cairo, ALL, hgu95av2.db, nlcv Enhances: gridSVG, JavaGD License: GPL-3 MD5sum: fb19bbf3dec5541efc4a5b34affdbffc Package: a4Classif Version: 1.58.0 Depends: a4Core, a4Preproc Imports: methods, Biobase, ROCR, pamr, glmnet, varSelRF, utils, graphics, stats Suggests: ALL, hgu95av2.db, knitr, rmarkdown License: GPL-3 MD5sum: ec96dc289f71312292bfed038ba501d9 Package: a4Core Version: 1.58.0 Imports: Biobase, glmnet, methods, stats Suggests: knitr, rmarkdown License: GPL-3 MD5sum: fa591e394ac3dc7affb340c9b6e0c593 Package: a4Preproc Version: 1.58.0 Imports: BiocGenerics, Biobase Suggests: ALL, hgu95av2.db, knitr, rmarkdown 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gridExtra, seqinr, GenomeInfoDb, nlme Suggests: testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 65de2d95d1f389ae1dc0c3ebf121674c Package: AlphaBeta Version: 1.24.0 Depends: R (>= 3.6.0) Imports: dplyr (>= 0.7), data.table (>= 1.10), stringr (>= 1.3), utils (>= 3.6.0), gtools (>= 3.8.0), optimx (>= 2018-7.10), expm (>= 0.999-4), stats (>= 3.6), BiocParallel (>= 1.18), igraph (>= 1.2.4), graphics (>= 3.6), ggplot2 (>= 3.2), grDevices (>= 3.6), plotly (>= 4.9) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 9a5516eb4bc2d6b0e245c6bd27b8ea5b Package: AlphaMissenseR Version: 1.6.0 Depends: R (>= 4.3.0), dplyr Imports: rjsoncons (>= 1.0.1), DBI, duckdb (>= 1.3.1), rlang, curl, BiocFileCache, spdl, memoise, BiocBaseUtils, utils, stats, tools, methods, whisker, ggplot2 Suggests: BiocManager, BiocGenerics, S4Vectors, Seqinfo, GenomeInfoDb, GenomicRanges, AnnotationHub, ExperimentHub, ensembldb, 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parallel, utils Suggests: mia (>= 1.6.0), DT, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, dplyr, knitr, magrittr, microbiome, phyloseq, rmarkdown, testthat, tidyr, tidyverse License: Artistic-2.0 MD5sum: 60b5851e234e5047a6b9db3da7082bda Package: ANF Version: 1.32.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 50f8dfa76b8758c5d01cca6ae9e3166e Package: anglemania Version: 1.0.0 Depends: R (>= 4.5.0) Imports: bigparallelr, bigstatsr, checkmate, digest, dplyr, Matrix, pbapply, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tidyr, withr LinkingTo: Rcpp, rmio, bigstatsr Suggests: batchelor, BiocStyle, bluster, knitr, magick, matrixStats, patchwork, RcppArmadillo, rmarkdown, scater, scran, Seurat, splatter, testthat (>= 3.0.0), UpSetR License: GPL (>= 3) MD5sum: c59c446779156e4f96c4087359565c26 Package: animalcules Version: 1.26.0 Depends: R (>= 4.3.0) Imports: ape, assertthat, caret, covr, DESeq2, dplyr, DT, forcats, ggforce, ggplot2, GUniFrac, lattice, limma, magrittr, Matrix, methods, MultiAssayExperiment, plotly, rentrez, reshape2, ROCit, S4Vectors (>= 0.23.19), scales, shiny, shinyjs, stats, SummarizedExperiment, tibble, tidyr, tsne, umap, utils, vegan, XML Suggests: BiocStyle, biomformat, devtools, glmnet, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 5c9b004787f0e76d37c828d3de1610c2 Package: annaffy Version: 1.82.0 Depends: R (>= 2.5.0), methods, Biobase, BiocManager, GO.db Imports: AnnotationDbi (>= 0.1.15), DBI Suggests: hgu95av2.db, multtest, tcltk License: LGPL MD5sum: 7cc7546566d01475a0f11c6f1b67970c Package: anndataR Version: 1.0.0 Depends: R (>= 4.5.0) Imports: cli, lifecycle, Matrix, methods, purrr, R6 (>= 2.4.0), reticulate (>= 1.41.1), rlang, stats Suggests: BiocFileCache, BiocStyle, knitr, processx, rhdf5 (>= 2.52.1), rmarkdown, S4Vectors, Seurat, SeuratObject, SingleCellExperiment, spelling, SummarizedExperiment, testthat (>= 3.0.0), vctrs, withr, yaml License: MIT + file LICENSE MD5sum: acf1512942a2a755e77c8286a6767792 Package: annmap Version: 1.52.0 Depends: R (>= 2.15.0), methods, GenomicRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice, Rsamtools, genefilter, IRanges, BiocGenerics Suggests: RUnit, rjson, Gviz License: GPL-2 MD5sum: 2b1020b890fe289dc54fd81bd5aca17d Package: annotate Version: 1.88.0 Depends: R (>= 2.10), AnnotationDbi (>= 1.27.5), XML Imports: Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), httr Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: e7b69e16e6f3183cc3d81ceb8b9619a0 Package: AnnotationDbi Version: 1.72.0 Depends: R (>= 2.7.0), methods, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges Imports: DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST Suggests: utils, 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: 96557e67bcc4aae7db6d1da9c4604eb2 Package: AnnotationFilter Version: 1.34.0 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: bf66f3c8b7374c6466e21e0358142d13 Package: AnnotationForge Version: 1.52.0 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, rmarkdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit License: Artistic-2.0 MD5sum: 11ff1d3de93bc4a7b062e37481c2d258 Package: AnnotationHub Version: 4.0.0 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 2.99.3) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr2, yaml, dplyr, BiocBaseUtils Suggests: IRanges, Seqinfo, GenomeInfoDb, GenomicRanges, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 16b4facb66f92559b543d439fdd57b0a Package: AnnotationHubData Version: 1.40.0 Depends: R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges (>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15) Imports: GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocManager, biocViews, BiocCheck, graph, AnnotationDbi, Biobase, Biostrings, DBI, Seqinfo, GenomeInfoDb (>= 1.45.5), OrganismDbi, RSQLite, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub License: Artistic-2.0 MD5sum: a4c39860c89d6c7a15e3c9afd25a6b61 Package: annotationTools Version: 1.84.0 Imports: Biobase, stats Suggests: BiocStyle License: GPL MD5sum: 58362e4ad8d477fcb5e557dea14a824f Package: annotatr Version: 1.36.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures (>= 1.61.4), GenomicRanges (>= 1.61.1), Seqinfo, ggplot2 (>= 3.5.0), IRanges, methods, readr, regioneR, reshape2, rlang, rtracklayer (>= 1.69.1), S4Vectors (>= 0.23.10), stats, utils Suggests: GenomeInfoDb, 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.Drerio.UCSC.danRer10.refGene, TxDb.Drerio.UCSC.danRer11.refGene, 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.Mmusculus.UCSC.mm39.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene License: GPL-3 MD5sum: bae64d2b66c48b40855fac1a9c5f8ff6 Package: anota Version: 1.58.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: 40b0024b1bf886eb088e0cc5848d913a Package: anota2seq Version: 1.32.0 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: afd1b3daaf72f401288aaa75338ee783 Package: antiProfiles Version: 1.50.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: 7faf4cd71b4bf415e35fcf45b5e9746f Package: AnVIL Version: 1.22.0 Depends: R (>= 4.5.0), dplyr, AnVILBase Imports: stats, utils, methods, futile.logger, GCPtools, jsonlite, httr, rapiclient, yaml, tibble, shiny, DT, miniUI, htmltools, BiocBaseUtils Suggests: knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools, AnVILAz, AnVILGCP, lifecycle License: Artistic-2.0 MD5sum: bb0a90b97062be688aba3f138a0ea39e Package: AnVILAz Version: 1.4.0 Depends: R (>= 4.5.0) Imports: AnVILBase, BiocBaseUtils, curl, httr2, jsonlite, methods, rjsoncons, tibble, utils Suggests: BiocStyle, dplyr, knitr, readr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: 9d0a8cbb3676ebfc5cfdceffcf5cdd17 Package: AnVILBase Version: 1.4.0 Depends: R (>= 4.5.0) Imports: httr, httr2, dplyr, jsonlite, methods, tibble Suggests: AnVIL, AnVILAz, AnVILGCP, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), tinytest License: Artistic-2.0 MD5sum: 3cccb69a8b85597351951f8a633a0cf5 Package: AnVILBilling Version: 1.20.0 Depends: R (>= 4.1) Imports: methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr, dplyr, lubridate, plotly, ggplot2 Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: c840808958ca3db65e4e205a1a45c878 Package: AnVILGCP Version: 1.4.0 Depends: R (>= 4.5.0) Imports: AnVILBase, BiocBaseUtils, dplyr, GCPtools (>= 0.99.4), httr, jsonlite, methods, rlang, stats, tibble, tidyr, utils Suggests: AnVIL, BiocStyle, knitr, rmarkdown, testthat, withr License: Artistic-2.0 MD5sum: 9637f03597e11a3ff2bd33e4e9e09d89 Package: AnVILPublish Version: 1.20.0 Imports: AnVIL, AnVILGCP, BiocBaseUtils, BiocManager, httr, jsonlite, rmarkdown, yaml, readr, whisker, tools, utils, stats Suggests: knitr, BiocStyle, GCPtools, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 771cdaf0cebe9f459ce65a1325f53749 Package: AnVILWorkflow Version: 1.10.0 Depends: R (>= 4.4.0), AnVILGCP, AnVILBase, httr Imports: AnVIL, dplyr, jsonlite, rlang, tibble, tidyr, utils, methods, plyr, stringr Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: 66f49a30e6ec465cbe24d8a7e4d06b87 Package: apComplex Version: 2.76.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: d17f6032aa8b2b257d364147d6298f3d Package: apeglm Version: 1.32.0 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 951ef7ceec7202ec14a44813a7066998 Package: APL Version: 1.14.0 Depends: R (>= 4.4.0) Imports: Matrix, RSpectra, ggrepel, ggplot2, viridisLite, plotly, SeuratObject, SingleCellExperiment, magrittr, SummarizedExperiment, topGO, methods, stats, utils, org.Hs.eg.db, org.Mm.eg.db, rlang Suggests: BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, sparseMatrixStats, testthat License: GPL (>= 3) MD5sum: 7f3a8e7e405e31b53d11facbec3c941a Package: appreci8R Version: 1.28.0 Imports: shiny, shinyjs, DT, VariantAnnotation, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, 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, stats, GenomicRanges, S4Vectors, GenomicFeatures, IRanges, GenomicScores, SummarizedExperiment Suggests: GO.db, org.Hs.eg.db, utils License: LGPL-3 MD5sum: 0845d013cd535e6aaa5bfe16da20bb07 Package: aroma.light Version: 3.40.0 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: 1f3a52557975e696801935122a9b1f05 Package: ArrayExpress Version: 1.70.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: oligo, limma, httr, utils, jsonlite, rlang, tools, methods Suggests: affy License: Artistic-2.0 MD5sum: 41a008e9996ceacdc52ca6b50d7ebd65 Package: arrayMvout Version: 1.68.0 Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy Imports: mdqc, affyContam, lumi Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf License: Artistic-2.0 MD5sum: a8f85524a34a54ed8cf00cbf8570154d Package: arrayQuality Version: 1.88.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL MD5sum: 3b9afa40a0bb9a7c407a25d8a01a915e Package: ARRmNormalization Version: 1.50.0 Depends: R (>= 2.15.1), ARRmData License: Artistic-2.0 MD5sum: d984fe2690be4a42b418be3735fc4dd8 Package: artMS Version: 1.28.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, bit64, circlize, cluster, corrplot, data.table, dplyr, getopt, ggdendro, ggplot2, gplots, ggrepel, graphics, grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db, pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml Suggests: BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat License: GPL (>= 3) + file LICENSE MD5sum: d8c5fa2c6f834728df2158be54109b06 Package: ASAFE Version: 1.36.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 MD5sum: cf7e35f8cbba9b0b90e1398f0a370bea Package: ASEB Version: 1.54.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) MD5sum: ee1bbdab534e3d5563a84bad8fa7b13e Package: ASGSCA Version: 1.44.0 Imports: Matrix, MASS Suggests: BiocStyle License: GPL-3 MD5sum: 196530a639eed4338ea8fe516895b3eb Package: ASICS Version: 2.26.0 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: b8889f371f39f92975797c51180aea6e Package: ASpli Version: 2.20.0 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, txdbmaker License: GPL MD5sum: 9ba6b7489f7361028a61b68336c633df Package: AssessORF Version: 1.28.0 Depends: R (>= 3.5.0), DECIPHER (>= 2.10.0) Imports: Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown, RSQLite (>= 1.1) License: GPL-3 MD5sum: 83512eaaa172bf84ccfea4a32efc2962 Package: ASSET Version: 2.28.0 Depends: R (>= 3.5.0), stats, graphics Imports: MASS, msm, rmeta Suggests: RUnit, BiocGenerics, knitr License: GPL-2 + file LICENSE MD5sum: 3e80e2c6c75c8418baa48ff8b739bd1e Package: ASSIGN Version: 1.46.0 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: f72c5a9495df40dea5828063e04bc33c Package: assorthead Version: 1.4.0 Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 556dd3968547aca6b1719af6fbce7779 Package: ASURAT Version: 1.14.0 Depends: R (>= 4.0.0) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp (>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize, grid, grDevices, graphics LinkingTo: Rcpp Suggests: ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 040dd483e7ec8c8537d9ceff3ccc17a6 Package: ATACseqQC Version: 1.34.0 Depends: R (>= 3.5.0), 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, BiocParallel Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown License: GPL (>= 2) MD5sum: d0d5a3e99b663937259018f8fdc46a2e Package: ATACseqTFEA Version: 1.12.0 Depends: R (>= 4.2) Imports: BiocGenerics, S4Vectors, IRanges, Matrix, GenomicRanges, GenomicAlignments, Seqinfo, SummarizedExperiment, Rsamtools, motifmatchr, TFBSTools, stats, pracma, ggplot2, ggrepel, dplyr, limma, methods, rtracklayer Suggests: BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle License: GPL-3 MD5sum: 429e3585af570474f9bc82df7fcf3234 Package: atena Version: 1.16.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, MatrixGenerics, BiocParallel, S4Vectors, IRanges, Seqinfo, GenomicFeatures, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats, cli Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer License: Artistic-2.0 MD5sum: c6a999380be5533fb8df8213392d07de Package: atSNP Version: 1.26.0 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: 0240614f81d485c2894d5e856c761ff4 Package: attract Version: 1.62.0 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: d9757afb5259d4e67bb5c077973f6782 Package: AUCell Version: 1.32.0 Imports: DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats, SummarizedExperiment, BiocGenerics, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: 71a5d90b280ac0bba23458e88c7eb373 Package: autonomics Version: 1.18.0 Depends: R (>= 4.0) Imports: abind, arrow, BiocFileCache, BiocGenerics, bit64, cluster, codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma, lme4, magrittr, matrixStats, methods, MultiAssayExperiment, parallel, RColorBrewer, rlang, R.utils, readxl, S4Vectors, scales, stats, stringi, SummarizedExperiment, survival, tidyr, tidyselect, tools, utils, vsn Suggests: affy, AnnotationDbi, AnnotationHub, apcluster, Biobase, BiocManager, BiocStyle, Biostrings, coin, diagram, DBI, e1071, ensembldb, GenomicDataCommons, GenomicRanges, GEOquery, ggstance, ggridges, ggtext, hgu95av2.db, ICSNP, jsonlite, knitr, lmerTest, MASS, mclust, mixOmics, mixtools, mpm, nlme, OlinkAnalyze, org.Hs.eg.db, org.Mm.eg.db, patchwork, pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite, remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer, statmod, testthat, UniProt.ws, writexl, XML License: GPL-3 MD5sum: 337011cda4a5fef9692ad0749c16ab48 Package: AWAggregator Version: 1.0.0 Depends: R (>= 4.5.0) Imports: dplyr, Peptides, progress, purrr, ranger, rlang, stats, stringr, tidyr, toOrdinal, utils Suggests: AWAggregatorData, BiocStyle, ExperimentHub, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 7110c4b821016ecfa0074961b7f1b3f6 Package: AWFisher Version: 1.24.0 Depends: R (>= 3.6) Imports: edgeR, limma, stats Suggests: knitr, tightClust License: GPL-3 MD5sum: c1a957f63ec1df2ee55e0abe16d72b82 Package: awst Version: 1.18.0 Imports: stats, methods, SummarizedExperiment Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown License: MIT + file LICENSE MD5sum: 97ebfce46f364787eb96270b4cc5aeca Package: BaalChIP Version: 1.36.0 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: a877577de4a8f23de4fce9df33fe736f Package: bacon Version: 1.38.0 Depends: R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 License: GPL (>= 2) MD5sum: 1535b98343d14b5e9c01bcca56cf9150 Package: BADER Version: 1.48.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 MD5sum: 5121fa864088b48ccc936c693be84e16 Package: BadRegionFinder Version: 1.38.0 Imports: VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 6aa8b7e5ff92aa3d58d21c276c1fa6a8 Package: BAGS Version: 2.50.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 MD5sum: f6b28059ddb352893b0822a413742a93 Package: ballgown Version: 2.42.0 Depends: R (>= 3.5.0), methods Imports: GenomicRanges (>= 1.17.25), IRanges (>= 1.99.22), S4Vectors (>= 0.9.39), RColorBrewer, splines, sva, limma, rtracklayer (>= 1.29.25), Biobase (>= 2.25.0), Seqinfo Suggests: testthat, knitr, markdown License: Artistic-2.0 MD5sum: 44402bbfcee4ef0a877815ca1ab1f463 Package: bambu Version: 3.12.0 Depends: R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>= 0.22.1), BSgenome, IRanges Imports: BiocGenerics, BiocParallel, data.table, dplyr, tidyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost LinkingTo: Rcpp, RcppArmadillo Suggests: AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq Enhances: parallel License: GPL-3 + file LICENSE MD5sum: 8a65f7b7581176735839c4c1d0cb52e2 Package: bamsignals Version: 1.42.0 Depends: R (>= 3.5.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges LinkingTo: Rcpp, Rhtslib (>= 1.13.1) Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 99f577d843e0201e118c2c863fdd323c Package: BANDITS Version: 1.26.0 Depends: R (>= 4.3.0) 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: f1c7a04718dfb5119686e623e972b198 Package: bandle Version: 1.14.0 Depends: R (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc Imports: Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr, knitr, methods, BiocParallel, robustbase, BiocStyle, ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils, grDevices, rlang, RColorBrewer, gtools, gridExtra, coda (>= 0.19-4) LinkingTo: Rcpp, RcppArmadillo, BH Suggests: testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling License: Artistic-2.0 MD5sum: 5d68150ad4d137a72271f2078aaf0289 Package: Banksy Version: 1.6.0 Depends: R (>= 4.4.0) Imports: aricode, BiocParallel, data.table, dbscan, SpatialExperiment, SingleCellExperiment, SummarizedExperiment, S4Vectors, stats, Matrix, MatrixGenerics, mclust, igraph, irlba, leidenAlg (>= 1.1.0), utils, uwot, RcppHungarian, GenomeInfoDb Suggests: knitr, rmarkdown, pals, scuttle, scater, scran, cowplot, ggplot2, testthat (>= 3.0.0), harmony, Seurat, ExperimentHub, spatialLIBD, BiocStyle License: file LICENSE MD5sum: fd6f17da183b9c7c161630ca16651130 Package: banocc Version: 1.34.0 Depends: R (>= 3.5.1), rstan (>= 2.17.4) Imports: coda (>= 0.18.1), mvtnorm, stringr Suggests: knitr, 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Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805 Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: c85400c0ebb0e02968cd409d84104b46 Package: BASiCS Version: 2.22.0 Depends: R (>= 4.1), SingleCellExperiment Imports: Biobase, BiocGenerics, coda, cowplot, ggExtra, ggplot2, graphics, grDevices, MASS, methods, Rcpp (>= 0.11.3), S4Vectors, scran, scuttle, stats, stats4, SummarizedExperiment, viridis, utils, Matrix (>= 1.5.0), matrixStats, assertthat, reshape2, BiocParallel, posterior, hexbin LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, magick License: GPL-3 MD5sum: 84f9792346fae0229aba09a8cd9a9db0 Package: BASiCStan Version: 1.12.0 Depends: R (>= 4.2), BASiCS, rstan (>= 2.18.1) Imports: methods, glmGamPoi, scran, scuttle, stats, utils, SingleCellExperiment, SummarizedExperiment, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstantools (>= 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rmarkdown, spelling, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: de6731ade7da34e869e06da5da238362 Package: BatchSVG Version: 1.2.0 Depends: R (>= 4.5.0) Imports: scry, dplyr, stats, rlang, cowplot, ggrepel, ggplot2, RColorBrewer, scales, SummarizedExperiment Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, spatialLIBD License: Artistic-2.0 MD5sum: 08ea34e37c6b61322913777a94780565 Package: BayesKnockdown Version: 1.36.0 Depends: R (>= 3.3) Imports: stats, Biobase License: GPL-3 MD5sum: cdae272357264a7c736aea6f420d4439 Package: BayesSpace Version: 1.20.0 Depends: R (>= 4.0.0), SingleCellExperiment Imports: Rcpp (>= 1.0.4.6), stats, methods, purrr, scater, scran, SummarizedExperiment, coda, rhdf5, S4Vectors, Matrix, magrittr, assertthat, arrow, mclust, RCurl, DirichletReg, xgboost (< 2.0.0), utils, dplyr, rlang, ggplot2, tibble, rjson, tidyr, scales, microbenchmark, BiocFileCache, BiocSingular, BiocParallel LinkingTo: Rcpp, RcppArmadillo, RcppDist, RcppProgress Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, viridis, patchwork, RColorBrewer, Seurat License: MIT + file LICENSE MD5sum: ec1c281e4e6e4e92dd2ff5dad76e6c33 Package: bayNorm Version: 1.28.0 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: 18291a0a3fe75dbff20a7fd34f3961e0 Package: baySeq Version: 2.44.0 Depends: R (>= 2.3.0), methods Imports: edgeR, GenomicRanges, abind, parallel, graphics, stats, utils Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: e3af72f0b938f29d6c3e8695850bd6f3 Package: BBCAnalyzer Version: 1.40.0 Imports: SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices, GenomicRanges, IRanges, Biostrings Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: e7c374cc8bfbb4800d9716a0d80268a6 Package: BCRANK Version: 1.72.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 MD5sum: eff9b9da177b39271a87a700673a023b Package: bcSeq Version: 1.32.0 Depends: R (>= 3.4.0) Imports: Rcpp (>= 0.12.12), Matrix, Biostrings LinkingTo: Rcpp, Matrix Suggests: knitr License: GPL (>= 2) MD5sum: 0d341f085dcd702267711afadfb152cc Package: beachmat Version: 2.26.0 Imports: methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics, Matrix, Rcpp LinkingTo: Rcpp, assorthead (>= 1.3.3) Suggests: testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array, beachmat.hdf5 License: GPL-3 MD5sum: 46b3d8a5f74d01f2ed48d5550a344b59 Package: beachmat.hdf5 Version: 1.8.0 Imports: methods, beachmat, HDF5Array, DelayedArray, Rcpp LinkingTo: Rcpp, assorthead, beachmat, Rhdf5lib Suggests: testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix License: GPL-3 MD5sum: f46edeabe0bb393c52f432fa23fd59d1 Package: beachmat.tiledb 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matrixStats, stats, ggplot2, methods, rtracklayer, S4Vectors, ggforce, GenomeInfoDb, ComplexHeatmap, RColorBrewer, lifecycle, rlang, forcats, dplyr, GenomicFeatures, IRanges, kableExtra, ggdist Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments, scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify, SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr, txdbmaker, ggrepel, stringr License: Artistic-2.0 MD5sum: 9f6a18f85b35fe8c92606ac849fa0819 Package: Biobase Version: 2.70.0 Depends: R (>= 2.10), BiocGenerics (>= 0.27.1), utils Imports: methods Suggests: tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr, limma License: Artistic-2.0 MD5sum: e664a4f6d0d68712c7da0c1379eefbe5 Package: biobroom Version: 1.42.0 Depends: R (>= 3.0.0), broom Imports: dplyr, tidyr, Biobase Suggests: limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, rmarkdown, SummarizedExperiment License: LGPL MD5sum: 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0.10.0) License: AGPL-3 | file LICENSE MD5sum: cb0e941b6efb945b70d97b16b45f034e Package: BioCartaImage Version: 1.8.0 Depends: R (>= 4.3.0) Imports: magick, grid, stats, grDevices, utils Suggests: testthat, knitr, BiocStyle, ragg License: MIT + file LICENSE MD5sum: 8ddbec0a8b8eed6b5dd48d8e98dd43be Package: BiocBaseUtils Version: 1.12.0 Depends: R (>= 4.2.0) Imports: methods, utils Suggests: knitr, rmarkdown, BiocStyle, tinytest License: Artistic-2.0 MD5sum: b9bb91baf0d23b1b9091cd305d2ef7ef Package: BiocBook Version: 1.8.0 Depends: R (>= 4.3) Imports: BiocGenerics, pak, cli, glue, gert, gh, gitcreds, httr, usethis, dplyr, purrr, tibble, methods, rprojroot, stringr, yaml, tools, utils, rlang, quarto, renv Suggests: BiocStyle, knitr, testthat (>= 3.0.0), rmarkdown License: MIT + file LICENSE MD5sum: 56ccd6cf8ca5722997b0cdb0b2af9636 Package: BiocCheck Version: 1.46.0 Depends: R (>= 4.4.0) Imports: BiocBaseUtils, BiocFileCache, BiocManager, biocViews, callr, cli, codetools, graph, httr2, knitr, methods, rvest, stringdist, tools, utils Suggests: BiocStyle, devtools, gert, jsonlite, rmarkdown, tinytest, usethis License: Artistic-2.0 MD5sum: 47382010725ffa053bfd95a7b85bf661 Package: BiocFHIR Version: 1.12.0 Depends: R (>= 4.2) Imports: DT, shiny, jsonlite, graph, tidyr, visNetwork, dplyr, utils, methods, BiocBaseUtils Suggests: knitr, testthat, rjsoncons, igraph, BiocStyle License: Artistic-2.0 MD5sum: 66a609319205062bf33ea0947c27d549 Package: BiocFileCache Version: 3.0.0 Depends: R (>= 3.4.0), dbplyr (>= 1.0.0) Imports: methods, stats, utils, dplyr, RSQLite, DBI, filelock, curl, httr2 Suggests: testthat, knitr, BiocStyle, rmarkdown, rtracklayer License: Artistic-2.0 MD5sum: 4000fc6fdcd5cbfc2b53532a81ee6104 Package: BiocGenerics Version: 0.56.0 Depends: R (>= 4.0.0), methods, utils, graphics, stats, generics Imports: methods, utils, graphics, stats Suggests: Biobase, S4Vectors, IRanges, S4Arrays, SparseArray, DelayedArray, HDF5Array, GenomicRanges, pwalign, Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase, annotate, MultiAssayExperiment, RUnit License: Artistic-2.0 MD5sum: 1e14e18c37308533b11794a5545caa85 Package: biocGraph Version: 1.72.0 Depends: Rgraphviz, graph Imports: Rgraphviz, geneplotter, graph, BiocGenerics, methods Suggests: fibroEset, geneplotter, hgu95av2.db License: Artistic-2.0 MD5sum: 4ccec2c24849d08e9f4f2097a1d04c40 Package: BiocHubsShiny Version: 1.10.0 Depends: R (>= 4.3.0), shiny Imports: AnnotationHub, ExperimentHub, DT, htmlwidgets, rclipboard, S4Vectors, shinyAce, shinybiocloader, shinyjs, shinythemes, utils Suggests: BiocManager, BiocStyle, curl, glue, knitr, rmarkdown, sessioninfo, shinytest2 License: Artistic-2.0 MD5sum: 7df196631d2347eb54c1b3a91643c5b5 Package: BiocIO Version: 1.20.0 Depends: R (>= 4.3.0) Imports: BiocGenerics, S4Vectors, methods, tools Suggests: testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 05ea2c3f0f12c7bcb570be5c7b2d9929 Package: biocmake Version: 1.2.0 Imports: utils, tools, dir.expiry Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE MD5sum: a7d995cd8322c42d265425679ac000b7 Package: BiocNeighbors Version: 2.4.0 Imports: Rcpp, methods LinkingTo: Rcpp, assorthead Suggests: BiocParallel, testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 617ced6257bf5f211d081856c3312a17 Package: BioCor Version: 1.34.0 Depends: R (>= 4.4) Imports: BiocParallel, GSEABase, Matrix, methods Suggests: airway, BiocStyle, boot, DESeq2, ggplot2 (>= 3.4.1), GOSemSim, Hmisc, knitr (>= 1.43), org.Hs.eg.db, reactome.db, rmarkdown, spelling, testthat (>= 3.1.5), WGCNA License: MIT + file LICENSE MD5sum: 3c3abba1113f70646707e0a02090f5cb Package: BiocParallel Version: 1.44.0 Depends: methods, R (>= 4.1.0) Imports: stats, utils, futile.logger, parallel, snow, codetools LinkingTo: BH (>= 1.87.0), cpp11 Suggests: BiocGenerics, tools, foreach, BBmisc, doParallel, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle, knitr, batchtools, data.table Enhances: Rmpi License: GPL-2 | GPL-3 | BSL-1.0 MD5sum: 619997208fa630f0109f353204870b1d Package: BiocPkgTools Version: 1.27.12 Depends: htmlwidgets, R (>= 4.1.0) Imports: BiocFileCache, BiocManager, biocViews, tibble, methods, rlang, stringr, stats, rvest, dplyr, xml2, readr, httr, httr2, htmltools, DT, tools, utils, igraph (>= 2.0.0), jsonlite, gh, RBGL, graph, curl, glue, lubridate, purrr, tidyr, yaml Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, networkD3, visNetwork, clipr, blastula, kableExtra, DiagrammeR, SummarizedExperiment License: MIT + file LICENSE MD5sum: c7e0cd7c34a3351c2c1f3214d399cac8 Package: biocroxytest Version: 1.6.0 Depends: R (>= 4.4.0) Imports: cli, glue, roxygen2, stringr Suggests: BiocStyle, here, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 0d6994c2b8e23c967198714ad85b1ed0 Package: BiocSet Version: 1.24.0 Depends: R (>= 3.6), dplyr Imports: methods, tibble, utils, rlang, plyr, S4Vectors, BiocIO, AnnotationDbi, KEGGREST, ontologyIndex, tidyr Suggests: GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache, GO.db, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: e9b8b58fbdbc747f853df2022e6c8eba Package: BiocSingular Version: 1.26.0 Imports: BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat (>= 2.25.1) LinkingTo: Rcpp, beachmat, assorthead Suggests: testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix License: GPL-3 MD5sum: 5faabeaa98ac40931a1908eba06987bf Package: BiocSklearn Version: 1.32.0 Depends: R (>= 4.0), reticulate, methods, SummarizedExperiment Imports: basilisk Suggests: testthat, HDF5Array, BiocStyle, rmarkdown, knitr License: Artistic-2.0 MD5sum: ffc9a5fdbce9765f252b260ed9f1304e Package: BiocStyle Version: 2.38.0 Imports: bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils, yaml, BiocManager 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81d2cdb69f8aedc307ecb9b2e9dd03e8 Package: biodb Version: 1.18.0 Depends: R (>= 4.1.0) Imports: R6, RSQLite, Rcpp, XML, chk, fscache (>= 1.0.2), jsonlite, lgr, lifecycle, methods, openssl, plyr, progress, rappdirs, sched (>= 1.0.1), sqlq, stats, stringr, tools, withr, yaml LinkingTo: Rcpp, testthat Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, xml2 License: AGPL-3 MD5sum: f2156d59b64be4229bf592b53788f18c Package: biodbChebi Version: 1.16.0 Depends: R (>= 4.1) Imports: R6, biodb (>= 1.3.1) Suggests: BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, lgr License: AGPL-3 MD5sum: e1c67d508992e0c0709aef20391dea58 Package: bioDist Version: 1.82.0 Depends: R (>= 2.0), methods, Biobase,KernSmooth Suggests: locfit License: Artistic-2.0 MD5sum: a189cebf6e750b4a8b34a9e8c16d1ca1 Package: BioGA Version: 1.4.0 Depends: R (>= 4.4) Imports: ggplot2, graphics, Rcpp, SummarizedExperiment, animation, rlang, biocViews, sessioninfo, BiocStyle LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: c5b572091850fbdf54c146507f6515f3 Package: biomaRt Version: 2.66.0 Depends: methods, R (>= 4.5.0) Imports: AnnotationDbi, BiocFileCache, curl, httr2, progress, stringr, utils, xml2 Suggests: BiocStyle, httptest2, knitr, mockery, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 43f82aa269fcdb93f0e07b26a997a32d Package: biomformat Version: 1.38.0 Depends: R (>= 3.2), methods Imports: plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5 Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) License: GPL-2 MD5sum: d35c1bb6a437995eda3aa45e8d1bb959 Package: BioMVCClass Version: 1.78.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz License: LGPL MD5sum: 01aa389275278c09668013f763aa2482 Package: biomvRCNS Version: 1.50.0 Depends: IRanges, GenomicRanges, Gviz Imports: methods, mvtnorm Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 0c4982fd5ed39e34841e7237c8634ff0 Package: BioNAR Version: 1.11.0 Depends: R (>= 3.5.0), igraph (>= 2.0.1.1), poweRlaw, latex2exp, RSpectra, Rdpack Imports: stringr, viridis, fgsea, grid, methods, AnnotationDbi, dplyr, GO.db, org.Hs.eg.db (>= 3.19.1), rSpectral, WGCNA, ggplot2, ggrepel, minpack.lm, cowplot, data.table, scales, stats, Matrix Suggests: knitr, BiocStyle, magick, rmarkdown, igraphdata, testthat (>= 3.0.0), vdiffr, devtools, pander, plotly, randomcoloR License: Artistic-2.0 MD5sum: 70784273ff70fe9353c68c29b563c777 Package: BioNERO Version: 1.18.0 Depends: R (>= 4.1) Imports: WGCNA, dynamicTreeCut, ggdendro, matrixStats, sva, RColorBrewer, ComplexHeatmap, ggplot2, rlang, ggrepel, patchwork, reshape2, igraph, ggnetwork, intergraph, NetRep, stats, grDevices, utils, methods, BiocParallel, minet, GENIE3, SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2, networkD3, covr License: GPL-3 MD5sum: e6f08d79c6473bf1f823d56730e0ead6 Package: BioNet Version: 1.70.0 Depends: R (>= 2.10.0), graph, RBGL Imports: igraph (>= 1.0.1), AnnotationDbi, Biobase Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML License: GPL (>= 2) MD5sum: 05fd4073631bbd0aecf8d9384a3b13eb Package: BioQC Version: 1.38.0 Depends: R (>= 3.5.0), Biobase Imports: edgeR, Rcpp, methods, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db, ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer License: GPL (>= 3) + file LICENSE MD5sum: f715b72c0ca18ce418a5952a3f0fcafc Package: Biostrings Version: 2.78.0 Depends: R (>= 4.1.0), BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.31.2), XVector (>= 0.37.1), Seqinfo Imports: methods, utils, grDevices, stats, crayon LinkingTo: S4Vectors, IRanges, XVector Suggests: graphics, pwalign, BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit, BiocStyle, knitr, testthat (>= 3.0.0), covr License: Artistic-2.0 MD5sum: 55808b995299b3e915da4692f793697d Package: BioTIP Version: 1.24.0 Depends: R (>= 3.6) Imports: igraph, cluster, psych, stringr, GenomicRanges, MASS, scran, methods, stats, utils, grDevices, graphics, foreach, doParallel Suggests: knitr, markdown, base, rmarkdown, ggplot2 License: GPL-2 MD5sum: 13e00a9cd6caea9d606cbe431e86da8e Package: biotmle Version: 1.34.0 Depends: R (>= 4.0) Imports: stats, methods, dplyr, tibble, ggplot2, ggsci, superheat, assertthat, drtmle (>= 1.0.4), S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, limma Suggests: testthat, knitr, rmarkdown, BiocStyle, arm, earth, ranger, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) License: MIT + file LICENSE MD5sum: 0f86afd0730c2c6f81933570412fcd6c Package: biovizBase Version: 1.58.0 Depends: R (>= 3.5.0), methods Imports: grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors (>= 0.23.19), IRanges (>= 1.99.28), Seqinfo, GenomeInfoDb (>= 1.45.5), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1), GenomicAlignments (>= 1.45.1), GenomicFeatures (>= 1.61.4), AnnotationDbi, VariantAnnotation (>= 1.55.1), ensembldb (>= 2.33.1), AnnotationFilter (>= 0.99.8), rlang Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit License: Artistic-2.0 MD5sum: 4691bc4a40c168a66c03e9c0eca510b4 Package: BiRewire Version: 3.41.0 Depends: igraph, slam, Rtsne, Matrix Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 9703736259bd8a41e166d49241f047ad Package: biscuiteer Version: 1.24.0 Depends: R (>= 4.1.0), biscuiteerData, bsseq Imports: readr, qualV, Matrix, impute, HDF5Array, S4Vectors, Rsamtools, data.table, Biobase, GenomicRanges, IRanges, BiocGenerics, VariantAnnotation, DelayedMatrixStats, SummarizedExperiment, GenomeInfoDb, Mus.musculus, Homo.sapiens, matrixStats, rtracklayer, QDNAseq, dmrseq, methods, utils, R.utils, gtools, BiocParallel Suggests: DSS, covr, knitr, rmarkdown, markdown, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10, BiocStyle License: GPL-3 MD5sum: 8efd420f4293d15f60fb22383b49a8bf Package: BiSeq Version: 1.50.0 Depends: R (>= 3.5.0), methods, S4Vectors, IRanges (>= 1.17.24), GenomicRanges, SummarizedExperiment (>= 0.2.0), Formula Imports: methods, BiocGenerics, Biobase, S4Vectors, IRanges, Seqinfo, GenomicRanges, SummarizedExperiment, rtracklayer, parallel, betareg, lokern, Formula, globaltest License: LGPL-3 MD5sum: 03bac9745ec9fc183e75baaca2e04afb Package: blacksheepr Version: 1.24.0 Depends: R (>= 3.6) Imports: grid, stats, grDevices, utils, circlize, viridis, RColorBrewer, ComplexHeatmap, SummarizedExperiment, pasilla Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl License: MIT + file LICENSE MD5sum: 473a3c1706100bdd53c0b529dbc46677 Package: blase Version: 1.0.0 Depends: R (>= 4.5.0) Imports: SummarizedExperiment, SingleCellExperiment, ggplot2, viridis, patchwork, Matrix, scater, methods, rlang, BiocParallel, boot, dplyr, mgcv, stats, MatrixGenerics, Seurat (>= 4.0.0) Suggests: knitr, rmarkdown, testthat (>= 3.2.3), covr, tradeSeq, scran, slingshot, tools, ami, reshape2, plyr, fs, sparseMatrixStats, ggVennDiagram, uwot, BiocStyle, DelayedMatrixStats, limma License: GPL (>= 3) MD5sum: bc2ad6c2c9d7139013a4f79f98e6c9a8 Package: BLMA Version: 1.34.0 Depends: ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel, Biobase, metafor, methods Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 188b331ce72d074fd1e4cd77ccd5b6da Package: BloodGen3Module Version: 1.18.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, ExperimentHub, methods, grid, graphics, stats, grDevices, circlize, testthat, ComplexHeatmap(>= 1.99.8), ggplot2, matrixStats, gtools, reshape2, preprocessCore, randomcoloR, V8, limma Suggests: RUnit, devtools, BiocGenerics, knitr, rmarkdown License: GPL-2 MD5sum: feac4604ea83c9c77c0c043ddc1effef Package: bluster Version: 1.20.0 Imports: stats, methods, utils, cluster, Matrix, Rcpp, igraph, S4Vectors, BiocParallel, BiocNeighbors LinkingTo: Rcpp, assorthead Suggests: knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut, scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans, kohonen, apcluster, DirichletMultinomial, vegan, fastcluster License: GPL-3 MD5sum: 0c27bfae9189a2e781792ec659693f9b Package: bnbc Version: 1.32.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, GenomicRanges Imports: Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, Seqinfo, S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage, utils, HiCBricks LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, RUnit, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 6506c9835a746af0a924b13455f45036 Package: bnem Version: 1.18.0 Depends: R (>= 4.1) Imports: CellNOptR, matrixStats, snowfall, Rgraphviz, cluster, flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods, utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown Suggests: knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit License: GPL-3 MD5sum: f823358214ed5c0a9f82f2286ffafd9c Package: BOBaFIT Version: 1.14.0 Depends: R (>= 2.10) Imports: dplyr, NbClust, ggplot2, ggbio, grDevices, stats, tidyr, GenomicRanges, ggforce, stringr, plyranges, methods, utils, magrittr Suggests: rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0), utils, testthat License: GPL (>= 3) MD5sum: 8ac2d3578a82b9de6443119d6176da23 Package: borealis Version: 1.14.0 Depends: R (>= 4.2.0), Biobase Imports: doParallel, snow, purrr, plyr, foreach, gamlss, gamlss.dist, bsseq, methods, DSS, R.utils, utils, stats, ggplot2, cowplot, dplyr, rlang, GenomicRanges Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, annotatr, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL-3 MD5sum: 8d9cee7be90c32dbca19b135cd0bde2d Package: BRAIN Version: 1.56.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 MD5sum: 85e42bc6b954f267592b35c78704a05f Package: breakpointR Version: 1.28.0 Depends: R (>= 3.5), GenomicRanges, cowplot, breakpointRdata Imports: methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>= 1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2, BiocGenerics, gtools, doParallel, foreach Suggests: knitr, BiocStyle, testthat License: file LICENSE MD5sum: 01191b54c23aac1606683b56995728ef Package: BreastSubtypeR Version: 1.2.0 Depends: R (>= 4.5.0) Imports: methods, Biobase, tidyselect, dplyr, ggplot2, magrittr, rlang, stringr, withr, edgeR, ComplexHeatmap, impute (>= 1.80.0), data.table (>= 1.16.0), RColorBrewer (>= 1.1-3), circlize (>= 0.4.16), ggrepel (>= 0.9.6), e1071 (>= 1.7-8), SummarizedExperiment, utils Suggests: lifecycle, tidyverse, shiny (>= 1.9.1), bslib (>= 0.8.0), BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: ccb0e347f30edeb7db3d74e890d2fba2 Package: brendaDb Version: 1.24.0 Imports: dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel, crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, devtools License: MIT + file LICENSE MD5sum: e7e1d87382dd9eac576f0ff4bfa1cb5c Package: BREW3R.r Version: 1.6.0 Imports: GenomicRanges, methods, rlang, S4Vectors, utils Suggests: testthat (>= 3.0.0), IRanges, knitr, rmarkdown, BiocStyle, rtracklayer License: GPL-3 MD5sum: 9325e53cbef6ec5f01912c3c114d67dc Package: BridgeDbR Version: 2.20.0 Depends: R (>= 3.3.0), rJava Imports: curl Suggests: BiocStyle, knitr, rmarkdown, testthat License: AGPL-3 MD5sum: f82edd76642ba050155af5cd2239f5a0 Package: BrowserViz Version: 2.32.0 Depends: R (>= 3.5.0), jsonlite (>= 1.5), httpuv(>= 1.5.0) Imports: methods, BiocGenerics Suggests: RUnit, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: c530adfc8d48a807e1ae5628c5830cb1 Package: BSgenome Version: 1.78.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.47.6), IRanges (>= 2.13.16), Seqinfo, GenomicRanges (>= 1.61.1), Biostrings (>= 2.77.2), BiocIO, rtracklayer (>= 1.69.1) Imports: utils, stats, matrixStats, XVector, Rsamtools (>= 2.25.1) Suggests: BiocManager, GenomeInfoDb, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit, BSgenomeForge License: Artistic-2.0 MD5sum: 757dfdc835b9d4d04622863d47bdcbda Package: BSgenomeForge Version: 1.10.0 Depends: R (>= 4.3.0), methods, BiocGenerics, IRanges, Seqinfo, GenomeInfoDb (>= 1.45.5), Biostrings (>= 2.77.2), BSgenome (>= 1.77.1) Imports: utils, stats, Biobase, S4Vectors (>= 0.47.6), GenomicRanges (>= 1.61.1), BiocIO, rtracklayer (>= 1.69.1) Suggests: GenomicFeatures, Rsamtools, testthat, knitr, rmarkdown, BiocStyle, devtools, BSgenome.Celegans.UCSC.ce2 License: Artistic-2.0 MD5sum: 0def4025e259097b16a36b0e185baff3 Package: bsseq Version: 1.46.0 Depends: R (>= 4.0), methods, BiocGenerics, GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5) Imports: IRanges (>= 2.23.9), Seqinfo, scales, stats, parallel, tools, 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, beachmat (>= 2.23.2) LinkingTo: Rcpp, beachmat, assorthead (>= 1.1.4) Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, batchtools License: Artistic-2.0 MD5sum: a2f74aeaab684ee3fe49bc00ee9812ae Package: BufferedMatrix Version: 1.74.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) MD5sum: b50ea72cad20a4d9bc4cd5a6d66813c9 Package: BufferedMatrixMethods Version: 1.74.0 Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods LinkingTo: BufferedMatrix Suggests: affyio, affy License: GPL (>= 2) MD5sum: 3b7e11e2c5e449088014a3192765f0d5 Package: bugsigdbr Version: 1.16.0 Depends: R (>= 4.1) Imports: BiocFileCache, methods, vroom, utils Suggests: BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 8fdb2e5e5617052b03b09b271f97f4ad Package: BulkSignalR Version: 1.2.0 Depends: R (>= 4.5) Imports: BiocFileCache, httr2, RCurl, cli, curl, rlang, jsonlite, matrixStats, methods, doParallel, glmnet, ggalluvial, ggplot2, gridExtra, grid, Rtsne, ggrepel, foreach, multtest, igraph, orthogene, stabledist, circlize (>= 0.4.14), ComplexHeatmap (>= 2.0.0), stats, scales, RANN, SpatialExperiment, SummarizedExperiment, tools Suggests: knitr, markdown, rmarkdown, STexampleData, testthat (>= 3.0.0), codetools, Matrix, lattice, cluster, survival, MASS, nlme License: CeCILL | file LICENSE MD5sum: c0d0c82c268106ff6eec7985e7c11563 Package: BUMHMM Version: 1.34.0 Depends: R (>= 3.5.0) Imports: devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges Suggests: testthat, knitr, BiocStyle License: GPL-3 MD5sum: 123137c3c0ba2824a2a1aac076028b21 Package: bumphunter Version: 1.52.0 Depends: R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), Seqinfo, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats Suggests: testthat, RUnit, doParallel, GenomeInfoDb, txdbmaker, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 284bdfe8c262cabdf53b10e94b784ced Package: BumpyMatrix Version: 1.18.0 Imports: utils, methods, Matrix, S4Vectors, IRanges Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: bb99ad79d89a0876021c5ee9b811562d Package: BUS Version: 1.66.0 Depends: R (>= 2.3.0), minet Imports: stats, infotheo License: GPL-3 MD5sum: d9123437358ae8face2a920fb5d57165 Package: BUScorrect Version: 1.28.0 Depends: R (>= 3.5.0) Imports: gplots, methods, grDevices, stats, SummarizedExperiment Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: f2854d56f1a76284a699e9695ffef0fb Package: BUSpaRse Version: 1.24.0 Depends: R (>= 3.6) Imports: AnnotationDbi, AnnotationFilter, AnnotationHub, biomaRt, BiocGenerics, Biostrings, BSgenome, dplyr, ensembldb, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, IRanges, lifecycle, magrittr, Matrix, methods, plyranges, Rcpp, S4Vectors, stats, stringr, tibble, tidyr, utils, zeallot LinkingTo: Rcpp, RcppArmadillo, RcppProgress, BH Suggests: knitr, rmarkdown, testthat, BiocStyle, txdbmaker, TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: BSD_2_clause + file LICENSE MD5sum: 2daeea44b8edd2ed7091d1202cfff9df Package: BUSseq Version: 1.16.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots, grDevices, methods, stats, utils Suggests: BiocStyle, knitr, BiocGenerics License: Artistic-2.0 MD5sum: f97755066ca34ada7dae09e9a2ade230 Package: CaDrA Version: 1.8.0 Depends: R (>= 4.4.0) Imports: doParallel, ggplot2, gplots, graphics, grid, gtable, knnmi, MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats, SummarizedExperiment Suggests: BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat (>= 3.1.6) License: GPL-3 + file LICENSE MD5sum: eebcc88326c8b74496cf516eb55db7b8 Package: CAEN Version: 1.18.0 Depends: R (>= 4.1) Imports: stats,PoiClaClu,SummarizedExperiment,methods Suggests: knitr,rmarkdown,BiocManager,SummarizedExperiment,BiocStyle License: GPL-2 MD5sum: f25ea064a1046ec11e87a250e34ee2e5 Package: CAFE Version: 1.46.0 Depends: R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio Imports: affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: dc621561bef08ecf8b931181af65a651 Package: CAGEfightR Version: 1.30.0 Depends: R (>= 3.5), GenomicRanges (>= 1.61.1), rtracklayer (>= 1.69.1), SummarizedExperiment (>= 1.39.1) Imports: pryr(>= 0.1.3), assertthat(>= 0.2.0), methods(>= 3.6.3), Matrix(>= 1.2-12), BiocGenerics(>= 0.24.0), S4Vectors(>= 0.16.0), IRanges(>= 2.12.0), Seqinfo, GenomicFeatures(>= 1.61.4), GenomicAlignments(>= 1.45.1), BiocParallel(>= 1.12.0), GenomicFiles(>= 1.14.0), Gviz(>= 1.22.2), InteractionSet(>= 1.9.4), GenomicInteractions(>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-3 + file LICENSE MD5sum: 1dc2688577c398f1a0d5c058995ed7b8 Package: cageminer Version: 1.16.0 Depends: R (>= 4.1) Imports: ggplot2, rlang, ggbio, ggtext, GenomeInfoDb, GenomicRanges, IRanges, reshape2, methods, BioNERO Suggests: testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo License: GPL-3 MD5sum: 17c2913b945103614f777ce8e8c26dc3 Package: CAGEr Version: 2.16.0 Depends: methods, MultiAssayExperiment, R (>= 4.1.0) Imports: BiocGenerics, BiocParallel, Biostrings, BSgenome, CAGEfightR, data.table, formula.tools, Seqinfo, GenomicAlignments (>= 1.45.1), GenomicFeatures (>= 1.61.4), GenomicRanges (>= 1.61.1), ggplot2 (>= 4.0.0), gtools, IRanges (>= 2.18.0), KernSmooth, Matrix, memoise, plyr, rlang, Rsamtools (>= 2.25.1), reshape2, rtracklayer (>= 1.69.1), S4Vectors (>= 0.27.5), scales, som, stringdist, stringi, SummarizedExperiment (>= 1.39.1), utils, vegan, VGAM Suggests: BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, DESeq2, FANTOM3and4CAGE, ggseqlogo, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 9f788acb6d40ae0975ea347335744905 Package: CalibraCurve Version: 1.0.0 Depends: R (>= 4.5.0) Imports: checkmate, dplyr, ggplot2, magrittr, openxlsx, scales, SummarizedExperiment, tidyr Suggests: BiocStyle, knitr, msqc1, RefManageR, rmarkdown, sessioninfo, testthat, vdiffr License: BSD 3-clause License + file LICENSE MD5sum: 69ff1191600d3d8dcdca59975b94c67c Package: calm Version: 1.24.0 Imports: mgcv, stats, graphics Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 96c5ff02da9f58f0ec6ae9adf1a9a09e Package: CaMutQC Version: 1.6.0 Depends: R (>= 4.5.0) Imports: ggplot2, dplyr, org.Hs.eg.db, vcfR, clusterProfiler, stringr, DT, MesKit, maftools, data.table, utils, stats, methods, tidyr Suggests: knitr, rmarkdown, BiocStyle, shiny License: GPL-3 MD5sum: 36a27a24e33dbf5db579e2aac96c64f1 Package: canceR Version: 1.44.0 Depends: R (>= 4.3), tcltk, cBioPortalData Imports: GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart, survival, Biobase, phenoTest, circlize, plyr, tidyr, dplyr, graphics, stats, utils, grDevices, R.oo, R.methodsS3 Suggests: testthat (>= 3.1), knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 546025bf042264b26410a52430da1816 Package: cancerclass Version: 1.54.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 MD5sum: 4104d95365dcfdcf246258a6938f9888 Package: cardelino Version: 1.12.0 Depends: R (>= 4.2), stats Imports: combinat, GenomeInfoDb, GenomicRanges, ggplot2, ggtree, Matrix, matrixStats, methods, pheatmap, snpStats, S4Vectors, utils, VariantAnnotation, vcfR Suggests: BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat, VGAM Enhances: doMC License: GPL-3 MD5sum: 78862748c93cb40ed034eda540588cdf Package: Cardinal Version: 3.12.0 Depends: R (>= 4.4), BiocParallel, BiocGenerics, ProtGenerics, S4Vectors, methods, stats, stats4 Imports: CardinalIO, Biobase, EBImage, graphics, grDevices, irlba, Matrix, matter (>= 2.7.10), nlme, parallel, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, emmeans, lme4, lmerTest License: Artistic-2.0 | file LICENSE MD5sum: 758d3923e1e9d63073774de1c88ce267 Package: CardinalIO Version: 1.8.0 Depends: R (>= 4.4), BiocParallel, matter, ontologyIndex Imports: methods, S4Vectors, stats, utils, tools Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: ebcd34b46c262abaed24fa8282410f46 Package: CARDspa Version: 1.2.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 1.0.7),RcppArmadillo, SummarizedExperiment, methods, MCMCpack, fields, wrMisc, concaveman, sp, dplyr, sf, Matrix, RANN, ggplot2, reshape2, RColorBrewer, S4Vectors, scatterpie, grDevices,ggcorrplot, stats, nnls, BiocParallel, RcppML, NMF, spatstat.random, gtools, SingleCellExperiment, SpatialExperiment LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 + file LICENSE MD5sum: 9b2c7b4283499e5c7e120d7d1afd6543 Package: CARNIVAL Version: 2.20.0 Depends: R (>= 4.0) Imports: readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson, rmarkdown Suggests: RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0), sessioninfo License: GPL-3 MD5sum: 3cd9d7e99ca489d539d79a546d477846 Package: CATALYST Version: 1.34.0 Depends: R (>= 4.5), SingleCellExperiment Imports: circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot, data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel, ggridges, graphics, grDevices, grid, gridExtra, 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: fccde2c639770bef4b798e56eb6ec4de Package: Category Version: 2.76.0 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: efa8fae73a7d25b89b7504c197f5942e Package: categoryCompare Version: 1.54.0 Depends: R (>= 2.10), Biobase, BiocGenerics (>= 0.13.8), Imports: AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1), GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29), methods, grDevices, utils Suggests: knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown License: GPL-2 MD5sum: f70386029e233c571547412773f82207 Package: CatsCradle Version: 1.3.3 Depends: R (>= 4.4.0) Imports: Seurat (>= 5.0.1), ggplot2, networkD3, stringr, pracma, reshape2, rdist, igraph, geometry, Rfast, data.table, abind, pheatmap, EBImage, S4Vectors, SeuratObject, SingleCellExperiment, SpatialExperiment, Matrix, methods, SummarizedExperiment, msigdbr Suggests: fossil, interp, knitr, BiocStyle, tictoc License: MIT + file LICENSE MD5sum: 44f54365ec329925a72710c585390984 Package: CausalR Version: 1.42.