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testthat, DT, tidyr, tidyverse, microbiome, magrittr License: Artistic-2.0 MD5sum: 42059f62faa03e818d0cd15b7bcf0094 NeedsCompilation: no Package: AneuFinder Version: 1.30.0 Depends: R (>= 3.5), GenomicRanges, ggplot2, cowplot, AneuFinderData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, Rsamtools, bamsignals, DNAcopy, ecp, Biostrings, GenomicAlignments, reshape2, ggdendro, ggrepel, mclust Suggests: knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: 421efa90a617606c8db2c947d302c6b1 NeedsCompilation: yes Package: ANF Version: 1.24.1 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 56d73dcafe0bc643f70111fa5670c5f7 NeedsCompilation: no Package: animalcules Version: 1.18.3 Depends: R (>= 4.3.0) Imports: ape, assertthat, caret, covr, DESeq2, dplyr, DT, forcats, ggplot2, GUniFrac, lattice, limma, magrittr, Matrix, methods, MultiAssayExperiment, plotly, rentrez, reshape2, ROCit, S4Vectors (>= 0.23.19), scales, shiny, shinyjs, stats, SummarizedExperiment, tibble, tsne, umap, utils, vegan, XML Suggests: BiocStyle, biomformat, devtools, glmnet, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: eb0d7e45ea49758bec2b9f248328b1eb NeedsCompilation: no Package: annaffy Version: 1.74.0 Depends: R (>= 2.5.0), methods, Biobase, BiocManager, GO.db Imports: AnnotationDbi (>= 0.1.15), DBI Suggests: hgu95av2.db, multtest, tcltk License: LGPL MD5sum: a590578d3e87dbab236a5531f0a5bce0 NeedsCompilation: no Package: annmap Version: 1.44.0 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: 4e793a7c30de8248f566e7c14bf3fa90 NeedsCompilation: no Package: annotate Version: 1.80.0 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, License: Artistic-2.0 MD5sum: 04d25cadc03401556364f8ca9c3b2a61 NeedsCompilation: no Package: AnnotationDbi Version: 1.64.1 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: 965300db0b7a8b527ed3eb00fdd6d10f NeedsCompilation: no Package: AnnotationFilter Version: 1.26.0 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: 512eececc247990236fd09aa1fc46966 NeedsCompilation: no Package: AnnotationForge Version: 1.44.0 Depends: R (>= 3.5.0), methods, utils, BiocGenerics (>= 0.15.10), Biobase (>= 1.17.0), AnnotationDbi (>= 1.33.14) Imports: DBI, RSQLite, XML, S4Vectors, RCurl Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, markdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit License: Artistic-2.0 MD5sum: 4aa011cdbdc464bbfe1542ec418e7749 NeedsCompilation: no Package: AnnotationHub Version: 3.10.1 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr, yaml, dplyr, interactiveDisplayBase Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 0f982a325d1e17a3702cd9b442d30eb1 NeedsCompilation: yes Package: AnnotationHubData Version: 1.32.1 Depends: R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges (>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15) Imports: GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocManager, biocViews, BiocCheck, graph, AnnotationDbi, Biobase, Biostrings, DBI, GenomeInfoDb (>= 1.15.4), OrganismDbi, RSQLite, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub License: Artistic-2.0 MD5sum: 16c917d10f4fe18cd1e2db8ae41ce6be NeedsCompilation: no Package: annotationTools Version: 1.76.0 Imports: Biobase, stats Suggests: BiocStyle License: GPL MD5sum: 3b0a795d7898c0b6112ed596f9d2de27 NeedsCompilation: no Package: annotatr Version: 1.28.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures, GenomicRanges, GenomeInfoDb (>= 1.10.3), ggplot2, IRanges, methods, readr, regioneR, reshape2, rtracklayer, S4Vectors (>= 0.23.10), stats, utils Suggests: BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene License: GPL-3 MD5sum: 433372717ce78a1ae23a91a80601f2b6 NeedsCompilation: no Package: anota Version: 1.50.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: 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Rsamtools, HybridMTest Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset License: LGPL-3 MD5sum: 88aebb2681d07ad9bc8b7e3499339d51 NeedsCompilation: no Package: apComplex Version: 2.68.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: 03418539dfa5904bf05f430718789fde NeedsCompilation: no Package: apeglm Version: 1.24.0 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 0f8e64bdd8eec2566238fdc487afabb8 NeedsCompilation: yes Package: APL Version: 1.6.1 Depends: R (>= 4.2) Imports: reticulate, ggrepel, ggplot2, viridisLite, plotly, Seurat, SingleCellExperiment, magrittr, SummarizedExperiment, topGO, methods, stats, utils, org.Hs.eg.db, org.Mm.eg.db, rlang Suggests: BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, testthat 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BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, Rsamtools, BiocStyle, igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid, graphics, pbmcapply