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: b89bca0abb17fd56c0384162d23d824c Package: cbaf Version: 1.32.0 Depends: R (>= 4.1) Imports: BiocFileCache, RColorBrewer, cBioPortalData, genefilter, gplots, grDevices, stats, utils, openxlsx, zip Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: d9790a006f6338fc9e756b37cee44f13 Package: cBioPortalData Version: 2.21.5 Depends: R (>= 4.5.0), AnVIL (>= 1.19.5), MultiAssayExperiment Imports: BiocBaseUtils, BiocFileCache (>= 1.5.3), digest, dplyr, Seqinfo, GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment, RTCGAToolbox (>= 2.19.7), S4Vectors, SummarizedExperiment, stats, tibble, tidyr, TCGAutils (>= 1.9.4), utils Suggests: BiocStyle, jsonlite, knitr, survival, survminer, rmarkdown, testthat License: AGPL-3 MD5sum: efdbb419ca2ae1da7ad053a26dbcd46e Package: CBN2Path Version: 1.0.0 Depends: R (>= 4.1.0) Imports: R6, ggraph, tidygraph, ggplot2, patchwork, cowplot, magrittr, igraph, rlang, grDevices, coda, graphics, stats, TCGAbiolinks, BiocParallel Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE OS_type: unix MD5sum: 78448e1deb7c280fde2165c6fc7d406f Package: CBNplot Version: 1.10.0 Depends: R (>= 4.3.0) Imports: ggplot2, magrittr, graphite, ggraph, igraph, bnlearn (>= 4.7), patchwork, org.Hs.eg.db, clusterProfiler, utils, enrichplot, reshape2, ggforce, dplyr, tidyr, stringr, depmap, ExperimentHub, Rmpfr, graphlayouts, BiocFileCache, ggdist, purrr, pvclust, stats, rlang Suggests: knitr, arules, concaveman, ReactomePA, bnviewer, rmarkdown, withr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: de37c114f93d79f427c1b7dacd61bbc9 Package: cbpManager Version: 1.18.0 Depends: shiny, shinydashboard Imports: utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite, rapportools, basilisk, reticulate, shinyBS, shinycssloaders, rintrojs, rlang, markdown Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 9e5fc4d9095ca88c9db5632a1a2d3e31 Package: CCAFE Version: 1.2.0 Depends: R (>= 4.4.0) Imports: dplyr, VariantAnnotation Suggests: testthat (>= 3.0.0), rmarkdown, markdown, knitr, tidyverse, DescTools, cowplot, BiocStyle, GenomicRanges, SummarizedExperiment, S4Vectors, IRanges License: GPL-3 MD5sum: 94ef597a35cfe00ea5d3aac346c6d6b6 Package: ccImpute Version: 1.12.0 Imports: Rcpp, sparseMatrixStats, stats, BiocParallel, irlba, SingleCellExperiment, Matrix, SummarizedExperiment LinkingTo: Rcpp, RcppEigen Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, mclust, testthat (>= 3.0.0), splatter License: GPL-3 MD5sum: c47cd3854afe9a5ff2fdd5d9bc4b15ba Package: CCPlotR Version: 1.8.0 Imports: plyr, tidyr, dplyr, ggplot2, forcats, ggraph, igraph, scatterpie, circlize, ComplexHeatmap, tibble, grid, ggbump, stringr, ggtext, ggh4x, patchwork, RColorBrewer, scales, viridis, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: bd79e2f6ef4ccc39a524783eeead5205 Package: CCPROMISE Version: 1.36.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: 0d7c7bfc080c419bb29a3d4999c89fda Package: ccrepe Version: 1.46.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat, RUnit License: MIT + file LICENSE MD5sum: 46d0f7e9c1e491b8bc810727fc6fbecd Package: CDI Version: 1.8.0 Depends: R(>= 3.6) Imports: matrixStats, Seurat, SeuratObject, stats, BiocParallel, ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment, SummarizedExperiment, methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle License: GPL-3 + file LICENSE MD5sum: d40f90d0efde39cf576127706d1cbc9d Package: celaref Version: 1.28.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang, BiocGenerics, S4Vectors, readr, tibble, DelayedArray Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat License: GPL-3 MD5sum: 470b3849426a2d3c83dee5e1efda4689 Package: celda Version: 1.26.0 Depends: R (>= 4.0), SingleCellExperiment, Matrix Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, reshape2, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, scater (>= 1.14.4), scran, dbscan, DelayedArray, stringr, ComplexHeatmap, gridExtra, circlize, dendextend, ggdendro, pROC LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData License: MIT + file LICENSE MD5sum: 0406900da613a68256763f021836d2ff Package: CellBarcode Version: 1.16.0 Depends: R (>= 4.1.0) Imports: methods, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr, ggplot2, stringr, magrittr, ShortRead (>= 1.48.0), Biostrings (>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors, seqinr, Rsamtools LinkingTo: Rcpp, BH Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: Artistic-2.0 MD5sum: 38e8105dfd05c062c4cc204aaca7f57d Package: cellbaseR Version: 1.34.0 Depends: R(>= 3.4) Imports: methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils, Rsamtools, BiocParallel, foreach, utils, parallel, doParallel Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation License: Apache License (== 2.0) MD5sum: ee7f708d468e751d98b711fcce51275b Package: CellBench Version: 1.26.0 Depends: R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils Imports: assertthat, BiocGenerics, BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, tidyselect, lubridate Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 License: GPL-3 MD5sum: c162d920f3db6011e0cf4cee9324403c Package: CelliD Version: 1.18.0 Depends: R (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment Imports: Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater, stringr, irlba, data.table, glue, pbapply, umap, Rtsne, reticulate, fastmatch, matrixStats, ggplot2, BiocParallel, SummarizedExperiment, fgsea LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel License: GPL-3 + file LICENSE MD5sum: e1ac6a6fa834be0fdf54f7c0ad11f96a Package: cellity Version: 1.38.0 Depends: R (>= 3.3) Imports: AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid, mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats, topGO, utils Suggests: BiocStyle, caret, knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: f40a51fc0c93f96a59ccd25c44c023bf Package: CellMapper Version: 1.36.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 MD5sum: 02d6accc8dcdb39ba6a2dcd5ec48229b Package: cellmig Version: 1.0.0 Depends: R (>= 4.5.0) Imports: base, ggplot2, ggforce, ggtree, patchwork, ape, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, utils, scales LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, testthat License: GPL-3 + file LICENSE MD5sum: d22c6a441cc6be679fc0abd8ec54950f Package: cellmigRation Version: 1.18.0 Depends: R (>= 4.1), methods, foreach Imports: tiff, graphics, stats, utils, reshape2, parallel, doParallel, grDevices, matrixStats, FME, SpatialTools, sp, vioplot, FactoMineR, Hmisc Suggests: knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl License: GPL-2 MD5sum: 345c62d38abbd8aa644c3ff511aa3b66 Package: CellMixS Version: 1.26.0 Depends: kSamples, R (>= 4.0) Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne License: GPL (>= 2) MD5sum: a7663ff165691dbd8502143fb2a4a3ea Package: CellNOptR Version: 1.56.0 Depends: R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML, ggplot2, rmarkdown Imports: igraph, stringi, stringr Suggests: data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics, Enhances: doParallel, foreach License: GPL-3 MD5sum: 5741c38a10ec78fc5a0f61a0c375e7c3 Package: cellscape Version: 1.34.0 Depends: R (>= 3.3) Imports: dplyr (>= 0.4.3), gtools (>= 3.5.0), htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 94ad680f76cb8ba088aca500f141b3ba Package: CellTrails Version: 1.28.0 Depends: R (>= 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gtable, fastcluster Suggests: testthat, BiocManager License: GPL-3 MD5sum: 8f10ea42cb7136a561dec81cef91ba79 Package: censcyt Version: 1.18.0 Depends: R (>= 4.0), diffcyt Imports: BiocParallel, broom.mixed, dirmult, dplyr, edgeR, fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp, purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment, survival, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 License: MIT + file LICENSE MD5sum: eb8869523a4ac208371f6309bc6095c2 Package: Cepo Version: 1.16.0 Depends: GSEABase, R (>= 4.1) Imports: DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors, methods, SingleCellExperiment, SummarizedExperiment, ggplot2, rlang, grDevices, patchwork, reshape2, BiocParallel, stats, dplyr, purrr Suggests: knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap License: MIT + file LICENSE MD5sum: b90e13127b0db67c936a4d2a6ddd061a Package: ceRNAnetsim Version: 1.22.0 Depends: R (>= 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prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b4.hg19, limma, DNAcopy, preprocessCore,impute, marray, wateRmelon, plyr,goseq,missMethyl,ggplot2, GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly (>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat Suggests: knitr,rmarkdown License: GPL-3 MD5sum: 76e50f13f83cd5092c8469aebaeea5a1 Package: ChemmineR Version: 3.62.0 Depends: R (>= 2.10.0), methods Imports: rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp (>= 0.11.0), ggplot2,grid,gridExtra, png,base64enc,DT,rsvg,jsonlite,stringi LinkingTo: Rcpp, BH Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png,rmarkdown, BiocManager,bibtex,codetools Enhances: ChemmineOB License: Artistic-2.0 MD5sum: 1b6f0540c32793c2473847b90305f429 Package: CHETAH Version: 1.26.0 Depends: R (>= 4.2), ggplot2, SingleCellExperiment Imports: shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr License: file LICENSE MD5sum: c4b6d4c2f4500b5db0cf53a4da33c847 Package: chevreulPlot Version: 1.2.0 Depends: R (>= 4.5.0), SingleCellExperiment, chevreulProcess Imports: base, cluster, clustree, ComplexHeatmap (>= 2.5.4), circlize, dplyr, EnsDb.Hsapiens.v86, forcats, fs, ggplot2, grid, plotly, purrr, S4Vectors, scales, scater, scran, scuttle, stats, stringr, tibble, tidyr, utils, wiggleplotr (>= 1.13.1), tidyselect, patchwork Suggests: BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 2db6b5ef117a1cf283c72d2368413c13 Package: chevreulProcess Version: 1.2.0 Depends: R (>= 4.5.0), SingleCellExperiment, scater Imports: batchelor, bluster, circlize, cluster, DBI, dplyr, EnsDb.Hsapiens.v86, ensembldb, fs, GenomicFeatures, glue, megadepth, methods, purrr, RSQLite, S4Vectors, scran, scuttle, stringr, tibble, tidyr, tidyselect, utils Suggests: BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: b9cf970db9e2cb2a844c0523ba1b5560 Package: Chicago Version: 1.38.0 Depends: R (>= 3.3.1), data.table Imports: matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, GenomeInfoDb, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub License: Artistic-2.0 MD5sum: a942b0a5d392f3d0d3dde290fe0919f0 Package: chihaya Version: 1.10.0 Depends: DelayedArray Imports: methods, Matrix, rhdf5, Rcpp, HDF5Array LinkingTo: Rcpp, Rhdf5lib Suggests: BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix, BiocStyle, testthat, rmarkdown, knitr License: GPL-3 MD5sum: 5038c4ecfb30735509e836b0b125c24e Package: chimeraviz Version: 1.36.0 Depends: Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, AnnotationFilter, data.table Imports: methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, checkmate, gtools, magick Suggests: testthat, roxygen2, devtools, knitr, lintr License: Artistic-2.0 MD5sum: b536c6d20ac9bc27f1dc8386c4637204 Package: ChIPanalyser Version: 1.32.0 Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb,RColorBrewer Suggests: BSgenome.Dmelanogaster.UCSC.dm6,knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: f29da706b12ba4805bac73f9dce4743a Package: ChIPComp Version: 1.40.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,rtracklayer,Seqinfo,S4Vectors Imports: Rsamtools,limma,BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,BiocGenerics Suggests: BiocStyle,RUnit License: GPL MD5sum: 46c95f788600217bb461bcb67fbfea8e Package: chipenrich Version: 2.34.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, chipenrich.data, Seqinfo, GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra, MASS, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer, S4Vectors (>= 0.23.10), stats, stringr, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat License: GPL-3 MD5sum: 7267fc325c9ff97ac9599e72d44adda4 Package: ChIPexoQual Version: 1.34.0 Depends: R (>= 3.5.0), GenomicAlignments (>= 1.45.1) Imports: methods, utils, Seqinfo, stats, BiocParallel, GenomicRanges (>= 1.61.1), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools (>= 2.25.1), IRanges (>= 1.6), S4Vectors (>= 0.8), biovizBase (>= 1.18), broom (>= 0.4), RColorBrewer (>= 1.1), dplyr (>= 0.5), scales (>= 0.4.0), viridis (>= 0.3), hexbin (>= 1.27), rmarkdown Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat License: GPL (>= 2) MD5sum: 907f8fac6dd757318263f6aed6de1d34 Package: ChIPpeakAnno Version: 3.44.0 Depends: R (>= 3.5), methods, IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), S4Vectors (>= 0.17.25) Imports: AnnotationDbi, BiocGenerics (>= 0.1.0), Biostrings (>= 2.47.6), pwalign, DBI, dplyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics, grid, InteractionSet, KEGGREST, matrixStats, multtest, regioneR, rtracklayer, stats, utils, universalmotif, stringr, tibble, tidyr, data.table, scales, ensembldb Suggests: AnnotationHub, BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, reshape2, testthat, trackViewer, motifStack, OrganismDbi, BiocFileCache License: GPL (>= 2) MD5sum: 562adc1a237126e5f498592c88ad7b72 Package: ChIPseeker Version: 1.45.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, aplot, BiocGenerics, boot, dplyr, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, graphics, grDevices, gtools, magrittr, methods, plotrix, parallel, RColorBrewer, rlang, rtracklayer, S4Vectors, scales, stats, tibble, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, yulab.utils (>= 0.1.5) Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, knitr, org.Hs.eg.db, prettydoc, ReactomePA, rmarkdown, testthat License: Artistic-2.0 MD5sum: 9fada587e3017374e23cac36d9d6232e Package: chipseq Version: 1.60.0 Depends: R (>= 3.5.0), 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, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr License: Artistic-2.0 MD5sum: 4a901551dc4d4e9eb627623be20b8eae Package: ChIPseqR Version: 1.64.0 Depends: R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25) Imports: Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14), graphics, grDevices, HilbertVis, ShortRead, stats, timsac, utils License: GPL (>= 2) MD5sum: 5fb816904f2a91989c9d7659979644ec Package: ChIPsim Version: 1.64.0 Depends: Biostrings (>= 2.29.2) Imports: IRanges, XVector, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) MD5sum: d5b5973dd7d2e439b71f9cd6ee18c987 Package: ChIPXpress Version: 1.54.0 Depends: R (>= 2.10), ChIPXpressData Imports: Biobase, GEOquery, frma, affy, bigmemory, biganalytics Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 8ad0773f292fe0006746ad99d17ebba0 Package: Chromatograms Version: 1.0.0 Depends: BiocParallel, ProtGenerics (>= 1.39.2), R (>= 4.5.0) Imports: methods, S4Vectors, MsCoreUtils (>= 1.7.5), Spectra Suggests: msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), testthat, knitr (>= 1.1.0), rmarkdown, mzR (>= 2.41.4), MsBackendMetaboLights (>= 1.3.1), vdiffr, RColorBrewer License: Artistic-2.0 MD5sum: e0f3f80bcdf3868594e3c554941bd14e Package: chromDraw Version: 2.40.0 Depends: R (>= 3.0.0) Imports: Rcpp (>= 0.11.1), GenomicRanges (>= 1.17.46) LinkingTo: Rcpp License: GPL-3 MD5sum: a698ce1bfcfbc15c3912c82de3d0f584 Package: ChromHeatMap Version: 1.64.0 Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0) Imports: Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer, GenomicRanges Suggests: ALL, hgu95av2.db License: Artistic-2.0 MD5sum: 883b935c0c27acb937dacd262d35a02d Package: chromPlot Version: 1.38.0 Depends: stats, utils, graphics, grDevices, datasets, base, biomaRt, GenomicRanges, R (>= 3.1.0) Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 1d02f2850fcb0abcfa898223a4942b06 Package: ChromSCape Version: 1.20.0 Depends: R (>= 4.1) Imports: shiny, colourpicker, shinyjs, rtracklayer, shinyFiles, shinyhelper, shinyWidgets, shinydashboardPlus, shinycssloaders, Matrix, plotly, shinydashboard, colorRamps, kableExtra, viridis, batchelor, BiocParallel, parallel, Rsamtools, ggplot2, ggrepel, gggenes, gridExtra, qualV, stringdist, stringr, fs, qs, DT, scran, scater, ConsensusClusterPlus, Rtsne, dplyr, tidyr, GenomicRanges, IRanges, irlba, rlist, umap, tibble, methods, jsonlite, edgeR, stats, graphics, grDevices, utils, S4Vectors, SingleCellExperiment, SummarizedExperiment, msigdbr, forcats, Rcpp, coop, matrixTests, DelayedArray LinkingTo: Rcpp Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr License: GPL-3 MD5sum: 90b9d9991e5ed746d861085d5f60efad Package: chromVAR Version: 1.32.0 Depends: R (>= 3.5.0) Imports: IRanges, Seqinfo, GenomicRanges, ggplot2, nabor, BiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools, S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats, utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment, RColorBrewer, BSgenome LinkingTo: Rcpp, RcppArmadillo Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr License: MIT + file LICENSE MD5sum: 576010f3735be7c613c6c0bf630f0b3a Package: cicero Version: 1.28.0 Depends: R (>= 3.5.0), monocle, Gviz (>= 1.22.3) Imports: assertthat (>= 0.2.0), Biobase (>= 2.37.2), BiocGenerics (>= 0.23.0), data.table (>= 1.10.4), dplyr (>= 0.7.4), FNN (>= 1.1), GenomicRanges (>= 1.30.3), ggplot2 (>= 2.2.1), glasso (>= 1.8), grDevices, igraph (>= 1.1.0), IRanges (>= 2.10.5), Matrix (>= 1.2-12), methods, parallel, plyr (>= 1.8.4), reshape2 (>= 1.4.3), S4Vectors (>= 0.14.7), stats, stringi, stringr (>= 1.2.0), tibble (>= 1.4.2), tidyr, VGAM (>= 1.0-5), utils Suggests: AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr License: MIT + file LICENSE MD5sum: 254830989be345d2c86e456b335bd32b Package: cigarillo Version: 1.0.0 Depends: methods, BiocGenerics, S4Vectors (>= 0.47.2), IRanges, Biostrings Imports: stats LinkingTo: S4Vectors, IRanges Suggests: Rsamtools, GenomicAlignments, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: d222c539062350b40250016ba4554788 Package: CIMICE Version: 1.18.0 Imports: dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork, ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat, tidygraph, expm, Matrix Suggests: BiocStyle, knitr, rmarkdown, testthat, webshot License: Artistic-2.0 MD5sum: 69cdf5abc916ddb5b6fc079566f783e8 Package: CINdex Version: 1.38.0 Depends: R (>= 3.3), GenomicRanges Imports: bitops,gplots,grDevices,som, dplyr,gridExtra,png,stringr,S4Vectors, IRanges, Seqinfo,graphics, stats, utils Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens, R.utils License: GPL (>= 2) MD5sum: 6de9495dd05bbfbd25155898f08a7f9d Package: circRNAprofiler Version: 1.24.0 Depends: R(>= 4.5.0) Imports: dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2, edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb, universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, Biostrings, gwascat, BSgenome, Suggests: testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager, License: GPL-3 MD5sum: 151789b758c36289a1867e83a824d5ec Package: CircSeqAlignTk Version: 1.12.0 Depends: R (>= 4.2) Imports: stats, tools, utils, R.utils, methods, S4Vectors, rlang, magrittr, dplyr, tidyr, ggplot2, BiocGenerics, Biostrings, IRanges, ShortRead, Rsamtools, Rbowtie2, Rhisat2, shiny, shinyFiles, shinyjs, plotly, parallel, htmltools Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 0eddb826c571bb979daaa9467a3164b2 Package: CiteFuse Version: 1.22.0 Depends: R (>= 4.0) Imports: SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>= 1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid, dbscan, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph, scales, scran (>= 1.14.6), graphics, methods, stats, utils, reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5, rlang, Rcpp, compositions LinkingTo: Rcpp Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown License: GPL-3 MD5sum: eb26132f73d6c113097c95868e75ee33 Package: ClassifyR Version: 3.14.0 Depends: R (>= 4.1.0), generics, methods, S4Vectors, MultiAssayExperiment, BiocParallel, survival Imports: grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2 (>= 3.5.0), ggpubr, reshape2, ggupset, broom, dcanr Suggests: limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, robustbase, glmnet, class, randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale, TOP, BiocNeighbors License: GPL-3 MD5sum: 35417bc62a62c5d22124a0c997fc7983 Package: cleanUpdTSeq Version: 1.48.0 Depends: R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods Imports: BSgenome, GenomicRanges, seqinr, e1071, Biostrings, Seqinfo, IRanges, utils, stringr, stats, S4Vectors Suggests: BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0) License: GPL-2 MD5sum: 1ef163d6b1f3fb09085f7478abe8eadb Package: CleanUpRNAseq Version: 1.4.0 Depends: R (>= 4.4.0) Imports: AnnotationFilter, BiocGenerics, Biostrings, BSgenome, DESeq2, edgeR, ensembldb, Seqinfo, GenomicRanges, ggplot2, ggrepel, graphics, grDevices, KernSmooth, limma, methods, pheatmap, qsmooth, R6, RColorBrewer, Rsamtools, Rsubread, reshape2, SummarizedExperiment, stats, tximport, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86, ggplotify, knitr, patchwork, R.utils, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: b42c4dae19216cacee565342f0ff7f73 Package: cleaver Version: 1.48.0 Depends: R (>= 3.0.0), methods, Biostrings (>= 1.29.8) Imports: S4Vectors, IRanges Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.36.5) License: GPL (>= 3) MD5sum: 588ebc9a9859a2f37a250f7c616b1f2b Package: clevRvis Version: 1.10.0 Imports: shiny, ggraph, igraph, ggiraph, cowplot, htmlwidgets, readxl, dplyr, readr, purrr, tibble, patchwork, R.utils, shinyWidgets, colorspace, shinyhelper, shinycssloaders, ggnewscale, shinydashboard, DT, colourpicker, grDevices, methods, utils, stats, ggplot2, magrittr, tools Suggests: knitr, rmarkdown, BiocStyle License: LGPL-3 MD5sum: 5c6e31f83f1288d6cb7ba7170d869e88 Package: clippda Version: 1.60.0 Depends: R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d, graphics, grDevices, stats, utils, Biobase, tools, methods License: GPL (>= 2) MD5sum: d08b0836e89bd1f5810af88796679254 Package: clipper Version: 1.50.0 Depends: R (>= 2.15.0), Matrix, graph Imports: methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph, KEGGgraph, corpcor Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle Enhances: RCy3 License: AGPL-3 MD5sum: 9e9a9812975f1a78d20d16f77bff9aa6 Package: cliProfiler Version: 1.16.0 Depends: S4Vectors, methods, R (>= 4.1) Imports: dplyr, rtracklayer, GenomicRanges, ggplot2, BSgenome, Biostrings, utils Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: 64f0146b366b3f301936c1831f0cfda4 Package: cliqueMS Version: 1.24.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, coop, slam, matrixStats, methods LinkingTo: Rcpp, BH, RcppArmadillo Suggests: BiocParallel, knitr, rmarkdown, testthat, CAMERA License: GPL (>= 2) MD5sum: 141fc98b2f38b539730ce92ebf71f8e8 Package: Clomial Version: 1.46.0 Depends: R (>= 2.10), matrixStats Imports: methods, permute License: GPL (>= 2) MD5sum: 83384d1c238834324283fcb239af701b Package: clst Version: 1.58.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 MD5sum: 36a43f0d93642202f9dced263b61a209 Package: clstutils Version: 1.58.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit License: GPL-3 MD5sum: 03cd88b9a0cf94ecd8e3f97cdbbac9db Package: ClustAll Version: 1.6.0 Depends: R (>= 4.2.0) Imports: FactoMineR, bigstatsr, clValid, doSNOW, parallel, foreach, dplyr, fpc, mice, modeest, flock, networkD3, methods, ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices, ggplot2, grid, stats, utils, pbapply Suggests: RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2 License: GPL-2 MD5sum: fccdeb5fe514606db0e48e0d8af693fa Package: clustComp Version: 1.38.0 Depends: R (>= 3.3) Imports: sm, stats, graphics, grDevices Suggests: Biobase, colonCA, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 4bcf3854cd92958272a142d72c606b16 Package: clusterExperiment Version: 2.30.0 Depends: R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>= 1.15.4), BiocGenerics Imports: methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, locfdr, matrixStats, graphics, parallel, BiocSingular, kernlab, stringr, S4Vectors, grDevices, DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma, mbkmeans LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown License: Artistic-2.0 MD5sum: d77d0cd1b1f8b99660086c0c5de53935 Package: ClusterFoldSimilarity Version: 1.6.0 Imports: methods, igraph, ggplot2, scales, BiocParallel, graphics, stats, utils, Matrix, cowplot, dplyr, reshape2, Seurat, SeuratObject, SingleCellExperiment, ggdendro Suggests: knitr, rmarkdown, kableExtra, scRNAseq, BiocStyle License: Artistic-2.0 MD5sum: 8e5cd940beb06d0931f3cc6ccb02d0bc Package: ClusterJudge Version: 1.32.0 Depends: R (>= 3.6), stats, utils, graphics, infotheo, lattice, latticeExtra, httr, jsonlite Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt License: Artistic-2.0 MD5sum: 3bef5c0c6f607b66efcac4eb1dd389c8 Package: clusterProfiler Version: 4.18.0 Depends: R (>= 4.2.0) Imports: AnnotationDbi, DOSE (>= 3.23.2), dplyr, enrichplot (>= 1.9.3), GO.db, GOSemSim (>= 2.27.2), gson (>= 0.0.7), httr, igraph, magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils (>= 0.1.6) Suggests: AnnotationHub, knitr, jsonlite, readr, rmarkdown, org.Hs.eg.db, prettydoc, BiocManager, testthat License: Artistic-2.0 MD5sum: 563fa2ba452a23859da78ce23984cb0a Package: clusterSeq Version: 1.34.0 Depends: R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats, utils Imports: BiocGenerics Suggests: BiocStyle License: GPL-3 MD5sum: 094ebac62a1d5264b6852d4780c9e0ae Package: ClusterSignificance Version: 1.38.0 Depends: R (>= 3.3.0) Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr License: GPL-3 MD5sum: 4ed24b72bb37bda92eb53333ebfd310e Package: clusterStab Version: 1.82.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 MD5sum: db09d016c7496cd105f314409d018086 Package: clustifyr Version: 1.22.0 Depends: R (>= 2.10) Imports: cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, SeuratObject, matrixStats, S4Vectors, proxy, httr, utils Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr, data.table, R.utils License: MIT + file LICENSE MD5sum: b48617580115cb25c246e55cad16982a Package: ClustIRR Version: 1.8.0 Depends: R (>= 4.3.0) Imports: blaster, future, future.apply, grDevices, igraph, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils, posterior, visNetwork, dplyr, tidyr, ggplot2, ggforce, scales LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork License: GPL-3 + file LICENSE MD5sum: babcf7a7ad80d0bc8cf639f139bdf32c Package: clustSIGNAL Version: 1.2.0 Depends: R (>= 4.4.0), SpatialExperiment Imports: BiocParallel, BiocNeighbors, bluster (>= 1.16.0), scater, harmony, SingleCellExperiment, SummarizedExperiment, methods, Matrix, reshape2 Suggests: knitr, BiocStyle, testthat (>= 3.0.0), aricode, ggplot2, patchwork, dplyr, scattermore License: GPL-2 MD5sum: 76c7a6a64c8682fe49ed3fe33eb2c126 Package: CMA Version: 1.68.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm License: GPL (>= 2) MD5sum: b3e2147e3bb7f134466ca784f4166631 Package: cmapR Version: 1.22.0 Depends: R (>= 4.0) Imports: methods, rhdf5, data.table, flowCore, SummarizedExperiment, matrixStats Suggests: knitr, testthat, BiocStyle, rmarkdown License: file LICENSE MD5sum: 787890111bc2709c67643dd48bd18d13 Package: cn.farms Version: 1.58.0 Depends: R (>= 3.0), Biobase, methods, ff, oligoClasses, snow Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice License: LGPL (>= 2.0) MD5sum: c88cc8b845d2638625260665fd2922ae Package: cn.mops Version: 1.56.0 Depends: R (>= 3.5.0), methods, utils, stats, graphics, parallel, GenomicRanges Imports: BiocGenerics, Biobase, IRanges, Rsamtools, Seqinfo, S4Vectors Suggests: DNAcopy License: LGPL (>= 2.0) MD5sum: 6b2fddc2945d47a26f8a434ca295cf1f Package: CNAnorm Version: 1.56.0 Depends: R (>= 2.10.1), methods Imports: DNAcopy License: GPL-2 MD5sum: 718ce64ee22815ab028109f5043e7ab7 Package: CNORdt Version: 1.52.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 MD5sum: c75b33628d18ba09c4a472ce8e2e76fa Package: CNORfeeder Version: 1.50.0 Depends: R (>= 4.0.0), graph Imports: CellNOptR (>= 1.4.0) Suggests: minet, Rgraphviz, RUnit, BiocGenerics, igraph Enhances: MEIGOR License: GPL-3 MD5sum: 18237b6a2fdc769146fd7b26fcc0b7c5 Package: CNORfuzzy Version: 1.52.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 MD5sum: d93dd5ece11b81953911892fa7512c24 Package: CNORode Version: 1.52.0 Depends: CellNOptR, genalg Suggests: knitr, rmarkdown Enhances: doParallel, foreach License: GPL-2 MD5sum: e19891c46bf1aff4041d27bda7668bf2 Package: CNTools Version: 1.66.0 Depends: R (>= 2.10), methods, tools, stats, genefilter License: LGPL MD5sum: bd0c5639a7e79c9bce3c5cbbe23ab484 Package: CNVfilteR Version: 1.24.0 Depends: R (>= 4.3) Imports: IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods Suggests: knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown License: Artistic-2.0 MD5sum: 31a23f27241cb8ca58683b4de588de3e Package: cnvGSA Version: 1.54.0 Depends: brglm, doParallel, foreach, GenomicRanges, methods, splitstackshape Suggests: cnvGSAdata, org.Hs.eg.db License: LGPL MD5sum: b961a7471b8e88abe6b1ffd559fdb97f Package: CNViz Version: 1.18.0 Depends: R (>= 4.0), shiny (>= 1.5.0) Imports: dplyr, stats, utils, grDevices, plotly, karyoploteR, CopyNumberPlots, GenomicRanges, magrittr, DT, scales, graphics Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: e01dc9e80285546aeccb26c0694ede61 Package: CNVMetrics Version: 1.14.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, S4Vectors, BiocParallel, methods, magrittr, stats, pheatmap, gridExtra, grDevices, rBeta2009 Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 62305ccb94d014a31cd2c850e9b86c50 Package: CNVPanelizer Version: 1.42.0 Depends: R (>= 3.2.0), GenomicRanges Imports: BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx Suggests: knitr, RUnit License: GPL-3 MD5sum: aaadee183a8185f1ce794b410b4bedea Package: CNVRanger Version: 1.26.0 Depends: GenomicRanges, RaggedExperiment Imports: BiocGenerics, BiocParallel, GDSArray, GenomeInfoDb, IRanges, S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR, gdsfmt, grDevices, lattice, limma, methods, plyr, qqman, rappdirs, reshape2, stats, utils Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, curatedTCGAData, ensembldb, grid, knitr, org.Hs.eg.db, regioneR, rmarkdown, statmod License: Artistic-2.0 MD5sum: f9be5d797b849095bb8110be2d9de6c8 Package: CNVrd2 Version: 1.48.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 MD5sum: b616ab31b68a1afc5c347d4d17913ca5 Package: CoCiteStats Version: 1.82.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL MD5sum: 91f1fbc0cab525cc4c1be0fb8c434f1c Package: COCOA Version: 2.24.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices, simpleCache, fitdistrplus Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: e20cea7fee1f3807cb9f7d5896978d6c Package: codelink Version: 1.78.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 MD5sum: eea535d75216b1ceeb7cd084ddc4c588 Package: CODEX Version: 1.42.0 Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors Suggests: WES.1KG.WUGSC License: GPL-2 MD5sum: 59a61ebb8a76c861002672dd1c73105f Package: CoGAPS Version: 3.30.0 Depends: R (>= 3.5.0) Imports: BiocParallel, cluster, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5, dplyr, fgsea, forcats, ggplot2 LinkingTo: Rcpp, BH, testthat Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject, BiocFileCache, xml2 License: BSD_3_clause + file LICENSE MD5sum: a8c15468ca1f419f41902bf5ee128f96 Package: cogena Version: 1.44.0 Depends: R (>= 3.6), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools Suggests: knitr, rmarkdown (>= 2.1) License: LGPL-3 MD5sum: e4b76fdd1e73e3aa574a1fb5bbd4ac8a Package: cogeqc Version: 1.14.0 Depends: R (>= 4.2.0) Imports: utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr License: GPL-3 MD5sum: 3d0aa4cfb88a3f80883cb22b6117e56f Package: Cogito Version: 1.16.0 Depends: R (>= 4.1), GenomicRanges, jsonlite, GenomicFeatures, entropy Imports: BiocManager, rmarkdown, Seqinfo, S4Vectors, AnnotationDbi, graphics, stats, utils, methods, magrittr, ggplot2, TxDb.Mmusculus.UCSC.mm9.knownGene Suggests: BiocStyle, knitr, markdown, testthat (>= 3.0.0) License: LGPL-3 MD5sum: b550f0e8943462550c979394106d4708 Package: coGPS Version: 1.54.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 MD5sum: df8215dec46d1427af457d768fbb831f Package: cola Version: 2.16.0 Depends: R (>= 4.0.0) Imports: grDevices, graphics, grid, stats, utils, ComplexHeatmap (>= 2.5.4), matrixStats (>= 1.2.0), GetoptLong, circlize (>= 0.4.7), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer, cluster, skmeans, png, mclust, crayon, methods, xml2, microbenchmark, httr, knitr (>= 1.4.0), markdown (>= 1.6), digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr, foreach, doParallel, doRNG, irlba LinkingTo: Rcpp Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 License: MIT + file LICENSE MD5sum: 10fdf3dd6ecefca45a87883e0e815132 Package: combi Version: 1.22.0 Depends: R (>= 4.0), DBI Imports: ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix (>= 1.6.0), BB, reshape2, alabama, cobs, Biobase, vegan, grDevices, graphics, methods, SummarizedExperiment Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 6f2e6dbdf722599dd22d6d8c21557977 Package: coMethDMR Version: 1.14.0 Depends: R (>= 4.1) Imports: AnnotationHub, BiocParallel, bumphunter, ExperimentHub, GenomicRanges, IRanges, lmerTest, methods, stats, utils Suggests: BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: GPL-3 MD5sum: 5677354ecf1a1d8a15d54409cce62298 Package: COMPASS Version: 1.48.0 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach, coda LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress License: Artistic-2.0 MD5sum: b4eeae2e6e6eb20183263e42c7f5a8ed Package: compcodeR Version: 1.46.0 Depends: R (>= 4.0), sm Imports: knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods, stats, utils, ape, phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny, shinydashboard Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk Enhances: rpanel, DSS License: GPL (>= 2) MD5sum: a6a7a4250fd1c0301c3327e67fa0319e Package: compEpiTools Version: 1.44.0 Depends: R (>= 3.5.0), methods, topGO, GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, Seqinfo Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer License: GPL MD5sum: 0ece61ca5298ec6d5f4947fe2f1f229a Package: ComplexHeatmap Version: 2.26.0 Depends: R (>= 4.0.0), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.14), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges, matrixStats, foreach, doParallel, codetools Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo, magick License: MIT + file LICENSE MD5sum: 1b5b93abc720e1a27d4f0a7164d01174 Package: CompoundDb Version: 1.14.0 Depends: R (>= 4.1), methods, AnnotationFilter, S4Vectors Imports: BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges, Spectra (>= 1.15.10), MsCoreUtils, MetaboCoreUtils, BiocParallel, stringi Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf License: Artistic-2.0 MD5sum: 8cd53d5c432f12c9ad88d7b02fd6ff66 Package: ComPrAn Version: 1.18.0 Imports: data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr, rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio, scales, shinydashboard, shinyjs, stats, tibble, grid Suggests: testthat (>= 2.1.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: e9f81fb4a0bd344c51478187c6591bcf Package: compSPOT Version: 1.8.0 Depends: R (>= 4.3.0) Imports: stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra, utils, data.table Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: f0cf0cddcc42a85429a299325e21ca24 Package: concordexR Version: 1.10.0 Depends: R (>= 4.5.0) Imports: BiocGenerics, BiocNeighbors, BiocParallel, bluster, cli, DelayedArray, Matrix, methods, purrr, rlang, SingleCellExperiment, sparseMatrixStats, SpatialExperiment, SummarizedExperiment Suggests: BiocManager, BiocStyle, ggplot2, glue, knitr, mbkmeans, patchwork, rmarkdown, scater, SFEData, SpatialFeatureExperiment, TENxPBMCData, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 6d4f8f36511d8a5b51a43d93c80515c8 Package: condiments Version: 1.18.0 Depends: R (>= 4.0) Imports: slingshot (>= 1.9), mgcv, RANN, stats, SingleCellExperiment, SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume (>= 0.9.1), methods, pbapply, matrixStats, BiocParallel, TrajectoryUtils, igraph, distinct Suggests: knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN, DelayedMatrixStats License: MIT + file LICENSE MD5sum: 676c5a0c6d006775603d86ef3ddb00da Package: CONFESS Version: 1.38.0 Depends: R (>= 3.3),grDevices,utils,stats,graphics Imports: methods,changepoint,cluster,contrast,data.table(>= 1.9.7),ecp,EBImage,flexmix,flowCore,flowClust,flowMeans,flowMerge,flowPeaks,foreach,ggplot2,grid,limma,MASS,moments,outliers,parallel,plotrix,raster,readbitmap,reshape2,SamSPECTRAL,waveslim,wavethresh,zoo Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata License: GPL-2 MD5sum: 629269b02a76a78346792fd9fc7a49fc Package: consensus Version: 1.28.0 Depends: R (>= 3.5), RColorBrewer Imports: matrixStats, gplots, grDevices, methods, graphics, stats, utils Suggests: knitr, RUnit, rmarkdown, BiocGenerics License: BSD_3_clause + file LICENSE MD5sum: dcc4a9c148404255f86c18abad108693 Package: ConsensusClusterPlus Version: 1.74.0 Imports: Biobase, ALL, graphics, stats, utils, cluster License: GPL-2 MD5sum: 467159a4a8037abe8fa223380682f3a9 Package: consensusDE Version: 1.28.0 Depends: R (>= 3.5), BiocGenerics Imports: airway, AnnotationDbi, BiocParallel, Biobase, Biostrings, data.table, dendextend, DESeq2 (>= 1.20.0), EDASeq, ensembldb, edgeR, EnsDb.Hsapiens.v86, GenomicAlignments, GenomicFeatures, limma, org.Hs.eg.db, pcaMethods, RColorBrewer, Rsamtools, RUVSeq, S4Vectors, stats, SummarizedExperiment, TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 60df6af7bd3b51fc30bbc224bdf068bb Package: consensusOV Version: 1.32.0 Depends: R (>= 3.6) Imports: Biobase, GSVA (>= 1.50.0), gdata, genefu, limma, matrixStats, randomForest, stats, utils, methods, BiocParallel Suggests: BiocStyle, ggplot2, knitr, rmarkdown, magick License: Artistic-2.0 MD5sum: 97b8294dd0e00a0e5ec285267475819a Package: consensusSeekeR Version: 1.38.0 Depends: R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, BiocParallel Imports: Seqinfo, rtracklayer, stringr, S4Vectors, methods Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 3fb871b99b828d8ecd848f5c2c9e0660 Package: consICA Version: 2.8.0 Depends: R (>= 4.2.0) Imports: fastICA (>= 1.2.1), sm, org.Hs.eg.db, GO.db, stats, SummarizedExperiment, BiocParallel, graph, ggplot2, methods, Rfast, pheatmap, survival, topGO, graphics, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat, Seurat License: MIT + file LICENSE MD5sum: c5f5894b9c2ed9d51826a25ab6bb678a Package: CONSTANd Version: 1.18.0 Depends: R (>= 4.1) Suggests: BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma License: file LICENSE MD5sum: 90790e351b6b2ed6fa0e19c5de480d57 Package: conumee Version: 1.44.0 Depends: R (>= 3.5.0), minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest Imports: methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges, Seqinfo Suggests: BiocStyle, knitr, rmarkdown, minfiData, RCurl License: GPL (>= 2) MD5sum: 05d20816099bc18e2fd6d94a5ff24b44 Package: convert Version: 1.86.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL MD5sum: 174acde17ec79693d003e7334fec0c41 Package: copa 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SingleR, MouseGastrulationData, testthat (>= 3.0.0), BiocStyle, scrapper License: GPL-3 MD5sum: 1b5cd423e4935b8e30566a7cecd094e8 Package: coRdon Version: 1.28.0 Depends: R (>= 3.5) Imports: methods, stats, utils, Biostrings, Biobase, dplyr, stringr, purrr, ggplot2, data.table Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: b2b0200513e7f2b2598d5b81e1804f27 Package: CoreGx Version: 2.14.0 Depends: R (>= 4.1), BiocGenerics, SummarizedExperiment Imports: Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics, piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods, stats, utils, graphics, grDevices, lsa, data.table, crayon, glue, rlang, bench Suggests: pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat License: GPL (>= 3) MD5sum: 4a5beca190ebd95f23058b1eab098b74 Package: Cormotif Version: 1.56.0 Depends: R (>= 2.12.0), affy, limma Imports: affy, graphics, grDevices License: GPL-2 MD5sum: e78757f7a84acf8c6d2910e46cee6f86 Package: corral Version: 1.20.0 Imports: ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix, methods, MultiAssayExperiment, pals, reshape2, SingleCellExperiment, SummarizedExperiment, transport Suggests: ade4, BiocStyle, CellBench, DuoClustering2018, knitr, rmarkdown, scater, testthat License: GPL-2 MD5sum: b8d557e9056929a9582587fa7cc2eae9 Package: coseq Version: 1.34.0 Depends: R (>= 4.0.0), SummarizedExperiment, S4Vectors Imports: edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2, scales, HTSFilter, corrplot, HTSCluster, grDevices, graphics, stats, methods, compositions, mvtnorm Suggests: Biobase, knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 201ba8cc9d31ebfd66b96dd1e72b18a2 Package: CoSIA Version: 1.10.0 Depends: R (>= 4.3.0), methods (>= 4.3.0), ExperimentHub (>= 2.7.0) Imports: dplyr (>= 1.0.7), magrittr (>= 2.0.1), RColorBrewer (>= 1.1-2), tidyr (>= 1.2.0), plotly (>= 4.10.0), stringr (>= 1.4.0), ggplot2 (>= 3.3.5), tibble (>= 3.1.7), org.Hs.eg.db (>= 3.12.0), org.Mm.eg.db (>= 3.12.0), org.Dr.eg.db (>= 3.12.0), org.Ce.eg.db (>= 3.12.0), org.Dm.eg.db (>= 3.12.0), org.Rn.eg.db (>= 3.12.0), AnnotationDbi (>= 1.52.0), biomaRt (>= 2.46.3), homologene (>= 1.4.68.19), annotationTools (>= 1.64.0), readr (>= 2.1.1), tidyselect (>= 1.1.2), stats (>= 4.1.2) Suggests: BiocStyle (>= 2.22.0), tidyverse (>= 1.3.1), knitr (>= 1.42), rmarkdown (>= 2.20), testthat (>= 3.1.6), qpdf (>= 1.3.0) License: MIT + file LICENSE MD5sum: cb92fffe3a958bf099a8279537a308e2 Package: cosmiq Version: 1.44.0 Depends: R (>= 3.6), Rcpp Imports: pracma, xcms, MassSpecWavelet, faahKO Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: c854cb1b5409ee246439531138de1458 Package: cosmosR Version: 1.18.0 Depends: R (>= 4.1) Imports: CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr, rlang, stringr, utils, visNetwork, decoupleR Suggests: testthat, knitr, rmarkdown, piano, ggplot2 License: GPL-3 MD5sum: 861be71868d619f4ed36f3f0743166f4 Package: COSNet Version: 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randtests, stats, utils, methods, ragg Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 3bdc5e1ba7b254f149f57d133789b413 Package: covEB Version: 1.36.0 Depends: R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats, LaplacesDemon, Matrix Suggests: curatedBladderData License: GPL-3 MD5sum: 295b83eed13ac5fc7b750c139c80b679 Package: CoverageView Version: 1.48.0 Depends: R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer Imports: S4Vectors (>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges, GenomicAlignments, parallel, tools License: Artistic-2.0 MD5sum: 64ee96c5795ac128fc563b04f16a64af Package: covRNA Version: 1.36.0 Depends: ade4, Biobase Imports: parallel, genefilter, grDevices, stats, graphics Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: ad73316bd6db70ec4037a4f57f4e9dd1 Package: CPSM Version: 1.2.0 Depends: R (>= 3.5.0) Imports: SummarizedExperiment, grDevices, reshape2 , survival , survminer , ggplot2 , MTLR , glmnet , rms , preprocessCore , Matrix , stats, Hmisc, ggfortify, randomForestSRC, caret, SurvMetrics, MASS, Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: GPL-3 | file LICENSE MD5sum: f997b375c35dbba54f3ac2eaa305a02c Package: cpvSNP Version: 1.42.0 Depends: R (>= 3.5.0), GenomicFeatures, GSEABase (>= 1.24.0) Imports: methods, corpcor, BiocParallel, ggplot2, plyr Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: c3dae2c99331b97fb6052e2f966d4f3c Package: cqn Version: 1.56.0 Depends: R (>= 2.10.0), mclust Imports: splines, graphics, nor1mix, stats, quantreg Suggests: scales, edgeR License: Artistic-2.0 MD5sum: 4c5d49b2e5dd7afac21fca17f1340f29 Package: CRImage Version: 1.58.0 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach, sgeostat License: Artistic-2.0 MD5sum: 1366ae3f617af65b24df7baed3e58b10 Package: crisprBase Version: 1.14.0 Depends: utils, methods, R (>= 4.1) Imports: BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges, S4Vectors, stringr Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: d2a134eafa0d8ac74be0bffa5b519b43 Package: crisprBowtie Version: 1.14.0 Depends: methods Imports: BiocGenerics, Biostrings, BSgenome, crisprBase (>= 0.99.15), Seqinfo, GenomicRanges, IRanges, Rbowtie, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 63e1b95e08c767094b4bb88fb0fb655b Package: crisprBwa Version: 1.14.0 Depends: methods Imports: BiocGenerics, BSgenome, crisprBase (>= 0.99.15), Seqinfo, Rbwa, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE OS_type: unix MD5sum: a51079bb3557d4b3efaebe336ffbd929 Package: crisprDesign Version: 1.12.0 Depends: R (>= 4.2.0), crisprBase (>= 1.1.3) Imports: AnnotationDbi, BiocGenerics, Biostrings (>= 2.77.2), BSgenome (>= 1.77.1), crisprBowtie (>= 0.99.8), crisprScore (>= 1.1.6), GenomeInfoDb (>= 1.45.7), GenomicFeatures (>= 1.61.4), GenomicRanges (>= 1.61.1), IRanges, Matrix, MatrixGenerics, methods, rtracklayer (>= 1.69.1), S4Vectors, Seqinfo, stats, txdbmaker (>= 1.5.6), utils, VariantAnnotation (>= 1.55.1) Suggests: biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat License: MIT + file LICENSE MD5sum: 86e9a2a5180b7f6637b44d525892bab3 Package: crisprScore Version: 1.14.0 Depends: R (>= 4.1), crisprScoreData (>= 1.1.3) Imports: basilisk (>= 1.9.2), BiocGenerics, Biostrings, IRanges, methods, randomForest, reticulate, stringr, utils, XVector Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: a0b9ed01ae61d9c852f52755c78e5c45 Package: CRISPRseek Version: 1.50.0 Depends: R (>= 3.5.0), BiocGenerics, Biostrings, GenomicFeatures Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges, BSgenome, hash, methods,reticulate,rhdf5,XVector, DelayedArray, Seqinfo, GenomicRanges, dplyr, keras, mltools, gtools, openxlsx, rio, rlang, stringr Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice, MASS, tensorflow, BSgenome.Hsapiens.UCSC.hg38, BiocFileCache, TxDb.Hsapiens.UCSC.hg38.knownGene, testthat, knitr License: file LICENSE MD5sum: aaf2636fc4a66597341ce8b100769fab Package: crisprShiny Version: 1.6.0 Depends: R (>= 4.4.0), shiny Imports: BiocGenerics, Biostrings, BSgenome, crisprBase, crisprDesign, crisprScore, crisprViz, DT, Seqinfo, htmlwidgets, methods, pwalign, S4Vectors, shinyBS, shinyjs, utils, waiter Suggests: BiocStyle, knitr, rmarkdown, shinyFeedback, testthat (>= 3.0.0), BSgenome.Hsapiens.UCSC.hg38 License: MIT + file LICENSE MD5sum: c710779721419916c5a4d435b88a680f Package: CrispRVariants Version: 1.38.0 Depends: R (>= 4.3.0), ggplot2 (>= 2.2.0) Imports: AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>= 0.9.38), utils Suggests: BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl, rtracklayer, sangerseqR, testthat, VariantAnnotation License: GPL-2 MD5sum: b69cf80f57196bc0331c55f37488fc93 Package: crisprVerse Version: 1.12.0 Depends: R (>= 4.2.0) Imports: BiocManager, cli, crisprBase, crisprBowtie, crisprScore, crisprScoreData, crisprDesign, crisprViz, rlang, tools, utils Suggests: BiocStyle, knitr, testthat License: MIT + file LICENSE MD5sum: 3577a89d170257c511381a50fa67d586 Package: crisprViz Version: 1.12.0 Depends: R (>= 4.2.0), crisprBase (>= 0.99.15), crisprDesign (>= 0.99.77) Imports: BiocGenerics, Biostrings, BSgenome, Seqinfo, GenomicFeatures, GenomicRanges, grDevices, Gviz, IRanges, methods, S4Vectors, txdbmaker Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, rtracklayer, testthat, utils License: MIT + file LICENSE MD5sum: 9de6e9c51cf3151dc17b4f0067a7970c Package: crlmm Version: 1.68.0 Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= 1.17.7) Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>= 1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats, VGAM, parallel, graphics, limma, beanplot LinkingTo: preprocessCore (>= 1.17.7) Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit License: Artistic-2.0 MD5sum: 6998154a4083d7fce831498577679152 Package: crumblr Version: 1.2.0 Depends: R (>= 4.4.0), ggplot2, methods Imports: Rdpack, viridis, tidytree, variancePartition (>= 1.36.3), SingleCellExperiment, ggtree, dplyr, stats, MASS, Rfast Suggests: BiocStyle, RUnit, knitr, rmarkdown, dreamlet, muscat, ExperimentHub, scater, HMP, reshape2, glue, tidyverse, BiocGenerics, compositions License: Artistic-2.0 MD5sum: ee82e54d010948284c22fe92c5f1b8ac Package: crupR Version: 1.2.0 Depends: R (>= 4.4.0) Imports: bamsignals, Rsamtools, GenomicRanges, preprocessCore, randomForest, rtracklayer, Seqinfo, S4Vectors, ggplot2, matrixStats, dplyr, IRanges, GenomicAlignments, GenomicFeatures, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, reshape2, magrittr, stats, utils, grDevices, SummarizedExperiment, BiocParallel, fs, methods Suggests: GenomeInfoDb, testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: ae97078bd1cfc0aa7ac25fedabfb1440 Package: CSAR Version: 1.62.0 Depends: R (>= 2.15.0), S4Vectors, IRanges, Seqinfo, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 MD5sum: ea340ad64d156d66623310a3d1b7f37f Package: csaw Version: 1.44.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1) Imports: Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods, S4Vectors, IRanges, Seqinfo, stats, BiocParallel, metapod, utils LinkingTo: Rhtslib, Rcpp Suggests: AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager License: GPL-3 MD5sum: 4e21113ea2260b4c7c03d658cc29e6bb Package: csdR Version: 1.16.0 Depends: R (>= 4.1.0) Imports: WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp LinkingTo: Rcpp Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr License: GPL-3 MD5sum: 661ca6399ee634ade69162f9216c383c Package: CSOA Version: 1.0.0 Imports: bayesbio, dplyr, ggplot2, henna, kerntools, methods, qs, reshape2, rlang, Seurat, SeuratObject, SummarizedExperiment, sgof, spatstat.utils, stats, textshape, wesanderson Suggests: BiocStyle, knitr, patchwork, rmarkdown, scRNAseq, scuttle, stringr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 6540aaede55835e4ba5a2e0c527daa0a Package: CSSQ Version: 1.22.0 Depends: SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, rtracklayer Imports: GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, markdown License: Artistic-2.0 MD5sum: 7dabba9db6bd52c741c41327832096fa Package: ctc Version: 1.84.0 Depends: amap License: GPL-2 MD5sum: ee0a13b7e4af72e27ec7abbfac1daa5e Package: CTdata Version: 1.10.0 Depends: R (>= 4.2) Imports: ExperimentHub, utils Suggests: testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown, SummarizedExperiment, SingleCellExperiment License: Artistic-2.0 MD5sum: d42c3de4c51397d51e9ccd6c44382309 Package: CTDquerier Version: 2.18.0 Depends: R (>= 4.1) Imports: RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils, grid, gridExtra, methods, stats, BiocFileCache Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 8937f8d1c2a6341565b3ba67f7e912f7 Package: CTexploreR Version: 1.6.0 Depends: R (>= 4.3), CTdata (>= 1.5.3) Imports: BiocGenerics, ComplexHeatmap, grid, SummarizedExperiment, GenomicRanges, IRanges, dplyr, tidyr, tibble, ggplot2, rlang, grDevices, stats, circlize, ggrepel, SingleCellExperiment, MatrixGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), InteractiveComplexHeatmap License: Artistic-2.0 MD5sum: f23758dfd52d92944098772cf4d9fd98 Package: cTRAP Version: 1.28.0 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: e20c1ef4d90456711323439e6cc3780b Package: ctsGE Version: 1.36.0 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: 827fb4ac9aa2889a39b2eaa651d36f93 Package: CTSV Version: 1.12.0 Depends: R (>= 4.2), Imports: stats, pscl, qvalue, BiocParallel, methods, knitr, SpatialExperiment, SummarizedExperiment Suggests: testthat, BiocStyle License: GPL-3 MD5sum: e50e4de04fb67f9e643edfd8da9477ed Package: CuratedAtlasQueryR Version: 1.8.0 Depends: R (>= 4.2.0) Imports: dplyr, SummarizedExperiment, SingleCellExperiment, purrr (>= 1.0.0), BiocGenerics, glue, HDF5Array, DBI, tools, httr, cli, assertthat, SeuratObject, Seurat, methods, rlang, stats, S4Vectors, tibble, utils, dbplyr (>= 2.3.0), duckdb, stringr Suggests: zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow, reticulate, spelling, forcats, ggplot2, tidySingleCellExperiment, rprojroot License: GPL-3 MD5sum: d367364aa7b168afbc9ebded3c267b8e Package: customCMPdb Version: 1.20.0 Depends: R (>= 4.0) Imports: AnnotationHub, RSQLite, XML, utils, ChemmineR, methods, stats, rappdirs, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: ea3709bf46fb7aeda12d6914197e3216 Package: cyanoFilter Version: 1.18.0 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: 57a4f6b9949cf652f5469b09be5514ab Package: cycle Version: 1.64.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 MD5sum: f2a8f13b9155b6467e2d46f48a5611cb Package: cydar Version: 1.34.0 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: ff6c0ab957b5cff2e5a940f462fa4b0f Package: cypress Version: 1.6.0 Depends: R(>= 4.4.0) Imports: stats, abind, sirt, MASS,TOAST, tibble, parallel, preprocessCore, SummarizedExperiment, TCA, PROPER, methods,dplyr, utils, RColorBrewer, graphics, edgeR, BiocParallel, checkmate, mvtnorm, DESeq2, rlang, e1071 Suggests: knitr, rmarkdown, MatrixGenerics, htmltools, RUnit, BiocGenerics, BiocManager, BiocStyle, Biobase License: GPL-2 | GPL-3 MD5sum: c26f26d578db698044f81aebb58fabfc Package: CytoDx Version: 1.30.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 8694175e7297bc7954a8f7b9ca3bdddd Package: CyTOFpower Version: 1.16.0 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: 75039bb01ff547e05e03c8ba2b07e97c Package: 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SingleCellExperiment, methods Imports: SpatialExperiment, S4Vectors, BiocParallel, HDF5Array, DelayedArray, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5, nnls Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest License: GPL (>= 2) MD5sum: d883d15d7232f123e7fae91f7140cb93 Package: CytoMDS Version: 1.6.0 Depends: R (>= 4.4), Biobase Imports: methods, stats, rlang, pracma, withr, flowCore, reshape2, ggplot2, ggrepel, ggforce, patchwork, transport, smacof, BiocParallel, CytoPipeline Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, HDCytoData License: GPL-3 MD5sum: f67c3a1f39b4e3719d56dccb8f55a7e8 Package: cytoMEM Version: 1.14.0 Depends: R (>= 4.2.0) Imports: gplots, tools, flowCore, grDevices, stats, utils, matrixStats, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 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(>= 4.4), CytoPipeline (>= 1.9.3) Imports: shiny, plotly, ggplot2, flowCore Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, patchwork License: GPL-3 MD5sum: fa700563ebb25d56b5dea1f16b58591d Package: cytoviewer Version: 1.10.0 Imports: shiny, shinydashboard, utils, colourpicker, shinycssloaders, svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite, EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 MD5sum: 25b96ba47d058a0f0df67767751a744e Package: dada2 Version: 1.38.0 Depends: R (>= 4.1.0), 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: 92dd60d27bf8540f9fb3cd2dca072453 Package: dagLogo Version: 1.48.0 Depends: R (>= 3.0.1), methods, grid Imports: pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils, biomaRt, motifStack, httr Suggests: XML, grImport, grImport2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: b9b53f5bb57033761bb66fbd30d8d6f6 Package: daMA Version: 1.82.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: 854f0209f9040d57a9c7c4d27bdc33be Package: DAMEfinder Version: 1.22.0 Depends: R (>= 4.0) Imports: stats, Seqinfo, 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: 6bf5f1514785dd055dac816acdb0114d Package: DaMiRseq Version: 2.22.0 Depends: R (>= 3.5.0), 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: c4e197bd7721c8304d5293498bedcc8b Package: Damsel Version: 1.6.0 Depends: R (>= 4.4.0) Imports: AnnotationDbi, Biostrings, ComplexHeatmap, dplyr, edgeR, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggbio, ggplot2, goseq, magrittr, patchwork, plyranges, reshape2, rlang, Rsamtools, Rsubread, stats, stringr, tidyr, utils Suggests: BiocStyle, biomaRt, biovizBase, BSgenome.Dmelanogaster.UCSC.dm6, knitr, limma, org.Dm.eg.db, rmarkdown, testthat (>= 3.0.0), TxDb.Dmelanogaster.UCSC.dm6.ensGene License: MIT + file LICENSE MD5sum: 1ad5cad501bb330873ffcef557d5409d Package: DAPAR Version: 1.42.0 Depends: R (>= 4.3.0) Imports: Biobase, MSnbase, DAPARdata (>= 1.30.0), utils, highcharter, foreach Suggests: testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph, diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR, factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster, forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr, norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr, limma, preprocessCore, stringr, tidyr, impute, gplots, grDevices, reshape2, graphics, stats, methods, ggplot2, RColorBrewer, Matrix, org.Sc.sgd.db License: Artistic-2.0 MD5sum: 371a5816337e455ae3a1b44d48d92c32 Package: DART Version: 1.58.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: 04b901caeda15d7964788e201cec7e03 Package: dcanr Version: 1.26.0 Depends: R (>= 3.6.0) Imports: igraph, foreach, plyr, stringr, reshape2, methods, Matrix, graphics, stats, RColorBrewer, circlize, doRNG Suggests: EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 MD5sum: 3692cd2534cb1e819f48172c9e2e50fd Package: DCATS Version: 1.8.0 Depends: R (>= 4.1.0), stats Imports: MCMCpack, matrixStats, robustbase, aod, e1071 Suggests: testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 7cdf60089c9facd6706cbdb7ab0dd411 Package: dcGSA Version: 1.38.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: 42798afbba3bf9d6c7b86f06f28ef947 Package: ddCt Version: 1.66.0 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: 046ee3c8a87a0b56eddf563bdcd94ab8 Package: ddPCRclust Version: 1.30.0 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: 3be69e0dbc8cda9070261bbc7e4f7b2d Package: dearseq Version: 1.22.0 Depends: R (>= 3.6.0) Imports: CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr, matrixStats, methods, patchwork, parallel, pbapply, reshape2, rlang, scattermore, stats, statmod, survey, tibble, viridisLite Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr License: GPL-2 | file LICENSE MD5sum: b6fdc125313a6fd211e75f5c61cbfe24 Package: debrowser Version: 1.38.0 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: 5c77e0f3ab0045d89086271bde0a493d Package: DECIPHER Version: 3.6.0 Depends: R (>= 3.5.0), Biostrings (>= 2.59.1), stats Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector Suggests: RSQLite (>= 1.1) License: GPL-3 MD5sum: ef0266b1637843fa508357e76352c6ca Package: decontam Version: 1.30.0 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: 4a6be9fc9662a929a415ae57808afa04 Package: decontX Version: 1.8.0 Depends: R (>= 4.3.0) Imports: celda, dbscan, DelayedArray, ggplot2, Matrix (>= 1.5.3), MCMCprecision, methods, patchwork, plyr, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.2.0), S4Vectors, scater, Seurat, SingleCellExperiment, SummarizedExperiment, withr LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 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stats, methods, foreach (>= 1.5.1), magrittr (>= 2.0.1), matrixStats (>= 0.61.0), e1071 (>= 1.7.9), quadprog (>= 1.5.8), nnls (>= 1.4), rsq (>= 2.2), MASS, utils, dplyr (>= 1.0.7), tidyr (>= 1.1.3), assertthat, minfi Suggests: testthat (>= 3.0.0), roxygen2 (>= 7.1.2), doParallel (>= 1.0.16), parallel, knitr (>= 1.34), BiocStyle (>= 2.20.2), reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), rmarkdown, devtools (>= 2.4.2), sessioninfo (>= 1.1.1), covr, granulator, RefManageR License: Artistic-2.0 MD5sum: 8e5ac271a12dbeb81726c36f39b522da Package: DeeDeeExperiment Version: 1.0.0 Depends: R (>= 4.5.0), SingleCellExperiment Imports: SummarizedExperiment, methods, S4Vectors, utils, DESeq2, edgeR, limma, cli Suggests: macrophage, knitr, BiocStyle, apeglm, mosdef, org.Hs.eg.db, topGO, clusterProfiler, DEFormats, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 64a17df11019e37f9deb9ca73e6cb53b Package: DeepPINCS Version: 1.18.0 Depends: keras, R (>= 4.1) Imports: tensorflow, CatEncoders, matlab, rcdk, stringdist, tokenizers, webchem, purrr, ttgsea, PRROC, reticulate, stats Suggests: knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: d5a777808c43970749a0fdc3b3bd0fb9 Package: deepSNV Version: 1.56.0 Depends: R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.27.6), Imports: Rhtslib LinkingTo: Rhtslib (>= 1.13.1) Suggests: RColorBrewer, knitr, rmarkdown License: GPL-3 MD5sum: 5bf0b128fdcf1026e493504ee11adc60 Package: DeepTarget Version: 1.4.0 Depends: R (>= 4.2.0) Imports: fgsea, ggplot2, stringr, ggpubr, BiocParallel, pROC, stats, grDevices, graphics, depmap, readr, dplyr Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 53293716763d2cb665368cc3c9ef7198 Package: DEFormats Version: 1.38.0 Imports: checkmate, data.table, DESeq2, edgeR (>= 3.13.4), GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat License: GPL-3 MD5sum: 7670c19aa93bf9b0d4e0d3502e0f3da5 Package: DegCre Version: 1.6.0 Depends: R (>= 4.4) Imports: GenomicRanges, InteractionSet, plotgardener, S4Vectors, stats, graphics, grDevices, BiocGenerics, Seqinfo, IRanges, BiocParallel, qvalue, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, utils Suggests: BSgenome, BSgenome.Hsapiens.UCSC.hg38, BiocStyle, magick, knitr, rmarkdown, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 5f68708c42d1a4449427d4575bcc337d Package: DegNorm Version: 1.20.0 Depends: R (>= 4.0.0), methods Imports: Rcpp (>= 1.0.2),GenomicFeatures, txdbmaker, parallel, foreach, S4Vectors, doParallel, Rsamtools (>= 1.31.2), GenomicAlignments, heatmaply, data.table, stats, ggplot2, GenomicRanges, IRanges, plyr, plotly, utils,viridis LinkingTo: Rcpp, RcppArmadillo,S4Vectors,IRanges Suggests: knitr,rmarkdown,formatR License: LGPL (>= 3) MD5sum: 3cf8b43723dbdc890c16be0908d3e057 Package: DEGreport Version: 1.46.0 Depends: R (>= 4.0.0) Imports: utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, dendextend, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, magrittr, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, stringi, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE MD5sum: 125b397116ee3d25cf621be36aaa1be5 Package: DEGseq Version: 1.64.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: 320e9c088e9086491d0c3757d1ae2460 Package: DelayedArray Version: 0.36.0 Depends: R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>= 0.53.3), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.47.6), IRanges (>= 2.17.3), S4Arrays (>= 1.9.3), SparseArray (>= 1.7.5) Imports: stats LinkingTo: S4Vectors Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit License: Artistic-2.0 MD5sum: 9bcaf8e75fa3866d9663bd24c980b95f Package: DelayedDataFrame Version: 1.26.0 Depends: R (>= 3.6), S4Vectors (>= 0.23.19), DelayedArray (>= 0.7.5) Imports: methods, stats, BiocGenerics Suggests: testthat, knitr, rmarkdown, BiocStyle, SeqArray, GDSArray License: GPL-3 MD5sum: 7768159acc962956862bbc20bad9463f Package: DelayedMatrixStats Version: 1.32.0 Depends: MatrixGenerics (>= 1.15.1), DelayedArray (>= 0.31.7) Imports: methods, sparseMatrixStats (>= 1.13.2), Matrix (>= 1.5-0), S4Vectors (>= 0.17.5), IRanges (>= 2.25.10), SparseArray (>= 1.5.19) Suggests: testthat, knitr, rmarkdown, BiocStyle, microbenchmark, profmem, HDF5Array, matrixStats (>= 1.0.0) License: MIT + file LICENSE MD5sum: 761c563943090e62cb4800f45630586a Package: DelayedRandomArray Version: 1.18.0 Depends: SparseArray (>= 1.5.15), DelayedArray (>= 0.31.6) Imports: methods, dqrng, Rcpp LinkingTo: dqrng, BH, Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, Matrix License: GPL-3 MD5sum: 2b72cfc4311a220f72e9cbf6f6ee8cb9 Package: DelayedTensor Version: 1.16.0 Depends: R (>= 4.1.0) Imports: methods, utils, S4Arrays, SparseArray, DelayedArray (>= 0.31.8), HDF5Array, BiocSingular, rTensor, DelayedRandomArray (>= 1.13.1), irlba, Matrix, einsum, Suggests: markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr, dplyr, reticulate License: Artistic-2.0 MD5sum: 585adb73f9060d2fc5df3001a43e43ae Package: deltaCaptureC Version: 1.24.0 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2, tictoc Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 1cd3dbf7c47ae25357604f5540f3a4a5 Package: deltaGseg Version: 1.50.0 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 MD5sum: 8eb1424545738ce584a9b26b38d2f595 Package: DeMAND Version: 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(>= 1.17.40), ggbio (>= 1.13.13), ggplot2, graphics, grDevices, IRanges (>= 1.99.28), limma, methods, plyr, RColorBrewer, reshape2, S4Vectors (>= 0.9.38), scales, utils Suggests: biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData (>= 0.99.0), sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, RefManageR, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, covr License: Artistic-2.0 MD5sum: 1dee38cc0ad9379009833b60c19f5e6b Package: DEScan2 Version: 1.30.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocParallel, BiocGenerics, ChIPpeakAnno, data.table, DelayedArray, Seqinfo, 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: c656a9b5bae821aaee3aeb9a0858f417 Package: DESeq2 Version: 1.50.0 Depends: 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assertthat, terra, sf, spatstat.explore, spatstat.geom, ggforce, ggnewscale, patchwork, BiocParallel, methods, scales, scuttle Suggests: knitr, rmarkdown, testthat, BiocStyle, muSpaData, ExperimentHub, spatialLIBD, purrr, reshape2, tidyverse, concaveman License: GPL-3 MD5sum: 0af402f66cfa90d162108f1e82650e35 Package: DEsubs Version: 1.36.0 Depends: R (>= 3.3), locfit Imports: graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq, stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix, jsonlite, tools, DESeq2, methods Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL-3 MD5sum: e71ddf37a17c4f31e3869fe6f684a7df Package: DEWSeq Version: 1.24.0 Depends: R(>= 4.0.0), R.utils, DESeq2, BiocParallel Imports: BiocGenerics, data.table(>= 1.11.8), Seqinfo, GenomicRanges, methods, S4Vectors, SummarizedExperiment, stats, utils Suggests: knitr, tidyverse, rmarkdown, testthat, BiocStyle, IHW License: LGPL (>= 3) MD5sum: 5de6a3629567172a29333d71f255fc76 Package: DExMA Version: 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RUnit License: GPL (> 2) MD5sum: 5c3610217540c1ba8a05474c46b6e295 Package: diffcyt Version: 1.30.0 Depends: R (>= 3.4.0) Imports: flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma, edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats, methods, utils, grDevices, graphics, ComplexHeatmap, circlize, grid Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST License: MIT + file LICENSE MD5sum: 38bac37d5b7f59b7a669632fd9f83b15 Package: DifferentialRegulation Version: 2.8.0 Depends: R (>= 4.3.0) Imports: methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, stats, BANDITS, Matrix, SingleCellExperiment, SummarizedExperiment, ggplot2, tximport, gridExtra LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 97c61b9a7f2ab7528d8c8c223c09c08f Package: diffGeneAnalysis Version: 1.92.0 Imports: graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils License: GPL MD5sum: 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reshape2, utils License: GPL-3 MD5sum: c69f489a0e4ed602e36e1577d55eb4b1 Package: diffUTR Version: 1.18.0 Depends: R (>= 4.0) Imports: S4Vectors, SummarizedExperiment, limma, edgeR, DEXSeq, GenomicRanges, Rsubread, ggplot2, rtracklayer, ComplexHeatmap, ggrepel, stringi, methods, stats, GenomeInfoDb, dplyr, matrixStats, IRanges, ensembldb, viridisLite Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 823a47eaca95c004bf350ba7610a593b Package: diggit Version: 1.42.0 Depends: R (>= 3.0.2), Biobase, methods Imports: ks, viper(>= 1.3.1), parallel Suggests: diggitdata License: file LICENSE MD5sum: b2834f33916a84e7aed9866cb93b7369 Package: Dino Version: 1.16.0 Depends: R (>= 4.0.0) Imports: BiocParallel, BiocSingular, SummarizedExperiment, SingleCellExperiment, S4Vectors, Matrix, Seurat, matrixStats, parallel, scran, grDevices, stats, methods Suggests: testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools, ggplot2, gridExtra, ggpubr, grid, magick, hexbin License: GPL-3 MD5sum: 21923256d15ee16586e4219a9c9d3541 Package: dinoR Version: 1.6.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, edgeR, GenomicRanges, ggplot2, Matrix, methods, rlang, stats, stringr, tibble, tidyr, tidyselect Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: dd637a652e7ca7a7fc802769b54aaa40 Package: dir.expiry Version: 1.18.0 Imports: utils, filelock Suggests: rmarkdown, knitr, testthat, BiocStyle License: GPL-3 MD5sum: 61f2b6e5025bf0976083ae64c63933f7 Package: DirichletMultinomial Version: 1.52.0 Depends: S4Vectors, IRanges Imports: stats4, methods, BiocGenerics Suggests: lattice, parallel, MASS, RColorBrewer, DT, knitr, rmarkdown, BiocStyle License: LGPL-3 MD5sum: 7db29bbc50a668fd54a09c078b52897e Package: discordant Version: 1.34.0 Depends: R (>= 4.1.0) Imports: Rcpp, Biobase, stats, biwt, gtools, MASS, tools, dplyr, methods, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat (>= 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cowplot, reshape2, pheatmap, grDevices, ggrepel, ggridges, stats, utils, SummarizedExperiment, SingleCellExperiment, S4Vectors Suggests: plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR, ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran, MASS License: MIT + file LICENSE MD5sum: a7548eec4c4fbfaec5f1c2e9d4b4e65e Package: divergence Version: 1.26.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 7b030d9892d8066962c500988305b002 Package: dks Version: 1.56.0 Depends: R (>= 2.8) Imports: cubature License: GPL MD5sum: d9a409ce3189e827b7bcbbda2f0a4d4f Package: DMCFB Version: 1.24.0 Depends: R (>= 4.0.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges Imports: utils, stats, speedglm, MASS, data.table, splines, arm, rtracklayer, benchmarkme, tibble, matrixStats, fastDummies, graphics Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 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GenomicAlignments, Biostrings, BSgenome, BiocManager, S4Vectors, IRanges, InteractionSet, stringr, inflection, BiocParallel, Seqinfo, GenomeInfoDb Suggests: knitr, RUnit, BiocGenerics, rmarkdown, bookdown, BiocStyle, betareg, rtracklayer, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 MD5sum: 1a2e89decf6bc8d85ca51baa38d67e85 Package: DMRcate Version: 3.6.0 Depends: R (>= 4.3.0) Imports: AnnotationHub, ExperimentHub, bsseq, Seqinfo, limma, edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment, biomaRt, grDevices Suggests: knitr, RUnit, BiocGenerics, GenomeInfoDb, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest License: file LICENSE MD5sum: c7928f8512ff013084251be11e125820 Package: DMRScan Version: 1.32.0 Depends: R (>= 3.6.0) Imports: Matrix, MASS, RcppRoll,GenomicRanges, IRanges, Seqinfo, methods, mvtnorm, stats, parallel Suggests: knitr, rmarkdown, BiocStyle, BiocManager License: GPL-3 MD5sum: 23514b68faac4f51bcb1b0e3f36f6e11 Package: dmrseq Version: 1.30.0 Depends: R (>= 3.5), bsseq Imports: GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer, bumphunter, DelayedMatrixStats (>= 1.1.13), matrixStats, BiocParallel, outliers, methods, locfit, IRanges, grDevices, graphics, stats, utils, annotatr, AnnotationHub, rtracklayer, Seqinfo, splines Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 483be508aee0b88a415977fb4dadfda1 Package: DNABarcodeCompatibility Version: 1.26.0 Depends: R (>= 3.6.0) Imports: dplyr, tidyr, numbers, purrr, stringr, stats, utils, methods, Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: file LICENSE MD5sum: ee707965a8ac1adc0893003459c9e59c Package: DNABarcodes Version: 1.40.0 Depends: Matrix, parallel Imports: Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, BiocStyle, rmarkdown License: GPL-2 MD5sum: dc20573b0e40772541a43bdd57b21535 Package: DNAcopy Version: 1.84.0 License: GPL (>= 2) MD5sum: cbeac936ea278453ef6dc8691619c7e8 Package: DNAcycP2 Version: 1.1.0 Depends: R (>= 4.4.0) Imports: basilisk, reticulate Suggests: knitr, rmarkdown, BiocGenerics, RUnit, tinytest, BiocStyle, Biostrings License: Artistic-2.0 MD5sum: 2ef8107465aa226552dc801b7dcae45d Package: DNAfusion Version: 1.12.0 Depends: R (>= 4.4.0) Imports: GenomicRanges, IRanges, Rsamtools, GenomicAlignments, BiocBaseUtils, S4Vectors, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocGenerics Suggests: knitr, rmarkdown, testthat, sessioninfo, BiocStyle License: GPL-3 MD5sum: b4aab8cefe63a9ddd9c3d1dd4bd86285 Package: DNAshapeR Version: 1.38.0 Depends: R (>= 3.4), GenomicRanges Imports: Rcpp (>= 0.12.1), Biostrings, fields LinkingTo: Rcpp Suggests: AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret License: GPL-2 MD5sum: d386f42d49aba915547e210ee020679f Package: DNEA Version: 1.0.0 Depends: R (>= 4.2) Imports: BiocParallel, dplyr, gdata, glasso, igraph (>= 2.0.3), janitor, Matrix, methods, netgsa, stats, stringr, utils, SummarizedExperiment Suggests: BiocStyle, ggplot2, Hmisc, kableExtra, knitr, pheatmap, rmarkdown, testthat (>= 3.0.0), withr, airway Enhances: massdataset License: MIT + file LICENSE MD5sum: 53e531fa1570f8e7b81d28018ccae91c Package: DominoEffect Version: 1.30.0 Depends: R(>= 3.5) Imports: biomaRt, data.table, utils, stats, Biostrings, pwalign, SummarizedExperiment, VariantAnnotation, AnnotationDbi, Seqinfo, IRanges, GenomicRanges, methods Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: f91ae02d6355342f120c17cc53e76fd8 Package: dominoSignal Version: 1.4.0 Depends: R(>= 4.2.0), Imports: biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid, igraph, Matrix, methods, plyr, stats, utils, magrittr, purrr, dplyr Suggests: knitr, patchwork, rmarkdown, Seurat, testthat, formatR, BiocFileCache, SingleCellExperiment License: GPL-3 | file LICENSE MD5sum: 2975a815e37f40e33a9c3c6d9771e672 Package: doppelgangR Version: 1.38.0 Depends: R (>= 3.5.0), Biobase, BiocParallel Imports: sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat License: GPL (>= 2.0) MD5sum: 38103807c2e36024bf7934d2b34852fe Package: Doscheda Version: 1.32.0 Depends: R (>= 3.4) Imports: methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy, limma, stringr, ggplot2, graphics, grDevices, calibrate, corrgram, gridExtra, DT, shiny, shinydashboard, readxl, prodlim, matrixStats Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 716e892c942670558b6d94812f05cf47 Package: DOSE Version: 4.4.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, BiocParallel, fgsea, ggplot2, GOSemSim 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SummarizedExperiment, DelayedMatrixStats, sparseMatrixStats, MatrixGenerics, Matrix, methods, purrr, GSEABase, data.table, zenith (>= 1.1.2), mashr (>= 0.2.52), ashr, dplyr, BiocParallel, ggbeeswarm, S4Vectors, IRanges, irlba, limma, metafor, remaCor, broom, tidyr, rlang, BiocGenerics, S4Arrays, SparseArray, DelayedArray, gtools, reshape2, ggrepel, scattermore, Rcpp, lme4 (>= 1.1-33), MASS, Rdpack, utils, stats LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub, RUnit, muscData, scater, scuttle License: Artistic-2.0 MD5sum: 850a41664f88f293064de175ca8bbfd1 Package: DRIMSeq Version: 1.38.0 Depends: R (>= 3.4.0) Imports: utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2 Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: bb9c141109866b0ee7254c064e2820c4 Package: DriverNet Version: 1.50.0 Depends: R (>= 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Imports: ape, Biostrings, data.table, DECIPHER, DESeq2, dplyr, edgeR, flextable, ggalluvial, ggnewscale, ggplot2, ggpubr, ggraph, ggrepel, ggridges, ggtree, ggtreeExtra, graphics, grDevices, igraph, limma, matrixStats, methods, microbiome, officer, grid, reshape2, patchwork, phangorn, phyloseq, randomForest, RColorBrewer, rlang, S4Vectors, scales, stats, tibble, tidyr, SummarizedExperiment, TreeSummarizedExperiment, utils, msa, xml2, ggstar Suggests: Biobase, mia, BiocGenerics, magrittr, BiocManager, cluster, devtools, DT, e1071, foreach, ggtext, intergraph, knitr, optparse, plyr, preprocessCore, qpdf, remotes, rmarkdown, ShortRead, testthat (>= 3.0.0), vegan, viridis License: MIT + file LICENSE MD5sum: d78ab4f6663e0a6039a0a889c1f75ad5 Package: DSS Version: 2.58.0 Depends: R (>= 3.5.0), methods, Biobase, BiocParallel, bsseq, parallel Imports: utils, graphics, stats, splines Suggests: BiocStyle, knitr, rmarkdown, edgeR License: GPL MD5sum: 12e577cdb92bf09ac426ec447ba9430e Package: dStruct Version: 1.16.0 Depends: R (>= 4.1) Imports: zoo, ggplot2, purrr, reshape2, parallel, IRanges, S4Vectors, rlang, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, tidyverse, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 49e4741e1db4792388221a045c0cebfb Package: DTA Version: 2.56.0 Depends: R (>= 2.10), LSD Imports: scatterplot3d License: Artistic-2.0 MD5sum: 4677aaa6382b3411f48ba2136406c93d Package: DuplexDiscovereR Version: 1.4.0 Depends: R (>= 4.5), InteractionSet Imports: Gviz, Biostrings, rtracklayer, GenomicAlignments, GenomicRanges, ggsci, igraph, rlang, scales, stringr, dplyr, tibble, tidyr, purrr, methods, grDevices, stats, utils, vctrs Suggests: knitr, UpSetR, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 6522248ccea511af1309dd079922dfa3 Package: dupRadar Version: 1.40.0 Depends: R (>= 3.2.0) Imports: Rsubread (>= 1.14.1), KernSmooth Suggests: BiocStyle, knitr, rmarkdown, AnnotationHub License: GPL-3 MD5sum: 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BiocStyle Suggests: knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools, BiocStyle License: Artistic-2.0 MD5sum: 2d76f508d3a5713c3bd4203e55aa007e Package: easylift Version: 1.8.0 Depends: R (>= 4.1.0), GenomicRanges, BiocFileCache Imports: rtracklayer, GenomeInfoDb, R.utils, tools, methods Suggests: testthat (>= 3.0.0), IRanges, knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: 29c1ef26581964bc274849fffc6cada2 Package: easyreporting Version: 1.22.0 Depends: R (>= 3.5.0) Imports: rmarkdown, methods, tools, shiny, rlang Suggests: distill, BiocStyle, knitr, readxl, edgeR, limma, EDASeq, statmod License: Artistic-2.0 MD5sum: 5ec6f122fd14182c6371ad5299eab6e2 Package: easyRNASeq Version: 2.46.0 Imports: Biobase (>= 2.64.0), BiocFileCache (>= 2.12.0), BiocGenerics (>= 0.50.0), BiocParallel (>= 1.38.0), biomaRt (>= 2.60.1), Biostrings (>= 2.77.2), edgeR (>= 4.2.1), Seqinfo, genomeIntervals (>= 1.60.0), GenomicAlignments (>= 1.45.1), GenomicRanges (>= 1.61.1), 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BiocStyle, digest, knitr, rmarkdown, shiny License: LGPL MD5sum: df6aabeacfa1f092fa75cfc9796dabbf Package: EBSEA Version: 1.38.0 Depends: R (>= 4.0.0) Imports: DESeq2, graphics, stats, EmpiricalBrownsMethod Suggests: knitr, rmarkdown License: GPL-2 MD5sum: e53a233ae5c7830a65082db992960e2f Package: EBSeq Version: 2.8.0 Depends: blockmodeling, gplots, testthat, R (>= 3.0.0) Imports: Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0), BH (<= 1.87.0-1) LinkingTo: Rcpp,RcppEigen,BH License: Artistic-2.0 MD5sum: dd906188170178e1050101f21572dd02 Package: ecolitk Version: 1.82.0 Depends: R (>= 2.10) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy License: GPL (>= 2) MD5sum: e9931c03958da4f6309817d67f9c74cd Package: EDASeq Version: 2.44.0 Depends: Biobase (>= 2.15.1), ShortRead (>= 1.11.42) Imports: methods, graphics, BiocGenerics, IRanges (>= 1.13.9), aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings, AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager Suggests: BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat, DESeq2, rmarkdown License: Artistic-2.0 MD5sum: 21288776ac9b03665b79b0954dee911e Package: edge Version: 2.42.0 Depends: R(>= 3.1.0), Biobase Imports: methods, splines, sva, qvalue(>= 1.99.0), MASS Suggests: testthat, knitr, ggplot2, reshape2 License: MIT + file LICENSE MD5sum: e1a2a68ee9a2bb511eb2491039b6a2e8 Package: edgeR Version: 4.8.0 Depends: R (>= 3.6.0), limma (>= 3.63.6) Imports: methods, graphics, stats, utils, locfit Suggests: arrow, jsonlite, knitr, Matrix, readr, rhdf5, SeuratObject, splines, AnnotationDbi, Biobase, BiocStyle, org.Hs.eg.db, SummarizedExperiment License: GPL (>= 2) MD5sum: cfe9f19394d771c9fc89c68b4affb5e1 Package: EDIRquery Version: 1.10.0 Depends: R (>= 4.2.0) Imports: tibble (>= 3.1.6), tictoc (>= 1.0.1), utils (>= 4.1.3), stats (>= 4.1.3), readr (>= 2.1.2), InteractionSet (>= 1.22.0), GenomicRanges (>= 1.46.1) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 02ac17c336092630bd0b07c6b8a55786 Package: eds Version: 1.12.0 Depends: Matrix Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, tximportData, testthat (>= 3.0.0) License: GPL-2 MD5sum: b985c20acebc73cb3096c21fbd67f163 Package: EGAD Version: 1.38.0 Depends: R(>= 3.5) Imports: gplots, Biobase, GEOquery, limma, impute, RColorBrewer, zoo, igraph, plyr, MASS, RCurl, methods Suggests: knitr, testthat, rmarkdown, markdown License: GPL-2 MD5sum: 3fe99e6b58be2389e96fc918e1cf9812 Package: EGSEA Version: 1.38.0 Depends: R (>= 4.3.0), Biobase, gage (>= 2.14.4), AnnotationDbi, topGO (>= 2.16.0), pathview (>= 1.4.2) Imports: PADOG (>= 1.6.0), GSVA (>= 1.12.0), globaltest (>= 5.18.0), limma (>= 3.20.9), edgeR (>= 3.6.8), HTMLUtils (>= 0.1.5), hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0), safe (>= 3.4.0), stringi (>= 0.5.0), parallel, stats, metap, grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, RColorBrewer, methods, EGSEAdata (>= 1.3.1), htmlwidgets, plotly, DT Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: 456d762194fcbe132c90638e53dfd59c Package: eiR Version: 1.50.0 Depends: R (>= 2.10.0), ChemmineR (>= 2.15.15), methods, DBI Imports: snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl, digest, BiocGenerics, RcppAnnoy (>= 0.0.9) Suggests: BiocStyle, knitcitations, knitr, knitrBootstrap,rmarkdown,RSQLite,codetools License: Artistic-2.0 MD5sum: b69ba2737f3d0ad6ad9b419fa9f6f96e Package: eisaR Version: 1.22.0 Depends: R (>= 4.1) Imports: graphics, stats, GenomicRanges, S4Vectors, IRanges, limma, edgeR (>= 4.0), methods, SummarizedExperiment, BiocGenerics, utils Suggests: knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, txdbmaker, rtracklayer, withr License: GPL-3 MD5sum: 5f7f63ca7bb8c037bf5af3e98ffe920c Package: ELMER Version: 2.33.1 Depends: R (>= 3.4.0), ELMER.data (>= 2.9.3) Imports: GenomicRanges, ggplot2, reshape, grid, grDevices, graphics, methods, parallel, stats, utils, IRanges, Seqinfo, S4Vectors, GenomicFeatures, TCGAbiolinks (>= 2.23.7), plyr, Matrix, dplyr, Gviz, ComplexHeatmap, circlize, MultiAssayExperiment, SummarizedExperiment, biomaRt, doParallel, downloader, ggrepel, lattice, magrittr, readr, scales, rvest, xml2, plotly, gridExtra, rmarkdown, stringr, tibble, tidyr, progress, purrr, reshape2, ggpubr, rtracklayer (>= 1.61.2), DelayedArray Suggests: BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData License: GPL-3 MD5sum: 939836da3ee32698dcbe2ceca6bd491b Package: ELViS Version: 1.2.0 Depends: R (>= 4.5.0) Imports: reticulate, BiocGenerics, circlize, ComplexHeatmap, data.table, dplyr, GenomicFeatures, GenomicRanges, ggplot2, glue, graphics, grDevices, igraph, IRanges, magrittr, memoise, methods, parallel, patchwork, scales, segclust2d, stats, stringr, txdbmaker, utils, uuid, zoo Suggests: Rsamtools, BiocManager, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 343abc43c769dc4df61278e2a87f55d0 Package: EMDomics Version: 2.40.0 Depends: R (>= 3.2.1) Imports: emdist, BiocParallel, matrixStats, ggplot2, CDFt, preprocessCore Suggests: knitr License: MIT + file LICENSE MD5sum: e8a54974187ddf2b734fc3c337f7ffa6 Package: EmpiricalBrownsMethod Version: 1.38.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: f09fa25851112b79699beba690772914 Package: enhancerHomologSearch Version: 1.16.0 Depends: R (>= 4.1.0), methods Imports: BiocGenerics, Biostrings, BSgenome, BiocParallel, BiocFileCache, Seqinfo, GenomicRanges, httr, IRanges, jsonlite, motifmatchr, Matrix, pwalign, rtracklayer, Rcpp, S4Vectors, stats, utils LinkingTo: Rcpp Suggests: GenomeInfoDb, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, MotifDb, testthat, TFBSTools License: GPL (>= 2) MD5sum: f2d9e80df8804d3aac2bef3ce2214519 Package: EnMCB Version: 1.22.0 Depends: R (>= 4.0) Imports: survivalROC, glmnet, rms, mboost, Matrix, igraph, methods, survivalsvm, ggplot2, boot, e1071, survival, BiocFileCache Suggests: SummarizedExperiment, testthat, Biobase, survminer, affycoretools, knitr, plotROC, limma, rmarkdown License: GPL-2 MD5sum: 281ec91fa8d8a6d8e8b478e6322d5de9 Package: ENmix Version: 1.46.0 Depends: parallel,doParallel,foreach,SummarizedExperiment,stats,R (>= 3.5.0) Imports: grDevices,graphics,matrixStats,methods,utils,irlba, geneplotter,impute,minfi,RPMM,illuminaio,dynamicTreeCut,IRanges,gtools, Biobase,ExperimentHub,AnnotationHub,genefilter,gplots,quadprog,S4Vectors Suggests: minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: bb4d36a51fe871f03bdc0db443a6e8b9 Package: EnrichDO Version: 1.4.0 Depends: R (>= 4.0.0) Imports: BiocGenerics, Rgraphviz, hash, S4Vectors, dplyr, ggplot2, graph, magrittr, methods, pheatmap, graphics, utils, purrr, tidyr, stats Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: MIT + file LICENSE MD5sum: f757caee126855e5f7b6c0651ba01cad Package: EnrichedHeatmap Version: 1.40.0 Depends: R (>= 3.6.0), methods, grid, ComplexHeatmap (>= 2.11.0), GenomicRanges Imports: matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize (>= 0.4.5), IRanges LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter, RColorBrewer License: MIT + file LICENSE MD5sum: 6b52501a826f7f78f5fc09e6bf371ea6 Package: EnrichmentBrowser Version: 2.40.0 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, statmod License: Artistic-2.0 MD5sum: 5d744410f57fe1ac9ec4930f8686fdc4 Package: enrichplot Version: 1.30.0 Depends: R (>= 4.1.0) Imports: aplot (>= 0.2.1), DOSE (>= 3.31.2), ggfun (>= 0.1.7), ggnewscale, ggplot2 (>= 3.5.0), ggrepel (>= 0.9.0), ggtangle (>= 0.0.5), graphics, grid, igraph, methods, plyr, purrr, RColorBrewer, reshape2, rlang, stats, utils, scatterpie, GOSemSim (>= 2.31.2), magrittr, ggtree, yulab.utils (>= 0.1.6) Suggests: clusterProfiler, dplyr, europepmc, ggarchery, ggupset, glue, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, ggHoriPlot, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggstar, scales, ggtreeExtra, tidydr License: Artistic-2.0 MD5sum: 7e2958b28e82ce27300a5353df192761 Package: enrichViewNet Version: 1.8.0 Depends: R (>= 4.2.0) Imports: gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, DOSE, igraph, reshape2, methods Suggests: BiocStyle, knitr, rmarkdown, ggplot2, scatterpie, ggtangle, ggrepel, testthat, ggnetwork, magick License: Artistic-2.0 MD5sum: 69f00213d0195732bf976d259e0a3b00 Package: ensembldb Version: 2.34.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.61.1), GenomicFeatures (>= 1.61.4), AnnotationFilter (>= 1.5.2) Imports: methods, RSQLite (>= 1.1), DBI, Biobase, Seqinfo, GenomeInfoDb (>= 1.45.5), AnnotationDbi (>= 1.31.19), rtracklayer (>= 1.69.1), S4Vectors (>= 0.23.10), Rsamtools, IRanges (>= 2.13.24), ProtGenerics, Biostrings (>= 2.77.2), curl Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), rmarkdown, AnnotationHub Enhances: RMariaDB, shiny License: LGPL MD5sum: e1414596f0ae868ab77a1f9344730eaf Package: epialleleR Version: 1.18.0 Depends: R (>= 4.1) Imports: stats, methods, utils, data.table, BiocGenerics, GenomicRanges, Rcpp LinkingTo: Rcpp, BH, Rhtslib Suggests: GenomeInfoDb, SummarizedExperiment, VariantAnnotation, RUnit, knitr, rmarkdown, ggplot2 License: Artistic-2.0 MD5sum: 57177ac9f76b354cde5d037b9d9125b9 Package: EpiCompare Version: 1.14.0 Depends: R (>= 4.2.0) Imports: AnnotationHub, ChIPseeker, data.table, genomation, GenomicRanges, IRanges (>= 2.41.3), Seqinfo (>= 0.99.2), GenomeInfoDb (>= 1.45.7), ggplot2 (>= 3.5.0), htmltools, methods, plotly, reshape2, rmarkdown, rtracklayer, stats, stringr, utils, BiocGenerics, downloadthis, parallel Suggests: rworkflows, BiocFileCache, BiocParallel, BiocStyle, clusterProfiler, GenomicAlignments, grDevices, knitr, org.Hs.eg.db, testthat (>= 3.0.0), tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, ComplexUpset, plyranges, scales, Matrix, consensusSeekeR, heatmaply, viridis License: GPL-3 MD5sum: 97408e5f8104723762333602b2a886c1 Package: epidecodeR Version: 1.18.0 Depends: R (>= 3.1.0) Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 5efe41e8379c65b5a53611e04c596de6 Package: EpiDISH Version: 2.26.0 Depends: R (>= 4.1) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat License: GPL-2 MD5sum: 3b7fd90b7663944ca1992e53b5577cc5 Package: epigraHMM Version: 1.18.0 Depends: R (>= 3.5.0) Imports: Rcpp, magrittr, data.table, SummarizedExperiment, methods, Seqinfo, GenomicRanges, rtracklayer, IRanges, Rsamtools, bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5, Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap, grDevices LinkingTo: Rcpp, RcppArmadillo, Rhdf5lib Suggests: GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle, BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData License: MIT + file LICENSE MD5sum: d7a75844e40eb7f42497b36f5e3312e1 Package: EpiMix Version: 1.12.0 Depends: R (>= 4.2.0), EpiMix.data (>= 1.2.2) Imports: AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table, doParallel, doSNOW, downloader, dplyr, ELMER.data, ExperimentHub, foreach, Seqinfo, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, impute, IRanges, limma, methods, parallel, plyr, progress, R.matlab, RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, utils Suggests: BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter License: GPL-3 MD5sum: 73543d982ce66dd6a8d8582b8b2dad86 Package: epimutacions Version: 1.14.0 Depends: R (>= 4.3.0), epimutacionsData Imports: minfi, bumphunter, isotree, robustbase, ggplot2, GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment, stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt, BiocParallel, GenomeInfoDb, Homo.sapiens, purrr, tibble, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, AnnotationDbi, AnnotationHub, ExperimentHub, reshape2, grid, ensembldb, gridExtra, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, ggrepel Suggests: testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices License: MIT + file LICENSE MD5sum: d55dc6abb9a62e6c03bb3a5c3579ff2b Package: epiNEM Version: 1.34.0 Depends: R (>= 4.1) Imports: BoutrosLab.plotting.general, BoolNet, e1071, gtools, stats, igraph, utils, lattice, latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph, mnem, latex2exp Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle License: GPL-3 MD5sum: 15df070809cf8f920b38a5d41ab23441 Package: EpipwR Version: 1.4.0 Depends: R (>= 4.4.0) Imports: EpipwR.data, ExperimentHub (>= 2.10.0), ggplot2 Suggests: knitr, rmarkdown, testthat (>= 3.0.0), sessioninfo License: Artistic-2.0 MD5sum: 7b25933a196f209cbd09f1b9814e4618 Package: epiregulon Version: 2.0.0 Depends: R (>= 4.4), SingleCellExperiment Imports: AnnotationHub, BiocParallel, ExperimentHub, Matrix, Rcpp, S4Vectors, SummarizedExperiment, checkmate, entropy, lifecycle, methods, scran, scuttle, stats, utils, AnnotationHub, GenomeInfoDb, GenomicRanges, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, motifmatchr, IRanges, scrapper LinkingTo: Rcpp Suggests: knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), coin, scater, scMultiome License: MIT + file LICENSE MD5sum: c0bf5662ecf8faeaa142c31ec2486232 Package: epiregulon.extra Version: 1.6.0 Depends: R (>= 4.4), SingleCellExperiment Imports: scran, ComplexHeatmap, Matrix, SummarizedExperiment, checkmate, circlize, clusterProfiler, ggplot2, ggraph, igraph, patchwork, reshape2, scales, scater Suggests: epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), msigdb, GSEABase, dorothea, scMultiome, S4Vectors, scuttle, vdiffr, ggrastr, ggrepel License: MIT + file LICENSE MD5sum: 99283cce4093ac36b20740e50e7b21b0 Package: epistack Version: 1.16.0 Depends: R (>= 4.1) Imports: GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, graphics, plotrix, grDevices, stats, methods Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick License: MIT + file LICENSE MD5sum: 2cf3edda2f1b763b189c5449c810e0e9 Package: epistasisGA Version: 1.12.0 Depends: R (>= 4.2) Imports: BiocParallel, data.table, matrixStats, stats, survival, igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid, bigmemory, graphics, utils LinkingTo: Rcpp, RcppArmadillo, BH, bigmemory Suggests: BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0) License: GPL-3 MD5sum: ec761f8a890fc34a5ce01ffffc741ed8 Package: EpiTxDb Version: 1.22.0 Depends: R (>= 4.0), AnnotationDbi, Modstrings Imports: methods, utils, httr, xml2, curl, rex, GenomicFeatures, txdbmaker, GenomicRanges, Seqinfo, BiocGenerics, BiocFileCache, S4Vectors, IRanges, RSQLite, DBI, Biostrings, tRNAdbImport Suggests: BiocStyle, knitr, rmarkdown, testthat, httptest, AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: 3cf87653a1a83cae5c845d1bce057578 Package: epivizr Version: 2.40.0 Depends: R (>= 3.5.0), 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: e896498aa57b7135bee5b963963445d0 Package: epivizrChart Version: 1.32.0 Depends: R (>= 3.5.0) 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: fb17e76ed2875182c0f00cd7e59e863a Package: epivizrData Version: 1.38.0 Depends: R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase Imports: S4Vectors, GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), OrganismDbi, GenomicFeatures (>= 1.61.4), Seqinfo, IRanges, ensembldb (>= 2.33.1) Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats License: MIT + file LICENSE MD5sum: 7805d8b5f0086df7c8b23b538823f9c8 Package: epivizrServer Version: 1.38.0 Depends: R (>= 3.2.3), methods Imports: httpuv (>= 1.3.0), R6 (>= 2.0.0), rjson, mime (>= 0.2) Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 096fee88269c8c6d71dc3431581f7298 Package: epivizrStandalone Version: 1.38.0 Depends: R (>= 3.2.3), epivizr (>= 2.3.6), methods Imports: git2r, epivizrServer, Seqinfo, BiocGenerics, GenomicFeatures, S4Vectors Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle License: MIT + file LICENSE MD5sum: cb235bedb0d6e2c2a398efd47bf643e8 Package: erccdashboard Version: 1.44.0 Depends: R (>= 4.0), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0) Imports: edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr, qvalue, reshape2, ROCR, scales, stringr, knitr Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 50443f3e56ec99e94b3a285940090054 Package: ERSSA Version: 1.28.0 Depends: R (>= 4.0.0) Imports: edgeR (>= 3.23.3), DESeq2 (>= 1.21.16), ggplot2 (>= 3.0.0), RColorBrewer (>= 1.1-2), plyr (>= 1.8.4), BiocParallel (>= 1.15.8), apeglm (>= 1.4.2), grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 6d92fa71c803158bc60f21c5e64a66bd Package: esATAC Version: 1.32.0 Depends: R (>= 4.0.0), Rsamtools, GenomicRanges, ShortRead, pipeFrame Imports: Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer, ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph, rJava, magrittr, digest, BSgenome, AnnotationDbi, GenomicAlignments, GenomicFeatures, R.utils, Seqinfo, BiocGenerics, S4Vectors, IRanges, rmarkdown, tools, VennDiagram, grid, JASPAR2018, TFBSTools, grDevices, graphics, stats, utils, parallel, corrplot, BiocManager, motifmatchr LinkingTo: Rcpp Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat, webshot, prettydoc License: GPL-3 | file LICENSE Archs: x64 MD5sum: 67afcbee221d4beff0e623e36458d83b Package: escape Version: 2.6.1 Depends: R (>= 4.1) Imports: ggdist, ggplot2 (>= 3.5.0), grDevices, Matrix, MatrixGenerics, methods, stats, SummarizedExperiment, utils Suggests: AUCell, BiocParallel, BiocStyle, DelayedMatrixStats, dplyr, fgsea, GSEABase, ggraph, ggridges, ggpointdensity, GSVA, hexbin, igraph, irlba, knitr, msigdb, patchwork, rmarkdown, rlang, scran, SeuratObject, Seurat, SingleCellExperiment, spelling, stringr, testthat (>= 3.0.0), UCell License: MIT + file LICENSE MD5sum: 7a010840f42575fba12d18a9ebece271 Package: escheR Version: 1.10.0 Depends: ggplot2, R (>= 4.3) Imports: SpatialExperiment (>= 1.6.1), SingleCellExperiment, rlang, SummarizedExperiment Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat, hexbin License: MIT + file LICENSE MD5sum: f2db8bd572797a2252ff402fa6aa73ab Package: esetVis Version: 1.36.0 Imports: mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils, grDevices, methods Suggests: ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db License: GPL-3 MD5sum: 7dc2b5877af9b80a141e0a8208030b7d Package: eudysbiome Version: 1.40.0 Depends: R (>= 3.1.0) Imports: plyr, Rsamtools, R.utils, Biostrings License: GPL-2 MD5sum: b830a479f2f0764cbd8c427c6d52c20e Package: evaluomeR Version: 1.26.0 Depends: R (>= 3.6), SummarizedExperiment, MultiAssayExperiment, cluster (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14), flexmix (>= 2.3.15), RSKC (>= 2.4.2), sparcl (>= 1.0.4) Imports: corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2, ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class, prabclus, mclust, kableExtra, dplyr, dendextend (>= 1.16.0) Suggests: BiocStyle, knitr, rmarkdown, magrittr License: GPL-3 MD5sum: ed5b28867949d302f01e87964bd4fdf9 Package: EventPointer Version: 3.18.0 Depends: R (>= 3.5.0), SGSeq, Matrix, SummarizedExperiment Imports: GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls, limma, matrixStats, RBGL, prodlim, graph, methods, utils, stats, doParallel, foreach, affxparser, GenomicRanges, S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome, Biostrings, glmnet, abind, iterators, lpSolve, poibin, speedglm, tximport, fgsea Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra License: Artistic-2.0 MD5sum: d26ab41eba65cfdc8d25ace92930576c Package: EWCE Version: 1.18.0 Depends: R (>= 4.2), RNOmni (>= 1.0) Imports: stats, utils, methods, ewceData (>= 1.7.1), dplyr, ggplot2, reshape2, limma, stringr, HGNChelper, Matrix, parallel, SingleCellExperiment, SummarizedExperiment, DelayedArray, BiocParallel, orthogene (>= 0.99.8), data.table Suggests: rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork License: GPL-3 MD5sum: bae77525f3112bb835d2ce88ce8703f3 Package: 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GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown, HubPub License: Artistic-2.0 MD5sum: a481a4d9e2e02010a47225b6df5a1ef0 Package: ExperimentSubset Version: 1.20.0 Depends: R (>= 4.0.0), SummarizedExperiment, SingleCellExperiment, SpatialExperiment, TreeSummarizedExperiment Imports: methods, Matrix, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran, scater, scds, TENxPBMCData, airway License: MIT + file LICENSE MD5sum: 9727f5eb1e410bb28b9b641b05b6f8d3 Package: ExploreModelMatrix Version: 1.22.0 Imports: shiny (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr, magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales, tibble, MASS, limma, S4Vectors, shinyjs, rlang Suggests: testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle License: MIT + file LICENSE MD5sum: 53efb423538501972d4355435d202476 Package: ExpressionAtlas Version: 2.2.0 Depends: R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2, RCurl, jsonlite, BiocStyle Imports: utils, XML, httr Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: f9cc1450efc836414e6a0eac3fff1b8e Package: extraChIPs Version: 1.14.0 Depends: BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 4.0.0), ggside (>= 0.4.0), Seqinfo, SummarizedExperiment (>= 1.39.1), tibble Imports: csaw, dplyr (>= 1.1.1), edgeR (>= 4.0), forcats, GenomeInfoDb, glue, ggrepel, InteractionSet, IRanges, matrixStats, methods, patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales, stats, stringr, tidyr, tidyselect, vctrs Suggests: apeglm, BiocStyle, SimpleUpset, covr, DESeq2, EnrichedHeatmap, GenomicAlignments, GenomicInteractions, Gviz, ggforce, harmonicmeanp, here, knitr, limma, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse, VennDiagram License: GPL-3 MD5sum: 16cfbf050bc1332a5ea86e6927ccd169 Package: fabia Version: 2.56.0 Depends: R (>= 3.6.0), Biobase Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: 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License: GPL-2 MD5sum: e0c5de52413d4df6598caf506510a6e5 Package: FastqCleaner Version: 1.28.0 Imports: methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12) LinkingTo: Rcpp Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 3dc48abdba99664f8a23968e058e903f Package: fastreeR Version: 2.0.0 Depends: R (>= 4.4) Imports: ape, data.table, dynamicTreeCut, methods, R.utils, rJava, stats, stringr, utils Suggests: BiocFileCache, BiocStyle, ggtree, graphics, knitr, memuse, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: 0e3391675d6bf4c62ecc19521b768385 Package: fastseg Version: 1.56.0 Depends: R (>= 2.13), GenomicRanges, Biobase Imports: methods, graphics, grDevices, stats, BiocGenerics, S4Vectors, IRanges Suggests: DNAcopy, BiocStyle, knitr License: LGPL (>= 2.0) MD5sum: b333b772f25c25a236e0cf267a2d7cf1 Package: fCCAC Version: 1.36.0 Depends: R (>= 4.2.0), S4Vectors, IRanges, 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stats, utils, irlba, TSCAN, SC3, matrixStats Suggests: rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-2 MD5sum: 19dd65395fe6deb4b1ba5b195639f762 Package: FeatSeekR Version: 1.10.0 Imports: pheatmap, MASS, pracma, stats, SummarizedExperiment, methods Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: c5c746057f0fe3b0507a3dda41014d1e Package: fedup Version: 1.18.0 Depends: R (>= 4.1) Imports: openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes, forcats, RColorBrewer, RCy3, utils, stats Suggests: biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr License: MIT + file LICENSE MD5sum: cbcb93e0fe40dd8848d60066f3b2a953 Package: fenr Version: 1.8.0 Depends: R (>= 4.1.0) Imports: tools, methods, assertthat, rlang, dplyr, tidyr, tidyselect, tibble, purrr, readr, stringr, httr2, rvest, progress, BiocFileCache, shiny, ggplot2 Suggests: BiocStyle, testthat, knitr, rmarkdown, topGO License: MIT + file LICENSE MD5sum: 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ggrepel, tibble, tidyr, SummarizedExperiment, MultiAssayExperiment, IRanges, progress, purrr, glmnet, methods Suggests: BiocStyle, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), TxDb.Athaliana.BioMart.plantsmart28 License: Artistic-2.0 MD5sum: cbe345de5dd21a02572d0efefd3aa52b Package: FinfoMDS Version: 1.0.0 Depends: R (>= 4.4.0) Imports: phyloseq Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 7c5ee7b6d763b68759989b358341d1f4 Package: FISHalyseR Version: 1.44.0 Depends: EBImage,abind Suggests: knitr License: Artistic-2.0 MD5sum: 0bc691504c997933935e10407c1ffbd2 Package: fishpond Version: 2.16.0 Imports: graphics, stats, utils, methods, abind, gtools, qvalue, S4Vectors, IRanges, SummarizedExperiment, GenomicRanges, matrixStats, svMisc, Matrix, SingleCellExperiment, jsonlite Suggests: testthat, knitr, rmarkdown, macrophage, tximeta, org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma, ensembldb, EnsDb.Hsapiens.v86, GenomicFeatures, 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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: 8301ca8aee5d6eed4187dff3dcded5e8 Package: GAprediction Version: 1.36.0 Depends: R (>= 3.3) Imports: glmnet, stats, utils, Matrix Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 78eeb87f748b24072fc80d82e1f62dae Package: garfield Version: 1.38.0 Suggests: knitr License: GPL-3 MD5sum: 210b31a59fd7cd8a3760e13b34b5e8be Package: GARS Version: 1.30.0 Depends: R (>= 3.5), ggplot2, cluster Imports: DaMiRseq, MLSeq, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: c4db5b76eeb853278b374600c4498697 Package: GateFinder Version: 1.30.0 Imports: splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: a50ae4b2307d0a8df808bffc0e2f1cc1 Package: gatom Version: 1.7.0 Depends: R (>= 4.3.0) Imports: data.table, igraph, BioNet, plyr, methods, XML, sna, intergraph, network, GGally, grid, ggplot2, mwcsr, pryr, htmlwidgets, htmltools, shinyCyJS (>= 1.0.0) Suggests: testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi, org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils License: MIT + file LICENCE MD5sum: 7cf4224c1e7919cf2388a85a655b6436 Package: GBScleanR Version: 2.3.2 Depends: SeqArray Imports: stats, utils, methods, ggplot2, tidyr, expm, Rcpp, RcppParallel, gdsfmt LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: e1f8de1418bd27535093dc704bc94828 Package: gcapc Version: 1.34.0 Depends: R (>= 3.4) Imports: BiocGenerics, Seqinfo, 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: b0481da620cad88a6710420e5210ca73 Package: gcatest Version: 2.10.0 Depends: R (>= 4.0) Imports: methods, lfa Suggests: knitr, ggplot2, testthat, BEDMatrix, genio License: GPL (>= 3) MD5sum: 562ecbfc21fe66b0ba3d595d8b6ba719 Package: GCPtools Version: 1.0.0 Depends: R (>= 4.5.0) Imports: AnVILBase, BiocBaseUtils, dplyr, httr, rlang, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: b458df64f638bbecd1da991b258ba3bb Package: gCrisprTools Version: 2.16.0 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: 27930f916591bddbe511f64a4aee87ea Package: gcrma Version: 2.82.0 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: a614f3402912490352a168d6cdf13b56 Package: GDCRNATools Version: 1.30.0 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, prettydoc, rmarkdown License: Artistic-2.0 MD5sum: a5029a4d2980dcdddba51b76f78e17e6 Package: gDNAx Version: 1.8.0 Depends: R (>= 4.3) Imports: methods, BiocGenerics, BiocParallel, matrixStats, Biostrings, S4Vectors, IRanges, Seqinfo, GenomeInfoDb, GenomicRanges, GenomicFiles, GenomicAlignments, GenomicFeatures, Rsamtools, AnnotationHub, RColorBrewer, AnnotationDbi, bitops, plotrix, SummarizedExperiment, grDevices, graphics, stats, utils, cli Suggests: BiocStyle, knitr, rmarkdown, RUnit, TxDb.Hsapiens.UCSC.hg38.knownGene, gDNAinRNAseqData License: Artistic-2.0 MD5sum: 08ef57e75561db713971d6c647ef8b41 Package: gDR Version: 1.8.0 Depends: R (>= 4.2), gDRcore (>= 1.7.1), gDRimport (>= 1.7.1), gDRutils (>= 1.7.1) Suggests: BiocStyle, BumpyMatrix, futile.logger, gDRstyle (>= 1.7.1), gDRtestData (>= 1.7.1), kableExtra, knitr, markdown, purrr, rmarkdown, SummarizedExperiment, testthat, yaml License: Artistic-2.0 MD5sum: 75411a1a3adca6dba97c1518df0cc090 Package: gDRcore Version: 1.8.0 Depends: R (>= 4.2) Imports: BumpyMatrix, BiocParallel, checkmate, futile.logger, gDRutils (>= 1.7.1), MultiAssayExperiment, purrr, stringr, S4Vectors, SummarizedExperiment, data.table Suggests: BiocStyle, gDRstyle (>= 1.7.1), gDRimport (>= 1.7.1), gDRtestData (>= 1.7.1), IRanges, knitr, pkgbuild, qs, testthat, yaml License: Artistic-2.0 MD5sum: bc79a40d3be30a540b0093b634e3947e Package: gDRimport Version: 1.8.0 Depends: R (>= 4.2) Imports: assertthat, BumpyMatrix, checkmate, CoreGx, PharmacoGx, data.table, futile.logger, gDRutils (>= 1.7.1), magrittr, methods, MultiAssayExperiment, readxl, rio, S4Vectors, stats, stringi, SummarizedExperiment, tibble, tools, utils, XML, yaml, openxlsx Suggests: BiocStyle, gDRtestData (>= 1.7.1), gDRstyle (>= 1.7.1), knitr, purrr, qs, testthat License: Artistic-2.0 MD5sum: 1eb0abca21ef013cdf1485f6980e9ced Package: gDRstyle Version: 1.8.0 Depends: R (>= 4.2) Imports: BiocCheck, BiocManager, BiocStyle, checkmate, desc, git2r, lintr (>= 3.0.0), rcmdcheck, remotes, yaml, rjson, pkgbuild, withr Suggests: knitr, pkgdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 63ffaa3abfcd111ed47e0996fe10a111 Package: gDRutils Version: 1.8.0 Depends: R (>= 4.2) Imports: BiocParallel, BumpyMatrix, checkmate, data.table, digest, drc, jsonlite, jsonvalidate, methods, MultiAssayExperiment, S4Vectors, stats, stringr, SummarizedExperiment, qs, utils Suggests: BiocManager, BiocStyle, futile.logger, gDRstyle (>= 1.7.1), gDRtestData (>= 1.7.1), IRanges, knitr, lintr, mockery, purrr, rcmdcheck, rmarkdown, scales, testthat, tools, withr, yaml License: Artistic-2.0 MD5sum: eb344c7dd0f36b19c95fd73d772b7175 Package: GDSArray Version: 1.30.0 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: ff0e66132222156fcc5bcf582a940651 Package: gdsfmt Version: 1.46.0 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics License: LGPL-3 MD5sum: 091a16ed4e3137d82cba980c5f8bc085 Package: GEM Version: 1.36.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown License: Artistic-2.0 MD5sum: e2e183b9fbf5b5f40a774245a02fa35a Package: gemini Version: 1.24.0 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: 3595270eb17b533c1dcf84834c2ad20c Package: gemma.R Version: 3.6.0 Imports: magrittr, glue, memoise, jsonlite, data.table, rlang, lubridate, utils, stringr, SummarizedExperiment, Biobase, tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat, digest, R.utils, kableExtra, base64enc Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, listviewer, shiny License: Apache License (>= 2) MD5sum: daf679643640215bdcf57d3d6ba63c53 Package: genArise Version: 1.86.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: 9d92af5e423d2383cbdcc207cad3228c Package: geneAttribution Version: 1.36.0 Imports: utils, GenomicRanges, org.Hs.eg.db, BiocGenerics, Seqinfo, GenomicFeatures, IRanges, rtracklayer Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 56e47895a89ee91c2864eb0b73aa1723 Package: GeneBreak Version: 1.40.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: 4d8b6c0d4efe7ba1f6a4636729466bc5 Package: geneClassifiers Version: 1.34.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: 0970ace81667f2563d3daecf3bc062a5 Package: GeneExpressionSignature Version: 1.56.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: d5072d92b57572defe46b60576efb301 Package: genefilter Version: 1.92.0 Imports: MatrixGenerics (>= 1.11.1), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 MD5sum: ac13b00f4b27f0c93c5dd8a7227845f4 Package: genefu Version: 2.42.0 Depends: R (>= 4.1), survcomp, biomaRt, iC10, AIMS Imports: amap, impute, mclust, limma, graphics, stats, utils, iC10TrainingData Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown License: Artistic-2.0 MD5sum: 9651233d15cdf1de589c26a7b07271ad Package: GeneMeta Version: 1.82.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: ab2bd98b3fdcc599f2a34d383f39851f Package: GeneNetworkBuilder Version: 1.52.0 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, RCy3, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db License: GPL (>= 2) MD5sum: 3d5d9e8ea0c043da6acff56a7cfaddc5 Package: GeneOverlap Version: 1.46.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: c4cf3fa4721d45fed86b9cf456e3f75d Package: geneplast Version: 1.36.0 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, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: 0dd81c4de393aa218f3229bd674fb871 Package: geneplotter Version: 1.88.0 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, BiocStyle, knitr License: Artistic-2.0 MD5sum: 38e89f04a7d80d9aedaa66dc2034a0d9 Package: geneRecommender Version: 1.82.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: 5e5a883f2109475388c028e0289a4688 Package: GeneRegionScan Version: 1.66.0 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: c763c63e2c313b0918a2246fd45ca1b5 Package: geneRxCluster Version: 1.46.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 49e2a58b590e7b718b2d33acdcefd9ae Package: GeneSelectMMD Version: 2.54.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: 40d7e4dfb952783e14b9421db83fc79b Package: GENESIS Version: 2.40.0 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, GenomeInfoDb License: GPL-3 MD5sum: 88148d1668a7a291547c9c80d4fe8ba1 Package: GeneStructureTools Version: 1.30.0 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: b5fa5d2857da25a771e999343caac0e0 Package: geNetClassifier Version: 1.50.0 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: 1c6f02e8146e4016f04f263085443241 Package: GeneticsPed Version: 1.72.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: d2c623344f44d2d33ede178d28a5d3a7 Package: geneXtendeR Version: 1.36.0 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: 245354a7fb3e8a2a7baa6148c4ad3d91 Package: GENIE3 Version: 1.32.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle License: GPL (>= 2) MD5sum: 1e8435cedd7c9176d3daf58c2008a5b6 Package: genomation Version: 1.42.0 Depends: R (>= 3.5.0), grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, Seqinfo, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 4b1a08002566dfcaad5d237f71206076 Package: GenomAutomorphism Version: 1.12.0 Depends: R (>= 4.4.0), Imports: Biostrings, BiocGenerics, BiocParallel, Seqinfo, GenomicRanges, IRanges, matrixStats, XVector, dplyr, data.table, parallel, doParallel, foreach, methods, S4Vectors, stats, numbers, utils Suggests: spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr License: Artistic-2.0 MD5sum: 9300687104d71f44ee31a15dae6b356c Package: GenomeInfoDb Version: 1.46.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.47.6), IRanges (>= 2.41.1), Seqinfo (>= 0.99.2) Imports: stats, utils, UCSC.utils Suggests: GenomeInfoDbData, R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: bd013963a3d41d68cda5788eb2c3387b Package: genomeIntervals Version: 1.66.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: Seqinfo, GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: 2c54a6d402c3d9079f355caf412901b0 Package: genomes Version: 3.40.0 Depends: readr, curl License: GPL-3 MD5sum: 18a91ff9c6b3daecfdfd27965768019c Package: GenomicAlignments Version: 1.46.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.47.6), IRanges (>= 2.23.9), Seqinfo, GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel, cigarillo (>= 0.99.2) LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, knitr, BiocStyle License: Artistic-2.0 MD5sum: d6fc6c9e0933653f24fc4c28ec7400df Package: GenomicDataCommons Version: 1.33.1 Depends: R (>= 4.1.0) Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, tibble, tidyr Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table License: Artistic-2.0 MD5sum: 53729d07bdbb273d95935f1d328953e3 Package: GenomicDistributions Version: 1.18.0 Depends: R (>= 4.0), IRanges, GenomicRanges Imports: data.table, ggplot2, reshape2, methods, utils, Biostrings, plyr, dplyr, scales, broom, GenomeInfoDb, stats Suggests: AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData Enhances: BSgenome, extrafont, ensembldb, GenomicFeatures License: BSD_2_clause + file LICENSE MD5sum: 41bf6b77261e43d653cd951d2a46518c Package: GenomicFeatures Version: 1.62.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.51.2), S4Vectors (>= 0.47.6), IRanges (>= 2.37.1), Seqinfo (>= 0.99.2), GenomicRanges (>= 1.61.1), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, DBI, XVector, Biostrings (>= 2.77.2), rtracklayer (>= 1.69.1) Suggests: GenomeInfoDb, txdbmaker, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown License: Artistic-2.0 MD5sum: 43378ae072fd52838b28f3c8da459913 Package: GenomicFiles Version: 1.46.0 Depends: BiocGenerics, BiocParallel, GenomicRanges, MatrixGenerics, methods, Rsamtools (>= 2.25.1), rtracklayer (>= 1.69.1), SummarizedExperiment (>= 1.39.1) Imports: BiocBaseUtils, GenomeInfoDb (>= 1.45.7), GenomicAlignments (>= 1.45.1), IRanges, S4Vectors, Seqinfo, VariantAnnotation (>= 1.55.1) Suggests: BiocStyle, Biostrings, deepSNV, genefilter, Homo.sapiens, knitr, RNAseqData.HNRNPC.bam.chr14, RUnit, snpStats License: Artistic-2.0 MD5sum: 820049a9fb95e06d38641e47687202ed Package: genomicInstability Version: 1.16.0 Depends: R (>= 4.1.0), checkmate Imports: mixtools, SummarizedExperiment Suggests: SingleCellExperiment, ExperimentHub, pROC License: file LICENSE MD5sum: b20ae6ef3475ccffcdedb58883785798 Package: GenomicInteractionNodes Version: 1.14.0 Depends: R (>= 4.2.0), stats Imports: AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, Seqinfo, methods, IRanges, RBGL, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: file LICENSE MD5sum: 3e1add3919373917f901759843a07c15 Package: GenomicInteractions Version: 1.44.0 Depends: R (>= 3.5), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, Seqinfo, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 2568250f7d5355dbead352321b87d4b1 Package: GenomicOZone Version: 1.24.0 Depends: R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2 Imports: grDevices, stats, utils, plyr, gridExtra, lsr, parallel, ggbio, S4Vectors, IRanges, Seqinfo, Rdpack Suggests: readxl, GEOquery, knitr, rmarkdown License: LGPL (>= 3) MD5sum: e70d54c1fab434ea39e6e6e96b85ba12 Package: GenomicPlot Version: 1.8.0 Depends: R (>= 4.4.0), GenomicRanges (>= 1.46.1) Imports: methods, Rsamtools, parallel, tidyr, rtracklayer (>= 1.54.0), plyranges (>= 1.14.0), cowplot (>= 1.1.1), VennDiagram, ggplotify, Seqinfo, IRanges, ComplexHeatmap, RCAS (>= 1.20.0), scales (>= 1.2.0), GenomicAlignments (>= 1.30.0), edgeR, circlize, viridis, ggsignif (>= 0.6.3), ggsci (>= 2.9), ggpubr, grDevices, graphics, stats, utils, GenomicFeatures, genomation (>= 1.36.0), txdbmaker, ggplot2 (>= 3.3.5), BiocGenerics, dplyr, grid Suggests: knitr, rmarkdown, R.utils, Biobase, BiocStyle, testthat, AnnotationDbi, GenomeInfoDb License: GPL-2 MD5sum: 329437fea4a9e56087020e271159e00a Package: GenomicRanges Version: 1.62.0 Depends: R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.45.2), IRanges (>= 2.43.6), Seqinfo (>= 0.99.3) Imports: utils, stats LinkingTo: S4Vectors, IRanges Suggests: GenomeInfoDb, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.77.2), SummarizedExperiment (>= 1.39.1), Rsamtools, GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, txdbmaker, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 51bc2fcb7322ebed2876ca9197d71b71 Package: GenomicScores Version: 2.22.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache, IRanges (>= 2.3.23), Biostrings, Seqinfo, GenomeInfoDb (>= 1.45.5), AnnotationHub, rhdf5, DelayedArray, HDF5Array Suggests: RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard, BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38, MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v4.0.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: a528c21335654d2e5a157ca2fe91ebbd Package: GenomicSuperSignature Version: 1.18.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils License: Artistic-2.0 MD5sum: 2a241aa3ba4c92110dfa82cf772fde2b Package: GenomicTuples Version: 1.44.0 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), Seqinfo, S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, covr, GenomicAlignments, Biostrings, GenomeInfoDb License: Artistic-2.0 MD5sum: e0cc71dc49629c1a7d8c7e07081c6b9f Package: GenProSeq Version: 1.14.0 Depends: keras, mclust, R (>= 4.2) Imports: tensorflow, word2vec, DeepPINCS, ttgsea, CatEncoders, reticulate, stats Suggests: VAExprs, stringdist, knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: c2583bbeba71af31e3c136461baf65b2 Package: GeoDiff Version: 1.16.0 Depends: R (>= 4.1.0), Biobase Imports: Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods, graphics, stats, testthat, GeomxTools, NanoStringNCTools LinkingTo: Rcpp, RcppArmadillo, roptim Suggests: knitr, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: e7e8dff3520557944774d90bd8efdde7 Package: GEOfastq Version: 1.18.0 Imports: xml2, rvest, stringr, RCurl, doParallel, foreach, plyr Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: a1d1513ebfedf3c52b36c4ee30bd2094 Package: GEOmetadb Version: 1.72.0 Depends: R.utils,RSQLite Suggests: knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud License: Artistic-2.0 MD5sum: 6abf2c8dab1d524c6d0262f6bb42434a Package: geomeTriD Version: 1.4.0 Depends: R (>= 4.4.0) Imports: aricode, BiocGenerics, Biostrings, clue, cluster, dbscan, future.apply, Seqinfo, GenomicRanges, graphics, grDevices, grid, htmlwidgets, igraph, InteractionSet, IRanges, MASS, Matrix, methods, plotrix, progressr, RANN, rgl, rjson, S4Vectors, scales, stats, trackViewer Suggests: RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, manipulateWidget, shiny, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 314f1f4f6deff77ceec9e863b67b3ff8 Package: GeomxTools Version: 3.14.0 Depends: R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors Imports: BiocGenerics, rjson, readxl, EnvStats, reshape2, methods, utils, stats, data.table, lmerTest, dplyr, stringr, grDevices, graphics, GGally, rlang, ggplot2, SeuratObject Suggests: rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork License: MIT MD5sum: 663c9c276a353db1bb3e677e773f4b50 Package: GEOquery Version: 2.78.0 Depends: R (>= 4.1.0), methods, Biobase Imports: readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr, limma, curl, rentrez, R.utils, stringr, SummarizedExperiment, S4Vectors, rvest, httr2 Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr, markdown, quarto, DropletUtils, SingleCellExperiment License: MIT + file LICENSE MD5sum: 9ea0c9596f67a1be1f7c5e29225e988d Package: GEOsubmission Version: 1.62.0 Imports: affy, Biobase, utils License: GPL (>= 2) MD5sum: e38740c32e0bab6d22abf02301f6cbe2 Package: GeoTcgaData Version: 2.10.0 Depends: R (>= 4.2.0) Imports: utils, data.table, plyr, cqn, topconfects, stats, SummarizedExperiment, methods Suggests: knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr, clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq, testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery, BiocGenerics License: Artistic-2.0 MD5sum: 2e238eac2d5e4bc240b829b7f0f26697 Package: gep2pep Version: 1.30.0 Imports: repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators Suggests: WriteXLS, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 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1.8.0 Depends: R (>= 4.3.0), ggplot2 Imports: DESeq2, dplyr, edgeR, ggrepel, glue, janitor, limma, magrittr, methods, purrr, rlang, scales, stats, stringr, tibble, tidyr Suggests: airway, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat, vdiffr License: MIT + file LICENSE MD5sum: fc1b77641a71f10d32323a4009bb2d82 Package: ggbio Version: 1.58.0 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), Seqinfo, GenomeInfoDb (>= 1.45.5), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1), GenomicAlignments (>= 1.45.1), BSgenome (>= 1.77.1), VariantAnnotation (>= 1.55.1), rtracklayer (>= 1.69.1), GenomicFeatures (>= 1.61.4), OrganismDbi, ensembldb (>= 2.33.1), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: c8b9a010d1c9c4bb45842938f56411da Package: ggcyto Version: 1.38.0 Depends: methods, ggplot2(>= 3.5.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 4.3.1) Imports: plyr, scales, hexbin, data.table, RColorBrewer, gridExtra, rlang Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr License: file LICENSE MD5sum: f5aa6378f8275e7b99c752ff0d937032 Package: ggkegg Version: 1.8.0 Depends: R (>= 4.3.0), ggplot2, ggraph, XML, igraph, tidygraph Imports: BiocFileCache, data.table, dplyr, magick, patchwork, shadowtext, stringr, tibble, methods, utils, stats, grDevices, gtable Suggests: knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, AnnotationDbi, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 51a1a3ad3b20b31918863ffa7ab1682d Package: ggmanh Version: 1.14.0 Depends: methods, ggplot2 Imports: gdsfmt, ggrepel, grDevices, paletteer, RColorBrewer, rlang, scales, SeqArray (>= 1.32.0), stats, tidyr, dplyr, pals, magrittr Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0), GenomicRanges License: MIT + file LICENSE MD5sum: 8f84bea3da3be6940954c022957acf16 Package: ggmsa Version: 1.16.0 Depends: R (>= 4.1.0) Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot, RColorBrewer, ggfun (>= 0.2.0), ggforce, dplyr, R4RNA, grDevices, seqmagick, grid, methods, ggtree (>= 1.17.1) Suggests: ggtreeExtra, ape, cowplot, knitr, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, statebins, prettydoc, testthat (>= 3.0.0), yulab.utils License: Artistic-2.0 MD5sum: 290c9a72e0d86d4646a992961775e76a Package: GGPA Version: 1.22.0 Depends: R (>= 4.0.0), stats, methods, graphics, GGally, network, sna, scales, matrixStats Imports: Rcpp (>= 0.11.3) LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle License: GPL (>= 2) MD5sum: 355c2ff48202d9cd88073e11e5e2109a Package: ggsc Version: 1.8.0 Depends: R (>= 4.1.0) Imports: Rcpp, RcppParallel, cli, dplyr, ggfun (>= 0.1.5), ggplot2, grDevices, grid, methods, rlang, scattermore, stats, Seurat, SingleCellExperiment, SummarizedExperiment, tidydr, tidyr, tibble, utils, RColorBrewer, yulab.utils, scales LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph, knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater, scatterpie (>= 0.2.4), scuttle, shadowtext, sf, SeuratObject, SpatialExperiment, STexampleData, testthat (>= 3.0.0), MASS License: Artistic-2.0 MD5sum: 8f4103328b6e69496dbb416ade7a3d2a Package: ggseqalign Version: 1.4.0 Depends: R (>= 4.4.0) Imports: pwalign, dplyr, ggplot2 Suggests: Biostrings, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 5a0b44248e256507256047de4e210538 Package: ggspavis Version: 1.16.0 Depends: ggplot2 Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, ggrepel, RColorBrewer, scales, grDevices, methods, stats Suggests: BiocStyle, rmarkdown, knitr, OSTA.data, VisiumIO, arrow, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork License: MIT + file LICENSE MD5sum: 9969c2855dccdbdae313e1cfbf6a969c Package: ggtree Version: 4.0.1 Depends: R (>= 4.2.0) Imports: ape, aplot, dplyr, ggplot2 (>= 4.0.0), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.1.7), yulab.utils (>= 0.1.6), tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0), utils, scales, stats, cli, ggiraph (>= 0.9.1) Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue, Biostrings License: Artistic-2.0 MD5sum: 499b7e3ba06410c79341e088fefc5363 Package: ggtreeDendro Version: 1.12.0 Depends: ggtree (>= 3.5.3) Imports: ggplot2, stats, tidytree, utils Suggests: aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust, rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils License: Artistic-2.0 MD5sum: 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globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: fd1c513d13901d485c86854df4d3591d Package: globalSeq Version: 1.38.0 Depends: R (>= 3.0.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 MD5sum: abbb5da4fc76eba1686be2874ed5a980 Package: GloScope Version: 2.0.0 Depends: R (>= 4.4.0) Imports: utils, stats, MASS, mclust, ggplot2, RANN, FNN, BiocParallel, mvnfast, SingleCellExperiment, rlang, RColorBrewer, pheatmap, vegan, cluster, boot, permute Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown, zellkonverter License: Artistic-2.0 MD5sum: 8dcc7fd44b26d332384b672f052d40fc Package: GmicR Version: 1.24.0 Imports: AnnotationDbi, ape, bnlearn, Category, DT, doParallel, foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db, org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics, reshape2, stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 + file LICENSE MD5sum: 1766d48f906a05a1bf3600649b6e160d Package: gmoviz Version: 1.22.0 Depends: circlize, GenomicRanges, graphics, R (>= 4.0) Imports: grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics, Biostrings, Seqinfo, methods, GenomicAlignments, GenomicFeatures, IRanges, rtracklayer, pracma, colorspace, S4Vectors Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager, GenomeInfoDb License: GPL-3 MD5sum: 8501df72004be256d578d5a8c6cbc6ab Package: GMRP Version: 1.38.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: 0aee57e3802d1ee1c31fda61b1476550 Package: GNET2 Version: 1.26.0 Depends: R (>= 3.6) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment,dplyr,igraph, grDevices, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 MD5sum: 3fd9658ef39982084fec3065d1d45c84 Package: GNOSIS Version: 1.8.0 Depends: R (>= 4.3.0), shiny, shinydashboard, shinydashboardPlus, dashboardthemes, shinyWidgets, shinymeta, tidyverse, operator.tools, maftools Imports: DT, fontawesome, shinycssloaders, cBioPortalData, shinyjs, reshape2, RColorBrewer, survival, survminer, stats, compareGroups, rpart, partykit, DescTools, car, rstatix, fabricatr, shinylogs, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 5a275676e0d23c09adb90a40621dea2d Package: GOexpress Version: 1.44.0 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), randomForest (>= 4.6), RCurl (>= 1.95) Suggests: BiocStyle License: GPL (>= 3) MD5sum: eee5070e2a46ebfcf53b7c230a0c0e96 Package: GOfuncR Version: 1.30.0 Depends: R (>= 3.4), vioplot (>= 0.2), Imports: Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils, grDevices, graphics, stats, LinkingTo: Rcpp Suggests: Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat License: GPL (>= 2) MD5sum: 11320a77b6f77b3f5f26f4c0eeeb04e0 Package: GOpro Version: 1.36.0 Depends: R (>= 3.5.0) 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: 2f262c6be61e3fd1337acab906c51f9f Package: goProfiles Version: 1.72.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: a04a9f6901bec825b3096ff75848e3a1 Package: GOSemSim Version: 2.36.0 Depends: R (>= 4.2.0) Imports: AnnotationDbi, DBI, digest, GO.db, methods, rlang, R.utils, stats, utils, yulab.utils (>= 0.2.1) LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, readr, rmarkdown, testthat, tidyr, tidyselect, ROCR License: Artistic-2.0 MD5sum: 435c15f95b31c56d4b4a5606517d016c Package: goseq Version: 1.62.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2) Imports: mgcv, graphics, stats, utils, AnnotationDbi, GO.db, BiocGenerics, methods, rtracklayer, GenomicFeatures, Seqinfo Suggests: edgeR, org.Hs.eg.db License: LGPL (>= 2) MD5sum: eddba5e3dd1fe8b77d8cf8d797e9de80 Package: goSorensen Version: 1.12.0 Depends: R (>= 4.4) Imports: clusterProfiler, goProfiles, org.Hs.eg.db, parallel, stats, stringr Suggests: BiocManager, BiocStyle, knitr, rmarkdown, org.At.tair.db, 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.EcSakai.eg.db, org.EcK12.eg.db, org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Pt.eg.db, org.Xl.eg.db, GO.db, ggplot2, ggrepel, DT, magick License: GPL-3 MD5sum: 582780424003dddc55b93a62b11bf300 Package: goSTAG Version: 1.34.0 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 6e641af1c467f7facc2e87145e60db11 Package: GOstats Version: 2.76.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.43.2), graph Imports: methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr License: Artistic-2.0 MD5sum: 030a191cac6c9592349a9cdc5c3aa1af Package: GOTHiC Version: 1.46.0 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, Seqinfo Suggests: HiCDataLymphoblast Enhances: parallel License: GPL-3 MD5sum: e98adc6c982bd37f721e000342288798 Package: goTools Version: 1.84.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 MD5sum: 0fc8cff50f88324237f1fc59ab90505f Package: GPA Version: 1.22.0 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: 90d77df98b16351db6d13273c81757a9 Package: gpls Version: 1.82.0 Imports: stats Suggests: MASS License: Artistic-2.0 MD5sum: 20b075e3f6ab6846a958e1622fc14418 Package: GrafGen Version: 1.6.0 Depends: R (>= 4.3.0) Imports: stats, utils, graphics, ggplot2, plotly, scales, RColorBrewer, dplyr, grDevices, GenomicRanges, shiny, cowplot, ggpubr, stringr, rlang Suggests: knitr, rmarkdown, RUnit, BiocManager, BiocGenerics, BiocStyle, devtools License: GPL-2 MD5sum: 20b519c01ad31d8ff308872e8c8750dd Package: GRaNIE Version: 1.14.0 Depends: R (>= 4.2.0) Imports: futile.logger, checkmate, patchwork (>= 1.2.0), reshape2, data.table, matrixStats, Matrix, GenomicRanges, RColorBrewer, ComplexHeatmap, DESeq2, circlize, progress, utils, methods, stringr, tools, scales, igraph, S4Vectors, ggplot2, rlang, Biostrings, GenomeInfoDb (>= 1.34.8), SummarizedExperiment, forcats, gridExtra, limma, tidyselect, readr, grid, tidyr (>= 1.3.0), dplyr, stats, grDevices, graphics, magrittr, tibble, viridis, colorspace, biomaRt, topGO, AnnotationHub, ensembldb Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Mmulatta.UCSC.rheMac10, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm39.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW, clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA, variancePartition, purrr, EDASeq, JASPAR2022, JASPAR2024, RSQLite, TFBSTools, motifmatchr, rbioapi, LDlinkR License: Artistic-2.0 MD5sum: b11d38d7b9d7c015b7056dc059966480 Package: graper Version: 1.26.0 Depends: R (>= 3.6) Imports: Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: a5e2e95b55c05406db656e93edff636f Package: graph Version: 1.88.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.11) Imports: stats, stats4, utils Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle, knitr Enhances: Rgraphviz License: Artistic-2.0 MD5sum: 7899aae4f9fe254fffba7f464ed08696 Package: GraphAlignment Version: 1.74.0 License: file LICENSE License_restricts_use: yes MD5sum: 4883ff753d4e6cabbda05f39fe02f893 Package: GraphAT Version: 1.82.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL MD5sum: 7f1ad7aebe22fdaf06c87ae0e9c20a97 Package: graphite Version: 1.56.0 Depends: R (>= 4.2), methods Imports: AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats, utils, graphics, rlang, lifecycle, purrr, dir.expiry Suggests: checkmate, a4Preproc, ALL, BiocStyle, clipper, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) License: AGPL-3 MD5sum: 106b4fbb24de6211bba3ad8cbe5e7173 Package: GRENITS Version: 1.62.0 Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) Imports: graphics, grDevices, reshape2, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: network License: GPL (>= 2) MD5sum: 0f2bce8103a3e1904432f27e0ebb20d3 Package: GreyListChIP Version: 1.42.0 Depends: R (>= 4.0), methods, GenomicRanges Imports: GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, Seqinfo, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, RUnit, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: f35bcd340639dbc5491e024e47469342 Package: GRmetrics Version: 1.36.0 Depends: R (>= 4.0), SummarizedExperiment Imports: drc, plotly, ggplot2, S4Vectors, stats Suggests: knitr, rmarkdown, BiocStyle, tinytex License: GPL-3 MD5sum: 931795c2e59931f2c534094537ac1ca6 Package: groHMM Version: 1.44.0 Depends: R (>= 4.1.0), MASS, parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Seqinfo, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), rtracklayer (>= 1.39.7) Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 4c4bc079638451724340515d33d2623b Package: GSALightning Version: 1.38.0 Depends: R (>= 3.3.0) Imports: Matrix, data.table, stats Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 36ac57895180cd8aac53d33946815d45 Package: GSAR Version: 1.44.0 Depends: R (>= 3.0.1), igraph (>= 0.7.1) Imports: stats, graphics Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle License: GPL (>= 2) MD5sum: 5ea3a3add825a76a6f28b2712c54e22d Package: GSCA Version: 2.40.0 Depends: shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5, R(>= 2.10.0) Imports: graphics Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr License: GPL (>= 2) MD5sum: 4a4c1ce068ddb1b763cd14fa8c8d40cd Package: gscreend Version: 1.24.0 Depends: R (>= 3.6) Imports: SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics Suggests: knitr, testthat, rmarkdown, BiocStyle License: GPL-3 MD5sum: a9b3ead92ccfaf2789fb2abace1123c5 Package: GSEABase Version: 1.72.0 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, RUnit License: Artistic-2.0 MD5sum: 7c8307c009cb196d95c32db475fbe42a Package: GSEABenchmarkeR Version: 1.30.0 Depends: R (>= 4.5.0), 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: 1c39de22444a00f6d282f2a6656f7268 Package: GSEAlm Version: 1.70.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: 8d4fa0979e0f8b56d1320404bde41947 Package: GSEAmining Version: 1.20.0 Depends: R (>= 4.0) Imports: dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud, stringr, gridExtra, rlang, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat, tm License: GPL-3 | file LICENSE MD5sum: 54542740969104a9388c229387d44835 Package: gsean Version: 1.30.0 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi, knitr, plotly, WGCNA, rmarkdown License: Artistic-2.0 MD5sum: d16d2f87f322ec15a7a979e4779ca3fb Package: GSgalgoR Version: 1.20.0 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: 576cfc1401b164639628496889513741 Package: GSReg Version: 1.44.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi Suggests: GenomicRanges, GSBenchMark License: GPL-2 MD5sum: 7f2e46865d44e487fb0c168ef574d046 Package: GSRI Version: 2.58.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 MD5sum: b20de43efbaadfb7f4c4bc4d6fd4f6d8 Package: GSVA Version: 2.4.0 Depends: R (>= 3.5.0) Imports: methods, stats, utils, graphics, BiocGenerics, MatrixGenerics, S4Vectors, S4Arrays, HDF5Array, SparseArray, DelayedArray, IRanges, Biobase, SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel, BiocParallel, SingleCellExperiment, SpatialExperiment, sparseMatrixStats, DelayedMatrixStats, BiocSingular, cli LinkingTo: cli Suggests: RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, sva, ggplot2, TENxPBMCData, scuttle, scran, igraph, shiny, shinydashboard, ggplot2, data.table, plotly, future, promises, shinybusy, shinyjs License: Artistic-2.0 MD5sum: e2b2aa340dcf1e9555e04fd225851025 Package: gtrellis Version: 1.42.0 Depends: R (>= 3.1.2), grid, IRanges, GenomicRanges Imports: circlize (>= 0.4.8), GetoptLong, grDevices, utils Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff License: MIT + file LICENSE MD5sum: d3814f4739e8ef6d4df8aad1af1e0797 Package: GUIDEseq Version: 1.40.0 Depends: R (>= 3.5.0), GenomicRanges, BiocGenerics Imports: Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma,dplyr, GenomicFeatures, rio, tidyr, tools, methods, purrr, ggplot2, openxlsx, patchwork, rlang Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 37e5ec9f8fce1d585bf725be0e510b61 Package: Guitar Version: 2.26.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges, magrittr, ggplot2, methods, stats,utils ,knitr,dplyr License: GPL-2 MD5sum: d4b52a09ba543032cc3ea259ec618ffe Package: gVenn Version: 1.0.0 Depends: R (>= 4.5.0) Imports: ComplexHeatmap, eulerr, GenomicRanges, IRanges, lubridate, methods, rtracklayer, stringr, writexl Suggests: testthat (>= 3.0.0), ggplot2, withr, knitr, rmarkdown License: MIT + file LICENSE MD5sum: e5c3afd52780cde44048769a0ec63466 Package: Gviz Version: 1.54.0 Depends: R (>= 4.3), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.61.1), grid Imports: XVector (>= 0.5.7), rtracklayer (>= 1.69.1), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.61.4), ensembldb (>= 2.11.3), BSgenome (>= 1.77.1), Biostrings (>= 2.77.2), biovizBase (>= 1.13.8), Rsamtools (>= 2.25.1), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>= 1.45.1), Seqinfo, GenomeInfoDb, BiocGenerics (>= 0.11.3), digest(>= 0.6.8), graphics, grDevices, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 961d706956f752199d64c75208f55ab4 Package: GWAS.BAYES Version: 1.20.0 Depends: R (>= 4.3.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), limma (>= 3.54.0), stats (>= 4.2.2), MASS (>= 7.3-58.1) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP License: GPL-3 + file LICENSE MD5sum: a133b7d05947a1de2607db9614e2d753 Package: gwascat Version: 2.42.0 Depends: R (>= 4.1.0), methods Imports: S4Vectors (>= 0.9.25), IRanges, Seqinfo, GenomeInfoDb, GenomicRanges (>= 1.29.6), GenomicFeatures, readr, Biostrings, AnnotationDbi, BiocFileCache, snpStats, VariantAnnotation, AnnotationHub, data.table, tibble Suggests: DO.db, DT, knitr, RBGL, testthat, rmarkdown, dplyr, Gviz, Rsamtools, rtracklayer, graph, ggbio, DelayedArray, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BiocStyle Enhances: SNPlocs.Hsapiens.dbSNP144.GRCh37 License: Artistic-2.0 MD5sum: 3bc22ea0559793d73db59f9a28f096d2 Package: GWASTools Version: 1.56.0 Depends: Biobase Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr License: Artistic-2.0 MD5sum: 88c24819f844f8e2aa2a1764b36dde95 Package: gwasurvivr Version: 1.28.0 Depends: R (>= 3.4.0) Imports: GWASTools, survival, VariantAnnotation, parallel, matrixStats, SummarizedExperiment, stats, utils, SNPRelate Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: f009bcad0f4fb1bbf5e8f3e99304af84 Package: GWENA Version: 1.20.0 Depends: R (>= 4.1) Imports: WGCNA (>= 1.67), dplyr (>= 0.8.3), dynamicTreeCut (>= 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LinkingTo: Rhdf5lib, S4Vectors Suggests: BiocParallel, ExperimentHub, TENxBrainData, HDF5Array, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 4510f6a3034e429604adec1d61c82203 Package: h5vc Version: 2.44.0 Depends: grid, gridExtra, ggplot2 Imports: rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>= 2.13.1), methods, GenomicRanges, abind, BiocParallel, BatchJobs, h5vcData, GenomeInfoDb LinkingTo: Rhtslib (>= 1.99.1) Suggests: knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown License: GPL (>= 3) MD5sum: 4f64ff679be88ef65ebb112ab3bd4516 Package: hapFabia Version: 1.52.0 Depends: R (>= 3.6.0), Biobase, fabia (>= 2.3.1) Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: 897313005f5d00702ec109492b88cba7 Package: Harman Version: 1.38.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel, methods, matrixStats LinkingTo: Rcpp Suggests: HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva License: GPL-3 + file LICENCE MD5sum: 64f2e3de92b0292f5655c4896ebd7d74 Package: HarmonizR Version: 1.8.0 Depends: R (>= 4.2.0) Imports: doParallel (>= 1.0.16), foreach (>= 1.5.1), janitor (>= 2.1.0), plyr (>= 1.8.6), sva (>= 3.36.0), seriation (>= 1.3.5), limma (>= 3.46.0), SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 1782247201597e85a9355d894940aab0 Package: HDF5Array Version: 1.37.0 Depends: R (>= 3.4), methods, SparseArray (>= 1.7.5), DelayedArray (>= 0.33.5), h5mread (>= 0.99.4) Imports: utils, stats, tools, Matrix, BiocGenerics (>= 0.51.2), S4Vectors, IRanges, S4Arrays (>= 1.1.1), rhdf5 Suggests: BiocParallel, GenomicRanges, SummarizedExperiment (>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, SingleCellExperiment, DelayedMatrixStats, genefilter, 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grDevices, stats, RColorBrewer Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) MD5sum: 51e999bb4726704d5f2491e323f0a479 Package: HelloRanges Version: 1.36.0 Depends: methods, BiocGenerics, S4Vectors (>= 0.17.39), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.10), Biostrings (>= 2.41.3), BSgenome, GenomicFeatures (>= 1.31.5), VariantAnnotation (>= 1.19.3), Rsamtools, GenomicAlignments (>= 1.15.7), rtracklayer (>= 1.33.8), Seqinfo, SummarizedExperiment, BiocIO Imports: docopt, stats, tools, utils Suggests: GenomeInfoDb, HelloRangesData, BiocStyle, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 0d0b5ccd69bf5353b7d8ee71285ad049 Package: HELP Version: 1.68.0 Depends: R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods License: GPL (>= 2) MD5sum: 620f97b71e3e9b1c11921efb8116ba63 Package: hermes Version: 1.14.0 Depends: ggfortify, R (>= 4.1), SummarizedExperiment (>= 1.16) Imports: assertthat, Biobase, BiocGenerics, biomaRt, checkmate (>= 2.1), circlize, 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ggrastr, scales, stats, utils Suggests: HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: dc8ffa9c3e503cdf7803c7fa72b35ae8 Package: HiCool Version: 1.10.0 Depends: R (>= 4.2), HiCExperiment Imports: BiocIO, S4Vectors, GenomicRanges, IRanges, InteractionSet, vroom, basilisk.utils, basilisk, reticulate, rmarkdown, rmdformats, plotly, dplyr, stringr, sessioninfo, utils Suggests: HiContacts, HiContactsData, AnnotationHub, BiocFileCache, BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: d9b3e57efa99d570b32ebd45293ecdab Package: HiCParser Version: 1.2.0 Imports: data.table, InteractionSet, GenomicRanges, SummarizedExperiment, Rcpp (>= 1.0.12), S4Vectors, gtools, pbapply, BiocGenerics, Seqinfo LinkingTo: Rcpp Suggests: rhdf5, BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0) License: LGPL MD5sum: 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tidyr, grDevices, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 574473354ca20b09ea81fdf525cd5694 Package: HIPPO Version: 1.22.0 Depends: R (>= 3.6.0) Imports: ggplot2, graphics, stats, reshape2, gridExtra, Rtsne, umap, dplyr, rlang, magrittr, irlba, Matrix, SingleCellExperiment, ggrepel Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: ddad4f0b71a5a6530201ceefa61f9806 Package: HIREewas Version: 1.28.0 Depends: R (>= 3.5.0) Imports: quadprog, gplots, grDevices, stats Suggests: BiocStyle, knitr, BiocGenerics License: GPL (>= 2) MD5sum: e50eaebdffda73c722791125613d0595 Package: HiTC Version: 1.54.0 Depends: R (>= 2.15.0), methods, IRanges, GenomicRanges Imports: Biostrings, graphics, grDevices, rtracklayer, RColorBrewer, Matrix, parallel, Seqinfo Suggests: BiocStyle, HiCDataHumanIMR90, BSgenome.Hsapiens.UCSC.hg18 License: Artistic-2.0 MD5sum: 364b875b819f3f05f02877eeee27c9a6 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Rcpp Suggests: testthat (>= 3.0.0), BiocStyle License: GPL-3 + file LICENSE MD5sum: f2f71ce19ba2ba12c7368b492586e18d Package: hopach Version: 2.70.0 Depends: R (>= 2.11.0), cluster, Biobase, methods Imports: graphics, grDevices, stats, utils, BiocGenerics License: GPL (>= 2) MD5sum: 18e47f8dc28ee2d5b9dca8de92ef7839 Package: HPAanalyze Version: 1.28.0 Depends: R (>= 3.5.0) Imports: dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils, gridExtra Suggests: knitr, rmarkdown, devtools, BiocStyle License: GPL-3 + file LICENSE MD5sum: 6a94e4ed3eca784c87c3d6bd786dbff1 Package: hpar Version: 1.52.0 Depends: R (>= 3.5.0) Imports: utils, ExperimentHub Suggests: org.Hs.eg.db, GO.db, AnnotationDbi, knitr, BiocStyle, testthat, rmarkdown, dplyr, DT License: Artistic-2.0 MD5sum: f95cdb29e107aa87ccaf0082183d66fc Package: HTqPCR Version: 1.64.0 Depends: Biobase, RColorBrewer, limma Imports: affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils Suggests: statmod License: Artistic-2.0 MD5sum: 3cbea9e9681365659f45353a24eea603 Package: HTSFilter Version: 1.50.0 Depends: R (>= 4.0.0) Imports: edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices, graphics, methods Suggests: EDASeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: ae1aa558ee0e5fecc4390b1ac9f4c11e Package: HuBMAPR Version: 1.4.0 Depends: R (>= 4.4.0) Imports: httr2, dplyr, tidyr, tibble, rjsoncons, utils, stringr, whisker, purrr, rlang Suggests: testthat (>= 3.0.0), knitr, ggplot2, rmarkdown, BiocStyle, pryr License: Artistic-2.0 MD5sum: 71edf40f6d4a368b136e920522c863bb Package: HubPub Version: 1.18.0 Imports: available, usethis, biocthis, dplyr, aws.s3, fs, BiocManager, utils Suggests: AnnotationHubData, ExperimentHubData, GenomeInfoDbData, testthat, knitr, rmarkdown, BiocStyle, License: Artistic-2.0 MD5sum: 779716792a61653863827e78f38b0df1 Package: hummingbird Version: 1.20.0 Depends: R (>= 4.0) Imports: Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 5d5bfb32c7cec310db98141a86bf7262 Package: HVP Version: 1.0.0 Imports: Matrix, methods, stats Suggests: SingleCellExperiment, SummarizedExperiment, Seurat, SeuratObject, ggplot2, progress, testthat, splatter, scater, devtools, knitr, rmarkdown, BiocStyle, ExperimentHub License: MIT + file LICENSE MD5sum: 33859db852e14b3045deab4e261899d2 Package: HybridExpress Version: 1.6.0 Depends: R (>= 4.3.0) Imports: ggplot2, patchwork, rlang, DESeq2, SummarizedExperiment, stats, methods, RColorBrewer, ComplexHeatmap, grDevices, BiocParallel Suggests: BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0) License: GPL-3 MD5sum: 9cc0cca7259430ea5a8543df2a0ebb5f Package: HybridMTest Version: 1.54.0 Depends: R (>= 2.9.0), Biobase, fdrtool, MASS, survival Imports: stats License: GPL (>= 2) MD5sum: ce576495ea9e2aa4b94e3884d19df9fd Package: hyperdraw Version: 1.62.0 Depends: R (>= 2.9.0) Imports: 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GenomeInfoDb, knitr, rmarkdown, Rsubread (>= 1.29.0), testthat License: GPL-3 + file LICENSE MD5sum: 1670dfdf3203a64b83d58426372b84f0 Package: iCheck Version: 1.40.0 Depends: R (>= 3.2.0), Biobase, lumi, gplots Imports: stats, graphics, preprocessCore, grDevices, randomForest, affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest, scatterplot3d, utils License: GPL (>= 2) MD5sum: b7727430d9768c58daaecaf94878204e Package: iChip Version: 1.64.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) MD5sum: b375f76aa400354708f6f3137134d685 Package: iClusterPlus Version: 1.46.0 Depends: R (>= 4.1.0), parallel Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 1c5f1b4d2894bb626e1271dd86c70922 Package: iCNV Version: 1.30.0 Depends: R (>= 3.3.1), CODEX Imports: fields, ggplot2, truncnorm, tidyr, data.table, dplyr, grDevices, graphics, stats, utils, rlang Suggests: knitr, rmarkdown, WES.1KG.WUGSC License: GPL-2 MD5sum: 59f79948a2a7b79184fadb29c67d84b2 Package: iCOBRA Version: 1.38.0 Depends: R (>= 4.4.0) Imports: shiny (>= 0.9.1.9008), shinydashboard, shinyBS, reshape2, ggplot2 (>= 3.4.0), scales, ROCR, dplyr, DT, limma, methods, UpSetR, utils, rlang Suggests: knitr, markdown, rmarkdown, testthat License: GPL (>= 2) MD5sum: 1cc570ec97d67894ac1325ee9753ee1b Package: ideal Version: 2.4.0 Depends: topGO Imports: DESeq2, SummarizedExperiment, mosdef (>= 1.1.0), GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0), heatmaply, plotly, pheatmap, IHW, gplots, UpSetR, goseq, stringr, dplyr, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, DT, rentrez, rintrojs, rlang, ggrepel, knitr, rmarkdown, shinyAce, BiocParallel, grDevices, graphics, base64enc, methods, utils, stats Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, htmltools, edgeR License: MIT + file LICENSE MD5sum: e8f5bf04aee43f2e980a602478efff07 Package: IdeoViz Version: 1.46.0 Depends: R (>= 3.5.0), Biobase, IRanges, 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(>= 0.4), htmltools (>= 0.3.6), knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: c0730ac2f8a304ace5d4075fc3966b50 Package: IFAA Version: 1.12.0 Depends: R (>= 4.2.0), Imports: mathjaxr, doRNG, foreach (>= 1.4.3), Matrix (>= 1.4-0), HDCI (>= 1.0-2), parallel (>= 3.3.0), doParallel (>= 1.0.11), parallelly , glmnet, stats, utils, SummarizedExperiment, stringr, S4Vectors, DescTools, MatrixExtra, methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle License: GPL-2 MD5sum: 3b8ebc499689d4c626b0eec811d20863 Package: igblastr Version: 1.0.0 Depends: R (>= 4.2.0), tibble, Biostrings Imports: methods, utils, stats, tools, R.utils, curl, httr, xml2, rvest, xtable, jsonlite, S4Vectors, IRanges, GenomeInfoDb Suggests: GenomicAlignments, parallel, testthat, knitr, rmarkdown, BiocStyle, ggplot2, dplyr, scales, ggseqlogo License: Artistic-2.0 MD5sum: 56114326480384a3028d151f1ced173d Package: iGC Version: 1.40.0 Depends: R (>= 3.2.0) Imports: plyr, data.table Suggests: BiocStyle, knitr, rmarkdown Enhances: doMC License: GPL-2 MD5sum: f4bee4552b3be2c353bad3dc9152212c Package: IgGeneUsage Version: 1.24.0 Depends: R (>= 4.2.0) Imports: methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0), SummarizedExperiment, tidyr LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, ggrepel, patchwork License: MIT + file LICENSE MD5sum: f6b75df1569f6f938f960f3b0c5c49c7 Package: igvR Version: 1.30.0 Depends: R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz (>= 2.17.1) Imports: methods, BiocGenerics, httpuv, utils, rtracklayer, VariantAnnotation, RColorBrewer, httr Suggests: RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo License: MIT + file LICENSE MD5sum: 786fc28d4d920b59939463a75b905fcb Package: igvShiny Version: 1.6.0 Depends: R (>= 3.5.0), GenomicRanges, methods, shiny Imports: BiocGenerics, checkmate, futile.logger, GenomeInfoDbData, htmlwidgets, httr, jsonlite, randomcoloR, utils Suggests: BiocStyle, GenomicAlignments, knitr, Rsamtools, rtracklayer, RUnit, shinytest2, VariantAnnotation License: MIT + file LICENSE MD5sum: 94f075e08f0fa2f0fcff71133c7ff26e Package: IHW Version: 1.38.0 Depends: R (>= 3.3.0) Imports: methods, slam, lpsymphony, fdrtool, BiocGenerics Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools License: Artistic-2.0 MD5sum: 41d6b75478c64e67fe89e2c90b560682 Package: illuminaio Version: 0.52.0 Imports: base64 Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2), BiocStyle License: GPL-2 MD5sum: 633f9b5156db77ffb7a757f5bc1a0cb0 Package: ILoReg Version: 1.20.0 Depends: R (>= 4.0.0) Imports: Matrix, parallel, foreach, aricode, LiblineaR, 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data.table, sf, concaveman, tidyselect, distances, MatrixGenerics, rlang, grDevices Suggests: CATALYST, grid, tidyr, BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 MD5sum: 8a64368bd3167c8ee11d711225f8aec3 Package: IMMAN Version: 1.30.0 Imports: STRINGdb, pwalign, igraph, graphics, utils, seqinr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 8d0a81e607b893c2a8f37718f39e78c3 Package: immApex Version: 1.4.0 Depends: R (>= 4.3.0) Imports: hash, httr, Matrix, matrixStats, methods, Rcpp, rvest, SingleCellExperiment, stats, stringr, utils LinkingTo: Rcpp Suggests: BiocStyle, dplyr, ggraph, ggplot2, igraph, knitr, markdown, Peptides, randomForest, rmarkdown, scRepertoire, spelling, testthat, tidygraph, viridis License: MIT + file LICENSE MD5sum: d28db481b7fdcc598cd8f92a7970ab5b Package: immunoClust Version: 1.42.0 Depends: R(>= 4.2), flowCore Imports: methods, stats, graphics, grid, lattice, grDevices Suggests: BiocStyle, utils, testthat License: 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curl, readxl, reshape2, vroom, here, enrichR, rmarkdown License: GPL-3 MD5sum: 10ceb0c0c380cc418aa0289bbe89a85f Package: IMPCdata Version: 1.46.0 Depends: R (>= 2.3.0) Imports: rjson License: file LICENSE MD5sum: 92374febb9d1ef71094e95b544119f00 Package: impute Version: 1.84.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: 1e5bc73662c1627dcc6efacbc9c25cdf Package: INDEED Version: 2.24.0 Depends: glasso (>= 1.8), R (>= 3.5) Imports: devtools (>= 1.13.0), graphics (>= 3.3.1), stats (>= 3.3.1), utils (>= 3.3.1), igraph (>= 1.2.4), visNetwork(>= 2.0.6) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0) License: Artistic-2.0 MD5sum: 336c93b7b4248091ff7a76ab1b3345fe Package: infercnv Version: 1.26.0 Depends: R(>= 4.0) Imports: graphics, grDevices, RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, phyclust, Matrix, fastcluster, parallelDist, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, digest, RANN, igraph, reshape2, rjags, fitdistrplus, future, foreach, doParallel, Seurat, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse Suggests: BiocStyle, knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: b445b1e2cb24bca567a7fc14263653b9 Package: infinityFlow Version: 1.20.0 Depends: R (>= 4.0.0), flowCore Imports: stats, grDevices, utils, graphics, pbapply, matlab, png, raster, grid, uwot, gtools, Biobase, generics, parallel, methods, xgboost Suggests: knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071 License: GPL-3 MD5sum: 210832d8a5fbfa80dd6c3506b669da2a Package: Informeasure Version: 1.20.0 Depends: R (>= 4.0) Imports: entropy Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), SummarizedExperiment License: Artistic-2.0 MD5sum: 3a8d2572d4e91cb5a054785aa7b8d08b Package: InPAS Version: 2.18.0 Depends: R (>= 3.5) Imports: AnnotationDbi,batchtools,Biobase,Biostrings,BSgenome,cleanUpdTSeq, depmixS4,dplyr,flock,future,future.apply,GenomeInfoDb,GenomicRanges, 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Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: af487b994133dd1b49e38bd0a53aae01 Package: INTACT Version: 1.10.0 Depends: R (>= 4.3.0) Imports: SQUAREM, bdsmatrix, numDeriv, stats, tidyr, ggplot2 Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 + file LICENSE MD5sum: 445bf6b745de93bee031ee82e0b7e9ce Package: InTAD Version: 1.30.0 Depends: R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges, MultiAssayExperiment, SummarizedExperiment,stats Imports: BiocGenerics,Biobase,rtracklayer,parallel,graphics,mclust,qvalue, ggplot2,utils,ggpubr Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 1cca495141d873bc191c3ea35ac3dfe0 Package: intansv Version: 1.50.0 Depends: R (>= 2.14.0), plyr, ggbio, GenomicRanges Imports: BiocGenerics, IRanges License: MIT + file LICENSE MD5sum: 0cb00cde6a17479d1b4c923cabed80d4 Package: interacCircos Version: 1.20.0 Depends: R (>= 4.1) Imports: RColorBrewer, htmlwidgets, plyr, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: dd8d03ebeed64cc732960dc4f29de39b Package: InteractionSet Version: 1.38.0 Depends: GenomicRanges, SummarizedExperiment Imports: methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.27.12), IRanges, Seqinfo LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: dd5249c4a61dfdebca4b187b43b63ae7 Package: InteractiveComplexHeatmap Version: 1.18.0 Depends: R (>= 4.0.0), ComplexHeatmap (>= 2.11.0) Imports: grDevices, stats, shiny, grid, GetoptLong, S4Vectors (>= 0.26.1), digest, IRanges, kableExtra (>= 1.3.1), utils, svglite, htmltools, clisymbols, jsonlite, RColorBrewer, fontawesome Suggests: knitr, rmarkdown, testthat, EnrichedHeatmap, GenomicRanges, data.table, circlize, GenomicFeatures, tidyverse, tidyHeatmap, cluster, org.Hs.eg.db, simplifyEnrichment, GO.db, SC3, GOexpress, SingleCellExperiment, scater, gplots, pheatmap, airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve (>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks License: MIT + file LICENSE MD5sum: 4c8fb20ed3c509c812bafaeb1e04fa27 Package: interactiveDisplay Version: 1.48.0 Depends: R (>= 3.5.0), 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: ba52ed62340195162b4d69861fbec3ce Package: interactiveDisplayBase Version: 1.48.0 Depends: R (>= 2.10), methods, BiocGenerics Imports: shiny, DT Suggests: knitr, markdown Enhances: rstudioapi License: Artistic-2.0 MD5sum: eb842fa9daac31e25da3905478d1547b Package: InterCellar Version: 2.16.0 Depends: R (>= 4.1) Imports: config, golem, shiny, DT, shinydashboard, shinyFiles, shinycssloaders, data.table, fs, dplyr, tidyr, circlize, colourpicker, dendextend, factoextra, ggplot2, plotly, plyr, shinyFeedback, shinyalert, tibble, umap, visNetwork, wordcloud2, readxl, htmlwidgets, colorspace, signal, scales, htmltools, ComplexHeatmap, grDevices, stats, tools, utils, biomaRt, rlang, fmsb, igraph Suggests: testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, httr License: MIT + file LICENSE MD5sum: 83424c9dcd5c9c0df6cd0d2d148a02b9 Package: IntEREst Version: 1.34.0 Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, SummarizedExperiment, edgeR, S4Vectors, GenomicFiles Imports: seqLogo, Biostrings, GenomicFeatures (>= 1.39.4), txdbmaker, IRanges, seqinr, graphics, grDevices, stats, utils, grid, methods, DBI, RMariaDB, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2 Suggests: clinfun, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-2 MD5sum: bc84c4cd61aa3374a31f5a939b036556 Package: IntramiRExploreR Version: 1.32.0 Depends: R (>= 3.4) Imports: igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats, utils, grDevices, graphics Suggests: gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat License: GPL-2 MD5sum: dffa0aae7dd010ce01b46224bbb7886a Package: IONiseR Version: 2.34.0 Depends: R (>= 3.4) Imports: rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2, methods, BiocGenerics, XVector, tibble, stats, BiocParallel, bit64, stringr, utils Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData License: MIT + file LICENSE MD5sum: 113f6ca5d3f0a2495e0d62716a00c366 Package: ipdDb Version: 1.28.0 Depends: R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1), AnnotationHub Imports: Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats, assertthat Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 034ce608dd8e7661be5bb062cba53321 Package: IRanges Version: 2.44.0 Depends: R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.47.6) Imports: stats4 LinkingTo: S4Vectors Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 83cbb25a8655dff7e1a658b670d97f17 Package: ISAnalytics Version: 1.20.0 Depends: R (>= 4.5) Imports: utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs, lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools, grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib, vegan, data.table, DT Suggests: testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown, roxygen2, withr, extraDistr, ggalluvial, scales, gridExtra, R.utils, RefManageR, flexdashboard, circlize, plotly, gtools, eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr, future, doFuture, foreach, psych, Rcapture License: CC BY 4.0 MD5sum: e337f09e29dd704717ad5f2d6a5be4e2 Package: iscream Version: 1.0.0 Depends: R (>= 4.5) Imports: Rcpp, Matrix, data.table, methods, pbapply, parallelly, stringfish, LinkingTo: Rcpp, RcppArmadillo, RcppProgress, RcppSpdlog, Rhtslib, stringfish Suggests: BiocFileCache, BiocStyle, bsseq, ggplot2, ggridges, knitr, microbenchmark, rmarkdown, GenomicRanges, IRanges, Rsamtools, SummarizedExperiment, S4Vectors, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: de3abb0f8ec0ce5b840e69f47326d636 Package: iSEE Version: 2.22.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, listviewer, ComplexHeatmap, circlize, grid Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools, GenomicRanges License: MIT + file LICENSE MD5sum: 01f8b34f82fcfdc8e2203a4f3268ee58 Package: iSEEde Version: 1.8.0 Depends: iSEE Imports: DESeq2, edgeR, methods, S4Vectors, shiny, SummarizedExperiment Suggests: airway, BiocStyle, covr, knitr, limma, org.Hs.eg.db, 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BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), nullrangesData Enhances: BioPlex, biscuiteerData, bodymapRat, CLLmethylation, CopyNeutralIMA, curatedAdipoArray, curatedAdipoChIP, curatedMetagenomicData, curatedTCGAData, DMRcatedata, DuoClustering2018, easierData, emtdata, epimutacionsData, FieldEffectCrc, GenomicDistributionsData, GSE103322, GSE13015, GSE62944, HDCytoData, HMP16SData, HumanAffyData, imcdatasets, mcsurvdata, MetaGxBreast, MetaGxOvarian, MetaGxPancreas, MethylSeqData, muscData, NxtIRFdata, ObMiTi, quantiseqr, restfulSEData, RLHub, sesameData, SimBenchData, SingleCellMultiModal, SingleMoleculeFootprintingData, spatialDmelxsim, STexampleData, TabulaMurisData, TabulaMurisSenisData, TENxVisiumData, tissueTreg, VectraPolarisData, xcoredata License: Artistic-2.0 MD5sum: 2ab51ad4c936436b05db5da47822f5f0 Package: iSEEindex Version: 1.8.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: BiocFileCache, DT, iSEE, methods, paws.storage, 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IRanges, XVector, Biostrings, Rcpp, S4Vectors Suggests: SparseM, Biobase, BiocGenerics, knitr License: GPL (>= 2.1) MD5sum: 9a998de065b3279c5669f34a349a132e Package: KEGGgraph Version: 1.70.0 Depends: R (>= 3.5.0) Imports: methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz Suggests: RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) MD5sum: 8510934200fe137b742d8e8e0b8d740a Package: KEGGlincs Version: 1.36.0 Depends: R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db (>= 3.3.0) Imports: AnnotationDbi,KEGGgraph,igraph,plyr,gtools,httr,RJSONIO,KEGGREST, methods,graphics,stats,utils, XML, grDevices Suggests: BiocManager (>= 1.20.3), knitr, graph License: GPL-3 MD5sum: 3e9581e301ae9580c0161825a2ed42cc Package: keggorthology Version: 2.62.0 Depends: R (>= 2.5.0), hgu95av2.db, graph Imports: AnnotationDbi, DBI, grDevices, methods, tools, utils Suggests: RBGL,ALL License: Artistic-2.0 MD5sum: 797f96c2e3cef52a273760f86665c272 Package: KEGGREST Version: 1.50.0 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doParallel, parallel, dplyr, tibble, tidyr, ggsci, tidyverse, methods, stats, SummarizedExperiment, S4Vectors Suggests: BiocStyle, pander, rmarkdown, car, gridExtra, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: b70dd5e82054aa5ad079b764bfdf2e03 Package: LimROTS Version: 1.2.0 Depends: R (>= 4.5.0), SummarizedExperiment Imports: limma, stringr, qvalue, utils, stats, BiocParallel, S4Vectors, dplyr Suggests: BiocStyle, ggplot2, magick, testthat (>= 3.0.0), knitr, rmarkdown, caret, ROTS License: Artistic-2.0 MD5sum: 3c24aa5a7632627ee0e03fde5ac3d82c Package: lineagespot Version: 1.14.0 Imports: VariantAnnotation, MatrixGenerics, SummarizedExperiment, data.table, stringr, httr, utils Suggests: BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 2e68019a259907a80c41dce93a376d2f Package: LinkHD Version: 1.24.0 Depends: R(>= 3.6.0), methods, ggplot2, stats Imports: scales, cluster, graphics, ggpubr, gridExtra, vegan, rio, 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rlang, dplyr, tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD, magrittr Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, spelling, testthat License: MIT + file LICENSE MD5sum: 2a1e20ecb64c762207fd756082e7d190 Package: LipidTrend Version: 1.0.0 Depends: R (>= 4.5.0) Imports: dplyr, ggnewscale, ggplot2, magrittr, methods, rlang, SummarizedExperiment, MKmisc, matrixTests Suggests: BiocStyle, devtools, knitr, roxygen2, rmarkdown, testthat (>= 3.0.0), S4Vectors, Enhances: data.table, License: MIT + file LICENSE MD5sum: c0f11df10d9e4aa3973b8db150ec833e Package: LiquidAssociation Version: 1.64.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>= 3) MD5sum: 5341360bff285fad20a1d0861d355e61 Package: lisaClust Version: 1.18.0 Depends: R (>= 4.1.0) Imports: ggplot2, class, concaveman, grid, BiocParallel, spatstat.explore, spatstat.geom, BiocGenerics, S4Vectors, methods, spicyR, purrr, stats, data.table, dplyr, 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Matrix, gplots, graphics, grDevices, stats, utils, Wrench Suggests: annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW License: Artistic-2.0 MD5sum: 0dd0b5eba856edd4c36727a97bf72ff6 Package: metahdep Version: 1.68.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 MD5sum: 3a4e5435b10ae2edce5430a295b60d78 Package: MetaNeighbor Version: 1.29.0 Depends: R(>= 3.5) Imports: grDevices, graphics, methods, stats (>= 3.4), utils (>= 3.4), Matrix (>= 1.2), matrixStats (>= 0.54), beanplot (>= 1.2), gplots (>= 3.0.1), RColorBrewer (>= 1.1.2), SummarizedExperiment (>= 1.12), SingleCellExperiment, igraph, dplyr, tidyr, tibble, ggplot2 Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2), UpSetR License: MIT + file LICENSE MD5sum: bc1ea30b9c86ee0704ddae419f94bd76 Package: MetaPhOR Version: 1.12.0 Depends: R (>= 4.2.0) Imports: utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats, clusterProfiler, RecordLinkage, RCy3 Suggests: BiocStyle, knitr, rmarkdown, kableExtra License: Artistic-2.0 MD5sum: 08c1f7deebc1261878f06be31e24caaa Package: metapod Version: 1.18.0 Imports: Rcpp LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: c1f24017935a5e986401f4636ae3c77d Package: metapone Version: 1.16.0 Depends: R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea, ggplot2, ggrepel Imports: methods Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: a58a9c8dbf0b61ebb3e9b9c859a8a84d Package: metaSeq Version: 1.50.0 Depends: R (>= 2.13.0), NOISeq, snow, Rcpp License: Artistic-2.0 MD5sum: 93d681bf6f6a8ceb99132e938a3a4a3c Package: metaseqR2 Version: 1.22.0 Depends: R (>= 4.0.0), DESeq2, limma, locfit, splines Imports: ABSSeq, Biobase, BiocGenerics, BiocParallel, biomaRt, Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter, Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, gplots, graphics, grDevices, harmonicmeanp, heatmaply, htmltools, httr, IRanges, jsonlite, lattice, log4r, magrittr, MASS, Matrix, methods, NBPSeq, pander, parallel, qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite, rtracklayer, S4Vectors, stats, stringr, SummarizedExperiment, survcomp, txdbmaker, utils, VennDiagram, vsn, yaml, zoo Suggests: BiocStyle, BiocManager, BSgenome, knitr, RMySQL, RUnit Enhances: TCC License: GPL (>= 3) MD5sum: 513110105583ca7834cc87102321449b Package: MetCirc Version: 1.40.0 Depends: R (>= 4.4), amap (>= 0.8), circlize (>= 0.4.16), scales (>= 1.3.0), shiny (>= 1.8.1.1), Spectra (>= 1.15.3) Imports: ggplot2 (>= 3.5.1), MsCoreUtils (>= 1.17.0), S4Vectors (>= 0.43.1) Suggests: BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr (>= 1.48), testthat (>= 3.2.1.1) License: GPL (>= 3) MD5sum: 39b101b5195540ee208a0c6542d3713d Package: methimpute Version: 1.32.0 Depends: R (>= 3.5.0), GenomicRanges, ggplot2 Imports: Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats, GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm, data.table LinkingTo: Rcpp Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: 3cb7a72d1af770f6613455b3c80b18d0 Package: methInheritSim Version: 1.32.0 Depends: R (>= 3.5.0) Imports: methylKit, GenomicRanges, Seqinfo, parallel, BiocGenerics, S4Vectors, methods, stats, IRanges, msm Suggests: BiocStyle, knitr, rmarkdown, RUnit, methylInheritance License: Artistic-2.0 MD5sum: ebcf92c7f3c343cdbbe33eec2f99864a Package: methodical Version: 1.6.0 Depends: GenomicRanges, ggplot2, R (>= 4.0), SummarizedExperiment Imports: AnnotationHub, annotatr, BiocCheck, BiocManager, BiocParallel, BiocStyle, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, cowplot, data.table, DelayedArray, devtools, dplyr, ExperimentHub, foreach, GenomeInfoDb, HDF5Array, IRanges, knitr, MatrixGenerics, R.utils, rcmdcheck, RcppRoll, remotes, rhdf5, rtracklayer, S4Vectors, scales, tibble, tidyr, tools, TumourMethData, usethis Suggests: BSgenome.Athaliana.TAIR.TAIR9, DESeq2, methrix, rmarkdown License: GPL (>= 3) MD5sum: c721766693a72187e21fc8701219fb4c Package: MethPed Version: 1.38.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 MD5sum: 3e1c13e6fe08a99d44f9718d24fb7965 Package: MethReg Version: 1.20.0 Depends: R (>= 4.0) Imports: dplyr, plyr, GenomicRanges, SummarizedExperiment, DelayedArray, ggplot2, ggpubr, tibble, tidyr, S4Vectors, sesameData, sesame, AnnotationHub, ExperimentHub, stringr, readr, methods, stats, Matrix, MASS, rlang, pscl, IRanges, sfsmisc, progress, utils, openxlsx, JASPAR2024, RSQLite, TFBSTools Suggests: rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, R.utils, doParallel, reshape2, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr, jpeg, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, data.table, downloader License: GPL-3 MD5sum: 5178f0762bec875660ef0960824f88f1 Package: methrix Version: 1.24.0 Depends: R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment Imports: rtracklayer, DelayedArray, HDF5Array, BSgenome, DelayedMatrixStats, parallel, methods, ggplot2, S4Vectors, matrixStats, graphics, stats, utils, GenomicRanges, IRanges Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: f6058f563dd2ca97e47ef4d3eb4d66db Package: MethTargetedNGS Version: 1.42.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign Imports: utils, graphics, stats License: Artistic-2.0 MD5sum: a71275c9d0190e03137f38d3a98438e4 Package: MethylAid Version: 1.44.0 Depends: R (>= 3.4) Imports: Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: 6269f1191fc1d5893f10d56e44459f26 Package: methylCC Version: 1.24.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: GPL-3 MD5sum: 17f9c407847111879db082b8360b05c0 Package: methylclock Version: 1.16.0 Depends: R (>= 4.1.0), methylclockData, devtools, quadprog Imports: Rcpp (>= 1.0.6), ExperimentHub, dplyr, impute, PerformanceAnalytics, Biobase, ggpmisc, tidyverse, ggplot2, ggpubr, minfi, tibble, RPMM, stats, graphics, tidyr, gridExtra, preprocessCore, dynamicTreeCut, planet LinkingTo: Rcpp Suggests: BiocStyle, knitr, GEOquery, rmarkdown License: MIT + file LICENSE MD5sum: 2c54e79b79328547b4473b1f24c8f619 Package: methylGSA Version: 1.28.0 Depends: R (>= 3.5) Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, shiny, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr, rmarkdown, testthat, enrichplot License: GPL-2 MD5sum: bf9025fc8e8e956ad9f850c355f9b7a1 Package: methyLImp2 Version: 1.6.0 Depends: R (>= 4.3.0), ChAMPdata Imports: BiocParallel, parallel, stats, methods, corpcor, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: 95112733f8cd3033b9b59d5a2c0e37a0 Package: methylInheritance Version: 1.34.0 Depends: R (>= 3.5) Imports: methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors, methods, parallel, ggplot2, gridExtra, rebus Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 130e99489859490e392e9788fa393ece Package: methylKit Version: 1.36.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.18.1), methods Imports: IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>= 0.13.13), Seqinfo, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils LinkingTo: Rcpp, Rhtslib (>= 1.13.1) Suggests: testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager License: Artistic-2.0 MD5sum: b0bff2d69bbcd6aaa58c04417507c565 Package: MethylMix Version: 2.40.0 Depends: R (>= 3.2.0) Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown License: GPL-2 MD5sum: 3375fb5364188cb8a5cae571dc8c5b9f Package: methylMnM Version: 1.48.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: 9ef38e990ff3d02f27728b9441404a12 Package: methylPipe Version: 1.44.0 Depends: R (>= 3.5.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, Seqinfo, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) MD5sum: 649f532219985d18ac248cc1a8ea6e9c Package: methylscaper Version: 1.18.0 Depends: R (>= 4.4.0) Imports: shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings, pwalign, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, devtools, R.utils License: GPL-2 MD5sum: 8171ea43677143201a993f3f584c10db Package: MethylSeekR Version: 1.50.0 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), graphics (>= 2.15.2), grDevices (>= 2.15.2), parallel (>= 2.15.2), stats (>= 2.15.2), utils (>= 2.15.2), GenomeInfoDb Suggests: BSgenome.Hsapiens.UCSC.hg38 License: GPL (>= 2) MD5sum: 0bc4cdd67e2f8ac18d4ceb20a4e80aa7 Package: methylSig Version: 1.22.0 Depends: R (>= 3.6) Imports: bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, Seqinfo, GenomicRanges, methods, parallel, stats, S4Vectors Suggests: BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr License: GPL-3 MD5sum: c1435ba6ce0bc3af3658e14e5eba14b1 Package: methylumi Version: 2.56.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio, GenomicFeatures Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 MD5sum: c26581fa735636f8d03f98890f465583 Package: MetID Version: 1.28.0 Depends: R (>= 3.5) Imports: utils (>= 3.3.1), stats (>= 3.4.2), devtools (>= 1.13.0), stringr (>= 1.3.0), Matrix (>= 1.2-12), igraph (>= 1.2.1), ChemmineR (>= 2.30.2) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) License: Artistic-2.0 MD5sum: d446fba83ea125c851a4ba40751e1d07 Package: MetNet Version: 1.28.0 Depends: R (>= 4.1), S4Vectors (>= 0.28.1), SummarizedExperiment (>= 1.20.0) Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), corpcor (>= 1.6.10), dplyr (>= 1.0.3), ggplot2 (>= 3.3.3), GeneNet (>= 1.2.15), GENIE3 (>= 1.7.0), methods (>= 4.1), parmigene (>= 1.0.2), psych (>= 2.1.6), rlang (>= 0.4.10), stabs (>= 0.6), stats (>= 4.1), tibble (>= 3.0.5), tidyr (>= 1.1.2) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1), Spectra (>= 1.4.1), MsCoreUtils (>= 1.6.0) License: GPL (>= 3) MD5sum: 73fd872beeef3042748629f3b4bf6774 Package: Mfuzz Version: 2.70.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 MD5sum: 64cc023f90a9d5a4a642102fac4a9b81 Package: MGFM Version: 1.44.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 MD5sum: de1624cdfac3dbc8f25318f80c768bac Package: mgsa Version: 1.58.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: f92e05a87bd54773229c455868541051 Package: miaSim Version: 1.16.0 Depends: TreeSummarizedExperiment Imports: SummarizedExperiment, deSolve, stats, poweRlaw, MatrixGenerics, S4Vectors Suggests: ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy License: Artistic-2.0 | file LICENSE MD5sum: 84519059bf0cdd902998c4b20396b693 Package: MiChip Version: 1.64.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: 629d655806cda9f7add544822a630e3a Package: microbiome Version: 1.32.0 Depends: R (>= 3.6.0), phyloseq, ggplot2 Imports: Biostrings, compositions, dplyr, reshape2, Rtsne, scales, stats, tibble, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE MD5sum: f759c37fc9ad98c1913bcbac49acf0ea Package: microbiomeDASim Version: 1.24.0 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: b2340b2fa5f1711ff9eed1822c6f5a23 Package: microbiomeExplorer Version: 1.20.0 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: bb608747e5228e3df76f64a00e7b7427 Package: MicrobiomeProfiler Version: 1.16.0 Depends: R (>= 4.2.0) Imports: clusterProfiler (>= 4.5.2), config, DT, enrichplot, golem, gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader, htmltools, ggplot2, graphics, stats, utils, yulab.utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), prettydoc License: GPL-2 MD5sum: a4c32feec5d66bbe741e22a885f1b215 Package: MicrobiotaProcess Version: 1.22.0 Depends: R (>= 4.0.0) Imports: ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>= 1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table, ggfun (>= 0.1.1) Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager License: GPL (>= 3.0) MD5sum: d2eda772ff3898f613c6f70f71ed6cba Package: microRNA Version: 1.68.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: 02f096302378911e0830ee22732da4b8 Package: MICSQTL Version: 1.8.0 Depends: R (>= 4.3.0), SummarizedExperiment, stats Imports: TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2, ggpubr, ggridges, glue, S4Vectors, dirmult Suggests: testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle License: GPL-3 MD5sum: 69c9b49ec25da38476261c23c3949b1a Package: miloR Version: 2.6.0 Depends: R (>= 4.0.0), edgeR Imports: BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>= 1.3-0), MatrixGenerics, S4Vectors, stats, stringr, methods, igraph, irlba, utils, cowplot, BiocParallel, BiocSingular, limma, ggplot2, tibble, matrixStats, ggraph, gtools, SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices, Rcpp, pracma, numDeriv LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppML Suggests: testthat, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, MASS, curl, scRNAseq, graphics, sparseMatrixStats License: GPL-3 + file LICENSE MD5sum: 89d8b76d016bcb1b5b2044eba9d6456a Package: mimager Version: 1.34.0 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: 627910b12a746f277a53ec4a0eb65742 Package: mina Version: 1.18.0 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: 218b3628f9d4c1de882feb3bbe3f85c3 Package: MineICA Version: 1.49.0 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: c836047d17c4c90c08e89cd57d8af03d Package: minet Version: 3.68.0 Imports: infotheo License: Artistic-2.0 MD5sum: 974b4d384da50cfb43930ce8016bd7fe Package: minfi Version: 1.56.0 Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), bumphunter (>= 1.1.9) Imports: S4Vectors, Seqinfo, 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: d3f37f0240637552d7ddad0fc7e07f9e Package: MinimumDistance Version: 1.54.0 Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1) Imports: methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges, Seqinfo, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: 2c5c8d338ffff9f007a313f72b307f66 Package: MiPP Version: 1.82.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: 21e2ea220e1b310de4052f027284c18d Package: miQC Version: 1.18.0 Depends: R (>= 3.5.0) Imports: SingleCellExperiment, flexmix, ggplot2, splines Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 5523afdd8d2104db66a1c4af829e56c5 Package: MIRA Version: 1.32.0 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: 38eb5b802f97735982599177a1aec72c Package: MiRaGE Version: 1.52.0 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: 7433fd7a8f04562fc99cad804d658833 Package: miRBaseConverter Version: 1.34.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown License: GPL (>= 2) MD5sum: 47cc3cf87654f695a1a5241527b425b6 Package: miRcomp Version: 1.40.0 Depends: R (>= 3.5.0), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: 08b62bb3dd87c2c877cd373f602724a2 Package: mirIntegrator Version: 1.40.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: fcd8b25b514433d30c19059e602a8cce Package: MIRit Version: 1.6.0 Depends: MultiAssayExperiment, R (>= 4.4.0) Imports: AnnotationDbi, BiocFileCache, BiocParallel, DESeq2, edgeR, fgsea, genekitr, geneset, ggplot2, ggpubr, graph, graphics, graphite, grDevices, httr, limma, methods, Rcpp, Rgraphviz (>= 2.44.0), rlang, stats, utils LinkingTo: Rcpp Suggests: BiocStyle, biomaRt, BSgenome.Hsapiens.UCSC.hg38, GenomicRanges, ggrepel, ggridges, Gviz, gwasrapidd, knitr, MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 8b14f44000b589e1c0335519c14411cd Package: miRLAB Version: 1.40.0 Imports: methods, stats, utils, RCurl, httr, stringr, Hmisc, energy, entropy, gplots, glmnet, impute, limma, pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc, InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit,rmarkdown License: GPL (>= 2) MD5sum: f0da561ad89e235948ff371aad6bdf7e Package: miRNAmeConverter Version: 1.38.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 8e5bb70563f933e8a47a5cf5f8cbaa21 Package: miRNApath Version: 1.70.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: 9d1bdf918fd462263a3957bba4933dde Package: miRNAtap Version: 1.44.0 Depends: R (>= 3.3.0), AnnotationDbi Imports: DBI, RSQLite, stringr, sqldf, plyr, methods Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat License: GPL-2 MD5sum: 3b688676fc2082620b436bdf6d3833ef Package: miRSM Version: 2.6.0 Depends: R (>= 4.4.0) Imports: WGCNA, flashClust, dynamicTreeCut, GFA, igraph, RColorBrewer, grid, MCL, fabia, NMF, biclust, iBBiG, BicARE, isa2, methods, rJava, BiBitR, rqubic, Biobase, PMA, stats, dbscan, mclust, SOMbrero, ppclust, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE, MatrixCorrelation, energy Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: c56e1fd22ce76b69fe735bce33d5350f Package: miRspongeR Version: 2.14.0 Depends: R (>= 4.4.0) Imports: corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, utils, Rcpp, RColorBrewer, grid, org.Hs.eg.db, foreach, doParallel Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: dfd0019a7ad823b06dd25875cb6a1d24 Package: mirTarRnaSeq Version: 1.18.0 Depends: R (>= 4.1.0), ggplot2 Imports: purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap, reshape2, corrplot, grDevices, graphics, stats, utils, data.table, R.utils, viridis Suggests: BiocStyle, knitr, rmarkdown, R.cache, SPONGE License: MIT + file LICENSE MD5sum: 96d1f02cba0cb373eeef7546ceab7065 Package: missMethyl Version: 1.44.0 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomeInfoDb, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICv2manifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub License: GPL-2 MD5sum: eb1e3c3c69919e42ffc21323b3890132 Package: missRows Version: 1.30.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: f4b0fb026f7cc4bd412bb670fe7685a9 Package: mist Version: 1.2.0 Depends: R (>= 4.5.0) Imports: BiocParallel, MCMCpack, Matrix, S4Vectors, methods, rtracklayer, car, mvtnorm, SummarizedExperiment, SingleCellExperiment, BiocGenerics, stats, rlang Suggests: knitr, rmarkdown, RUnit, ggplot2, BiocStyle License: MIT + file LICENSE MD5sum: 48a976747b1e1c5b7587ba8fd4c8c9e3 Package: mitch Version: 1.22.0 Depends: R (>= 4.4) Imports: stats, grDevices, graphics, utils, MASS, plyr, reshape2, parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r, kableExtra, dplyr, network Suggests: stringi, testthat (>= 2.1.0), HGNChelper, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: CC BY-SA 4.0 + file LICENSE MD5sum: 0c643e3bcef76606a7d08dc123e7a9c8 Package: mitoClone2 Version: 1.16.0 Depends: R (>= 4.4.0) Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, Matrix, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2 LinkingTo: Rhtslib (>= 1.13.1) Suggests: knitr, rmarkdown, Biostrings, testthat License: GPL-3 MD5sum: 00db42e94dad9e4412bab513f7add189 Package: mitology Version: 1.2.0 Depends: R (>= 4.5.0) Imports: AnnotationDbi, ape, circlize, clusterProfiler, ComplexHeatmap, ggplot2, ggtree, magrittr, org.Hs.eg.db, ReactomePA, scales Suggests: Biobase, BiocStyle, GSVA, methods, rmarkdown, knitr, SummarizedExperiment, testthat License: AGPL-3 MD5sum: 2d05510f1079a16a058228720654bbf7 Package: mixOmics Version: 6.34.0 Depends: R (>= 4.4.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, ggrepel, BiocParallel, utils, gsignal, rgl Suggests: BiocStyle, knitr, rmarkdown, mime, testthat, microbenchmark, magick, vdiffr, kableExtra, devtools License: GPL (>= 2) MD5sum: 59d2b65969959567692357feed067a34 Package: MLInterfaces Version: 1.90.0 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, SummarizedExperiment 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, BiocStyle, knitr, testthat, airway Enhances: parallel License: LGPL MD5sum: d47700effec1d6c65436d2f3f96ad7c7 Package: MLSeq Version: 2.28.0 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: e89279f1dd26cefe0769063a985eb960 Package: MMDiff2 Version: 1.38.0 Depends: R (>= 3.5.0), 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: 32d7dd28b00b3cccf0eb65d73625d3f2 Package: mnem Version: 1.26.0 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, BiocStyle License: GPL-3 MD5sum: 94ba94d2f993029427e3769eee89f903 Package: moanin Version: 1.18.0 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: e358b50badcf5cd40c5f42d396963f99 Package: mobileRNA Version: 1.5.1 Depends: R (>= 4.3.0) Imports: dplyr, tidyr, ggplot2, BiocGenerics, DESeq2, edgeR, ggrepel, grDevices, pheatmap, utils, tidyselect, progress, RColorBrewer, GenomicRanges, rtracklayer, data.table, SimDesign, scales, IRanges, stats, methods, Biostrings, reticulate, S4Vectors, Seqinfo, SummarizedExperiment, rlang, bioseq, grid Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 188c575e9904b04b8a46358d1fb77fe9 Package: MODA Version: 1.36.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 28b32831622300fe55262353d787eeea Package: ModCon Version: 1.18.0 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: a4eb2e8e6c38bf58fc9f2d1bf44950f9 Package: Modstrings Version: 1.26.0 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: 9aed0f026e6a10ed52a4e30729266894 Package: MOGAMUN Version: 1.20.0 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: knitr, markdown License: GPL-3 + file LICENSE MD5sum: 42de3c283971c84d4fea319716f636a5 Package: mogsa Version: 1.44.0 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: 1c1120ad0db228187c86b18788949415 Package: MoleculeExperiment Version: 1.10.0 Depends: R (>= 4.1.0) Imports: SpatialExperiment, Matrix, purrr, data.table, dplyr (>= 1.1.1), magrittr, rjson, utils, methods, terra, ggplot2, rlang, cli, EBImage, rhdf5, BiocParallel, S4Vectors, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 79cca61d097be801ce2208a48f1d81a8 Package: MOMA Version: 1.22.0 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: 3abb8c9826c700873e08cb9e909baaf5 Package: monaLisa Version: 1.16.0 Depends: R (>= 4.1) Imports: BiocGenerics, BiocParallel, Biostrings, BSgenome, circlize, ComplexHeatmap (>= 2.11.1), Seqinfo, GenomicRanges, cli, ggplot2 (>= 4.0.0), glmnet, grDevices, grid, IRanges, methods, rlang, RSQLite, stabs, stats, SummarizedExperiment, S4Vectors, TFBSTools, tidyr, tools, utils, XVector Suggests: BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, ggrepel, gridExtra, JASPAR2020, JASPAR2024, knitr, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL (>= 3) MD5sum: 440903be5b7a413e4686e3e3cac37d89 Package: monocle Version: 2.38.0 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, Rtsne, MASS, reshape2, leidenbase (>= 0.1.9), limma, tibble, dplyr, 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: 39bc2579b5aab1540fd2bd86fa6a431d Package: Moonlight2R Version: 1.8.0 Depends: R (>= 4.5), doParallel, foreach Imports: parmigene, randomForest, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, grDevices, graphics, GEOquery, stats, purrr, RISmed, grid, utils, ComplexHeatmap, GenomicRanges, dplyr, fuzzyjoin, rtracklayer, magrittr, qpdf, readr, seqminer, stringr, tibble, tidyHeatmap, tidyr, AnnotationHub, easyPubMed, org.Hs.eg.db, EpiMix, BiocGenerics, ggplot2, ExperimentHub, rlang, withr, data.table Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), devtools, roxygen2, png License: GPL-3 MD5sum: 8f60f0430434dbeaabe9ecdc13d6b074 Package: MoonlightR Version: 1.36.0 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, edgeR License: GPL (>= 3) MD5sum: b2740573ca83856564d0dbde1c31dcff Package: mosaics Version: 2.48.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, Seqinfo, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: de3d21bd2c28298b2c5c5abfce79a67b Package: mosbi Version: 1.16.0 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: b1bd513868b48691384d3da298e9c50f Package: MOSClip Version: 1.4.0 Depends: R (>= 4.4.0) Imports: MultiAssayExperiment, methods, survminer, graph, graphite, AnnotationDbi, checkmate, ggplot2, gridExtra, igraph, pheatmap, survival, RColorBrewer, SuperExactTest, reshape, NbClust, S4Vectors, grDevices, graphics, stats, utils, ComplexHeatmap, FactoMineR, circlize, corpcor, coxrobust, elasticnet, gRbase, ggplotify, qpgraph, org.Hs.eg.db, Matrix Suggests: RUnit, BiocGenerics, MASS, BiocStyle, knitr, EDASeq, rmarkdown, kableExtra, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 332b7975c588163398b74f75587cfa04 Package: mosdef Version: 1.6.0 Depends: R (>= 4.4.0) Imports: DT, ggplot2, ggforce, ggrepel, graphics, grDevices, htmltools, methods, AnnotationDbi, topGO, GO.db, clusterProfiler, goseq, utils, RColorBrewer, rlang, DESeq2, scales, SummarizedExperiment, S4Vectors, stats Suggests: knitr, rmarkdown, macrophage, org.Hs.eg.db, GeneTonic, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene, BiocStyle License: MIT + file LICENSE MD5sum: ce4a2bd28ce6e865e1417c4afa139e64 Package: MOSim Version: 2.6.0 Depends: R (>= 4.2.0) Imports: HiddenMarkov, zoo, IRanges, S4Vectors, dplyr, ggplot2, lazyeval, matrixStats, methods, rlang, stringi, stringr, scran, Seurat, Signac, edgeR, Rcpp LinkingTo: cpp11, Rcpp Suggests: testthat, knitr, rmarkdown, codetools, BiocStyle, stats, utils, purrr, scales, tibble, tidyr, Biobase, scater, SingleCellExperiment, decor, markdown, Rsamtools, igraph, leiden, bluster License: GPL-3 MD5sum: 8ef94811f31d25781780d582c67c87e5 Package: Motif2Site Version: 1.14.0 Depends: R (>= 4.1) Imports: S4Vectors, stats, utils, methods, grDevices, graphics, BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges, GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools Suggests: BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805 License: GPL-2 MD5sum: fb7f483a26f28a698d1a67b0342feb0e Package: motifbreakR Version: 2.24.0 Depends: R (>= 4.4.0), grid, MotifDb Imports: methods, grDevices, stringr, parallel, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment, pwalign, DT, bsicons, BiocFileCache, biomaRt, bslib, shiny, vroom Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Hsapiens.UCSC.hg38 License: GPL-2 MD5sum: 0363b48aa23574cd2b5c4867f955e922 Package: motifcounter Version: 1.34.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: a937ef321e21b244709b4aca4d5878f7 Package: MotifDb Version: 1.52.0 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: bd95aa9c50455614bd2dfebfada434ef Package: motifmatchr Version: 1.32.0 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, Seqinfo LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 + file LICENSE MD5sum: e7daf8d336a1c616f61dd8dd351f7c65 Package: MotifPeeker Version: 1.2.0 Depends: R (>= 4.4.0) Imports: BiocFileCache, BiocParallel, DT, ggplot2, plotly, universalmotif, GenomicRanges, IRanges, rtracklayer, tools, htmltools, rmarkdown, viridis, SummarizedExperiment, htmlwidgets, Rsamtools, GenomicAlignments, Seqinfo, Biostrings, BSgenome, memes, S4Vectors, dplyr, purrr, tidyr, heatmaply, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, downloadthis, knitr, markdown, methods, remotes, rworkflows, testthat (>= 3.0.0), withr, emoji, curl, jsonlite License: GPL (>= 3) MD5sum: 74f14fc1079e0544cd9b1de363b89c52 Package: motifStack Version: 1.54.0 Depends: R (>= 2.15.1), methods, grid Imports: ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets, stats, stats4, utils, XML, TFBSTools Suggests: Cairo, grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020 License: GPL (>= 2) MD5sum: e548cee0a0347b5ee690dec0232f3dac Package: motifTestR Version: 1.6.0 Depends: Biostrings, GenomicRanges, ggplot2 (>= 4.0.0), R (>= 4.5.0), Imports: Seqinfo, graphics, harmonicmeanp, IRanges, matrixStats, methods, parallel, patchwork, rlang, S4Vectors, stats, universalmotif, Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, extraChIPs (>= 1.13.3), ggdendro, knitr, MASS, MotifDb, rmarkdown, rtracklayer, SimpleUpset, testthat (>= 3.0.0), VGAM License: GPL-3 MD5sum: d2f778dd8cc015dbc100c39f498808e1 Package: MouseFM Version: 1.20.0 Depends: R (>= 4.0.0) Imports: httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales, gtools, tidyr, data.table, jsonlite, rlist, Seqinfo, methods, biomaRt, stats, IRanges Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: e2d86ff4ec70a4e948743b9589dfaa3f Package: MPAC 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bc136d4a8a014a176b77faff9ac18052 Package: MPRAnalyze Version: 1.28.0 Imports: BiocParallel, methods, progress, stats, SummarizedExperiment Suggests: knitr License: GPL-3 MD5sum: c394dfeee6ffe10474c961827bbeea55 Package: msa Version: 1.42.0 Depends: R (>= 3.3.0), methods, Biostrings (>= 2.40.0) Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors, tools LinkingTo: Rcpp Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign License: GPL (>= 2) MD5sum: 8962b8e5074b3a5e97cd58b693eb3a0a Package: MSA2dist Version: 1.14.0 Depends: R (>= 4.4.0) Imports: Rcpp, Biostrings, GenomicRanges, IRanges, ape, doParallel, dplyr, foreach, methods, parallel, pwalign, rlang, seqinr, stats, stringi, stringr, tibble, tidyr, utils LinkingTo: Rcpp, RcppThread Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle License: GPL-3 + file LICENSE MD5sum: ec0b3f917ee51a6ccb6de0140dcfdc64 Package: MsBackendMassbank Version: 1.18.0 Depends: R (>= 4.0), Spectra (>= 1.15.10) 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IRanges, MsCoreUtils, methods, stats Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown License: Artistic-2.0 MD5sum: 930b7cb9feb33bee613b9cdf7c970d6e Package: MsBackendRawFileReader Version: 1.16.0 Depends: R (>= 4.1), methods, Spectra (>= 1.15.10) Imports: ProtGenerics (>= 1.35.3), MsCoreUtils, S4Vectors, IRanges, rawrr (>= 1.17.2), utils, BiocParallel Suggests: BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr, lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat License: GPL-3 MD5sum: d4c204e63760f8e5b41ddbe38dddd9af Package: MsBackendSql Version: 1.10.0 Depends: R (>= 4.2.0), Spectra (>= 1.19.8) Imports: BiocParallel, S4Vectors, methods, ProtGenerics (>= 1.35.3), DBI, MsCoreUtils, IRanges, data.table, progress, stringi, fastmatch, BiocGenerics Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, msdata, rmarkdown, microbenchmark, mzR License: Artistic-2.0 MD5sum: 2301641268cdc21dd96399904f69cd53 Package: MsCoreUtils Version: 1.21.0 Depends: R (>= 3.6.0) Imports: methods, S4Vectors, MASS, stats, clue LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD, impute, norm, pcaMethods, vsn, Matrix, preprocessCore, missForest Enhances: HDF5Array License: Artistic-2.0 MD5sum: 724af37e5ea828591ea5ed1f7c9403b5 Package: MsDataHub Version: 1.10.0 Imports: ExperimentHub, utils Suggests: ExperimentHubData, DT, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), Spectra, mzR, PSMatch, QFeatures (>= 1.13.3) License: Artistic-2.0 MD5sum: c08adac50034211d98237d96569016db Package: MsExperiment Version: 1.12.0 Depends: R (>= 4.2), ProtGenerics (>= 1.35.2), Imports: methods, S4Vectors, IRanges, Spectra, SummarizedExperiment, QFeatures, DBI, BiocGenerics Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown, rpx, mzR, msdata, MsBackendSql (>= 1.3.2), RSQLite License: Artistic-2.0 MD5sum: 3c57a31ea761f7c28f365116b62406e9 Package: MsFeatures 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BiocGenerics, DelayedArray, GenomicRanges, IRanges, MatrixGenerics, methods, S4Vectors, tidyr, utils Suggests: BiocStyle, HDF5Array, h5mread, knitr, maftools, RaggedExperiment, reshape2, rmarkdown, survival, survminer, testthat, UpSetR License: Artistic-2.0 MD5sum: a41bfbca8793ea68b45b88230476e1ae Package: MultiBaC Version: 1.20.0 Imports: Matrix, ggplot2, MultiAssayExperiment, ropls, graphics, methods, plotrix, grDevices, pcaMethods Suggests: knitr, rmarkdown, BiocStyle, devtools License: GPL-3 MD5sum: 839d6a0310b102971f7c5f30a1328462 Package: multiClust Version: 1.40.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) MD5sum: 3135bab4297a5b6c1fde15b8fd69c1fb Package: multicrispr Version: 1.20.0 Depends: R (>= 4.0) Imports: BiocGenerics, Biostrings, BSgenome, CRISPRseek, data.table, Seqinfo, 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, GenomeInfoDb, knitr, magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL-2 MD5sum: 4dd8af8d1466b3bf16d5263aa1892f11 Package: MultiDataSet Version: 1.38.0 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: 7e0b30e090620c4c0bafab4cab699a3d Package: multiGSEA Version: 1.20.0 Depends: R (>= 4.0.0) Imports: magrittr, graphite, AnnotationDbi, metaboliteIDmapping, dplyr, fgsea, metap, rappdirs, rlang, methods 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testthat (>= 1.0.2) License: MIT + file LICENSE MD5sum: ae0396f0c2224785ea0674fe5861d3bb Package: MultimodalExperiment Version: 1.10.0 Depends: R (>= 4.3.0), IRanges, S4Vectors Imports: BiocGenerics, MultiAssayExperiment, methods, utils Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 5120c04a1ebcfc88028ff0b54d1d2fdf Package: MultiRNAflow Version: 1.8.0 Depends: Mfuzz (>= 2.64.0), R (>= 4.4) Imports: Biobase (>= 2.54.0), ComplexHeatmap (>= 2.20.0), DESeq2 (>= 1.44.0), factoextra (>= 1.0.7), FactoMineR (>= 2.11), ggalluvial (>= 0.12.5), ggplot2 (>= 3.5.1), ggplotify (>= 0.1.2), ggrepel (>= 0.9.5), gprofiler2 (>= 0.2.3), graphics (>= 4.2.2), grDevices (>= 4.2.2), grid (>= 4.2.2), plot3D (>= 1.4.1), plot3Drgl (>= 1.0.4), reshape2 (>= 1.4.4), rlang (>= 1.1.6), S4Vectors (>= 0.42.0), stats (>= 4.2.2), SummarizedExperiment (>= 1.34.0), UpSetR (>= 1.4.0), utils (>= 4.2.2) Suggests: BiocGenerics (>= 0.40.0), BiocStyle (>= 2.32.1), e1071 (>= 1.7.12), knitr (>= 1.47), rmarkdown (>= 2.27), testthat (>= 3.0.0) License: GPL-3 | file LICENSE MD5sum: c126ee4f6cd7d7af20f639b2465eff71 Package: multiscan Version: 1.70.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) MD5sum: a27e83a872736a0613733a7e03236a62 Package: multistateQTL Version: 2.2.0 Depends: QTLExperiment, SummarizedExperiment, ComplexHeatmap, collapse Imports: methods, S4Vectors, data.table, grid, dplyr, tidyr, matrixStats, stats, fitdistrplus, viridis, ggplot2, circlize, mashr, grDevices Suggests: testthat, BiocStyle, knitr, covr, rmarkdown License: GPL-3 MD5sum: 7aef00acfddb7112e646ba7e729d6b93 Package: multiWGCNA Version: 1.7.0 Depends: R (>= 4.3.0), ggalluvial Imports: stringr, readr, WGCNA, dplyr, reshape2, data.table, patchwork, scales, igraph, flashClust, ggplot2, dcanr, cowplot, ggrepel, methods, SummarizedExperiment Suggests: BiocStyle, doParallel, ExperimentHub, knitr, markdown, rmarkdown, testthat (>= 3.0.0), vegan License: GPL-3 MD5sum: 4d7a792df322159aadd8abdc6c28b350 Package: multtest Version: 2.66.0 Depends: R (>= 2.10), methods, BiocGenerics, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL MD5sum: 366ef999847e3ddf5afab8681bbbe3dd Package: mumosa Version: 1.18.0 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: 81272c278da7982cbfe5f1f44e50a8e6 Package: MungeSumstats Version: 1.18.0 Depends: R(>= 4.1) Imports: data.table, utils, R.utils, dplyr, stats, GenomicRanges, GenomeInfoDb, IRanges, ieugwasr(>= 1.0.1), BSgenome, Biostrings, stringr, VariantAnnotation, methods, parallel, rtracklayer(>= 1.59.1), RCurl Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, Rsamtools, MatrixGenerics, badger, BiocParallel, GenomicFiles License: Artistic-2.0 MD5sum: 9ddd0af5963cc4dfc5dfca4453b792ff Package: muscat Version: 1.24.0 Depends: R (>= 4.5) Imports: BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, IHW, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, rlang, S4Vectors, scales, scater, scuttle, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition Suggests: BiocStyle, cowplot, countsimQC, AnnotationHub, ExperimentHub, iCOBRA, knitr, patchwork, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, stageR, testthat, tidyr, UpSetR License: GPL-3 MD5sum: 08033150e0fd37dc353723071a87a08a Package: muscle Version: 3.52.0 Depends: Biostrings License: Unlimited MD5sum: 0ecfbe123ed16450f2905ca20a3ce05e Package: musicatk Version: 2.4.0 Depends: R (>= 4.4.0), NMF Imports: SummarizedExperiment, VariantAnnotation, 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, decompTumor2Sig, topicmodels, ggrepel, plotly, utils, factoextra, cluster, ComplexHeatmap, philentropy, maftools, shiny, stringi, tidyverse, ggpubr, Matrix (>= 1.6.1), scales Suggests: TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard, shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr, shinyWidgets, cowplot, withr License: LGPL-3 MD5sum: 222185ee8e367b43f18a7cea57241e9c Package: mutscan Version: 1.0.0 Depends: R (>= 4.5.0) Imports: BiocGenerics, S4Vectors, methods, SummarizedExperiment, Rcpp, edgeR (>= 3.42.0), dplyr, Matrix, limma, tidyr, stats, GGally, ggplot2, tidyselect (>= 1.2.0), tibble, rlang, grDevices, csaw, rmarkdown, xfun, DT, ggrepel, IRanges, utils, DelayedArray, tools LinkingTo: Rcpp Suggests: testthat (>= 3.0.0), BiocStyle, knitr, Biostrings, pwalign, plotly, scattermore, BiocManager License: MIT + file LICENSE MD5sum: 8e05068357bda1e85ff307ac9a4c2ef9 Package: MVCClass Version: 1.84.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: 17a35832cf2f529a742ccb2cdda99327 Package: MWASTools Version: 1.34.0 Depends: R (>= 3.5.0) 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: c56d9f94c5ee36de9644f09f29718f39 Package: mygene Version: 1.46.0 Depends: R (>= 3.2.1), GenomicFeatures, txdbmaker Imports: methods, utils, stats, httr (>= 0.3), jsonlite (>= 0.9.7), Hmisc, sqldf, plyr, S4Vectors Suggests: BiocStyle License: Artistic-2.0 MD5sum: 9c3f902f06ff049421c6975e4cffc0bc Package: myvariant Version: 1.40.0 Depends: R (>= 3.2.1), VariantAnnotation Imports: httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, Seqinfo, GenomeInfoDb Suggests: BiocStyle License: Artistic-2.0 MD5sum: 1be61249bd2184a8a337a1c9b6b87a20 Package: mzID Version: 1.48.0 Depends: methods Imports: XML, plyr, parallel, doParallel, foreach, iterators, ProtGenerics Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 0a993e43f73b0e968b029d0ab6289d3f Package: mzR Version: 2.44.0 Depends: R (>= 4.0.0), Rcpp (>= 0.10.1), methods, utils Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3), ncdf4 LinkingTo: Rcpp, Rhdf5lib (>= 1.1.4) Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown License: Artistic-2.0 MD5sum: 736d955f9e32838c22562ae55e4e8146 Package: NADfinder Version: 1.34.0 Depends: R (>= 3.5.0), 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: ec932c54fa52abf20292186b965339d9 Package: NanoMethViz Version: 3.6.0 Depends: R (>= 4.0.0), methods, ggplot2 (>= 3.4.0) Imports: cpp11 (>= 0.2.5), readr, cli, S4Vectors, SummarizedExperiment, BiocSingular, bsseq, forcats, assertthat, AnnotationDbi, Rcpp, dplyr, dbscan, e1071, fs, GenomicRanges, Biostrings, ggrastr, glue, graphics, IRanges, limma (>= 3.44.0), patchwork, purrr, rlang, R.utils, Rsamtools, scales (>= 1.2.0), stats, stringr, tibble, tidyr, utils, withr LinkingTo: Rcpp Suggests: BiocStyle, DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm39.refGene, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr License: Apache License (>= 2.0) MD5sum: 7254d708d6de669065264a39e2366c9f Package: NanoStringDiff Version: 1.40.0 Depends: Biobase Imports: matrixStats, methods, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle License: GPL MD5sum: 0832062b33df5cbf99dca97e4805b57b Package: NanoStringNCTools Version: 1.18.0 Depends: R (>= 3.6), Biobase, S4Vectors, ggplot2 Imports: BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes, grDevices, IRanges, methods, pheatmap, RColorBrewer, stats, utils Suggests: biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf License: MIT MD5sum: bfd0e03f89ce1a9b3f22a23cded890a9 Package: NanoTube Version: 1.16.0 Depends: R (>= 4.1), Biobase, ggplot2, limma Imports: fgsea, methods, reshape, stats, utils Suggests: grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly, rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx License: GPL-3 + file LICENSE MD5sum: af6dc64f510bec00a47bea90d0b01759 Package: NBAMSeq Version: 1.26.0 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: b2c5fe9080d7ade94cb66804a584adcc Package: ncdfFlow Version: 2.56.0 Depends: R (>= 2.14.0), flowCore(>= 1.51.7), methods, BH Imports: Biobase,BiocGenerics,flowCore LinkingTo: cpp11,BH, Rhdf5lib Suggests: testthat,parallel,flowStats,knitr MD5sum: 2f1460beb0b5e7a264b3d567f3b61574 Package: ncGTW Version: 1.24.0 Depends: methods, BiocParallel, xcms Imports: Rcpp, grDevices, graphics, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-2 MD5sum: 9f2cbe91a4e70bb9c07e2c56060d9b88 Package: ncRNAtools Version: 1.20.0 Imports: httr, xml2, utils, methods, grDevices, ggplot2, IRanges, GenomicRanges, S4Vectors Suggests: knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics License: GPL-3 MD5sum: 12f833959b4f2eb59b1804a8b26f9031 Package: ndexr Version: 1.32.0 Depends: RCX Imports: httr, jsonlite, plyr, tidyr Suggests: BiocStyle, testthat, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: e2040b553ae4c2da3ed803bc9e69c9a8 Package: nearBynding Version: 1.20.0 Depends: R (>= 4.0) Imports: R.utils, matrixStats, plyranges, transport, Rsamtools, S4Vectors, grDevices, graphics, rtracklayer, dplyr, Seqinfo, 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: 805038193a6db41f84346d57c2272f36 Package: Nebulosa Version: 1.20.0 Depends: R (>= 4.0), ggplot2, patchwork Imports: SingleCellExperiment, SummarizedExperiment, SeuratObject, ks, Matrix, stats, methods, ggrastr Suggests: testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, Seurat License: GPL-3 MD5sum: ebbb2e550a9fd8f9e98c0841b464bb0e Package: nempi Version: 1.18.0 Depends: R (>= 4.1), mnem Imports: e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats, epiNEM Suggests: knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle License: GPL-3 MD5sum: fa28b0ec83c41165f38cb69dd2a1a733 Package: NetActivity Version: 1.12.0 Depends: R (>= 4.1.0) Imports: airway, DelayedArray, DelayedMatrixStats, DESeq2, methods, methods, NetActivityData, SummarizedExperiment, utils Suggests: AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse License: MIT + file LICENSE MD5sum: a575af54e8ac2aa960492b40fe86dba0 Package: netboost Version: 2.18.0 Depends: R (>= 4.0.0) Imports: Rcpp, RcppParallel, parallel, grDevices, graphics, stats, utils, dynamicTreeCut, WGCNA, impute, colorspace, methods, BiocStyle, R.utils LinkingTo: Rcpp, RcppParallel Suggests: knitr, rmarkdown License: GPL-3 OS_type: unix MD5sum: 0ac417f2f9e10f999e925a4ee1dd1715 Package: nethet Version: 1.42.0 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: c533745a016629b0702442e736b281b6 Package: NetPathMiner Version: 1.46.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: f3fd0d6fc27193d1b314b0c4383227b3 Package: netprioR Version: 1.36.0 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: b7fe2b3904b590453f348b3ded580180 Package: netresponse Version: 1.70.0 Depends: R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods, minet, mclust, reshape2 Imports: ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer Suggests: knitr License: GPL (>= 2) MD5sum: 5d53358af0a935c5406f783d549fe333 Package: NetSAM Version: 1.50.0 Depends: R (>= 3.0.0), seriation (>= 1.0-6), igraph (>= 2.0.0), 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: 69d548ae9b390575514641269d85d5a7 Package: netSmooth Version: 1.30.0 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: fce8d94f98e9d9478fd1d51fcb50fa5d Package: NewWave Version: 1.20.0 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: 585e99c99d201e6fc4baef559a86d060 Package: ngsReports Version: 2.12.0 Depends: R (>= 4.2.0), BiocGenerics, ggplot2 (>= 4.0.0), patchwork (>= 1.1.1), tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro, grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate, methods, plotly (>= 4.9.4), rlang, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo Suggests: BiocStyle, Cairo, DT, knitr, pander, readr, testthat, truncnorm License: LGPL-3 MD5sum: 277668050a6b02e5266cf69dc34f02d9 Package: nipalsMCIA Version: 1.8.0 Depends: R (>= 4.3.0) Imports: ComplexHeatmap, dplyr, fgsea, ggplot2 (>= 3.0.0), graphics, grid, methods, MultiAssayExperiment, SummarizedExperiment, pracma, rlang, RSpectra, scales, stats Suggests: BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0) License: GPL-3 MD5sum: 28473e024d9601e0fd9f68d518abbad0 Package: nnNorm Version: 2.74.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: 73401589b17007fff1481d91f461618b Package: nnSVG Version: 1.14.0 Depends: R (>= 4.2) Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat License: MIT + file LICENSE MD5sum: 2c1e6aeb75d7e23c9e43a3bec22c9037 Package: NOISeq Version: 2.54.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 MD5sum: 71cea4fe5a8283855d06b60950782083 Package: nondetects Version: 2.40.0 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: 8aabf8e6386ca4172f49be2199e236bb Package: NoRCE Version: 1.22.0 Depends: R (>= 4.4.0) Imports: KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,stringr,Seqinfo, S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl, dbplyr,utils,ggplot2,igraph,stats,reshape2,readr, GO.db, biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi,methods 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, markdown License: MIT + file LICENSE MD5sum: 3af91454a512d28bdc30be254d62a725 Package: normalize450K Version: 1.38.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 14af9cb702f2b15c7a61af8081c4ae49 Package: NormalyzerDE Version: 1.28.0 Depends: R (>= 4.1.0) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 MD5sum: bed6ba8d6a4b2bfea6b8855f166aaacf Package: NormqPCR Version: 1.56.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: 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knitr, lmerTest, mixOmics, MuMIn, MUVR2, notameViz, PERMANOVA, PK, randomForest, rmcorr, testthat License: MIT + file LICENSE MD5sum: 061306c537891aff25e4bdf79a8fd388 Package: notameViz Version: 1.0.0 Depends: R (>= 4.5.0), ggplot2, SummarizedExperiment Imports: BiocGenerics, cowplot, devEMF, dplyr, ggbeeswarm, ggdendro, ggrepel, grDevices, methods, notame, scales, stringr, stats, tibble, tidyr, utils Suggests: batchCorr, BiocStyle, igraph, knitr, notameStats, pcaMethods, Rtsne, testthat License: MIT + file LICENSE MD5sum: f8346ba55a741c432900d0fd0d0ba94d Package: NPARC Version: 1.22.0 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: 135cc4c21b9d0029ea9accf600e6a56e Package: npGSEA Version: 1.46.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, 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1.12.0 Depends: R (>= 4.2.0), magrittr, dplyr, ggplot2, edgeR, RUVSeq, DESeq2, limma, rhdf5, foreach, Rfast, octad.db, stats, httr, qpdf, ExperimentHub, AnnotationHub, Biobase, S4Vectors Imports: EDASeq, GSVA, data.table, htmlwidgets, plotly, reshape2, grDevices, utils Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: d2546bd5c98dfc893fa0f1fdc5ac8255 Package: odseq Version: 1.38.0 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: f7c07de451c3135417452c5776c4f1b7 Package: OGRE Version: 1.14.0 Depends: R (>= 4.2.0), S4Vectors Imports: GenomicRanges, methods, data.table, assertthat, ggplot2, Gviz, IRanges, AnnotationHub, grDevices, stats, Seqinfo, GenomeInfoDb, shiny, shinyFiles, DT, rtracklayer, shinydashboard, shinyBS,tidyr Suggests: testthat (>= 3.0.0), knitr (>= 1.36), rmarkdown (>= 2.11) License: Artistic-2.0 MD5sum: dc9141e4226ffbe3fe170dfe52827a86 Package: oligo Version: 1.74.0 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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: ae0e332acd5cc4178dc8b11fc944787d Package: OLIN Version: 1.88.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 MD5sum: 0d0191268f905018dc069c02beae060c Package: OLINgui Version: 1.84.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 MD5sum: a006c30ae230a75d4a7287bc2b0aabef Package: omada Version: 1.12.0 Depends: pdfCluster (>= 1.0-3), kernlab (>= 0.9-29), R (>= 4.2), fpc (>= 2.2-9), Rcpp (>= 1.0.7), diceR (>= 0.6.0), ggplot2 (>= 3.3.5), reshape (>= 0.8.8), genieclust (>= 1.1.3), clValid (>= 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omicRexposome Version: 1.32.0 Depends: R (>= 3.5.0), 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: 9b77090eeaf06c5e7811ff052433177b Package: omicsGMF Version: 1.0.0 Depends: R (>= 4.5.0), sgdGMF, SingleCellExperiment, scuttle, scater Imports: stats, utils, Matrix, S4Vectors, SummarizedExperiment, DelayedArray, MatrixGenerics, BiocSingular, BiocParallel, beachmat, ggplot2, methods, QFeatures Suggests: knitr, dplyr, testthat, BiocGenerics, BiocStyle, graphics, grDevices License: Artistic-2.0 MD5sum: 1dc40d231bbbd71f9c8ee80488740b93 Package: OMICsPCA Version: 1.28.0 Depends: R (>= 3.5.0), OMICsPCAdata Imports: HelloRanges, fpc, stats, MultiAssayExperiment, pdftools, methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown, kableExtra, rtracklayer, IRanges, Seqinfo, reshape2, ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR, PerformanceAnalytics, tidyr, data.table, cluster, magick Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: b72ddeccc8740b4d599c05288483c784 Package: omicsPrint Version: 1.30.0 Depends: R (>= 3.5), MASS Imports: methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 2) MD5sum: b6351f3419ce406034eddd6f8b8c7846 Package: omicsViewer Version: 1.14.0 Depends: R (>= 4.2) Imports: survminer, survival, fastmatch, reshape2, stringr, beeswarm, grDevices, DT, shiny, shinythemes, shinyWidgets, plotly, networkD3, httr, matrixStats, RColorBrewer, Biobase, fgsea, openxlsx, psych, shinybusy, ggseqlogo, htmlwidgets, graphics, grid, stats, utils, methods, shinyjs, curl, flatxml, ggplot2, S4Vectors, SummarizedExperiment, RSQLite, Matrix, shinycssloaders, ROCR, drc Suggests: BiocStyle, knitr, rmarkdown, unittest License: GPL-2 MD5sum: f1f4d02e379ae0b301a1c45f09b43201 Package: Omixer Version: 1.20.0 Depends: R (>= 4.0.0) Imports: dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr, tidyselect, grid, stats, stringr Suggests: knitr, rmarkdown, BiocStyle, magick, testthat License: MIT + file LICENSE MD5sum: 12585ebb6a9ede288eb7e7ab3f5104e0 Package: ompBAM Version: 1.14.0 Imports: utils, Rcpp Suggests: RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: bf19f159149ae41bfe94740a29ce323a Package: omXplore Version: 1.3.0 Depends: R (>= 4.4.0), methods Imports: DT, shiny, bs4Dash, waiter, thematic, MSnbase, PSMatch, SummarizedExperiment, MultiAssayExperiment, shinyBS, shinyjs, shinyjqui, RColorBrewer, gplots, highcharter, visNetwork, tibble, grDevices, stats, utils, htmlwidgets, vioplot, graphics, FactoMineR, dendextend, dplyr, factoextra, tidyr, nipals Suggests: knitr, rmarkdown, BiocStyle, testthat, Matrix, graph License: Artistic-2.0 MD5sum: fc916d2aec33006e39f177d7b8f6142d Package: oncomix Version: 1.32.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: bc7a1a4f708e7162fb078886056be44f Package: oncoscanR Version: 1.12.0 Depends: R (>= 4.2), IRanges (>= 2.30.0), GenomicRanges (>= 1.48.0), magrittr Imports: readr, S4Vectors, methods, utils Suggests: testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 48fe2e5f0a43bbed8efaa09f7dc7e61c Package: OncoScore Version: 1.38.0 Depends: R (>= 4.1.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: 5d73c59d625c3a3e83b74db5952cbf9a Package: ontoProc Version: 2.4.0 Depends: R (>= 4.1), ontologyIndex Imports: Biobase, S4Vectors, methods, stats, utils, BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph, AnnotationHub, SummarizedExperiment, reticulate, R.utils, httr, basilisk, jsonlite, RBGL, ellmer Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi, magick, License: Artistic-2.0 MD5sum: 9fc1f4fb7faed139c15b971385ac448f Package: openCyto Version: 2.22.0 Depends: R (>= 3.5.0) Imports: methods, Biobase, BiocGenerics, flowCore(>= 1.99.17), flowViz, ncdfFlow(>= 2.11.34), flowWorkspace(>= 3.99.1), flowClust(>= 3.11.4), RBGL, graph, data.table, RColorBrewer, grDevices LinkingTo: cpp11, BH(>= 1.62.0-1) Suggests: flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS MD5sum: 3e516a51fe01592a51f1e8102e15d074 Package: openPrimeR Version: 1.32.0 Depends: R (>= 4.0.0) Imports: Biostrings (>= 2.38.4), pwalign, XML (>= 3.98-1.4), scales (>= 0.4.0), reshape2 (>= 1.4.1), seqinr (>= 3.3-3), IRanges (>= 2.4.8), GenomicRanges (>= 1.22.4), ggplot2 (>= 2.1.0), plyr (>= 1.8.4), dplyr (>= 0.5.0), stringdist (>= 0.9.4.1), stringr (>= 1.0.0), RColorBrewer (>= 1.1-2), DECIPHER (>= 1.16.1), lpSolveAPI (>= 5.5.2.0-17), digest (>= 0.6.9), Hmisc (>= 3.17-4), ape (>= 3.5), BiocGenerics (>= 0.16.1), S4Vectors (>= 0.8.11), foreach (>= 1.4.3), magrittr (>= 1.5), uniqtag (>= 1.0), openxlsx (>= 4.0.17), grid (>= 3.1.0), grDevices (>= 3.1.0), stats (>= 3.1.0), utils (>= 3.1.0), methods (>= 3.1.0) Suggests: testthat (>= 1.0.2), knitr (>= 1.13), rmarkdown (>= 1.0), devtools (>= 1.12.0), doParallel (>= 1.0.10), pander (>= 0.6.0), learnr (>= 0.9) License: GPL-2 MD5sum: 15db1343811c49c17e88b69c7a2e4478 Package: OpenStats Version: 1.22.0 Depends: nlme Imports: MASS, jsonlite, Hmisc, methods, knitr, AICcmodavg, car, rlist, summarytools, graphics, stats, utils Suggests: rmarkdown License: GPL (>= 2) MD5sum: 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BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat License: Artistic-2.0 MD5sum: acb5675a2d2d572ea5ddff7dc3c4f1ff Package: OrderedList Version: 1.82.0 Depends: R (>= 3.6.1), Biobase, twilight Imports: methods License: GPL (>= 2) MD5sum: 920746eb17eca0c8e4958c6b7794dbcd Package: ORFhunteR Version: 1.18.0 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: MIT License MD5sum: 6af48a272dbe5a51b27a1f466719eacd Package: ORFik Version: 1.30.0 Depends: R (>= 4.1.0), IRanges (>= 2.17.1), GenomicRanges (>= 1.35.1), GenomicAlignments (>= 1.19.0) Imports: AnnotationDbi (>= 1.45.0), Biostrings (>= 2.51.1), biomaRt, biomartr (>= 1.0.7), BiocFileCache, BiocGenerics (>= 0.29.1), BiocParallel (>= 1.19.0), BSgenome, cowplot (>= 1.0.0), data.table (>= 1.11.8), DESeq2 (>= 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1.0.0), TreeTools, ggimage, OmaDB License: GPL-3 MD5sum: db02acd08dc0bcd53c3139f6d658cab3 Package: orthos Version: 1.7.4 Depends: R (>= 4.3), SummarizedExperiment Imports: AnnotationHub, basilisk, BiocParallel, colorspace, cowplot, DelayedArray, dplyr, ExperimentHub, ggplot2 (>= 3.4.0), ggpubr, ggrepel, ggsci, grDevices, grid, HDF5Array, keras (>= 2.16.0), methods, orthosData, parallel, plyr, reticulate, rlang, S4Vectors, stats, tensorflow, tidyr Suggests: BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 521d0cc49f19f8fe873399f04b86becf Package: OSAT Version: 1.58.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 MD5sum: 9aecbbdace6298a3311fcdf9a7fbe920 Package: Oscope Version: 1.40.0 Depends: EBSeq, cluster, testthat, BiocParallel Suggests: BiocStyle License: Artistic-2.0 MD5sum: b64394ccf2dad9a2d09cbf8b4c0c4550 Package: OSTA.data Version: 1.1.2 Depends: R (>= 4.5) Imports: osfr, utils, BiocFileCache 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GenomicRanges, igraph, motifmatchr, stats, utils, grDevices, graphics Suggests: bcellViper, BSgenome.Hsapiens.UCSC.hg19, JASPAR2018, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, TFBSTools, GenomicFeatures, annotate License: GPL-2 MD5sum: 4d0d2a44c1ed728e7765c375ffb90438 Package: PAIRADISE Version: 1.26.0 Depends: R (>= 3.6), nloptr Imports: SummarizedExperiment, S4Vectors, stats, methods, abind, BiocParallel Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: e431baffb1ce902e41852439751d11ff Package: paircompviz Version: 1.48.0 Depends: R (>= 2.10), Rgraphviz Imports: Rgraphviz Suggests: multcomp, reshape, rpart, plyr, xtable License: GPL (>= 3.0) MD5sum: caa6b0dbf4b899fbe79c044a822df3c5 Package: pairedGSEA Version: 1.10.0 Depends: R (>= 4.4.0) Imports: DESeq2, DEXSeq, limma, fgsea, msigdbr, sva, SummarizedExperiment, S4Vectors, BiocParallel, ggplot2, aggregation, stats, utils, methods, showtext Suggests: writexl, readxl, readr, rhdf5, plotly, 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phantasusLite, XML Suggests: testthat, BiocStyle, knitr, rmarkdown, org.Hs.eg.db, org.Mm.eg.db License: MIT + file LICENSE MD5sum: 113e424cda6961e2984dfba559bbae27 Package: phantasusLite Version: 1.8.0 Depends: R (>= 4.2) Imports: data.table, rhdf5client(>= 1.25.1), httr, stringr, stats, utils, Biobase, methods Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5, GEOquery License: MIT + file LICENSE MD5sum: aa0cec67e639b2db91d79e2ba77cd016 Package: PharmacoGx Version: 3.14.0 Depends: R (>= 4.1.0), CoreGx Imports: BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, RColorBrewer, magicaxis, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, checkmate, boot, coop LinkingTo: Rcpp Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils License: GPL (>= 3) MD5sum: ca46a08150fa8b589e6994740c588247 Package: PhenoGeneRanker Version: 1.18.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 International License MD5sum: 7dcf12e48430732817dc0271cf0e010d Package: phenomis Version: 1.12.0 Depends: SummarizedExperiment Imports: Biobase, biodb, biodbChebi, data.table, futile.logger, ggplot2, ggrepel, graphics, grDevices, grid, htmlwidgets, igraph, limma, methods, MultiAssayExperiment, MultiDataSet, PMCMRplus, plotly, ranger, RColorBrewer, ropls, stats, tibble, tidyr, utils, VennDiagram Suggests: BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4, rmarkdown, testthat License: CeCILL MD5sum: 8f91276bc8d8610b8c138b50a4386385 Package: phenopath Version: 1.34.0 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: 760c18748ce51cfdf282ae167c1a27e2 Package: phenoTest Version: 1.58.0 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: db51c7cf5f7ed1d4b24366b551d9ead4 Package: philr Version: 1.36.0 Imports: ape, phangorn, tidyr, ggplot2, ggtree, methods Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia License: GPL-3 MD5sum: 4f97297e465a4df161c1ecd820082c6f Package: PhIPData Version: 1.18.0 Depends: R (>= 4.1.0), SummarizedExperiment (>= 1.3.81) Imports: BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors, edgeR, cli, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr License: MIT + file LICENSE MD5sum: 0e762e93c274f24ebe05058adf91423c Package: phosphonormalizer Version: 1.34.0 Depends: R (>= 4.0) Imports: plyr, stats, graphics, matrixStats, methods Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) MD5sum: 7a58c7787d3cf769a3e29387103959f3 Package: PhosR Version: 1.20.0 Depends: R (>= 4.2.0) 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, stringi 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: ea9e074b188e6890e98d0301e9bfc6cf Package: PhyloProfile Version: 2.2.0 Depends: R (>= 4.5.0) Imports: ape, bioDist, BiocStyle, Biostrings, bsplus, colourpicker, data.table, dplyr, DT, energy, fastcluster, ggplot2, gridExtra, htmlwidgets, pbapply, plotly, RColorBrewer, RCurl, Rfast, scattermore, shiny, shinycssloaders, shinyFiles, shinyjs, stringr, tsne, svglite, umap, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat, OmaDB License: MIT + file LICENSE MD5sum: 0d7462a7d525098a0495f8386305f0bf Package: piano Version: 2.26.0 Depends: R (>= 3.5) Imports: BiocGenerics, Biobase, gplots, igraph, relations, marray, fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard, visNetwork, scales, grDevices, graphics, stats, utils, methods Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 5732f8e273f429dfe3ea2d32141af273 Package: PICB Version: 1.2.0 Imports: utils, Seqinfo, GenomicRanges, GenomicAlignments, Biostrings, Rsamtools, data.table, IRanges, seqinr, stats, openxlsx, dplyr, S4Vectors, methods Suggests: GenomeInfoDb, knitr, rtracklayer, testthat, BiocStyle, prettydoc, BSgenome, BSgenome.Dmelanogaster.UCSC.dm6, BiocManager, rmarkdown, ggplot2 License: CC0 MD5sum: 9882d491e1ce8739a9f5811f6c38c764 Package: pickgene Version: 1.82.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: da84fd782769c25810cc92c96c0c0d35 Package: pipeComp Version: 1.20.0 Depends: R (>= 4.1) Imports: BiocParallel, S4Vectors, ComplexHeatmap, SingleCellExperiment, SummarizedExperiment, Seurat, matrixStats, Matrix, cluster, aricode, methods, utils, dplyr, grid, scales, scran, viridisLite, clue, randomcoloR, ggplot2, cowplot, intrinsicDimension, scater, knitr, reshape2, stats, Rtsne, uwot, circlize, RColorBrewer Suggests: BiocStyle, rmarkdown License: GPL MD5sum: 9640d40bc201ea1edc738821bcf01389 Package: pipeFrame Version: 1.26.0 Depends: R (>= 4.0.0), Imports: BSgenome, digest, visNetwork, magrittr, methods, Biostrings, Seqinfo, parallel, stats, utils, rmarkdown Suggests: BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19 License: 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BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene License: MIT + file LICENSE MD5sum: d8dd4164763577a3141915969cc34f0c Package: plotGrouper Version: 1.28.0 Depends: R (>= 3.5) Imports: ggplot2 (>= 3.0.0), dplyr (>= 0.7.6), tidyr (>= 0.2.0), tibble (>= 1.4.2), stringr (>= 1.3.1), readr (>= 1.1.1), readxl (>= 1.1.0), scales (>= 1.0.0), stats, grid, gridExtra (>= 2.3), egg (>= 0.4.0), gtable (>= 0.2.0), ggpubr (>= 0.1.8), shiny (>= 1.1.0), shinythemes (>= 1.1.1), colourpicker (>= 1.0), magrittr (>= 1.5), Hmisc (>= 4.1.1), rlang (>= 0.2.2) Suggests: knitr, htmltools, BiocStyle, rmarkdown, testthat License: GPL-3 MD5sum: 33d89fe6984bb3b88c088850d1dbf4ce Package: PLPE Version: 1.70.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) MD5sum: 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BiocStyle, CoGAPS, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap, gplots, SeuratObject License: GPL (== 2) MD5sum: 707e7dadeb994318d2e33637caef6e09 Package: pRoloc Version: 1.50.0 Depends: R (>= 3.5), MSnbase (>= 1.19.20), MLInterfaces (>= 1.67.10), methods, Rcpp (>= 0.10.3), BiocParallel Imports: stats4, Biobase, mclust (>= 4.3), caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS, knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools, plyr, ggplot2, biomaRt, utils, grDevices, graphics, colorspace LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, rmarkdown, pRolocdata (>= 1.43.2), roxygen2, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape, magick, umap License: GPL-2 MD5sum: 21c443abfb0fb3fa10ff8382de18d5f3 Package: pRolocGUI Version: 2.20.0 Depends: methods, R (>= 3.1.0), 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vegan Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, DT License: GPL (>= 3) MD5sum: 74a04fd5045a396577ae17d4f5a646a4 Package: PROPER Version: 1.42.0 Depends: R (>= 3.3) Imports: edgeR Suggests: BiocStyle,DESeq2,DSS,knitr License: GPL MD5sum: b42e47024dcbe6e1716cb96026cd6f79 Package: PROPS Version: 1.32.0 Imports: bnlearn, reshape2, sva, stats, utils, Biobase Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 7b7e6d49b9410eb4305eb690753b3726 Package: Prostar Version: 1.42.0 Depends: R (>= 4.4.0) Imports: DAPAR (>= 1.35.1), DAPARdata (>= 1.30.0), rhandsontable, data.table, shiny, shinyBS, shinyAce, highcharter, htmlwidgets, webshot, shinythemes, later, shinycssloaders, future, promises, shinyjqui, tibble, ggplot2, gplots, shinyjs, vioplot, Biobase, DT, R.utils, RColorBrewer, XML, colourpicker, gtools, markdown, rclipboard, sass, shinyTree, shinyWidgets Suggests: BiocStyle, BiocManager, testthat, knitr License: Artistic-2.0 MD5sum: f822c6cfe7ce568c42eaea7f88615e57 Package: 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jsonlite, limma, pairsD3, plyr, purrr, Rcpp (>= 0.12.14), recount, Rfast, R.utils, reshape2, shinyjs, stringr, stats, SummarizedExperiment, survival, tools, utils, XML, xtable, methods LinkingTo: Rcpp Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling License: MIT + file LICENSE MD5sum: d1c60d8d3bcf5b15d073f90e7a8fd8ff Package: PSMatch Version: 1.14.0 Depends: S4Vectors, R (>= 4.1.0) Imports: utils, stats, igraph, methods, Spectra (>= 1.17.10), Matrix, BiocParallel, BiocGenerics, ProtGenerics (>= 1.27.1), QFeatures, MsCoreUtils, IRanges Suggests: msdata, rpx, mzID, mzR, SummarizedExperiment, BiocStyle, rmarkdown, knitr, factoextra, vdiffr (>= 1.0.0), testthat License: Artistic-2.0 MD5sum: 12642e61bdbc616e99536dba15e54808 Package: ptairMS Version: 1.18.0 Imports: Biobase, bit64, chron, data.table, doParallel, DT, enviPat, foreach, ggplot2, graphics, grDevices, ggpubr, gridExtra, Hmisc, methods, minpack.lm, MSnbase, parallel, plotly, rhdf5, rlang, Rcpp, shiny, shinyscreenshot, signal, scales, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData, ropls License: GPL-3 MD5sum: 0d469765483af8f4e07559df66e27ed1 Package: puma Version: 3.52.0 Depends: R (>= 3.2.0), oligo (>= 1.32.0),graphics,grDevices, methods, stats, utils, mclust, oligoClasses Imports: Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses Suggests: pumadata, affydata, snow, limma, ROCR,annotate License: LGPL MD5sum: 54573a72afbb0fc8dc4b430cdada4c80 Package: PureCN Version: 2.16.0 Depends: R (>= 3.5.0), DNAcopy, VariantAnnotation (>= 1.14.1) Imports: GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer, S4Vectors, data.table, grDevices, graphics, stats, utils, SummarizedExperiment, Seqinfo, GenomeInfoDb, GenomicFeatures, Rsamtools, Biobase, Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra, futile.logger, VGAM, tools, methods, mclust, rhdf5, Matrix Suggests: BiocParallel, BiocStyle, PSCBS, R.utils, TxDb.Hsapiens.UCSC.hg19.knownGene, covr, knitr, optparse, org.Hs.eg.db, jsonlite, markdown, rmarkdown, testthat Enhances: genomicsdb (>= 0.0.3) License: Artistic-2.0 MD5sum: d6997895a86421906d58a31ee59910d8 Package: pvac Version: 1.58.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) MD5sum: e7e557944c8d4908b40250cf4bc13c6b Package: pvca Version: 1.50.0 Depends: R (>= 2.15.1) Imports: Matrix, Biobase, vsn, stats, lme4 Suggests: golubEsets License: LGPL (>= 2.0) MD5sum: 300932d27ef159bf591f77d42cd45527 Package: Pviz Version: 1.44.0 Depends: R(>= 3.0.0), Gviz(>= 1.7.10) Imports: biovizBase, Biostrings, GenomicRanges, IRanges, data.table, methods Suggests: knitr, pepDat License: Artistic-2.0 MD5sum: 03fbc8e497d1c7e1f2553215ae1848df Package: pwalign Version: 1.6.0 Depends: BiocGenerics, S4Vectors, IRanges, Biostrings (>= 2.71.5) Imports: methods, utils LinkingTo: S4Vectors, IRanges, XVector, 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Suggests: rmarkdown, BiocStyle, knitr, pander, markdown License: GPL-3 MD5sum: 73fa68b87c801769356d437c76017020 Package: raer Version: 1.8.0 Imports: stats, methods, GenomicRanges, IRanges, Rsamtools, BSgenome, Biostrings, SummarizedExperiment, SingleCellExperiment, S4Vectors, Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicFeatures, BiocGenerics, BiocParallel, rtracklayer, Matrix, cli LinkingTo: Rhtslib Suggests: testthat (>= 3.0.0), knitr, DESeq2, edgeR, limma, rmarkdown, BiocStyle, ComplexHeatmap, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38, scater, scran, scuttle, AnnotationHub, covr, raerdata, txdbmaker License: MIT + file LICENSE MD5sum: 23a2afe03750fc83ca537809ad69c299 Package: RaggedExperiment Version: 1.34.0 Depends: R (>= 4.5.0), GenomicRanges (>= 1.61.1) Imports: BiocBaseUtils, BiocGenerics, Seqinfo, IRanges, Matrix, MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment (>= 1.39.1), utils Suggests: BiocStyle, knitr, rmarkdown, testthat, GenomeInfoDb, MultiAssayExperiment License: Artistic-2.0 MD5sum: 5e610f91b0d55fae2c1bdc937d2f1083 Package: RAIDS Version: 1.8.0 Depends: R (>= 4.2.0), gdsfmt, SNPRelate, stats, utils, GENESIS, dplyr, Rsamtools Imports: S4Vectors, GenomicRanges, ensembldb, BSgenome, AnnotationDbi, methods, class, pROC, IRanges, AnnotationFilter, rlang, VariantAnnotation, MatrixGenerics, ggplot2, stringr Suggests: testthat, knitr, rmarkdown, BiocStyle, withr, Seqinfo, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: Apache License (>= 2) MD5sum: 8396812ea7d834dfe556e8c10af2e2c6 Package: rain Version: 1.44.0 Depends: R (>= 2.10), gmp, multtest Suggests: lattice, BiocStyle License: GPL-2 MD5sum: c9795531a11127c1c93571d74188a214 Package: ramr Version: 1.18.0 Depends: R (>= 4.1) Imports: methods, data.table, Seqinfo, GenomicRanges, IRanges, BiocGenerics, S4Vectors, Rcpp LinkingTo: Rcpp Suggests: RUnit, knitr, rmarkdown, ggplot2, gridExtra, annotatr, LOLA, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, parallel, doParallel, foreach, doRNG, matrixStats, EnvStats, ExtDist, gamlss, gamlss.dist License: Artistic-2.0 MD5sum: be3ddf3758755f2c9d29d772e16af1a9 Package: ramwas Version: 1.34.0 Depends: R (>= 3.3.0), methods, filematrix Imports: graphics, stats, utils, digest, glmnet, KernSmooth, grDevices, GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings, BiocGenerics Suggests: knitr, rmarkdown, pander, BiocStyle, BSgenome.Ecoli.NCBI.20080805 License: LGPL-3 MD5sum: 5008cf18bd69f94dc797a3336113eaa9 Package: randPack Version: 1.56.0 Depends: methods Imports: Biobase License: Artistic-2.0 MD5sum: a4be672ce95faa7c474bb78738c2d8d2 Package: RankProd Version: 3.36.0 Depends: R (>= 3.2.1), stats, methods, Rmpfr, gmp Imports: graphics License: file LICENSE License_restricts_use: yes MD5sum: bc6299f90f2fdda8f7595adf0870bce8 Package: RAREsim Version: 1.14.0 Depends: R (>= 4.1.0) Imports: nloptr Suggests: markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 8d1e907eade6dcbcdc09381580d8025a Package: RareVariantVis Version: 2.38.0 Depends: BiocGenerics, VariantAnnotation, googleVis, GenomicFeatures Imports: S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, SummarizedExperiment, GenomicScores Suggests: knitr License: Artistic-2.0 MD5sum: a1548894ef491ddb5f9ff6d73493e698 Package: Rarr Version: 1.10.0 Depends: BiocGenerics, DelayedArray, R (>= 4.1.0) Imports: curl, jsonlite, methods, paws.storage, R.utils, utils Suggests: BiocStyle, covr, knitr, testthat (>= 3.0.0), withr License: MIT + file LICENSE MD5sum: 47b3f58a28abcb58742b2c3ff8954791 Package: rawDiag Version: 1.6.0 Depends: R (>= 4.4) Imports: dplyr, ggplot2 (>= 3.4), grDevices, hexbin, htmltools, BiocManager, BiocParallel, rawrr (>= 1.15.5), rlang, reshape2, scales, shiny (>= 1.5), stats, utils Suggests: BiocStyle (>= 2.28), ExperimentHub, tartare, knitr, testthat License: GPL-3 MD5sum: 0325330ff6287c4c0c17830690ab5280 Package: rawrr Version: 1.18.0 Depends: R (>= 4.5) Imports: grDevices, graphics, stats, utils Suggests: BiocStyle (>= 2.5), ExperimentHub, knitr, protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat License: GPL-3 MD5sum: 3407211580228db4a392f5a06eb27941 Package: RbcBook1 Version: 1.78.0 Depends: R (>= 2.10), Biobase, graph, rpart License: Artistic-2.0 MD5sum: aadc25ee46da3d6ac6777a28aab9131f Package: RBGL Version: 1.86.0 Depends: graph, methods Imports: methods LinkingTo: BH Suggests: Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr License: Artistic-2.0 MD5sum: 68ea16f0f72d17daf62bef3fd2b524d3 Package: RBioFormats Version: 1.10.0 Imports: EBImage, methods, rJava (>= 0.9-6), S4Vectors, stats Suggests: BiocStyle, knitr, testthat, xml2 License: GPL-3 MD5sum: 9a541d451cf7b52797c4b2f675a8f835 Package: rBiopaxParser Version: 2.50.0 Depends: R (>= 4.0), data.table Imports: XML Suggests: 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BiocGenerics, testthat, BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW, parallel, rmarkdown License: LGPL-3 + file LICENSE MD5sum: 581ae4633482d2cfc31c2b523ea48d78 Package: rCGH Version: 1.40.0 Depends: R (>= 3.4),methods,stats,utils,graphics Imports: plyr,DNAcopy,lattice,ggplot2,grid,shiny (>= 0.11.1), limma,affy,mclust,TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db,GenomicFeatures,Seqinfo,GenomicRanges,AnnotationDbi, parallel,IRanges,grDevices,aCGH Suggests: BiocStyle, knitr, BiocGenerics, RUnit License: Artistic-2.0 MD5sum: 5fa23b7a6d4a52052084b66af38fa3b2 Package: RcisTarget Version: 1.29.0 Depends: R (>= 3.5.0) Imports: AUCell (>= 1.1.6), BiocGenerics, data.table, graphics, GenomeInfoDb, GenomicRanges, arrow (>= 2.0.0), dplyr, tibble, GSEABase, methods, R.utils, stats, SummarizedExperiment, S4Vectors, utils, zoo Suggests: Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, gplots, rtracklayer, 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BiocStyle, rmarkdown, mclust, tidyverse, tinytex License: Artistic-2.0 MD5sum: d40f8d1dc1b656a37a09749ff414695d Package: Rcwl Version: 1.25.0 Depends: R (>= 3.6), yaml, methods, S4Vectors Imports: utils, stats, BiocParallel, batchtools, DiagrammeR, shiny, R.utils, codetools, basilisk Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-2 | file LICENSE MD5sum: 3ac9c082eae1708f21117cfb692efc7b Package: RcwlPipelines Version: 1.26.0 Depends: R (>= 3.6), Rcwl, BiocFileCache Imports: rappdirs, methods, utils, git2r, httr, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: a48859a92c41250fea140bc56ae18a2e Package: RCX Version: 1.14.0 Depends: R (>= 4.2.0) Imports: jsonlite, plyr, igraph, methods Suggests: BiocStyle, testthat, knitr, rmarkdown, base64enc, graph License: MIT + file LICENSE MD5sum: 787b9b9cfee67b1f748a6c6844eb81a6 Package: RCy3 Version: 2.30.0 Imports: httr, methods, RJSONIO, XML, utils, BiocGenerics, stats, graph, fs, uuid, stringi, glue, 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BiocStyle Suggests: testthat, igraph, XML, BiocManager, RCurl, bookdown, rappdirs, yaml, BiocParallel, OSCA.intro, OSCA.workflows License: GPL-3 MD5sum: 841c3d2ca7d74b1b6cab32d75fe70c19 Package: reconsi Version: 1.22.0 Imports: phyloseq, ks, reshape2, ggplot2, stats, methods, graphics, grDevices, matrixStats, Matrix Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 8ea7f4958c2df41f4e5551b7ac531d64 Package: recount Version: 1.36.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb, GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer (>= 1.35.3), S4Vectors, stats, utils Suggests: AnnotationDbi, BiocManager, BiocStyle (>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, txdbmaker, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport (>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap, DT, edgeR, ggplot2, RColorBrewer License: Artistic-2.0 MD5sum: 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grDevices, httr, IRanges, methods, parallel, RSQLite, Rsamtools, rtracklayer, S4Vectors, stats, stringr, txdbmaker, utils Suggests: GenomeInfoDb, grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RMySQL License: GPL (>= 3) MD5sum: 0a042d1f5241b725cc566e46a263cfbf Package: RedeR Version: 3.6.0 Depends: R (>= 4.0), methods Imports: scales, igraph Suggests: knitr, rmarkdown, markdown, BiocStyle, TreeAndLeaf License: GPL-3 MD5sum: b1d6608020edddda2d5ebed36e59bbce Package: RedisParam Version: 1.12.0 Depends: R (>= 4.2.0), BiocParallel (>= 1.29.12) Imports: methods, redux, withr, futile.logger Suggests: rmarkdown, knitr, testthat, BiocStyle License: Artistic-2.0 MD5sum: cd490182cf615fb04f3d3a5e12393ff2 Package: REDseq Version: 1.56.0 Depends: R (>= 3.5.0), BiocGenerics, BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno Imports: AnnotationDbi, graphics, IRanges (>= 1.13.5), stats, utils License: GPL (>= 2) MD5sum: e1b31b256b094fb150ff4eb9d8f68ad2 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testthat (>= 2.1.0), covr License: Artistic-2.0 MD5sum: 23ba89553bdb19c9795572fc1009893b Package: REMP Version: 1.34.0 Depends: R (>= 3.6), SummarizedExperiment(>= 1.1.6), minfi (>= 1.22.0) Imports: readr, rtracklayer, graphics, stats, utils, methods, settings, BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges, Seqinfo, BiocParallel, doParallel, parallel, foreach, caret, kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db, impute, iterators Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC License: GPL-3 MD5sum: 8c62497ca0b3316b6a2a3fd1d792f0d5 Package: ReportingTools Version: 2.50.0 Depends: methods, knitr, utils Imports: Biobase,hwriter,Category,GOstats,limma(>= 3.17.5),lattice,AnnotationDbi,edgeR, annotate,PFAM.db, GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils, DESeq2(>= 1.3.41), ggplot2, ggbio, IRanges Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db, rmarkdown, markdown License: Artistic-2.0 MD5sum: 94e712b8334a33483002b45afa8e50f8 Package: ResidualMatrix Version: 1.20.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular License: GPL-3 MD5sum: e52d8ecf862d4ab231cc2384f9160ac9 Package: RESOLVE Version: 1.12.0 Depends: R (>= 4.1.0) Imports: Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5, cluster, data.table, GenomeInfoDb, GenomicRanges, glmnet, ggplot2, gridExtra, IRanges, lsa, MutationalPatterns, nnls, parallel, reshape2, S4Vectors, RhpcBLASctl, survival Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 02cd84f306e630d100546afc0cb33662 Package: retrofit Version: 1.10.0 Depends: R (>= 4.2), Rcpp LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2, corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl License: GPL-3 MD5sum: 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GenomicRanges, stats, ranger Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data, RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer, keras License: Artistic-2.0 MD5sum: ed9b3e774ffd6c6dca6d90452dd914de Package: RNAmodR.RiboMethSeq Version: 1.24.0 Depends: R (>= 4.0), RNAmodR (>= 1.5.3) Imports: methods, S4Vectors, BiocGenerics, IRanges, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, Seqinfo, RNAmodR.Data License: Artistic-2.0 MD5sum: a528fde2e72c369d630539ccfc0d20e1 Package: RNAsense Version: 1.24.0 Depends: R (>= 3.6) Imports: ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment, stats, utils, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: ae901fc0254eade431bdf7bcf4200695 Package: rnaseqcomp Version: 1.40.0 Depends: R (>= 3.2.0) Imports: RColorBrewer, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 0a875d5ff87565d101a7e0657b95112b Package: RNAseqCovarImpute Version: 1.8.0 Depends: R (>= 4.3.0) Imports: Biobase, BiocGenerics, BiocParallel, stats, limma, dplyr, magrittr, rlang, edgeR, foreach, mice Suggests: BiocStyle, knitr, PCAtools, rmarkdown, tidyr, stringr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 4cc63f144f72ac32e23c3b1947669bc6 Package: RNASeqPower Version: 1.50.0 License: LGPL (>= 2) MD5sum: d677ff58c4b4c66d4b003ed2f785e109 Package: RnBeads Version: 2.28.0 Depends: R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25), GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, grid, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr, reshape2 Imports: IRanges Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, RnBeads.hg38, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame License: GPL-3 MD5sum: 63162f49af3a3e796d98ae29bd5b8cf4 Package: Rnits Version: 1.44.0 Depends: R (>= 3.6.0), Biobase, ggplot2, limma, methods Imports: affy, boot, impute, splines, graphics, qvalue, reshape2 Suggests: BiocStyle, knitr, GEOquery, stringr License: GPL-3 MD5sum: 73769c268450158c3c9f5fe9d9e58d35 Package: roar Version: 1.46.0 Depends: R (>= 3.0.1) Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, GenomicAlignments (>= 0.99.4), rtracklayer, GenomeInfoDb Suggests: RNAseqData.HNRNPC.bam.chr14, testthat License: GPL-3 MD5sum: 0c07b4a2da6ef5e2f439314ce3e84fd3 Package: roastgsa Version: 1.8.0 Depends: R (>= 4.3.0) Imports: parallel, grDevices, graphics, utils, stats, methods, grid, RColorBrewer, gplots, ggplot2, limma, Biobase Suggests: BiocStyle, knitr, rmarkdown, GSEABenchmarkeR, EnrichmentBrowser, preprocessCore, DESeq2 License: GPL-3 MD5sum: 26aaa92e2eb35db61a2c639425f94b22 Package: ROC Version: 1.86.0 Depends: R (>= 1.9.0), utils, methods Imports: knitr Suggests: rmarkdown, Biobase, BiocStyle License: Artistic-2.0 MD5sum: 63c9e5aa528e44bdb3d5beafb7980974 Package: ROCpAI Version: 1.22.0 Depends: boot, SummarizedExperiment, fission, knitr, methods Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 96996d3f0c42a8a84d2ba5af691d3287 Package: RolDE Version: 1.14.0 Depends: R (>= 4.2.0) Imports: stats, methods, ROTS, matrixStats, foreach, parallel, doParallel, doRNG, rngtools, SummarizedExperiment, nlme, qvalue, grDevices, graphics, utils Suggests: knitr, printr, rmarkdown, testthat License: GPL-3 MD5sum: bbba83dd7b7c58cc0d2034135ffb450c Package: ROntoTools Version: 2.38.0 Depends: methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz Suggests: RUnit, BiocGenerics License: CC BY-NC-ND 4.0 + file LICENSE MD5sum: 8820933a47b3fdbc4dd9c51f6965258b Package: ropls Version: 1.42.0 Depends: R (>= 3.5.0) Imports: Biobase, ggplot2, graphics, grDevices, methods, plotly, stats, MultiAssayExperiment, MultiDataSet, SummarizedExperiment, utils Suggests: BiocGenerics, BiocStyle, knitr, multtest, omicade4, phenomis, rmarkdown, testthat License: CeCILL MD5sum: 472d16cee94222a33c60080e8aeda1b1 Package: ROSeq Version: 1.22.0 Depends: R (>= 4.0) Imports: pbmcapply, edgeR, limma Suggests: knitr, rmarkdown, testthat, RUnit, BiocGenerics License: GPL-3 MD5sum: 1d4faf6be7482481038f3a901b5d493c Package: ROTS Version: 2.2.0 Depends: R (>= 3.6) Imports: Rcpp, stats, Biobase, methods, BiocParallel, lme4 LinkingTo: Rcpp Suggests: testthat License: GPL (>= 2) MD5sum: 11755dd4bcc648559bf1c123e0921471 Package: RPA Version: 1.66.0 Depends: R (>= 3.1.1), affy, BiocGenerics, BiocStyle, methods, rmarkdown Imports: phyloseq Suggests: knitr, parallel License: BSD_2_clause + file LICENSE MD5sum: b63c19e3492d4b383aa4bbc77ea676e9 Package: rprimer Version: 1.14.0 Depends: R (>= 4.1) Imports: Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods, patchwork, reshape2, S4Vectors, shiny, shinycssloaders, shinyFeedback Suggests: BiocStyle, covr, kableExtra, knitr, rmarkdown, styler, testthat (>= 3.0.0) License: GPL-3 MD5sum: d948c72cd1d25d3e2d8e81dc6520d2be Package: RProtoBufLib Version: 2.22.0 Suggests: knitr, rmarkdown License: BSD_3_clause MD5sum: 26481354997e65612ea81d4549fc7bdc Package: rpx Version: 2.18.0 Depends: R (>= 3.5.0), methods Imports: BiocFileCache, jsonlite, xml2, RCurl, curl, utils Suggests: Biostrings, BiocStyle, testthat, knitr, tibble, rmarkdown License: GPL-2 MD5sum: c663d73d956647720900a80b5565f86a Package: Rqc Version: 1.44.0 Depends: BiocParallel, ShortRead, ggplot2 Imports: BiocGenerics (>= 0.25.1), Biostrings, IRanges, methods, S4Vectors, knitr (>= 1.7), BiocStyle, plyr, markdown, grid, reshape2, Rcpp (>= 0.11.6), biovizBase, shiny, Rsamtools, GenomicAlignments, GenomicFiles LinkingTo: Rcpp Suggests: rmarkdown, testthat License: GPL (>= 2) MD5sum: 074b12412fa3585f573216f50539bd66 Package: rqt Version: 1.36.0 Depends: R (>= 3.4), SummarizedExperiment Imports: stats,Matrix,ropls,methods,car,RUnit,metap,CompQuadForm,glmnet,utils,pls Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: 7ad68620a02bcfc140026e24d7975af6 Package: rqubic Version: 1.56.0 Imports: methods, Biobase, BiocGenerics, biclust Suggests: RColorBrewer License: GPL-2 MD5sum: 24688938d4d020d516c70d47fa8be2f1 Package: rRDP Version: 1.44.0 Depends: Biostrings (>= 2.26.2) Imports: rJava, utils Suggests: rRDPData, knitr, rmarkdown License: GPL-2 + file LICENSE MD5sum: 56d07d4f1e08dd52c749283026c83163 Package: RRHO Version: 1.50.0 Depends: R (>= 2.10), grid Imports: VennDiagram Suggests: lattice License: GPL-2 MD5sum: 22b292aca90eb99142c266072be07783 Package: rrvgo Version: 1.22.0 Imports: GOSemSim, AnnotationDbi, GO.db, pheatmap, ggplot2, ggrepel, treemap, tm, wordcloud, shiny, grDevices, grid, stats, methods, umap Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), shinydashboard, DT, plotly, heatmaply, magrittr, utils, clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db License: GPL-3 MD5sum: 3743367b9ce224fa904c1e063a87d752 Package: Rsamtools Version: 2.26.0 Depends: R (>= 3.5.0), methods, Seqinfo, GenomicRanges (>= 1.61.1), Biostrings (>= 2.77.2) Imports: utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), bitops, BiocParallel, stats LinkingTo: Rhtslib (>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, VariantAnnotation, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr License: Artistic-2.0 | file LICENSE MD5sum: 35a3d019904446788e05da8d02830e47 Package: rScudo Version: 1.26.0 Depends: R (>= 3.6) Imports: methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, SummarizedExperiment, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel License: GPL-3 MD5sum: 75fa4aa3b35a0ea819e110637cd0643d Package: rsemmed Version: 1.20.0 Depends: R (>= 4.0), igraph Imports: methods, magrittr, stringr, dplyr Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: c98745a69797c317905134ed70fadc23 Package: RSeqAn Version: 1.30.0 Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 35c1c185d5e0c26fe97e5c8a5c374e55 Package: Rsubread Version: 2.24.0 Imports: grDevices, stats, utils, Matrix License: GPL (>= 3) MD5sum: 902444c371cf40bdd35499019d2e83da Package: RSVSim Version: 1.50.0 Depends: R (>= 3.5.0), Biostrings, GenomicRanges Imports: methods, IRanges, ShortRead Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer, pwalign License: LGPL-3 MD5sum: 8fc3eb4b7077415e0bd05cd75d2a35b2 Package: rSWeeP Version: 1.22.0 Depends: foreach, doParallel, parallel, Biostrings, methods, utils Imports: tools, stringi, Suggests: Rtsne, ape, Seurat, knitr, rmarkdown, tictoc, BiocStyle, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 057d3fb9b8bc7bf14e9fd978f605edeb Package: RTCA Version: 1.62.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 MD5sum: 6d35fb465adfcfe50674af36eed00254 Package: RTCGA Version: 1.40.0 Depends: R (>= 3.3.0) Imports: XML, RCurl, assertthat, stringi, rvest, data.table, xml2, dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr, scales, rmarkdown, htmltools Suggests: devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, magrittr, tidyr License: GPL-2 MD5sum: 3bd1cc43d1960ced902ca44984fb1030 Package: RTCGAToolbox Version: 2.40.0 Depends: R (>= 4.3.0) Imports: BiocGenerics, data.table, DelayedArray, GenomicRanges, Seqinfo, httr, methods, RaggedExperiment, RCurl, RJSONIO, rvest, S4Vectors, stats, stringr, SummarizedExperiment, TCGAutils, utils Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown License: GPL-2 MD5sum: a16c4a3aca4860f020652631f2aea765 Package: RTN Version: 2.34.0 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: cb544891d78570f210575f74a383a11e Package: RTNduals Version: 1.34.0 Depends: R(>= 3.6.3), RTN(>= 2.14.1), methods Imports: graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: c38cb536967d69feed6ce92e6e2b4d76 Package: RTNsurvival Version: 1.34.0 Depends: R(>= 4.4.0), RTN(>= 2.29.1), RTNduals(>= 1.29.1), methods Imports: survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: f7fde23ef693629c55e461e960ce66fe Package: RTopper Version: 1.56.0 Depends: R (>= 2.12.0), Biobase Imports: limma, multtest Suggests: org.Hs.eg.db, KEGGREST, GO.db License: GPL (>= 3) + file LICENSE MD5sum: fa4d82425d01069bf156a14d7909bbc9 Package: Rtpca Version: 1.20.0 Depends: R (>= 4.0.0), stats, dplyr, tidyr Imports: Biobase, methods, ggplot2, pROC, fdrtool, splines, utils, tibble Suggests: knitr, BiocStyle, TPP, testthat, rmarkdown License: GPL-3 MD5sum: db24441c0cf252c27271c1e71eba55c2 Package: rtracklayer Version: 1.70.0 Depends: R (>= 3.5), methods, GenomicRanges (>= 1.37.2) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.35.3), S4Vectors (>= 0.23.18), IRanges (>= 2.13.13), XVector (>= 0.19.7), Seqinfo, Biostrings (>= 2.77.2), curl, httr, Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), BiocIO, tools, restfulr (>= 0.0.13) LinkingTo: S4Vectors, IRanges, XVector Suggests: GenomeInfoDb, BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit License: Artistic-2.0 + file LICENSE MD5sum: 33dbad88829596f773d81216a095a9b1 Package: rTRM Version: 1.48.0 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: b6e78b51344d89130b35db7934686e2c Package: rTRMui Version: 1.48.0 Imports: shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 00dac7fecc8bef9da20819184583e76b Package: RUCova Version: 1.2.0 Depends: R (>= 4.4.0) Imports: dplyr, fastDummies, ggplot2, stringr, tibble, Matrix, ComplexHeatmap, grid, circlize, SingleCellExperiment, SummarizedExperiment, tidyverse, tidyr, magrittr, S4Vectors Suggests: knitr, rmarkdown, BiocManager, BiocStyle, remotes, ggpubr, ggcorrplot, ggh4x, testthat (>= 3.0.0) License: GPL-3 MD5sum: 97ff13177fbae1af687c67148f54f2dc Package: RUVcorr Version: 1.42.0 Imports: corrplot, MASS, stats, lattice, grDevices, gridExtra, snowfall, psych, BiocParallel, grid, bladderbatch, reshape2, graphics Suggests: knitr, hgu133a2.db, rmarkdown License: GPL-2 MD5sum: cc06244d889eebd19c32da35f0818f57 Package: RUVnormalize Version: 1.44.0 Depends: R (>= 2.10.0) Imports: RUVnormalizeData, Biobase Enhances: spams License: GPL-3 MD5sum: c91cae90acac3416f6c6015d43900505 Package: RUVSeq Version: 1.44.0 Depends: Biobase, EDASeq (>= 1.99.1), edgeR Imports: methods, MASS Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 License: Artistic-2.0 MD5sum: ec63c094befaaeb732115b0dd452cef6 Package: Rvisdiff Version: 1.8.0 Depends: R (>= 4.5.0) Imports: edgeR, utils Suggests: knitr, rmarkdown, DESeq2, limma, SummarizedExperiment, airway, BiocStyle, matrixTests, BiocManager License: GPL-2 | GPL-3 MD5sum: b9f4fe521b15c48d4a19fa09963bfa15 Package: RVS Version: 1.32.0 Depends: R (>= 3.5.0) Imports: GENLIB, gRain, snpStats, kinship2, methods, stats, utils, R.utils Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation License: GPL-2 MD5sum: 22c96ba88815f4aff228ce3dcec75e67 Package: rWikiPathways Version: 1.30.0 Imports: httr, utils, XML, rjson, data.table, RCurl, dplyr, tidyr, readr, stringr, purrr, lubridate Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 7ebb1f62bd4c43d6229b17fdb8c5ee85 Package: S4Arrays Version: 1.10.0 Depends: R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>= 0.45.2), S4Vectors (>= 0.47.6), IRanges Imports: stats LinkingTo: S4Vectors Suggests: BiocParallel, SparseArray (>= 0.0.4), DelayedArray, HDF5Array, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 3bc81c9e6f4b99034c18893d32541a9f Package: S4Vectors Version: 0.48.0 Depends: R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>= 0.53.2) Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: ba56095246b9c4af6ffe68df745f04a2 Package: safe Version: 3.50.0 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: GPL (>= 2) MD5sum: 2ddad0902ee1b62c91a654836aefa82d Package: sagenhaft Version: 1.80.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: 3bf49d13ad379cf9ea90415ae1966e00 Package: SAIGEgds Version: 2.10.0 Depends: R (>= 4.0.0), gdsfmt (>= 1.28.0), SeqArray (>= 1.49.6), Rcpp Imports: methods, stats, utils, Matrix, RcppParallel, SKAT, CompQuadForm, survey LinkingTo: Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0) Suggests: parallel, markdown, rmarkdown, crayon, SNPRelate, RUnit, knitr, ggmanh, BiocGenerics License: GPL-3 MD5sum: 454e4a63ef25607da9fc7166d369fc57 Package: SamSPECTRAL Version: 1.64.0 Depends: R (>= 3.3.3) Imports: methods License: GPL (>= 2) MD5sum: b1431848fb686d7af0b1e217d8c30bc1 Package: sangeranalyseR Version: 1.19.0 Depends: R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER, parallel, reshape2, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle, logger Suggests: testthat (>= 2.1.0) License: GPL-2 MD5sum: 7786d582d899ffc12e2b540faff46111 Package: sangerseqR Version: 1.46.0 Depends: R (>= 3.5.0), Biostrings, pwalign, stringr Imports: methods, shiny Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 MD5sum: 0d1bac132fb6400704a5202610e119ef Package: SanityR Version: 1.0.0 Imports: Rcpp, BiocGenerics, BiocParallel, MatrixGenerics, methods, S4Vectors, scuttle, SingleCellExperiment, SummarizedExperiment LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), scater, Rtsne License: GPL (>= 3) MD5sum: a823beeb30c1e45d48be0a10cd68a090 Package: SANTA Version: 2.46.0 Depends: R (>= 4.1), igraph Imports: graphics, Matrix, methods, stats Suggests: BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db, markdown, rmarkdown, RUnit License: GPL (>= 2) MD5sum: 45e6b9770507c9f5f5390f439cc2760e Package: sarks Version: 1.22.0 Depends: R (>= 4.0) Imports: rJava, Biostrings, IRanges, utils, stats, cluster, binom Suggests: RUnit, BiocGenerics, ggplot2 License: BSD_3_clause + file LICENSE MD5sum: 65a7a6643e36a9ea620f20f645c99740 Package: saseR Version: 1.6.0 Depends: R (>= 4.3.0) Imports: ASpli, BiocGenerics, BiocParallel, data.table, DESeq2, dplyr, edgeR, GenomicAlignments, GenomicFeatures, GenomicRanges, igraph, IRanges, limma, methods, MASS, MatrixGenerics, S4Vectors, stats, SummarizedExperiment, parallel, PRROC Suggests: rrcov, knitr, txdbmaker License: Artistic-2.0 MD5sum: 52c099df37b073bbe309ea7f34e94483 Package: satuRn Version: 1.18.0 Depends: R (>= 4.1) Imports: locfdr, SummarizedExperiment, BiocParallel, limma, pbapply, ggplot2, boot, Matrix, stats, methods, graphics Suggests: knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray License: Artistic-2.0 MD5sum: 2abd3b12637d990cd129f2f50637c24f Package: SBGNview Version: 1.24.0 Depends: R (>= 3.6), pathview, SBGNview.data Imports: Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi, httr, KEGGREST, bookdown Suggests: testthat, gage License: AGPL-3 MD5sum: c2babdba9262a9aa24da9f00b8f46fde Package: SBMLR Version: 2.6.0 Depends: XML, deSolve Suggests: rsbml License: GPL-2 MD5sum: 45b1204364a94cdf83a7001080611256 Package: SC3 Version: 1.38.0 Depends: R(>= 3.3) Imports: graphics, stats, utils, methods, e1071, parallel, foreach, doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR, robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1), SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, mclust, scater, BiocStyle License: GPL-3 MD5sum: 6c14b92720ee29bf7312b3d878b6a3aa Package: scafari Version: 1.0.0 Depends: R (>= 4.5.0) Imports: magrittr, shiny, shinycssloaders, DT, dplyr, waiter, ggplot2, tibble, stringr, reshape2, shinyjs, shinyBS, shinycustomloader, factoextra, markdown, plotly, ggbio, GenomicRanges, rhdf5, ComplexHeatmap, biomaRt, org.Hs.eg.db, SummarizedExperiment, SingleCellExperiment, S4Vectors, parallel, httr, jsonlite, scales, tidyr, txdbmaker, circlize, R.utils, dbscan, igraph, RANN Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: LGPL-3 MD5sum: 63b0f5834f13bccb8d90170d9a204bd1 Package: Scale4C Version: 1.32.0 Depends: R (>= 3.5.0), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: be233a293295f11a7f472f76762d37e7 Package: ScaledMatrix Version: 1.18.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular, DelayedMatrixStats License: GPL-3 MD5sum: 4ee2012b98152d6adf1a7594745ba925 Package: SCAN.UPC Version: 2.52.0 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva Imports: utils, methods, MASS, tools, IRanges Suggests: pd.hg.u95a License: MIT MD5sum: 42fe1c56b88fb925c13a335882093498 Package: scanMiR Version: 1.16.0 Depends: R (>= 4.0) Imports: Biostrings, pwalign, GenomicRanges, IRanges, data.table, BiocParallel, methods, Seqinfo, S4Vectors, ggplot2, stats, stringi, utils, graphics, grid, seqLogo, cowplot Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 5039ff3c5dbd4cb94fccc5778d1f0fdc Package: scanMiRApp Version: 1.16.0 Depends: R (>= 4.0), scanMiR Imports: AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel, Biostrings, data.table, digest, DT, ensembldb, fst, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs, rtracklayer, S4Vectors, scanMiRData, shiny, shinycssloaders, shinydashboard, shinyjqui, stats, utils, txdbmaker, waiter Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-3 MD5sum: d13c828bfb8f05187bd2e6a4ad408b8c Package: scAnnotatR Version: 1.16.0 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: 2fed6086cada3d2ac278370567fbdacb Package: SCANVIS Version: 1.24.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file LICENSE MD5sum: 24c41c4144c564b997ab818875330f12 Package: SCArray Version: 1.18.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.36.0), methods, DelayedArray (>= 0.31.5) Imports: S4Vectors, utils, Matrix, SparseArray (>= 1.5.13), BiocParallel, DelayedMatrixStats, SummarizedExperiment, SingleCellExperiment, BiocSingular Suggests: BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array License: GPL-3 MD5sum: a5bd6c141bb0f889e79990eed5a8c3a1 Package: SCArray.sat Version: 1.9.0 Depends: methods, SCArray (>= 1.13.1), SeuratObject (>= 5.0), Seurat (>= 5.0) Imports: S4Vectors, utils, stats, BiocGenerics, BiocParallel, gdsfmt, DelayedArray, BiocSingular, SummarizedExperiment, Matrix Suggests: future, RUnit, knitr, markdown, rmarkdown, BiocStyle License: GPL-3 MD5sum: 88a9c8d42ffdb67d39313f8a3341b2fb Package: scatterHatch Version: 1.16.0 Depends: R (>= 4.1) Imports: grid, ggplot2, plyr, spatstat.geom, stats, grDevices Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 6df86efb7fb6318480948782e7bf9dac Package: scBFA Version: 1.24.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods, Matrix Suggests: knitr, rmarkdown, testthat, Rtsne License: GPL-3 + file LICENSE MD5sum: 46d392c0bf174608ba947ffe53074d4c Package: SCBN Version: 1.28.0 Depends: R (>= 3.5.0) Imports: stats Suggests: knitr,rmarkdown,BiocStyle,BiocManager License: GPL-2 MD5sum: 8e1e02257f7557f11ed0395761941ad5 Package: scBubbletree Version: 1.12.0 Depends: R (>= 4.2.0) Imports: reshape2, BiocParallel, ape, scales, Seurat, ggplot2, ggtree, patchwork, proxy, methods, stats, base, utils, dplyr Suggests: BiocStyle, knitr, testthat, cluster, SingleCellExperiment License: GPL-3 + file LICENSE MD5sum: 0b61bb5ec8617a3c002208da1e08be30 Package: scCB2 Version: 1.20.0 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: de42db4f90a1d2f247359ed87cc5eb20 Package: scClassify Version: 1.22.0 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: 01a4d4090bc3db2d3df262a6c53e1ef0 Package: sccomp Version: 2.2.0 Depends: R (>= 4.3.0), instantiate (>= 0.2.3) Imports: stats, boot, utils, scales, lifecycle, rlang, tidyselect, magrittr, crayon, cli, fansi, dplyr, tidyr, purrr, tibble, ggplot2, ggrepel, patchwork, forcats, readr, stringr, glue, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), markdown, loo, prettydoc, SeuratObject, tidyseurat, tidySingleCellExperiment, bayesplot, posterior License: GPL-3 MD5sum: f3dee4f8415e12249a7b1c9749ef3d67 Package: scDataviz Version: 1.20.0 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: a1777b95e35073d95719f72617cf3756 Package: scDblFinder Version: 1.24.0 Depends: R (>= 4.0), SingleCellExperiment Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost, stats, utils, MASS, IRanges, GenomicRanges, GenomeInfoDb, Rsamtools, rtracklayer Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans License: GPL-3 + file LICENSE MD5sum: b1cc04a60e91a78f1255ce78572842ac Package: scDD Version: 1.34.0 Depends: R (>= 3.5.0) Imports: fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm, SingleCellExperiment, SummarizedExperiment, grDevices, graphics, stats, S4Vectors, scran Suggests: BiocStyle, knitr, gridExtra License: GPL-2 MD5sum: fb7d768eb825044d3b9b4009b16119c7 Package: scDDboost Version: 1.12.0 Depends: R (>= 4.2), ggplot2 Imports: Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0),EBSeq, BiocParallel, mclust, SingleCellExperiment, cluster, Oscope, SummarizedExperiment, stats, methods LinkingTo: Rcpp, RcppEigen, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: b14e79f48b13031c487d02a20532a8b6 Package: scde Version: 2.38.0 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: c4dd279c66d04e63a310ed5856e52e51 Package: scDesign3 Version: 1.8.0 Depends: R (>= 4.3.0) Imports: dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist, SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm, parallel, pbmcapply, umap, ggplot2, irlba, viridis, BiocParallel, matrixStats, Matrix, sparseMVN, coop Suggests: mvnfast, igraph, rvinecopulib, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle License: MIT + file LICENSE MD5sum: b0e7a1beafa0c6a3c66845c62f02c905 Package: scDiagnostics Version: 1.4.0 Depends: R (>= 4.4.0) Imports: SingleCellExperiment, methods, isotree, FNN, igraph, ggplot2, GGally, ggridges, SummarizedExperiment, ranger, transport, cramer, rlang, bluster, scales, MASS, stringr, Matrix, grDevices Suggests: AUCell, BiocStyle, knitr, rmarkdown, scran, scRNAseq, SingleR, celldex, scuttle, scater, dplyr, ComplexHeatmap, grid, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 517b1a30147c9cf08e840523493542e4 Package: scDotPlot Version: 1.4.0 Depends: R (>= 4.4.0) Imports: aplot, BiocGenerics, cli, dplyr, ggplot2, ggsci, ggtree, grDevices, magrittr, purrr, rlang, scales, scater, Seurat, SingleCellExperiment, stats, stringr, tibble, tidyr Suggests: AnnotationDbi, BiocStyle, knitr, rmarkdown, scran, scRNAseq, scuttle, SeuratObject, testthat, vdiffr License: Artistic-2.0 MD5sum: dd8d7f7bccfbc669a02d1fcf72eb24aa Package: scds Version: 1.26.0 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: b2be95164545f160440e4e79dc64129d Package: SCFA Version: 1.20.0 Depends: R (>= 4.0) Imports: matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph, Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival Suggests: knitr, rmarkdown, BiocStyle License: LGPL MD5sum: c8db388729b7186a6cdfd82f78b3475e Package: scFeatureFilter Version: 1.30.0 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: 4f9a97853d30cb9df6ee51773d197d3d Package: scGPS Version: 1.24.0 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: 27e9603fb18799944f0b800e876b9a32 Package: scGraphVerse Version: 1.0.0 Depends: R (>= 4.5.0) Imports: BiocBaseUtils, BiocParallel (>= 1.30.0), doParallel, doRNG, GENIE3, Matrix, MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, distributions3, dplyr, grDevices, graphics, httr, igraph, jsonlite, methods, parallel, reticulate, tidyr, glmnet, MASS, utils, stats, S4Vectors, graph, mpath Suggests: AnnotationDbi, BiocStyle, clusterProfiler, DOSE, enrichplot, fmsb, ggplot2, ggraph, gridExtra, INetTool, org.Hs.eg.db, org.Mm.eg.db, patchwork, pROC, RColorBrewer, ReactomePA, rentrez, robin, scales, Seurat, STRINGdb, testthat (>= 3.0.0), knitr, rmarkdown, tidyverse, magick, celldex, SingleR, TENxPBMCData, scater, GenomeInfoDb, GenomicRanges, License: GPL-3 + file LICENSE MD5sum: 3b8aa76cbf7cc791cfe944946cceb468 Package: schex Version: 1.24.0 Depends: SingleCellExperiment (>= 1.7.4), ggplot2 (>= 3.2.1) Imports: hexbin, stats, methods, cluster, dplyr, entropy, ggforce, grid, rlang, concaveman Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, Seurat, shinydashboard, iSEE, igraph, scran, tibble, scuttle License: GPL-3 MD5sum: cc35f24198fc15ab70d34397caf41ebe Package: scHiCcompare Version: 1.2.0 Depends: R (>= 4.5.0) Imports: grDevices, graphics, stats, utils, dplyr, ggplot2, gtools, HiCcompare, lattice, mclust, mice, miceadds, ranger, rstatix, tidyr, rlang, data.table, BiocParallel Suggests: knitr, rmarkdown, testthat, BiocStyle, DT, gridExtra License: MIT + file LICENSE MD5sum: d34190bd6afae6456f1cd0934676d5fb Package: scHOT Version: 1.22.0 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: 40c941cfa6fc8b41f4576f61072204ab Package: scider Version: 1.8.0 Depends: R (>= 4.3) Imports: SpatialExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, sf, lwgeom, SpatialPack, ggplot2, stats, pheatmap, plotly, shiny, igraph, janitor, knitr, methods, utils, isoband, S4Vectors, grDevices, dbscan, hexDensity, hexbin, uwot, SingleCellExperiment, BiocNeighbors, irlba Suggests: edgeR, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: c7812cb299aab7557106c96aa391db5a Package: scifer Version: 1.12.0 Imports: dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra, tibble, scales, rlang, flowCore, methods, basilisk, basilisk.utils, reticulate, here, pwalign, utils Suggests: BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0) Enhances: parallel License: MIT + file LICENSE MD5sum: e82465d1aadf416fed0bebd535efc36c Package: scLANE Version: 1.0.0 Depends: glm2, magrittr, R (>= 4.5.0) Imports: geeM, MASS, mpath, dplyr, stats, utils, withr, purrr, tidyr, furrr, doSNOW, gamlss, scales, future, Matrix, ggplot2, splines, foreach, glmmTMB, parallel, RcppEigen, bigstatsr, tidyselect, broom.mixed, Rcpp LinkingTo: Rcpp, RcppEigen Suggests: covr, grid, coop, uwot, scran, ggh4x, knitr, UCell, irlba, rlang, magick, igraph, scater, gtable, ggpubr, viridis, bluster, cluster, circlize, speedglm, rmarkdown, gridExtra, BiocStyle, slingshot, gprofiler2, GenomeInfoDb, BiocParallel, BiocGenerics, BiocNeighbors, ComplexHeatmap, Seurat (>= 5.0.0), testthat (>= 3.0.0), SingleCellExperiment, SummarizedExperiment License: MIT + file LICENSE MD5sum: 246466c0c4cf1c6de7825be3ced994c9 Package: scmap Version: 1.32.0 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, BiocStyle License: GPL-3 MD5sum: 6a21f782a74f117dfcfa7574aec1b47f Package: scMerge Version: 1.26.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, BiocNeighbors, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), proxyC, ruv, cvTools, scater, batchelor, scran, methods, S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3), SummarizedExperiment Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger License: GPL-3 MD5sum: 10b9b451a03a68b287cad9080e9b8988 Package: scMET Version: 1.12.0 Depends: R (>= 4.2.0) Imports: methods, Rcpp (>= 1.0.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), rstantools (>= 2.1.0), VGAM, data.table, MASS, logitnorm, ggplot2, matrixStats, assertthat, viridis, coda, BiocStyle, cowplot, stats, SummarizedExperiment, SingleCellExperiment, Matrix, dplyr, S4Vectors LinkingTo: BH (>= 1.66.0), Rcpp (>= 1.0.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), StanHeaders (>= 2.21.0.7) Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: d4498ac6eab9bd6ffa3805b273d38021 Package: scmeth Version: 1.30.0 Depends: R (>= 3.5.0) Imports: BiocGenerics, bsseq, AnnotationHub, Seqinfo, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: knitr, rmarkdown, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, ggplot2, ggthemes License: GPL-2 MD5sum: 4092804349f83e3586899a02dcb98164 Package: scMitoMut Version: 1.6.0 Depends: R (>= 4.3.0) Imports: data.table, Rcpp, magrittr, plyr, stringr, utils, stats, methods, ggplot2, pheatmap, RColorBrewer, rhdf5, readr, parallel, grDevices LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils License: Artistic-2.0 MD5sum: befb0f01d0a754c391dbcd8ac4d972fc Package: scMultiSim Version: 1.6.0 Depends: R (>= 4.4.0) Imports: foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats, phytools, KernelKnn, gplots, zeallot, crayon, assertthat, igraph, methods, grDevices, graphics, stats, utils, markdown, SummarizedExperiment, BiocParallel Suggests: knitr, rmarkdown, roxygen2, shiny, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: f25c9f64b8d26e24185558e0a31e8bae Package: SCnorm Version: 1.32.0 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: 99af0f3240fd5ec053218c31b3ce88f3 Package: scone Version: 1.34.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment, DelayedMatrixStats, sparseMatrixStats, SparseArray (>= 1.7.6) Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, DelayedArray, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData License: Artistic-2.0 MD5sum: 1e196de30e3c7a2cdbc3a997677d6139 Package: Sconify Version: 1.30.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 440cf5e6053a94ade505d35e83ae8b7c Package: SCOPE Version: 1.22.0 Depends: R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19 Imports: stats, grDevices, graphics, utils, DescTools, RColorBrewer, gplots, foreach, parallel, doParallel, DNAcopy, BSgenome, Biostrings, BiocGenerics, S4Vectors Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) License: GPL-2 MD5sum: 31ec3f2a15881894447911fd42d11c81 Package: scoreInvHap Version: 1.32.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: a7134e8fe9266bc0b65a8dbbaa65d495 Package: scoup Version: 1.4.0 Depends: R (>= 4.4), Matrix Imports: Biostrings, methods Suggests: BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat (>= 3.0.0), yaml License: GPL (>= 2) MD5sum: 209dced35b8da6856e1947e4dd7c01f2 Package: scPCA Version: 1.24.0 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: e9282a85a83f305aecd8ebbf8bf4c867 Package: scPipe Version: 2.10.0 Depends: R (>= 4.2.0), SingleCellExperiment Imports: AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings, data.table, dplyr, DropletUtils, flexmix, GenomicRanges, GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grDevices, graphics, hash, IRanges, magrittr, MASS, Matrix (>= 1.5.0), mclust, methods, MultiAssayExperiment, org.Hs.eg.db, org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate, Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer, SummarizedExperiment, S4Vectors, scales, stats, stringr, tibble, tidyr, tools, utils, vctrs (>= 0.5.2) LinkingTo: Rcpp, Rhtslib (>= 1.13.1), testthat Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap License: GPL (>= 2) MD5sum: 0f86dae2252cf1bf387853a422448097 Package: scran Version: 1.38.0 Depends: SingleCellExperiment, scuttle Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, MatrixGenerics, S4Arrays, DelayedArray, BiocSingular, bluster, metapod, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, DelayedMatrixStats, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, pheatmap, scater License: GPL-3 MD5sum: 319f6dfb1c1c2e77ca5c4918a9fa7e00 Package: scrapper Version: 1.4.0 Imports: methods, Rcpp, beachmat (>= 2.25.1), DelayedArray, BiocNeighbors (>= 1.99.0), Rigraphlib, parallel LinkingTo: Rcpp, assorthead (>= 1.3.10), beachmat, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, MatrixGenerics, sparseMatrixStats, Matrix, S4Vectors, SummarizedExperiment, SingleCellExperiment, scRNAseq, igraph License: MIT + file LICENSE MD5sum: a5a6c61573e07688d95961e27d049ea4 Package: scReClassify Version: 1.16.0 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: 5d7229478dfa021b4a238790e49c798a Package: scRecover Version: 1.26.0 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), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL MD5sum: 5a74e2678446195b082685b45ac424ad Package: screenCounter Version: 1.10.0 Depends: S4Vectors, SummarizedExperiment Imports: Rcpp, BiocParallel LinkingTo: Rcpp Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 9eedb5ce4f6d96a9601f562aa33ff8ac Package: scRepertoire Version: 2.5.8 Depends: ggplot2, R (>= 4.0) Imports: dplyr, evmix, ggalluvial, ggdendro, ggraph, grDevices, igraph, immApex, iNEXT, Matrix, quantreg, Rcpp, rjson, rlang, S4Vectors, SeuratObject, SingleCellExperiment, SummarizedExperiment, tidygraph, purrr, lifecycle, methods LinkingTo: Rcpp Suggests: BiocManager, BiocStyle, circlize, knitr, Peptides, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: bcd030fb4954954cbd7c87af9e0cfef5 Package: scRNAseqApp Version: 1.10.0 Depends: R (>= 4.3.0) Imports: bibtex, bslib, circlize, ComplexHeatmap, colourpicker, data.table, DBI, DT, fs, GenomicRanges, GenomeInfoDb, ggdendro, ggforce, ggplot2, ggrepel, ggridges, grDevices, grid, gridExtra, htmltools, IRanges, jsonlite, Matrix, magrittr, methods, patchwork, plotly, RColorBrewer, RefManageR, reshape2, rhdf5, Rsamtools, RSQLite, rtracklayer, S4Vectors, scales, scrypt, Seurat, SeuratObject, shiny, shinyhelper, shinymanager, slingshot, SingleCellExperiment, sortable, stats, tools, xfun, xml2, utils Suggests: rmarkdown, knitr, testthat, BiocStyle, shinytest2 Enhances: celldex, future, SingleR, SummarizedExperiment, tricycle License: GPL-3 MD5sum: c258d18ba5cf9add2171af03d6846acf Package: scruff Version: 1.28.0 Depends: R (>= 4.0) Imports: data.table, GenomicAlignments, GenomicFeatures, txdbmaker, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread, parallelly, patchwork Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 8a370032f1fd7ab20911ab2f955fd8a7 Package: scry Version: 1.22.0 Depends: R (>= 4.0), stats, methods Imports: DelayedArray, glmpca (>= 0.2.0), Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array, knitr, markdown, rmarkdown, TENxPBMCData, testthat License: Artistic-2.0 MD5sum: a30c8506295c5182ab1ef24d6c5d8e1a Package: scShapes Version: 1.16.0 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: e9fb99febee3d47a6d85dca05455778b Package: scTensor Version: 2.20.0 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: 65a96bd76810cfb9194a61977a5d527a Package: scTGIF Version: 1.24.0 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: 1b11d8d8bbbb8dba042f9fb0a695b2f5 Package: scTHI Version: 1.22.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: ebe19b047d9da0ed0f8633a39cce5ea5 Package: scTreeViz Version: 1.16.0 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: c87f0e677ba244c2b94e89b6896c08de Package: scuttle Version: 1.20.0 Depends: SingleCellExperiment Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays, MatrixGenerics, SparseArray, DelayedArray, beachmat LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, sparseMatrixStats, DelayedMatrixStats, scran License: GPL-3 MD5sum: ea3104872e60259262c2cc45d5d1adf8 Package: SDAMS Version: 1.30.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: a116b4777e017881ad1e0b1213d81de8 Package: seahtrue Version: 1.4.0 Depends: R (>= 4.2.0) Imports: dplyr (>= 1.1.2), readxl (>= 1.4.1), logger (>= 0.2.2), tidyxl (>= 1.0.8), purrr (>= 0.3.5), tidyr (>= 1.3.0), lubridate (>= 1.8.0), stringr (>= 1.4.1), tibble (>= 3.1.8), validate (>= 1.1.1), rlang (>= 1.0.0), glue (>= 1.6.2), cli (>= 3.4.1), janitor (>= 2.2.0), ggplot2 (>= 3.5.0), RColorBrewer (>= 1.1.3), colorspace (>= 2.1.0), forcats (>= 1.0.0), ggridges (>= 0.5.6), readr (>= 2.1.5), scales (>= 1.3.0) Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: Artistic-2.0 MD5sum: ac68ebd65f59477203b9736bbc7304c3 Package: sechm Version: 1.18.0 Depends: R (>= 4.0), SummarizedExperiment, ComplexHeatmap Imports: S4Vectors, seriation, circlize, methods, randomcoloR, stats, grid, grDevices, matrixStats Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 64270bd1582a0df51f4d58227033b999 Package: segmenter Version: 1.16.0 Depends: R (>= 4.1) Imports: ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges, S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils, methods, chromhmmData Suggests: testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz License: GPL-3 MD5sum: 9fdafaa164ced9f129de6319ce0eaf5f Package: segmentSeq Version: 2.44.0 Depends: R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, Seqinfo, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown License: GPL-3 MD5sum: b9bf2cfeaf19ae73a0789e45369004d7 Package: selectKSigs Version: 1.22.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: 99abd7633ee959b451b8fe52123146ec Package: SELEX Version: 1.42.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: 6c3b611a972200c4e52610396aacb213 Package: SemDist Version: 1.44.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) MD5sum: 52cf3aa216a94f23f92853cd679dc841 Package: semisup Version: 1.34.0 Depends: R (>= 3.0.0) Imports: VGAM Suggests: knitr, testthat, SummarizedExperiment License: GPL-3 MD5sum: babe8720d2b15fe2a8339b42d15a1fb8 Package: seq.hotSPOT Version: 1.10.0 Depends: R (>= 3.5.0) Imports: R.utils, hash, stats, base, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 2b78f69d6eeacd4fb62b6887c0819a2e Package: SeqArray Version: 1.50.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.31.1) Imports: methods, parallel, digest, S4Vectors, IRanges, GenomicRanges, Seqinfo, Biostrings LinkingTo: gdsfmt Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation License: GPL-3 MD5sum: 9e148d3e222f9d64dcbb1c31f81dbe78 Package: seqCAT Version: 1.32.0 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 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bd5e4a1790019ef966954763677361ca Package: Seqinfo Version: 1.0.0 Depends: methods, BiocGenerics Imports: stats, S4Vectors (>= 0.47.6), IRanges Suggests: GenomeInfoDb, GenomicRanges, BSgenome, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Celegans.UCSC.ce2, RUnit, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: eef563db1e8385d4250ca89e2957771d Package: seqLogo Version: 1.76.0 Depends: R (>= 4.2), methods, grid Imports: stats4, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: LGPL (>= 2) MD5sum: 77bc8973fffb0fd66c7e0298a3a01e4e Package: seqPattern Version: 1.42.0 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: b4fcab744640cfc607b9fd267d45f48b Package: seqsetvis Version: 1.30.0 Depends: R (>= 4.3), ggplot2 Imports: cowplot, data.table, eulerr, Seqinfo, GenomicAlignments, GenomicRanges, ggplotify, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, scales, stats, UpSetR Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, GenomeInfoDb, covr, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 312a3a1852b188e676cf986cd82ea9cf Package: SeqSQC Version: 1.32.0 Depends: R (>= 3.4), ExperimentHub (>= 1.3.7), SNPRelate (>= 1.10.2) Imports: e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, plotly, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: 001f4c6268115462d9621b644c654497 Package: SeqVarTools Version: 1.48.0 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: 7479ee73e36566ef708842daa1143789 Package: SEraster Version: 1.2.0 Depends: R (>= 4.5.0) Imports: BiocParallel, ggplot2, Matrix, methods, rearrr, sf, SpatialExperiment, SummarizedExperiment Suggests: CooccurrenceAffinity, nnSVG, testthat (>= 3.0.0), knitr, rmarkdown, BiocManager, remotes License: GPL-3 MD5sum: f795e55d6fc0b02d10e95d52627c7a13 Package: sesame Version: 1.28.0 Depends: R (>= 4.5.0), sesameData Imports: graphics, BiocParallel, utils, methods, stringr, readr, tibble, MASS, wheatmap (>= 0.2.0), GenomicRanges (>= 1.61.1), IRanges, grid, preprocessCore, S4Vectors, ggplot2, BiocFileCache, Seqinfo, stats, SummarizedExperiment (>= 1.39.1), dplyr, reshape2 Suggests: scales, BiocManager, GenomeInfoDb, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals License: MIT + file LICENSE MD5sum: f3ad5824b075765d5bee6f3752c1a4fa Package: SETA Version: 1.0.0 Depends: R (>= 4.5.0) Imports: dplyr, MASS, Matrix, SingleCellExperiment (>= 1.30.1), stats, tidygraph, rlang, utils Suggests: BiocStyle, caret, glmnet, corrplot, ggplot2, ggraph, knitr, methods, patchwork, reshape2, rmarkdown, SeuratObject, Seurat, SummarizedExperiment, TabulaMurisSenisData, tidyr, tidytext, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: ffae11d245c21adc5f805af23c253a15 Package: SEtools Version: 1.24.0 Depends: R (>= 4.0), SummarizedExperiment, sechm Imports: BiocParallel, Matrix, DESeq2, S4Vectors, data.table, edgeR, openxlsx, pheatmap, stats, circlize, methods, sva Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL MD5sum: 8397d0de0aaa1ea43c423b2b3dbdcf3e Package: sevenbridges Version: 1.40.0 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: 3794408b5073d332d545f21cfb82ddbf Package: sevenC Version: 1.30.0 Depends: R (>= 3.5), InteractionSet (>= 1.2.0) Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), Seqinfo, 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: 7914f496d027aec1eebb34b8d91d6f3a Package: SGSeq Version: 1.44.0 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), Seqinfo, 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: 6ed8e6022fc69399670547331a8a3313 Package: SharedObject Version: 1.24.0 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, Rcpp Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 77568d0fc7835dc85055eb46a9555faa Package: shiny.gosling Version: 1.5.0 Depends: R (>= 4.1.0) Imports: htmltools, jsonlite, rlang, shiny, shiny.react, fs, digest, rjson Suggests: config, covr, knitr, lintr, mockery (>= 0.4.3), rcmdcheck, rmarkdown, sessioninfo, spelling, testthat (>= 3.0.0), GenomicRanges, VariantAnnotation, StructuralVariantAnnotation, biovizBase, ggbio License: LGPL-3 MD5sum: 8a120b2685a024aaf70697bde7395bae Package: shinybiocloader Version: 1.0.0 Depends: htmltools Imports: shiny Suggests: shinydashboard, tinytest, quarto License: Artistic-2.0 MD5sum: 80d4b403e25b807ecb660882daf7cef1 Package: shinyDSP Version: 1.2.0 Depends: R (>= 4.5) Imports: AnnotationHub, BiocGenerics, bsicons, bslib, circlize, ComplexHeatmap, cowplot, dplyr, DT, edgeR, ExperimentHub, ggplot2, ggpubr, ggrepel, grDevices, grid, htmltools, limma, magrittr, pals, readr, S4Vectors, scales, scater, shiny, shinycssloaders, shinyjs, shinyvalidate, shinyWidgets, SingleCellExperiment, standR, stats, stringr, SummarizedExperiment, tibble, tidyr, utils, withr Suggests: BiocStyle, knitr, rmarkdown, shinytest2, spelling, svglite, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 5e7bd74c2547fd331a50ff6e9de17ef3 Package: shinyepico Version: 1.18.0 Depends: R (>= 4.3.0) Imports: DT (>= 0.15.0), data.table (>= 1.13.0), doParallel (>= 1.0.0), dplyr (>= 1.0.9), 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 (>= 1.0.2), rmarkdown (>= 2.3.0), rtracklayer (>= 1.46.0), shiny (>= 1.5.0), shinyWidgets (>= 0.5.0), shinycssloaders (>= 0.3.0), shinyjs (>= 1.1.0), shinythemes (>= 1.1.0), statmod (>= 1.4.0), tidyr (>= 1.2.0), zip (>= 2.1.0) Suggests: knitr (>= 1.30.0), mCSEA (>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData, BiocStyle License: AGPL-3 + file LICENSE MD5sum: 02cdb318401a7b66b975982e9380edf1 Package: shinyMethyl Version: 1.46.0 Imports: Biobase, BiocGenerics, graphics, grDevices, htmltools, MatrixGenerics, methods, minfi, RColorBrewer, shiny, stats, utils Suggests: shinyMethylData, minfiData, BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 54732cde1d53188924bd9b4d7335317e Package: ShortRead Version: 1.68.0 Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Seqinfo, GenomicRanges (>= 1.31.8), pwalign, hwriter, methods, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi, knitr License: Artistic-2.0 MD5sum: 82e386403537bfa8907efd0e38c17021 Package: SIAMCAT Version: 2.14.0 Depends: R (>= 4.2.0), mlr3, phyloseq Imports: beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot, lmerTest, mlr3learners, mlr3tuning, paradox, lgr Suggests: BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr License: GPL-3 MD5sum: f502cb05817de0da4633074bb302e6ab Package: SICtools Version: 1.40.0 Depends: R (>= 3.0.0), methods, Rsamtools (>= 1.18.1), doParallel (>= 1.0.8), Biostrings (>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges (>= 1.22.4), IRanges (>= 2.4.8) Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: ce641c8c0e6e745567249ba96929217b Package: SigCheck Version: 2.42.0 Depends: R (>= 4.0.0), MLInterfaces, Biobase, e1071, BiocParallel, survival Imports: graphics, stats, utils, methods Suggests: BiocStyle, breastCancerNKI, qusage License: Artistic-2.0 MD5sum: 147398c34c6fbb4cb6c3fa0173c2a528 Package: sigFeature Version: 1.28.0 Depends: R (>= 3.5.0) Imports: biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer, Matrix, SparseM, graphics, stats, utils, SummarizedExperiment, BiocParallel, methods Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL (>= 2) MD5sum: e5fc7c1c4032890b04161bf2845b09f3 Package: siggenes Version: 1.84.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: 9a7ff4cd0c3f852b1e0c8df180d7ccbb Package: sights Version: 1.36.0 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: c4ce28c2f850db468cedeff679076372 Package: signatureSearch Version: 1.24.0 Depends: R(>= 4.2.0), Rcpp, SummarizedExperiment, org.Hs.eg.db 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, tibble LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT License: Artistic-2.0 MD5sum: f4fcff1cb7c92b5b4927287d8166b4e7 Package: signeR Version: 2.12.0 Depends: R (>= 4.1.0), NMF Imports: BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat, future, VGAM, MASS, kknn, glmnet, e1071, randomForest, ada, future.apply, ggplot2, pROC, pheatmap, RColorBrewer, listenv, reshape2, scales, survminer, dplyr, ggpubr, cowplot, tibble, readr, shiny, shinydashboard, shinycssloaders, shinyWidgets, bsplus, DT, magrittr, tidyr, BiocFileCache, proxy, rtracklayer, BSgenome, broom, VariantAnnotation LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown License: GPL-3 MD5sum: 4dc53b01370e0caa37017e8a7c382170 Package: signifinder Version: 1.12.0 Depends: R (>= 4.4.0) Imports: AnnotationDbi, BiocGenerics, ComplexHeatmap, consensusOV, cowplot, DGEobj.utils, dplyr, ensembldb, ggplot2, ggridges, GSVA, IRanges, magrittr, matrixStats, maxstat, methods, openair, org.Hs.eg.db, patchwork, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, SpatialExperiment, stats, scales, SummarizedExperiment, survival, survminer, viridis Suggests: BiocStyle, edgeR, grid, kableExtra, knitr, limma, testthat (>= 3.0.0) License: AGPL-3 MD5sum: efd9c3be159942532e56a845c981ae92 Package: SigsPack Version: 1.24.0 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: 507f67ccd33f6d8074446dbefa8b0995 Package: sigsquared Version: 1.42.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 2eb82ab9d7667a5ea8602ff1c59902bf Package: SIM Version: 1.80.0 Depends: R (>= 3.5), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) MD5sum: 0dde3adfb1c3a39e6125d6e347de6a43 Package: SIMAT Version: 1.42.0 Depends: R (>= 3.5.0), Rcpp (>= 0.11.3) Imports: mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 2c8b3391c8e1432931e5b5a175a48a33 Package: SimBu Version: 1.12.0 Imports: basilisk, BiocParallel, data.table, dplyr, ggplot2, tools, Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer, RCurl, reticulate, sparseMatrixStats, SummarizedExperiment, tidyr Suggests: curl, knitr, matrixStats, rmarkdown, Seurat (>= 5.0.0), SeuratObject (>= 5.0.0), testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 847b2f2f70778a11208c3948e0eee6b1 Package: SIMD Version: 1.28.0 Depends: R (>= 3.5.0) Imports: edgeR, statmod, methylMnM, stats, utils Suggests: BiocStyle, knitr,rmarkdown License: GPL-3 MD5sum: 0900337e0d1a38babaef325a2415963a Package: SimFFPE Version: 1.22.0 Depends: Biostrings Imports: dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods Suggests: BiocStyle License: LGPL-3 MD5sum: 78dfd2acb876ce35ed3b062153f52e70 Package: similaRpeak Version: 1.42.0 Depends: R6 (>= 2.0) Imports: stats Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 2045ba39db2127bce3338ba1ee6d08cf Package: SIMLR Version: 1.36.0 Depends: R (>= 4.1.0), Imports: parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra LinkingTo: Rcpp Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph License: file LICENSE MD5sum: 879cb47f55711f2c28b6bae51c0632a5 Package: simona Version: 1.8.0 Depends: R (>= 4.1.0) Imports: methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions, igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize, ComplexHeatmap, grDevices, stats, utils, shiny, fastmatch LinkingTo: Rcpp Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png, InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment, AnnotationHub, jsonlite License: MIT + file LICENSE MD5sum: bec2cffbaf7d7f368132389024d5f01d Package: simPIC Version: 1.6.0 Depends: R (>= 4.5.0), SingleCellExperiment Imports: BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, actuar, Matrix, stats, SummarizedExperiment, rlang, S4Vectors, methods, scales, scuttle, edgeR, withr Suggests: ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), scater, scran, magick License: GPL-3 MD5sum: 8592c848102b181aa5091d31d8e6c5f7 Package: simpleSeg Version: 1.12.0 Depends: R (>= 3.5.0) Imports: BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors, grDevices, SummarizedExperiment, methods, cytomapper Suggests: BiocStyle, testthat (>= 3.0.0), knitr, ggplot2 License: GPL-3 MD5sum: ec06f10a13c9a0d48c4279f5247349ab Package: simplifyEnrichment Version: 2.4.0 Depends: R (>= 4.1.0) Imports: simona, ComplexHeatmap (>= 2.7.4), grid, circlize, GetoptLong, digest, tm, GO.db, AnnotationDbi, slam, methods, clue, grDevices, stats, utils, cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0) Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc License: MIT + file LICENSE MD5sum: b6ab507f46aff942f56d7e8ff8100825 Package: sincell Version: 1.42.0 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: 47a6e7a81f14f66bdf0f0914397f61fe Package: SingleCellAlleleExperiment Version: 1.6.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: SummarizedExperiment, BiocParallel, DelayedArray, methods, utils, Matrix, S4Vectors, stats Suggests: scaeData, knitr, rmarkdown, BiocStyle, scran, scater, scuttle, ggplot2, patchwork, org.Hs.eg.db, AnnotationDbi, DropletUtils, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: d1ef80476c02ec409e3d745b8bd237c9 Package: SingleCellExperiment Version: 1.32.0 Depends: SummarizedExperiment Imports: methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne License: GPL-3 MD5sum: d1d41bc465fa669810b5d6a795193274 Package: SingleCellSignalR Version: 2.0.0 Depends: R (>= 4.5) Imports: stats, utils, methods, ggplot2, matrixTests, matrixStats, foreach, BulkSignalR Suggests: knitr, markdown, rmarkdown License: CeCILL | file LICENSE MD5sum: 61716e51a508ceecc7b775f10cdabf69 Package: singleCellTK Version: 2.20.0 Depends: R (>= 4.0), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase Imports: ape, anndata, AnnotationHub, batchelor, BiocParallel, celldex, colourpicker, colorspace, cowplot, cluster, ComplexHeatmap, data.table, DelayedMatrixStats, DESeq2, dplyr, DT, ExperimentHub, ensembldb, fields, ggplot2, ggplotify, ggrepel, ggtree, gridExtra, grid, GSVA (>= 1.50.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix (>= 1.6-1), matrixStats, methods, msigdbr, multtest, plotly, plyr, ROCR, Rtsne, S4Vectors, scater, scMerge (>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, stringr, SoupX, sva, reshape2, shinyalert, circlize, enrichR (>= 3.2), celda, shinycssloaders, DropletUtils, scds (>= 1.2.0), reticulate (>= 1.14), tools, tximport, tidyr, eds, withr, GSEABase, R.utils, zinbwave, scRNAseq (>= 2.0.2), TENxPBMCData, yaml, rmarkdown, magrittr, scDblFinder, metap, VAM (>= 0.5.3), tibble, rlang, TSCAN, TrajectoryUtils, scuttle, utils, stats, zellkonverter, lifecycle Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony, SeuratObject, optparse License: MIT + file LICENSE MD5sum: c3989f6704c1319f06aff66c645511f9 Package: SingleMoleculeFootprinting Version: 2.4.0 Depends: R (>= 4.4.0) Imports: BiocGenerics, Biostrings, BSgenome, cluster, dplyr, Seqinfo, GenomicRanges, ggpointdensity, ggplot2, ggrepel, grDevices, IRanges, magrittr, Matrix, methods, miscTools, parallel, parallelDist, patchwork, plyranges, qs, QuasR, RColorBrewer, rlang, S4Vectors, stats, stringr, tibble, tidyr, utils, viridis Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, qs, rmarkdown, readr, rrapply, SingleMoleculeFootprintingData, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: 87329e897a0f53f729c81bbaf575227b Package: SingleR Version: 2.12.0 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocNeighbors, stats, utils, Rcpp, beachmat (>= 2.25.1) LinkingTo: Rcpp, beachmat, assorthead (>= 1.3.5), BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scrapper (>= 1.3.14), scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 MD5sum: 09ff43fcfe719218cdc4de6bcf8052e6 Package: singscore Version: 1.30.0 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: pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: db4a0cab8dc88fca1bc6f344b4e74dee Package: SiPSiC Version: 1.10.0 Depends: Matrix, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle License: file LICENSE MD5sum: 91bd1c9203300cc52eb2af1ed9721ed0 Package: sitadela Version: 1.18.0 Depends: R (>= 4.1.0) Imports: Biobase, BiocGenerics, biomaRt, Biostrings, Seqinfo, GenomicFeatures, GenomicRanges, IRanges, methods, parallel, Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, txdbmaker, utils Suggests: GenomeInfoDb, BiocStyle, BSgenome, knitr, rmarkdown, RMySQL, RUnit License: Artistic-2.0 MD5sum: 28511d6d6dc0778d86d496bf42a64bd6 Package: Site2Target Version: 1.2.0 Depends: R (>= 4.4) Imports: S4Vectors, stats, utils, BiocGenerics, GenomeInfoDb, MASS, IRanges, GenomicRanges Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-2 MD5sum: 1145556991338a1ff307906c4a5cd509 Package: sitePath Version: 1.26.0 Depends: R (>= 4.2) Imports: RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree, graphics, grDevices, gridExtra, methods, parallel, seqinr, stats, tidytree, utils LinkingTo: Rcpp Suggests: BiocStyle, devtools, knitr, magick, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 97a1d03a58673e22919a567956e2a038 Package: sizepower Version: 1.80.0 Depends: stats License: LGPL MD5sum: d122d1d9bfabdc595236113777c5d9b1 Package: sketchR Version: 1.6.0 Imports: basilisk, Biobase, DelayedArray, dplyr, ggplot2, methods, reticulate, rlang, scales, stats Suggests: rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle, scran, scater, SingleR, celldex, cowplot, SummarizedExperiment, beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment, snifter, uwot, bluster, class License: MIT + file LICENSE MD5sum: 7d4600c8be27bfada8e4e73d610e5611 Package: skewr Version: 1.42.0 Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports: minfi, S4Vectors (>= 0.19.1), RColorBrewer Suggests: GEOquery, knitr, minfiData License: GPL-2 MD5sum: 9a752e0c95304116ebc0be90d69845e3 Package: slingshot Version: 2.18.0 Depends: R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils Imports: graphics, grDevices, igraph, matrixStats, methods, S4Vectors, SingleCellExperiment, SummarizedExperiment Suggests: BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr License: Artistic-2.0 MD5sum: 14942ea6f792212ff1143d921a930160 Package: SLqPCR Version: 1.76.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) MD5sum: 75bb328f40653ef8b1a7ff60cca20b64 Package: SMAD Version: 1.26.0 Depends: R (>= 3.6.0), RcppAlgos Imports: magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 90cb4b1127778aa6542db2e915f959b3 Package: smartid Version: 1.6.0 Depends: R (>= 4.4) Imports: dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools, sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater, splatter, testthat (>= 3.0.0), tidytext, UpSetR License: MIT + file LICENSE MD5sum: a84b09fd784cef6442dda5340c265ed2 Package: SmartPhos Version: 1.0.0 Depends: R (>= 4.4.0) Imports: MultiAssayExperiment, SummarizedExperiment, data.table, shiny, shinythemes, shinyjs, shinyBS, shinyWidgets, parallel, DT, tools, stats, ggplot2, plotly, ggbeeswarm, pheatmap, grid, XML, MsCoreUtils, imputeLCMD, missForest, limma, proDA, decoupleR, piano, BiocParallel, doParallel, doRNG, e1071, magrittr, matrixStats, rlang, stringr, tibble, dplyr, tidyr, Biobase, vsn, factoextra, cowplot Suggests: knitr, BiocStyle, PhosR, testthat License: GPL-3 MD5sum: a2b5477c593fc3958aef214819d70efe Package: SMITE Version: 1.38.0 Depends: R (>= 3.5), GenomicRanges Imports: scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2, reactome.db, KEGGREST, BioNet, goseq, methods, IRanges, igraph, Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: e203da77236edcea8a415cd4be614cda Package: smoothclust Version: 1.6.0 Depends: R (>= 4.4.0) Imports: SpatialExperiment, SummarizedExperiment, BiocNeighbors, Matrix, methods, utils Suggests: BiocStyle, knitr, STexampleData, scuttle, scran, scater, ggspavis, testthat License: MIT + file LICENSE MD5sum: 75655086316e4980fa2f4fb2f43dd2ee Package: smoppix Version: 1.2.0 Depends: R (>= 4.4.0) Imports: spatstat.geom(>= 3.2.0),spatstat.random,methods,BiocParallel,SummarizedExperiment,SpatialExperiment,scam,Rdpack,stats,utils,extraDistr,lmerTest,lme4,ggplot2,graphics,grDevices,Rcpp (>= 1.0.11),spatstat.model,openxlsx,Rfast LinkingTo: Rcpp Suggests: testthat,rmarkdown,knitr,DropletUtils,polyCub,RImageJROI,sp,ape,htmltools,funkycells,glmnet,doParallel License: GPL-2 MD5sum: 185c9e8e9eb3676482b0545934809036 Package: SNAGEE Version: 1.50.0 Depends: R (>= 2.6.0), SNAGEEdata Suggests: ALL, hgu95av2.db Enhances: parallel License: Artistic-2.0 MD5sum: 74eacceb4945dd09e45adf55ca5dc25c Package: snapcount Version: 1.22.0 Depends: R (>= 4.0.0) Imports: R6, httr, rlang, purrr, jsonlite, assertthat, data.table, Matrix, magrittr, methods, stringr, stats, IRanges, GenomicRanges, SummarizedExperiment Suggests: BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 48bac852d21431913b4969a40f740f8b Package: snifter Version: 1.20.0 Depends: R (>= 4.0.0) Imports: basilisk, reticulate, irlba, stats, assertthat Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) License: GPL-3 MD5sum: c225622ce98fc21f2135165e7ea99a1e Package: snm Version: 1.58.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL MD5sum: 9a1c6cb91cc9ca8c680b740809377b0a Package: SNPediaR Version: 1.36.0 Depends: R (>= 3.0.0) Imports: RCurl, jsonlite Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 17c4ff8d748fd4a5dd005c89e912a84f Package: SNPhood Version: 1.40.0 Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, data.table, checkmate Imports: DESeq2, cluster, ggplot2, lattice, GenomeInfoDb (>= 1.34.8), BiocParallel, VariantAnnotation, BiocGenerics, IRanges, methods, SummarizedExperiment, RColorBrewer, Biostrings, grDevices, gridExtra, stats, grid, utils, reshape2, scales, S4Vectors Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot License: LGPL (>= 3) MD5sum: 13d4774716fbc7610d2eda95e195a57e Package: SNPRelate Version: 1.44.0 Depends: R (>= 2.15), gdsfmt (>= 1.8.3) Imports: methods, RhpcBLASctl LinkingTo: gdsfmt Suggests: parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics Enhances: SeqArray (>= 1.12.0) License: GPL-3 MD5sum: 1cd878f59783ab54c23a1d90204f524d Package: snpStats Version: 1.60.0 Depends: R(>= 2.10.0), survival, Matrix, methods Imports: graphics, grDevices, stats, utils, BiocGenerics Suggests: hexbin License: GPL-3 MD5sum: 954d80a819868794e0aed71d746437e3 Package: SOMNiBUS Version: 1.18.0 Depends: R (>= 4.1.0) Imports: Matrix, mgcv, stats, VGAM, IRanges, GenomeInfoDb, GenomicRanges, rtracklayer, S4Vectors, BiocManager, annotatr, yaml, utils, bsseq, reshape2, data.table, ggplot2, tidyr, Suggests: BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, License: MIT + file LICENSE MD5sum: aeac11311d47f048751ed0a458efad62 Package: sosta Version: 1.2.0 Depends: R (>= 4.4.0) Imports: terra, sf, smoothr, spatstat.explore, spatstat.geom, SpatialExperiment, SingleCellExperiment, dplyr, ggplot2, patchwork, SummarizedExperiment, stats, rlang, parallel, EBImage, spatstat.random, S4Vectors Suggests: knitr, rmarkdown, BiocStyle, ExperimentHub, lme4, lmerTest, ggfortify, tidyr, testthat (>= 3.0.0) License: GPL (>= 3) + file LICENSE MD5sum: 71b3b7bdcb1424634d318a5336389747 Package: SpaceMarkers Version: 2.0.0 Depends: R (>= 4.4.0) Imports: matrixStats, matrixTests, rstatix, spatstat.explore, spatstat.geom, ape, hdf5r, nanoparquet, jsonlite, Matrix, qvalue, stats, utils, methods, ggplot2, reshape2, RColorBrewer, circlize, mixtools, dplyr, readbitmap, rlang, effsize, viridis Suggests: data.table, devtools, knitr, cowplot, rjson, rmarkdown, BiocStyle, testthat (>= 3.0.0), CoGAPS, ComplexHeatmap Enhances: BiocParallel License: MIT + file LICENSE MD5sum: c240aa237c18ae7378d4c56a4c8f8605 Package: SpaceTrooper Version: 1.0.0 Depends: R (>= 4.4.0), SpatialExperiment Imports: DropletUtils, S4Vectors, SummarizedExperiment, arrow, data.table, dplyr, e1071, ggplot2, ggpubr, robustbase, scater, scuttle, sf, sfheaders, cowplot, glmnet, rhdf5, methods, rlang, SpatialExperimentIO Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), withr, viridis License: MIT + file LICENSE MD5sum: e1eddaceb68b8391bf9ac7a2b012c0c7 Package: spacexr Version: 1.2.0 Depends: R (>= 4.5.0) Imports: ggplot2, Matrix, parallel, quadprog, httr, methods, memoise, BiocParallel, BiocFileCache, SummarizedExperiment, scatterpie, SpatialExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 3) MD5sum: 72f2b9af805d744416714ff6704d9b84 Package: Spaniel Version: 1.24.0 Depends: R (>= 4.0) Imports: Seurat, SingleCellExperiment, SummarizedExperiment, dplyr, methods, ggplot2, scater (>= 1.13), scran, igraph, shiny, jpeg, magrittr, utils, S4Vectors, DropletUtils, jsonlite, png Suggests: knitr, rmarkdown, testthat, devtools License: MIT + file LICENSE MD5sum: e6279b4d490c0beec48df8cc6527e7ac Package: SpaNorm Version: 1.4.0 Depends: R (>= 4.4) Imports: edgeR, ggplot2, Matrix, matrixStats, methods, rlang, scran, SeuratObject, SingleCellExperiment, SpatialExperiment, stats, SummarizedExperiment, S4Vectors, utils Suggests: testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown, covr, BiocStyle, Seurat, patchwork, ggforce, ggnewscale License: GPL (>= 3) MD5sum: c6e1be68b1d394abebecb918249e06d3 Package: spARI Version: 1.0.0 Depends: R (>= 4.1.0) Imports: Rcpp, stats, Matrix, SpatialExperiment, SummarizedExperiment, BiocParallel (>= 1.0) LinkingTo: Rcpp Suggests: FNN, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 6bed2388fe1093d50c55da845ea3b66b Package: sparrow Version: 1.16.0 Depends: R (>= 4.1.0) Imports: babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet, checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>= 1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>= 2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix, methods, plotly (>= 4.9.0), stats, utils, viridis Suggests: AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, KernSmooth, knitr, magrittr, matrixStats, msigdbr (>= 10.0), orthogene, PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot License: MIT + file LICENSE MD5sum: cfc6112eedd3e3bd5fa6c2b70b46b617 Package: SparseArray Version: 1.10.1 Depends: R (>= 4.3.0), methods, Matrix, BiocGenerics (>= 0.43.1), MatrixGenerics (>= 1.11.1), S4Vectors (>= 0.43.2), S4Arrays (>= 1.9.3) Imports: utils, stats, matrixStats, IRanges, XVector LinkingTo: S4Vectors, IRanges, XVector Suggests: HDF5Array, ExperimentHub, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: aef8e2c23d69a8e90dca1d9d5a30974b Package: sparseMatrixStats Version: 1.22.0 Depends: MatrixGenerics (>= 1.5.3) Imports: Rcpp, Matrix, matrixStats (>= 0.60.0), methods LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: fdf055c9549f7483ee896e001bc9e57e Package: sparsenetgls Version: 1.28.0 Depends: R (>= 4.0.0), Matrix, MASS Imports: methods, glmnet, huge, stats, graphics, utils Suggests: testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) License: GPL-3 MD5sum: a8e1945256d68b680e70b50d976abf28 Package: SparseSignatures Version: 2.20.0 Depends: R (>= 4.1.0), NMF Imports: nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2, gridExtra, reshape2, RhpcBLASctl Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr, License: file LICENSE MD5sum: f6411dadf5fe36e54c93a699a44088d9 Package: spaSim Version: 1.12.0 Depends: R (>= 4.2.0) Imports: ggplot2, methods, stats, dplyr, spatstat.geom, spatstat.random, SpatialExperiment, SummarizedExperiment, RANN Suggests: RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown License: Artistic-2.0 MD5sum: 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ggplot2, ggrepel, scales, gridExtra Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 93118403d4c5c8a31787e2268477b4db Package: SpatialDecon Version: 1.20.0 Depends: R (>= 4.0.0) Imports: grDevices, stats, utils, graphics, SeuratObject, Biobase, GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4) Suggests: testthat, knitr, rmarkdown, qpdf, Seurat License: MIT + file LICENSE MD5sum: b70ecd78bd7bb58c38c87fc80b0f86aa Package: SpatialExperiment Version: 1.20.0 Depends: R (>= 4.1.0), methods, SingleCellExperiment Imports: rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils, VisiumIO License: GPL-3 MD5sum: 0ed2d89fe572e1d83a109de799d4c512 Package: SpatialExperimentIO Version: 1.2.0 Depends: R (>= 4.1.0) Imports: DropletUtils, SpatialExperiment, SingleCellExperiment, methods, data.table, arrow, purrr, S4Vectors Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: Artistic-2.0 MD5sum: ff163394664a335635b09ec4241a8dca Package: spatialFDA Version: 1.2.0 Depends: R (>= 4.3.0) Imports: dplyr, ggplot2, parallel, patchwork, purrr, refund, SpatialExperiment, spatstat.explore, spatstat.geom, SummarizedExperiment, methods, stats, fda, tidyr, graphics, ExperimentHub, scales, S4Vectors Suggests: stringr, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), mgcv License: GPL (>= 3) + file LICENSE MD5sum: 832ce09d2f2d1b88538dd323e6fbce60 Package: spatialHeatmap Version: 2.15.2 Depends: R (>= 3.5.0) Imports: data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid, gridExtra, igraph, methods, Matrix, rsvg, shiny, grDevices, graphics, ggplotify, parallel, reshape2, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2 Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend, DT, dynamicTreeCut, flashClust, gplots, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, scater, scuttle, scran, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, xlsx, yaml License: Artistic-2.0 MD5sum: e5e5661012b32c5767eda929fef0ce83 Package: SpatialOmicsOverlay Version: 1.10.0 Depends: R (>= 4.1.0) Imports: S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML, scattermore, dplyr, pbapply, data.table, readxl, magick, grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats, utils, methods, ggtext, tools, RBioFormats Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf License: MIT MD5sum: 3ac70a514bf7ac9ff78cb1c1140973b1 Package: spatialSimGP Version: 1.4.0 Depends: R (>= 4.4) Imports: SpatialExperiment, MASS, SummarizedExperiment Suggests: testthat (>= 3.0.0), STexampleData, ggplot2, knitr License: MIT + file LICENSE MD5sum: 34cbc94a78217916b1a6f9f24659b615 Package: speckle Version: 1.10.0 Depends: R (>= 4.2.0) Imports: limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods, stats, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 342d0ccb121fd1fda279703fefcca888 Package: specL Version: 1.44.0 Depends: R (>= 4.1), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.7), RSQLite (>= 1.1), seqinr (>= 3.3) Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) License: GPL-3 MD5sum: a87911b3ce6a439ac531630443b43e95 Package: SpeCond Version: 1.64.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) MD5sum: efc142df1ba286cd93f09515e60a7384 Package: Spectra Version: 1.20.0 Depends: R (>= 4.1.0), S4Vectors, BiocParallel Imports: ProtGenerics (>= 1.39.2), methods, IRanges, MsCoreUtils (>= 1.7.5), graphics, grDevices, stats, tools, utils, fs, BiocGenerics, MetaboCoreUtils Suggests: testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick License: Artistic-2.0 MD5sum: 3f858f42b702dfb72562c70c1eb16d13 Package: SpectralTAD Version: 1.26.0 Depends: R (>= 3.6) Imports: dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges, utils Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr License: MIT + file LICENSE MD5sum: cae56b1cdf796d94f5c091db6cffb869 Package: SpectraQL Version: 1.4.0 Depends: R (>= 4.4.0), ProtGenerics (>= 1.25.1) Imports: Spectra (>= 1.5.6), MsCoreUtils, methods Suggests: testthat, msdata (>= 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alphahull, Rtsne, umap, ComplexHeatmap, elsa License: Artistic-2.0 + file LICENSE MD5sum: 1aca891727e39e6e1942bc38503db0e0 Package: SPICEY Version: 1.0.0 Depends: R (>= 4.5.0), utils, stats, grDevices Imports: GenomicRanges, GenomicFeatures, AnnotationDbi, S4Vectors, ggplot2, dplyr, tidyr, tibble, GenomeInfoDb, scales, cowplot Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 38085595234bd4a93ead56c13a92eea9 Package: spicyR Version: 1.22.0 Depends: R (>= 4.1) Imports: BiocParallel, ClassifyR, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, cli, concaveman, coxme, data.table, dplyr, ggforce, ggh4x, ggnewscale, ggplot2, ggthemes, grDevices, lifecycle, lmerTest, magrittr, methods, pheatmap, rlang, scales, scam, simpleSeg, spatstat.explore, spatstat.geom, stats, survival, tibble, tidyr Suggests: SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, testthat (>= 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knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 4902a4c95b10dd8fe330b72aeecf03be Package: SpotClean Version: 1.12.0 Depends: R (>= 4.2.0), Imports: stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment, SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap, rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling License: GPL-3 MD5sum: 46d7c3158709e2bf1d4293300c058984 Package: SPOTlight Version: 1.14.0 Depends: R (>= 4.5.0) Imports: ggplot2, Matrix, SingleCellExperiment, sparseMatrixStats, stats LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, colorBlindness, DelayedArray, DropletUtils, ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat License: GPL-3 MD5sum: f44aa5f7191a1f44ef19dddf342e7a08 Package: SpotSweeper 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BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: 231b6f5f5837fd4d1a923963f5af436a Package: ssPATHS Version: 1.24.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: ROCR, dml, MESS Suggests: ggplot2, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: eeefed2f122c0a33d50e602b7bf6b2f4 Package: ssrch Version: 1.26.0 Depends: R (>= 3.6), methods Imports: shiny, DT, utils Suggests: knitr, testthat, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 77046151eed9450e160a74fa32c41453 Package: ssviz Version: 1.44.0 Depends: R (>= 3.5.0), methods, Rsamtools, Biostrings, reshape, ggplot2, RColorBrewer, stats Suggests: knitr License: GPL-2 MD5sum: f8fc1c78164dba04b40d8dd97d6b1d68 Package: StabMap Version: 1.4.0 Depends: R (>= 4.4.0), Imports: igraph, slam, BiocNeighbors, Matrix, MASS, abind, SummarizedExperiment, methods, MatrixGenerics, BiocGenerics, BiocSingular, BiocParallel 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testthat (>= 3.0.0), ClassifyR, spicyR, ggsurvfit, lisaClust, survival License: GPL-3 MD5sum: 385901c814442e5d3866185c1baaecec Package: statTarget Version: 1.40.0 Depends: R (>= 3.6.0) Imports: randomForest,plyr,pdist,ROC,utils,grDevices,graphics,rrcov,stats, pls,impute Suggests: testthat, BiocStyle, knitr, rmarkdown License: LGPL (>= 3) MD5sum: ef59206c4f472218d739895e473e845c Package: stepNorm Version: 1.82.0 Depends: R (>= 1.8.0), marray, methods Imports: marray, MASS, methods, stats License: LGPL MD5sum: 0a736c67ee23c79257eb781fffdde6ce Package: stJoincount Version: 1.12.0 Depends: R (>= 4.2.0) Imports: graphics, stats, dplyr, magrittr, sp, raster, spdep, ggplot2, pheatmap, grDevices, Seurat, SpatialExperiment, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: e0d06770c5fd64690e177d4a3b0820c8 Package: stPipe Version: 1.0.0 Depends: R (>= 4.5.0) Imports: basilisk, data.table, DropletUtils, dplyr, ggplot2, methods, 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annotate, AnnotationDbi, GenomicFeatures, SparseArray, SingleCellExperiment, TxDb.Hsapiens.UCSC.hg19.knownGene, hgu95av2.db, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit, testthat, digest License: Artistic-2.0 MD5sum: 417567fe8602c2ee6458f90f1dc4bafc Package: Summix Version: 2.16.0 Depends: R (>= 4.3) Imports: dplyr, nloptr, magrittr, methods, tibble, tidyselect, BEDASSLE, scales, visNetwork, randomcoloR Suggests: rmarkdown, markdown, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 47c0a5ee4c902a3564022549d7bc4af0 Package: SuperCellCyto Version: 1.0.0 Imports: SuperCell, data.table, Matrix, BiocParallel Suggests: flowCore, knitr, rmarkdown, usethis, testthat (>= 3.0.0), BiocSingular, bluster, scater, scran, Seurat, SingleCellExperiment, BiocStyle, magick, qs2 License: GPL-3 + file LICENSE MD5sum: 1930fce1118cac3d290420822814034d Package: supersigs Version: 1.18.0 Depends: R (>= 4.1) Imports: assertthat, caret, dplyr, tidyr, rsample, methods, rlang, utils, Biostrings, stats, SummarizedExperiment Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, testthat, VariantAnnotation License: GPL-3 MD5sum: 65e031193ecb9de165dd8afd008f1715 Package: surfaltr Version: 1.16.0 Depends: R (>= 4.0) Imports: dplyr (>= 1.0.6), biomaRt (>= 2.46.0), protr (>= 1.6-2), seqinr (>= 4.2-5), ggplot2 (>= 3.3.2), utils (>= 2.10.1), stringr (>= 1.4.0), Biostrings (>= 2.58.0),readr (>= 1.4.0), httr (>= 1.4.2), testthat(>= 3.0.0), xml2(>= 1.3.2), msa (>= 1.22.0), methods (>= 4.0.3) Suggests: knitr, rmarkdown, devtools, kableExtra License: MIT + file LICENSE MD5sum: 51654d085b5175079fc4f1a70f43f0a3 Package: SurfR Version: 1.6.0 Depends: R (>= 4.4.0) Imports: httr, BiocFileCache, SPsimSeq, DESeq2, edgeR, openxlsx, stringr, rhdf5, ggplot2, ggrepel, stats, magrittr, assertr, tidyr, dplyr, TCGAbiolinks, biomaRt, metaRNASeq, scales, venn, gridExtra, SummarizedExperiment, knitr, rjson, grDevices, graphics, curl, utils Suggests: BiocStyle, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 5fee86a4e2855959408c81c65fa9dee4 Package: survClust Version: 1.4.0 Depends: R (>= 3.5.0) Imports: Rcpp, MultiAssayExperiment, pdist, survival LinkingTo: Rcpp Suggests: knitr, testthat (>= 3.0.0), gplots, htmltools, BiocParallel License: MIT + file LICENSE MD5sum: 979960aa50dd642466c90162e3e69afa Package: survcomp Version: 1.60.0 Depends: survival, prodlim, R (>= 3.4) Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta, stats, graphics Suggests: Hmisc, clinfun, xtable, Biobase, BiocManager License: Artistic-2.0 MD5sum: 100428925e583a269a24fbd935fc10d1 Package: survtype Version: 1.26.0 Depends: SummarizedExperiment, pheatmap, survival, survminer, clustvarsel, stats, utils Suggests: maftools, scales, knitr, rmarkdown License: Artistic-2.0 MD5sum: f6d2303ab87eed06ec7ec86b74839c9b Package: sva Version: 3.58.0 Depends: R (>= 3.2), mgcv, genefilter, BiocParallel Imports: matrixStats, stats, graphics, utils, limma, edgeR Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat License: Artistic-2.0 MD5sum: b7c4249ea44e312b9b3678bb1f422bb4 Package: svaNUMT Version: 1.16.0 Depends: GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>= 4.0) Imports: assertthat, stringr, dplyr, methods, rlang, S4Vectors, Seqinfo, GenomeInfoDb, GenomicFeatures, pwalign Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown License: GPL-3 + file LICENSE MD5sum: 04cd702a8064cd6a13adb197e7b32347 Package: svaRetro Version: 1.15.1 Depends: GenomicRanges, rtracklayer, BiocGenerics, StructuralVariantAnnotation, R (>= 4.0) Imports: VariantAnnotation, assertthat, Biostrings, stringr, dplyr, methods, rlang, S4Vectors, Seqinfo, GenomeInfoDb, GenomicFeatures, utils Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges, circlize, tictoc, IRanges, stats, SummarizedExperiment, rmarkdown License: GPL-3 + file LICENSE MD5sum: 0dba342ac244a33189bf507bcacf2f35 Package: SVMDO Version: 1.10.0 Depends: R(>= 4.4), shiny (>= 1.7.4) Imports: shinyFiles (>= 0.9.3), shinytitle (>= 0.1.0), golem (>= 0.3.5), nortest (>= 1.0-4), e1071 (>= 1.7-12), BSDA (>= 1.2.1), data.table (>= 1.14.6), sjmisc (>= 2.8.9), klaR (>= 1.7-1), caTools (>= 1.18.2), caret (>= 6.0-93), survival (>= 3.4-0), DT (>= 0.33.0), DOSE (>= 3.24.2), AnnotationDbi (>= 1.60.0), org.Hs.eg.db (>= 3.16.0), dplyr (>= 1.0.10), SummarizedExperiment (>= 1.28.0), grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.1.6) License: GPL-3 MD5sum: 7e1788be96f4551a831a94ab0da54178 Package: SVP Version: 1.2.0 Depends: R (>= 4.1.0) Imports: Rcpp, RcppParallel, methods, cli, dplyr, rlang, S4Vectors, SummarizedExperiment, SingleCellExperiment, SpatialExperiment, BiocGenerics, BiocParallel, fastmatch, pracma, stats, withr, Matrix, DelayedMatrixStats, deldir, utils, BiocNeighbors, ggplot2, ggstar, ggtree, ggfun LinkingTo: Rcpp, RcppArmadillo (>= 14.0), RcppParallel, RcppEigen, dqrng Suggests: rmarkdown, prettydoc, broman, RSpectra, BiasedUrn, knitr, ks, igraph, testthat (>= 3.0.0), scuttle, magrittr, DropletUtils, tibble, tidyr, harmony, aplot, scales, ggsc, scatterpie, scran, scater, STexampleData, ape License: GPL-3 MD5sum: a6aa211f7e9209ba557a21023c4237b8 Package: SWATH2stats Version: 1.40.0 Depends: R(>= 2.10.0) Imports: data.table, reshape2, ggplot2, stats, grDevices, graphics, utils, biomaRt, methods Suggests: testthat, knitr, rmarkdown Enhances: MSstats, PECA, aLFQ License: GPL-3 MD5sum: 0b88ae6528846d7bd3581376ef92fe64 Package: SwathXtend Version: 2.32.0 Depends: e1071, openxlsx, VennDiagram, lattice License: GPL-2 MD5sum: f521d5deb17e35a9418b4d154142c9fe Package: switchBox Version: 1.46.0 Depends: R (>= 2.13.1), pROC, 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rmarkdown, testthat, devtools, prettydoc, glue License: GPL-2 MD5sum: 5b6f6dcabb77fcdf5048dc1861a40786 Package: syntenet Version: 1.12.0 Depends: R (>= 4.2) Imports: Rcpp (>= 1.0.8), BiocParallel, GenomicRanges, rlang, Biostrings, utils, methods, igraph, stats, grDevices, RColorBrewer, pheatmap, ggplot2, ggnetwork, intergraph LinkingTo: Rcpp, testthat Suggests: rtracklayer, BiocStyle, ggtree, labdsv, covr, knitr, rmarkdown, testthat (>= 3.0.0), xml2, networkD3 License: GPL-3 MD5sum: 39425a46c53ce25007c2b04434fd19f5 Package: systemPipeR Version: 2.16.0 Depends: Rsamtools (>= 1.31.2), Biostrings, ShortRead (>= 1.37.1), methods Imports: GenomicRanges, SummarizedExperiment, ggplot2, yaml, stringr, magrittr, S4Vectors, crayon, BiocGenerics, htmlwidgets Suggests: BiocStyle, knitr, rmarkdown, systemPipeRdata, GenomicAlignments, grid, dplyr, testthat, rjson, annotate, AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT, rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools, GenomicFeatures, 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ggplot2, glmnet, GSVA (>= 1.51.3), HGNChelper, magrittr, methods, pROC, RColorBrewer, reshape2, ROCit, S4Vectors, singscore, stats, SummarizedExperiment, tibble Suggests: BiocStyle, caret, circlize, class, covr, dplyr, e1071, impute, knitr, lintr, MASS, plyr, randomForest, rmarkdown, shiny, spelling, sva, testthat License: MIT + file LICENSE MD5sum: b77906944f12580c0ed10517d8740aa8 Package: TCC Version: 1.50.0 Depends: R (>= 3.0), methods, DESeq2, edgeR, ROC Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: c1dff32b47d14375afc65860038c8159 Package: TCGAbiolinks Version: 2.38.0 Depends: R (>= 4.1.0) 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 (>= 1.15.1), readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1) Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, Biobase, affy, testthat, sesame, AnnotationHub, ExperimentHub, pathview, clusterProfiler, Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid, DT License: GPL (>= 3) MD5sum: ac54f9825b0bc7b886a7828e2830e4b6 Package: TCGAutils Version: 1.29.5 Depends: R (>= 4.5.0) Imports: AnnotationDbi, BiocGenerics, BiocBaseUtils, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment, rvest, S4Vectors, Seqinfo, stats, stringr, SummarizedExperiment, utils, xml2 Suggests: AnnotationHub, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox, rtracklayer, R.utils, testthat, 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Package: terraTCGAdata Version: 1.14.0 Depends: AnVILGCP, MultiAssayExperiment Imports: AnVIL, BiocFileCache, dplyr, GenomicRanges, methods, RaggedExperiment, readr, S4Vectors, stats, tidyr, TCGAutils, utils Suggests: AnVILBase, knitr, rmarkdown, BiocStyle, withr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: e1c675b326dc2679c2c4349d692536bb Package: TFARM Version: 1.32.0 Depends: R (>= 3.5.0) Imports: arules, fields, GenomicRanges, graphics, stringr, methods, stats, gplots Suggests: BiocStyle, knitr, plyr License: Artistic-2.0 MD5sum: c5504cbd7fa9b1d3fad3af8a86f68321 Package: TFBSTools Version: 1.48.0 Depends: R (>= 3.2.2) Imports: Biobase(>= 2.28), Biostrings(>= 2.36.4), pwalign, BiocGenerics(>= 0.14.0), BiocParallel(>= 1.2.21), BSgenome(>= 1.36.3), caTools(>= 1.17.1), DirichletMultinomial(>= 1.10.0), Seqinfo, 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(>= 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methods, ORFik Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 929b2f3e813a8a0180283c1a52090003 Package: TFutils Version: 1.30.0 Depends: R (>= 4.1.0) Imports: methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase, rjson, BiocFileCache, DT, httr, readxl, AnnotationDbi, org.Hs.eg.db, utils, GenomicFiles, SummarizedExperiment Suggests: knitr, data.table, testthat, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, Seqinfo, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer, rmarkdown License: Artistic-2.0 MD5sum: 88ecf80e613025a9e772f386a8041ab1 Package: tidybulk Version: 2.0.0 Depends: R (>= 4.4.0), ttservice (>= 0.3.6) Imports: tibble, dplyr (>= 1.1.0), magrittr, tidyr, stringr, rlang, purrr, tidyselect, stats, parallel, utils, lifecycle, scales, ggplot2, SummarizedExperiment, GenomicRanges, methods, S4Vectors, crayon, Matrix 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, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, preprocessCore, igraph, EGSEA, IRanges, here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS, pkgconfig, enrichplot, patchwork, airway License: GPL-3 MD5sum: 4ed436e12de0c972964089bd832bb803 Package: tidyCoverage Version: 1.6.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, BiocParallel, BiocIO, rtracklayer, methods, tidyr, ggplot2, dplyr, fansi, pillar, rlang, scales, cli, purrr, vctrs, stats Suggests: tidySummarizedExperiment, plyranges, TxDb.Hsapiens.UCSC.hg19.knownGene, AnnotationHub, GenomicFeatures, BiocStyle, hues, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + file 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Depends: R (>= 4.1.0) Imports: assertthat, caret, ClassifyR, directPA, doParallel, dplyr, ggnewscale, ggplot2, ggraph, ggrepel, ggthemes, glmnet, Hmisc, igraph, latex2exp, limma, magrittr, methods, plotly, pROC, purrr, reshape2, stats, stringr, survival, tibble, tidygraph, tidyr, statmod Suggests: knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse License: GPL-3 MD5sum: 04f7ead16acd94ecd6ccb2315d7d072f Package: topconfects Version: 1.26.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, assertthat, ggplot2, scales, grid, grDevices 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: 94fa01f6fef0b31b2cb7853345f1ea86 Package: topdownr Version: 1.32.0 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.20.0), ProtGenerics (>= 1.10.0), Biostrings (>= 2.42.1), S4Vectors (>= 0.12.2) Imports: grDevices, 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rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools, PharmacoGx, xtable, markdown License: MIT + file LICENSE MD5sum: f859b862adb6987e7f43a02e5df980fc Package: TPP Version: 3.38.0 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: 5cb44147d0f8a30c7b2fbb0c4abf6e7b Package: TPP2D Version: 1.26.0 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, BiocStyle License: GPL-3 MD5sum: 880de4ba72f7f9e291d844437824832b Package: tpSVG Version: 1.6.0 Depends: mgcv, R (>= 4.4) Imports: stats, BiocParallel, MatrixGenerics, methods, SingleCellExperiment, SummarizedExperiment, SpatialExperiment Suggests: BiocStyle, knitr, nnSVG, rmarkdown, scran, scuttle, STexampleData, escheR, ggpubr, colorspace, BumpyMatrix, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 6059ebf48b57a06f63fe46b7175d086b Package: tracktables Version: 1.44.0 Depends: R (>= 3.5.0) Imports: IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base, stringr, RColorBrewer, methods Suggests: knitr, BiocStyle License: GPL (>= 3) MD5sum: 7f8d277531fcf0de11ba7382dbfdee91 Package: trackViewer Version: 1.46.0 Depends: R (>= 3.5.0), grDevices, methods, GenomicRanges, grid Imports: Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, InteractionSet, utils, rhdf5, strawr, txdbmaker Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack License: GPL (>= 2) MD5sum: 0045634b76db2a02e8001f4c528a4fad Package: tradeSeq Version: 1.24.0 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, DelayedMatrixStats License: MIT + file LICENSE MD5sum: 7c49dcab7bdcd03ff37bd0d0fdd3c82d Package: TrajectoryGeometry Version: 1.18.0 Depends: R (>= 4.1) Imports: pracma, rgl, ggplot2, stats, methods Suggests: dplyr, knitr, RColorBrewer, rmarkdown License: MIT + file LICENSE MD5sum: b2402259e8e91bbbeacc69e882a655fe Package: TrajectoryUtils Version: 1.18.0 Depends: SingleCellExperiment Imports: methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 63673c302d059c95357fd020ae5e2116 Package: transcriptogramer Version: 1.32.0 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: d79a9b87ba0532aff7bde98268635394 Package: transcriptR Version: 1.37.0 Depends: R (>= 3.5.0), methods 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: 813195fe4b9a05c7ae2ceded9cbf5ef6 Package: transformGamPoi Version: 1.16.0 Imports: glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp LinkingTo: Rcpp Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 63da203c8e3b391b151bc4c004f61a6f Package: transite Version: 1.28.0 Depends: R (>= 3.5) Imports: BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), stringr (>= 1.5.1), 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: 53c75df0b4d0213e56fd609671d4e5fb Package: tRanslatome Version: 1.48.0 Depends: R (>= 2.15.0), methods, limma, anota, DESeq2, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 MD5sum: 80a18ca56763a9f300b9eae5828a259a Package: transmogR Version: 1.6.0 Depends: R (>= 4.1.0), Biostrings, GenomicRanges Imports: BSgenome, data.table, Seqinfo, GenomicFeatures, ggplot2 (>= 4.0.0), IRanges, jsonlite, matrixStats, methods, parallel, patchwork, scales, stats, S4Vectors, SummarizedExperiment, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, edgeR, extraChIPs, InteractionSet, knitr, readr, rmarkdown, rtracklayer, SimpleUpset, testthat (>= 3.0.0) License: GPL-3 MD5sum: 8f3787b71354dc71fb05e565a3d6f232 Package: transomics2cytoscape Version: 1.20.0 Imports: RCy3, KEGGREST, dplyr, purrr, tibble, pbapply Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 123faeaeca64b39744c4e5dc0c0c8d46 Package: TransView Version: 1.54.0 Depends: methods, GenomicRanges Imports: BiocGenerics, S4Vectors (>= 0.9.25), IRanges, gplots LinkingTo: Rhtslib (>= 1.99.1) Suggests: RUnit, pasillaBamSubset, BiocManager License: GPL-3 MD5sum: bcbdb0df561bec29f23946cf9db8ac04 Package: traseR Version: 1.40.0 Depends: R (>= 3.5.0), GenomicRanges, IRanges, BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL MD5sum: 789a5c750536a37a10b7c08c97a181a0 Package: TreeAndLeaf Version: 1.22.0 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: 2caa6e9ec21c5723c9fd79bbdc4b519a Package: treeclimbR Version: 1.6.0 Depends: R (>= 4.4.0) Imports: TreeSummarizedExperiment (>= 1.99.0), edgeR, methods, SummarizedExperiment, S4Vectors, dirmult, dplyr, tibble, tidyr, ape, diffcyt, ggnewscale, ggplot2 (>= 3.4.0), viridis, ggtree, stats, utils, rlang Suggests: knitr, rmarkdown, scales, testthat (>= 3.0.0), BiocStyle, GenomeInfoDb License: Artistic-2.0 MD5sum: 6c5d46200402b7fe819d52cd18b931ef Package: treeio Version: 1.34.0 Depends: R (>= 4.1.0) Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble, tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6) Suggests: Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml License: Artistic-2.0 MD5sum: 76db182db8acf0b37ed710e1c0d17594 Package: treekoR Version: 1.18.0 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: 67a7b8e9977ba0671f00dd2b188535b0 Package: TreeSummarizedExperiment Version: 2.18.0 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: 62bbd7bc11827dafdd3fe7d497825be6 Package: TREG Version: 1.14.0 Depends: R (>= 4.2), SummarizedExperiment Imports: Matrix, purrr, rafalib Suggests: BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment License: Artistic-2.0 MD5sum: 864e2b6284ca427507f731611be84076 Package: Trendy Version: 1.32.0 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: 6577afb4e7f1c99a33aae8dab25c0fc8 Package: TRESS Version: 1.16.0 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: 185b97c2e6332e31b2b14e4950e8e31f Package: tricycle Version: 1.18.0 Depends: R (>= 4.0), SingleCellExperiment Imports: methods, circular, ggplot2, ggnewscale, 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 MD5sum: 262ed070ac2b3c17daf0587123f25cf3 Package: TrIdent Version: 1.2.0 Depends: R (>= 4.2.0) Imports: graphics, utils, stats, dplyr, ggplot2, patchwork, stringr, tidyr, roll Suggests: BiocStyle, knitr, rmarkdown, kableExtra, testthat (>= 3.0.0) License: GPL-2 MD5sum: c82d30a3376eab356a99a1467ba99eef Package: trio Version: 3.48.0 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1), data.table Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 MD5sum: 86f040e5f714d487a4078182cd59bb52 Package: triplex Version: 1.50.0 Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27), XVector (>= 0.11.6), Biostrings (>= 2.39.10) Imports: methods, grid, GenomicRanges LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer License: BSD_2_clause + file LICENSE MD5sum: dbc4d0d22a4baffcd6f6d9bf8ff0dd6c Package: tripr Version: 1.16.0 Depends: R (>= 4.1.0), shiny (>= 1.6.0), shinyBS Imports: shinyjs, shinyFiles, plyr, data.table, DT, stringr, stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices, graphics, stats, utils, vegan Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr Enhances: parallel License: MIT + file LICENSE MD5sum: 659086735130a919c76b8b733c898fbe Package: tRNA Version: 1.28.0 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: afc399507a2b36d560182d623cdd974b Package: tRNAdbImport Version: 1.28.0 Depends: R (>= 3.6), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, stringr, httr2, xml2, S4Vectors, methods, IRanges, utils Suggests: BiocGenerics, knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE MD5sum: 2bee2ab6d7da95ec1218e29895c0d4e1 Package: tRNAscanImport Version: 1.30.0 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, stringr, BiocGenerics, Biostrings, Structstrings, S4Vectors, IRanges, XVector, Seqinfo, rtracklayer, BSgenome, Rsamtools Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 + file LICENSE MD5sum: 10dcabea43fe21e919c46469543e8747 Package: TRONCO Version: 2.42.0 Depends: R (>= 4.1.0), Imports: bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick License: GPL-3 MD5sum: 4ac5112a438abd0bee83b855e711dbf8 Package: TSAR Version: 1.8.0 Depends: R (>= 4.3.0) Imports: dplyr (>= 1.0.7), ggplot2 (>= 3.3.5), ggpubr (>= 0.4.0), magrittr (>= 2.0.3), mgcv (>= 1.8.38), readxl (>= 1.4.0), stringr (>= 1.4.0), tidyr (>= 1.1.4), utils (>= 4.3.1), shiny (>= 1.7.4.1), plotly (>= 4.10.2), shinyjs (>= 2.1.0), jsonlite (>= 1.8.7), rhandsontable (>= 0.3.8), openxlsx (>= 4.2.5.2), shinyWidgets (>= 0.7.6), minpack.lm (>= 1.2.3) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 5a2fb28b9839b642cc43ceed10db2456 Package: TSCAN Version: 1.48.0 Depends: R (>= 4.4.0), SingleCellExperiment, TrajectoryUtils Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, SparseArray (>= 1.5.23), DelayedArray (>= 0.31.9), S4Vectors Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor License: GPL (>= 2) MD5sum: b6a647c5c5412f949c92860163e120f8 Package: ttgsea Version: 1.18.0 Depends: keras Imports: tm, text2vec, tokenizers, textstem, stopwords, data.table, purrr, DiagrammeR, stats Suggests: fgsea, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: 838c828e8e2f711c01d7bb7f23896fec Package: TTMap Version: 1.32.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 MD5sum: 8133105ada4e100d77de23829c29dd06 Package: TurboNorm Version: 1.58.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata, hgu95av2cdf License: LGPL MD5sum: 461e0cc710ecf15921addfd22611f447 Package: TVTB Version: 1.36.0 Depends: R (>= 3.4), methods, utils, stats Imports: AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel, Biostrings, ensembldb, Seqinfo, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges (>= 2.21.6), reshape2, Rsamtools, S4Vectors (>= 0.25.14), SummarizedExperiment, VariantAnnotation (>= 1.19.9) Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander License: Artistic-2.0 MD5sum: 6e7f3b6ec908130149bac1bfe2af0763 Package: tweeDEseq Version: 1.56.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn, grDevices, graphics, stats, utils LinkingTo: Rcpp Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) MD5sum: 01f70ab369428cc7ef1a51e069b45eaf Package: twilight Version: 1.86.0 Depends: R (>= 2.10) Imports: Biobase, graphics, grDevices, splines, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) MD5sum: 63ffa9a535b372f35584b9502d35ad2c Package: twoddpcr Version: 1.34.0 Depends: R (>= 3.4) Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: e711210f109de06c1b05a04cdf91a098 Package: txcutr Version: 1.16.0 Depends: R (>= 4.5.0) Imports: AnnotationDbi, GenomicFeatures, txdbmaker, IRanges, GenomicRanges, BiocGenerics, Biostrings, S4Vectors, rtracklayer, BiocParallel, stats, methods, utils Suggests: RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3, GenomeInfoDbData License: GPL-3 MD5sum: e9e17252973beb0652f24936956986ac Package: txdbmaker Version: 1.6.0 Depends: BiocGenerics, S4Vectors (>= 0.47.6), Seqinfo, GenomicRanges (>= 1.61.1), GenomicFeatures (>= 1.61.4) Imports: methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>= 2.0), IRanges, UCSC.utils, GenomeInfoDb, AnnotationDbi, Biobase, BiocIO, rtracklayer, biomaRt (>= 2.59.1) Suggests: RMariaDB, ensembldb, GenomeInfoDbData, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 518779571957fd2980f586e79aaa5c9b Package: tximeta Version: 1.28.0 Depends: R (>= 4.1.0) Imports: SummarizedExperiment (>= 1.39.1), tximport, jsonlite, S4Vectors, IRanges, GenomicRanges (>= 1.61.1), AnnotationDbi, GenomicFeatures, txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, Seqinfo, tools, utils, methods, Matrix Suggests: knitr, rmarkdown, testthat, tximportData (>= 1.37.5), org.Dm.eg.db, DESeq2, edgeR, limma, devtools, macrophage License: GPL-2 MD5sum: 29da3481ba5a1f137a6bcea309a849cc Package: tximport Version: 1.38.0 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds License: LGPL (>= 2) MD5sum: bebf696d565620c7ce17bd7450499348 Package: UCell Version: 2.14.0 Depends: R(>= 4.3.0) Imports: methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel, BiocNeighbors, SingleCellExperiment, SummarizedExperiment Suggests: scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: ad281d49a42c0c05f48e2b68670b6df3 Package: UCSC.utils Version: 1.6.0 Imports: methods, stats, httr, jsonlite, S4Vectors (>= 0.47.6) Suggests: DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 315c1c384e7ecfadc3156c0ee571b94a Package: Ularcirc Version: 1.28.0 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, moments, Organism.dplyr, plotgardener,R.utils, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, yaml Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: e9ec7705fbfc39268f69e2c5f76cf39d Package: UMI4Cats Version: 1.20.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats, annotate, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat License: Artistic-2.0 MD5sum: eb9fb12009534f4157da0311f8dcf128 Package: uncoverappLib Version: 1.20.0 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,S4Vectors, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, processx, Rsamtools, GenomicRanges Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: 6a4b7b63f7b8708c8de5026ab19834ae Package: UNDO Version: 1.52.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 84c3a6ec7cbc5db9ef4f14733482e334 Package: unifiedWMWqPCR Version: 1.46.0 Depends: methods Imports: BiocGenerics, limma, stats, graphics License: GPL (>= 2) MD5sum: ad6088d6e8cdf14029fbbc7337ca2ce8 Package: UniProt.ws Version: 2.50.0 Depends: R (>= 4.5.0) Imports: AnnotationDbi, BiocFileCache, BiocBaseUtils, BiocGenerics, httr2, jsonlite, methods, progress, rjsoncons, rlang, utils Suggests: BiocStyle, knitr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: 6ea477f96a32ea902e0a0672605e3481 Package: Uniquorn Version: 2.30.0 Depends: R (>= 3.5) Imports: stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation, data.table Suggests: testthat, knitr, rmarkdown, BiocGenerics License: Artistic-2.0 MD5sum: 2eb7c7309080639368aa429a95eddc1d Package: universalmotif Version: 1.28.0 Depends: R (>= 4.1.0) Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid, MatrixGenerics 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: 02339eb3a1a3b38b2aa72ca7e002de21 Package: updateObject Version: 1.14.0 Depends: R (>= 4.2.0), methods, BiocGenerics (>= 0.51.1), S4Vectors Imports: utils, digest Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, SingleCellExperiment, MultiAssayExperiment, BiSeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: ce365760b4e7d4e95105a74c1e65e147 Package: UPDhmm Version: 1.6.0 Depends: R (>= 4.1.0) Imports: HMM, utils, VariantAnnotation, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, Biobase, stats, BiocParallel, GenomeInfoDb Suggests: knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown, karyoploteR, regioneR, dplyr, BiocManager License: MIT + file LICENSE MD5sum: f8fba9fbaa80638af7055e794f2a37ff Package: uSORT Version: 1.36.0 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: 8cc5f4ca5154e53e6218892c35c13a9b Package: VAExprs Version: 1.16.0 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: b10e3549cdc1d63d063131ce5e91e68b Package: VanillaICE Version: 1.72.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, human610quadv1bCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 MD5sum: 68f3d7d8dea3a8609a99aaff27330fdc Package: VarCon Version: 1.18.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: b811657fcf6878fd122416fda816bac3 Package: variancePartition Version: 1.40.0 Depends: R (>= 4.3.0), ggplot2, limma (>= 3.62.2), BiocParallel Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2, gtools, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack, rlang, lme4 (>= 1.1.33), grDevices, graphics, Biobase, methods, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr License: GPL-2 MD5sum: 6dbf78331fd9f1d8aea1786eb62eef2f Package: VariantAnnotation Version: 1.56.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, Seqinfo, GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Rsamtools (>= 2.25.1) Imports: utils, DBI, Biobase, S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.77.2), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.69.1), BSgenome (>= 1.77.1), GenomicFeatures (>= 1.61.4), curl LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0) Suggests: GenomeInfoDb, RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr, magick, jsonlite, httr, rjsoncons License: Artistic-2.0 MD5sum: 2d4d96026a0664f491a58ef165714517 Package: VariantFiltering Version: 1.46.0 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, Seqinfo (>= 0.99.2), GenomeInfoDb (>= 1.45.7), Biostrings (>= 2.77.2), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), GenomicFeatures (>= 1.61.4), Rsamtools (>= 2.25.1), BSgenome (>= 1.77.1), GenomicScores (>= 2.21.4), Gviz (>= 1.53.1), 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: e6b74be7563d0e0a44e5247bb03101a2 Package: VaSP Version: 1.22.0 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 59c712664ec79afe33f544576106cc3e Package: vbmp Version: 1.78.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: 1c981de5a1adc61164a73e48bc4aa997 Package: VCFArray Version: 1.26.0 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: 2efa7bde0a844b382a539686334dc42d Package: VDJdive Version: 1.12.0 Depends: R (>= 4.2) Imports: BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix, methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils LinkingTo: Rcpp Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: 87bb549dd6990dbc0267f4cc925dd890 Package: VegaMC Version: 3.48.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods License: GPL-2 MD5sum: 7bbf551c860802732ef2232b7b0070ac Package: velociraptor Version: 1.20.0 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: 95c6974133e927f325a766654da8a100 Package: veloviz Version: 1.16.0 Depends: R (>= 4.1) Imports: Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 03625970a3f317c9de48328425e42ebf Package: VennDetail Version: 1.26.0 Depends: R (>= 4.0.0), Imports: dplyr, DT, methods, ggplot2, grDevices, magrittr, patchwork, plotly, purrr, rlang, shiny, stats, tibble, tidyr, htmlwidgets, utils Suggests: knitr, markdown, RColorBrewer, rmarkdown, rstudioapi, testthat (>= 3.0.0) License: GPL-2 MD5sum: fd3886f42b908a5cafe0a1f38f5426dd Package: VERSO Version: 1.20.0 Depends: R (>= 4.1.0) Imports: utils, data.tree, ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 5e3dbf9a5e4d62b5e5d1ee6249e87d65 Package: vidger Version: 1.30.0 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: 091105e0a3b41c876701d5a2f0913d34 Package: viper Version: 1.44.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: e8e0ad563a9fe0bf8df0ec09970de863 Package: ViSEAGO Version: 1.24.0 Depends: R (>= 3.6) Imports: data.table, AnnotationDbi, dendextend, dynamicTreeCut, GOSemSim, GO.db, heatmaply, topGO, AnnotationForge, DT, DiagrammeR, R.utils, RColorBrewer, UpSetR, biomaRt, fgsea, ggplot2, htmlwidgets, igraph, methods, plotly, scales, ComplexHeatmap, circlize Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager, stats, utils, grDevices, processx MD5sum: 76f08beb209b82d36ae8fe0ecf61f79c Package: VisiumIO Version: 1.6.0 Depends: R (>= 4.5.0), TENxIO Imports: BiocBaseUtils, BiocGenerics, BiocIO (>= 1.15.1), jsonlite, methods, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment Suggests: arrow, BiocStyle, data.table, knitr, readr, rmarkdown, sf, tinytest License: Artistic-2.0 MD5sum: 62763fbb7df75e64973011992fd5ed16 Package: visiumStitched Version: 1.2.0 Depends: R (>= 4.4), SpatialExperiment Imports: BiocBaseUtils, BiocGenerics, clue, dplyr, DropletUtils, grDevices, imager, Matrix, methods, pkgcond, readr, rjson, S4Vectors, SingleCellExperiment, spatialLIBD (>= 1.17.8), stringr, SummarizedExperiment, tibble, tidyr, xml2 Suggests: BiocFileCache, BiocStyle, ggplot2, knitr, RefManageR, rmarkdown, sessioninfo, Seurat, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 2f2e5221ca8fe18cc0361dcf485b6efd Package: vissE Version: 1.18.0 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: 8e6b9cfe15af5ed757db19c25b574664 Package: vmrseq Version: 1.2.0 Depends: R (>= 4.5.0) Imports: bumphunter, dplyr, BiocParallel, DelayedArray, GenomicRanges, ggplot2, methods, tidyr, locfit, gamlss.dist, recommenderlab, HDF5Array, data.table, SummarizedExperiment, IRanges, S4Vectors, devtools Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 93d11f5d03e21a8cae76571314308d3f Package: Voyager Version: 1.12.0 Depends: R (>= 4.2.0), SpatialFeatureExperiment (>= 1.7.3) Imports: BiocParallel, bluster, DelayedArray, ggnewscale, ggplot2 (>= 3.4.0), grDevices, grid, lifecycle, Matrix, MatrixGenerics, memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, spdep, stats, SummarizedExperiment, terra, utils, zeallot Suggests: arrow, automap, BiocSingular, BiocStyle, cowplot, data.table, DelayedMatrixStats, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, matrixStats, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, xml2 License: Artistic-2.0 MD5sum: 2e4f9e79bca33c3988bc49d021c7ca1b Package: VplotR Version: 1.20.0 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, Seqinfo, 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: abbc8779ad2d0a9016267d3de5e35b86 Package: vsclust Version: 1.12.0 Depends: R (>= 4.2.0) Imports: matrixStats, limma, parallel, shiny, qvalue, grDevices, stats, MultiAssayExperiment, clusterProfiler, DOSE, httr, graphics LinkingTo: Rcpp Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, httr License: GPL-2 MD5sum: b46b05867603383ca46e60cc7c315213 Package: vsn Version: 3.78.0 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: 94d498ec4c9a77d42f8d45a3be3ee4ae Package: vtpnet Version: 0.50.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: 89f64f4af0fd051921c45d66d1150fc6 Package: vulcan Version: 1.32.0 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: 2b8ce1c16517ea60f846a59144a9484d Package: wateRmelon Version: 2.16.0 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: de36836c2b28cff3ac88a6f2de3058bb Package: wavClusteR Version: 2.44.0 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: 1c5a034ccfcb729a187937d73bcb2699 Package: weaver Version: 1.76.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 MD5sum: 60ca6da7abec1661f1354571bbe7ac0c Package: webbioc Version: 1.82.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocManager License: GPL (>= 2) MD5sum: 02e79948a16bec79db43afd76d9fe881 Package: weitrix Version: 1.22.0 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: 3445b9847233a61d7c4768976d6a964b Package: widgetTools Version: 1.88.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: 8f6d88b491fd2345a0a2771cc0085885 Package: wiggleplotr Version: 1.34.0 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: bfcdabe36712a0919ab5cfb6accb7707 Package: wpm Version: 1.20.0 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: 99fa66ca1d3d7ff7cdc04b98587477f6 Package: Wrench Version: 1.28.0 Depends: R (>= 3.5.0) Imports: limma, matrixStats, locfit, stats, graphics Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR License: Artistic-2.0 MD5sum: d9ee0e7a904d27b20d2a5185113764cc Package: XAItest Version: 1.2.0 Depends: R (>= 3.5.0) Imports: limma, randomForest, kernelshap, caret, lime, DT, methods, SummarizedExperiment, ggplot2 Suggests: knitr, ggforce, shapr (>= 1.0.1), airway, xgboost, BiocGenerics, RUnit, S4Vectors License: MIT + file LICENSE MD5sum: 98da71e374bf7badfd2ba3b282f1f7d1 Package: xCell2 Version: 1.2.0 Depends: R (>= 4.0.0) Imports: SummarizedExperiment, SingleCellExperiment, Rfast, singscore, AnnotationHub, ontologyIndex, tibble, dplyr, BiocParallel, Matrix, minpack.lm, pracma, methods, readr, magrittr, progress, quadprog Suggests: testthat, knitr, rmarkdown, ggplot2, randomForest, tidyr, EnhancedVolcano, BiocStyle License: GPL (>= 3) MD5sum: a58e51f94cf6a4f47e8580f2bd65fb38 Package: xcms Version: 4.8.0 Depends: R (>= 4.1.0), BiocParallel (>= 1.8.0) Imports: MSnbase (>= 2.33.3), mzR (>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics (>= 1.37.1), lattice, MassSpecWavelet (>= 1.66.0), S4Vectors, IRanges, SummarizedExperiment, MsCoreUtils (>= 1.19.2), MsFeatures, MsExperiment (>= 1.5.4), Spectra (>= 1.16.1), progress, RColorBrewer, MetaboCoreUtils (>= 1.11.2), data.table Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>= 0.25.1), ncdf4, testthat (>= 3.1.9), pander, rmarkdown, MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal, mgcv, rhdf5 Enhances: Rgraphviz, rgl License: GPL (>= 2) + file LICENSE MD5sum: 457b3c555da044ce53d0c9fa00686744 Package: xcore Version: 1.14.0 Depends: R (>= 4.2) Imports: DelayedArray (>= 0.18.0), edgeR (>= 3.34.1), foreach (>= 1.5.1), GenomicRanges (>= 1.44.0), glmnet (>= 4.1.2), IRanges (>= 2.26.0), iterators (>= 1.0.13), magrittr (>= 2.0.1), Matrix (>= 1.3.4), methods (>= 4.1.1), MultiAssayExperiment (>= 1.18.0), stats, S4Vectors (>= 0.30.0), utils Suggests: AnnotationHub (>= 3.0.2), BiocGenerics (>= 0.38.0), BiocParallel (>= 1.28), BiocStyle (>= 2.20.2), data.table (>= 1.14.0), devtools (>= 2.4.2), doParallel (>= 1.0.16), ExperimentHub (>= 2.2.0), knitr (>= 1.37), pheatmap (>= 1.0.12), proxy (>= 0.4.26), ridge (>= 3.0), rmarkdown (>= 2.11), rtracklayer (>= 1.52.0), testthat (>= 3.0.0), usethis (>= 2.0.1), xcoredata License: GPL-2 MD5sum: 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SFEData, tiff License: Artistic-2.0 MD5sum: 415c16d04df347063ee09d29cba19629 Package: Xeva Version: 1.26.0 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: 16a5cacefe69b6b38b61cdba8e61a87d Package: XINA Version: 1.28.0 Depends: R (>= 3.5) Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 71d2fa43d9b3623507e86db67dbef1ba Package: xmapbridge Version: 1.68.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 MD5sum: 020b0a76fca7ccb24fc295160470e895 Package: XVector Version: 0.50.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.43.8) Imports: methods, utils, stats, tools, BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 MD5sum: 73e6e8c2196e85b3731b99765b72a756 Package: yamss Version: 1.36.0 Depends: R (>= 4.3.0), methods, BiocGenerics (>= 0.15.3), SummarizedExperiment Imports: IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table, grDevices, limma Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat License: Artistic-2.0 MD5sum: e223aa3d69d6797f7ac7d99a30a818ce Package: YAPSA Version: 1.36.0 Depends: R (>= 4.0.0), GenomicRanges, ggplot2, grid Imports: limSolve, SomaticSignatures, VariantAnnotation, Seqinfo, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, doParallel, parallel, PMCMRplus, ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings, BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: fc8627bc61dd9391416a6cf7d7923dad Package: yarn Version: 1.36.0 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: c304910b5fb1aa75baf4757aa25bc2d4 Package: zellkonverter Version: 1.19.2 Imports: basilisk, cli, DelayedArray, Matrix, methods, reticulate, S4Vectors, SingleCellExperiment (>= 1.11.6), SparseArray, SummarizedExperiment, utils Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rhdf5 (>= 2.45.1), rmarkdown, scRNAseq, SpatialExperiment, spelling, testthat, withr License: MIT + file LICENSE MD5sum: 76d2900e06cd0df48016c8138ac1478a Package: zenith Version: 1.12.0 Depends: R (>= 4.2.0), limma, methods Imports: variancePartition (>= 1.26.0), EnrichmentBrowser (>= 2.22.0), GSEABase (>= 1.54.0), msigdbr, Rfast, ggplot2, tidyr, dplyr, reshape2, progress, utils, Rdpack, stats Suggests: BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit License: Artistic-2.0 MD5sum: 99b32b8393cc91175cdf40965d53c391 Package: zFPKM Version: 1.32.0 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: b03a3fb026ef150479a28000ee7222ee Package: zinbwave Version: 1.32.0 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, sparseMatrixStats License: Artistic-2.0 MD5sum: 06716c7abee4e429fcf080b1ea05ed6a Package: zitools Version: 1.4.0 Depends: R (>= 4.4.0), methods Imports: phyloseq, pscl, ggplot2, MatrixGenerics, SummarizedExperiment, stats, VGAM, matrixStats, tidyr, tibble, dplyr, DESeq2, reshape2, RColorBrewer, magrittr, BiocGenerics, graphics, utils Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), tidyverse, microbiome License: BSD_3_clause + file LICENSE MD5sum: a5fc85aea255a645e5556b079f6669ec Package: ZygosityPredictor Version: 1.10.0 Depends: R (>= 4.3.0) Imports: GenomicAlignments, GenomicRanges, Rsamtools, IRanges, VariantAnnotation, DelayedArray, dplyr, stringr, purrr, tibble, methods, knitr, igraph, readr, stats, magrittr, rlang Suggests: rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: 900da4f365b7d8889d37ae92092cebfa