License: GPL MD5sum: abf86e5478e3191f21892ba2eb35e442 NeedsCompilation: no Package: AssessORF Version: 1.20.0 Depends: R (>= 3.5.0), DECIPHER (>= 2.10.0) Imports: Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: b11ca260fff21c6afe98ee471d79b3ec NeedsCompilation: no Package: ASSET Version: 2.20.0 Depends: R (>= 3.5.0), stats, graphics Imports: MASS, msm, rmeta Suggests: RUnit, BiocGenerics, knitr License: GPL-2 + file LICENSE MD5sum: 395bcc1b0256acc248c5d3440bf5dfeb NeedsCompilation: no Package: ASSIGN Version: 1.38.0 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: c03c8eedec6379aa0fac65d11377fdf8 NeedsCompilation: no Package: ASURAT Version: 1.6.0 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: a1cb615f6ddab8cb8b9ccb1a73ba39de NeedsCompilation: yes Package: ATACCoGAPS Version: 1.4.0 Depends: R (>= 4.2.0), CoGAPS (>= 3.5.13) Imports: gtools, GenomicRanges, projectR, TFBSTools, GeneOverlap, msigdbr, tidyverse, gplots, motifmatchr, chromVAR, GenomicFeatures, IRanges, fgsea, rGREAT, JASPAR2016, Homo.sapiens, Mus.musculus, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, stringr, dplyr Suggests: knitr, viridis License: Artistic-2.0 MD5sum: f8cf8dd559b05caf23934090510297de NeedsCompilation: no Package: ATACseqQC Version: 1.26.0 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 Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown License: GPL (>= 2) MD5sum: 6742da3bbb4073be7aa5f2544b65df23 NeedsCompilation: no Package: ATACseqTFEA Version: 1.4.0 Depends: R (>= 4.2) Imports: BiocGenerics, S4Vectors, IRanges, Matrix, GenomicRanges, GenomicAlignments, GenomeInfoDb, SummarizedExperiment, Rsamtools, motifmatchr, TFBSTools, stats, pracma, ggplot2, ggrepel, dplyr, limma, methods Suggests: BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle License: GPL-3 MD5sum: 30284cc31687d97f23d2a7c023e8561d NeedsCompilation: no Package: atena Version: 1.8.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, BiocParallel, S4Vectors, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer License: Artistic-2.0 MD5sum: c7ae11b12240ed1d848301b4c40b019e NeedsCompilation: no Package: atSNP Version: 1.18.0 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: e7de15cd417026f8449b14841ff89bd2 NeedsCompilation: yes Package: attract Version: 1.54.0 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: e7d563026d5d00b5dd3bd906268af221 NeedsCompilation: no Package: AUCell Version: 1.24.0 Imports: DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, shiny, stats, SummarizedExperiment, BiocGenerics, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, rbokeh, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: 4d095823da2fd13bf83c831c037564ff NeedsCompilation: no Package: autonomics Version: 1.10.2 Depends: R (>= 4.0) Imports: abind, assertive.base, assertive.files, assertive.numbers, assertive.sets, BiocFileCache, BiocGenerics, bit64, colorspace, data.table, dplyr, edgeR, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma, magrittr, matrixStats, methods, MultiAssayExperiment, parallel, pcaMethods, rappdirs, rlang, R.utils, readxl, S4Vectors, scales, stats, stringi, SummarizedExperiment, tidyr, tools, utils Suggests: affy, AnnotationDbi, BiocManager, BiocStyle, diagram, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, knitr, lme4, lmerTest, MASS, mixOmics, mpm, nlme, org.Hs.eg.db, org.Mm.eg.db, RCurl, remotes, rmarkdown, ropls, Rsubread, rtracklayer, seqinr, statmod, testthat License: GPL-3 MD5sum: 9034c755764d54d8bf0eb0e330f4e54f NeedsCompilation: no Package: AWFisher Version: 1.16.0 Depends: R (>= 3.6) Imports: edgeR, limma, stats Suggests: knitr, tightClust License: GPL-3 MD5sum: ba9b2824782018cc7626ebc72b6bb81e NeedsCompilation: yes Package: awst Version: 1.10.0 Imports: stats, methods, SummarizedExperiment Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown License: MIT + file LICENSE MD5sum: a7ca0636a8f728b63d6cf56729b856eb NeedsCompilation: no Package: BaalChIP Version: 1.28.0 Depends: R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools, Imports: GenomicAlignments, GenomeInfoDb, doParallel, parallel, 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apeglm, utils, DEXSeq Enhances: parallel License: GPL-3 + file LICENSE MD5sum: 33f2e8428308b620b204e8366c309094 NeedsCompilation: yes Package: bamsignals Version: 1.34.0 Depends: R (>= 3.5.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: e7b42351aa9651bdf7d429a6377143f5 NeedsCompilation: yes Package: BANDITS Version: 1.18.1 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: 2a65b9a4669d4075f5882047445491eb NeedsCompilation: yes Package: bandle Version: 1.6.0 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 LinkingTo: Rcpp, RcppArmadillo, BH Suggests: coda (>= 0.19-4), testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling License: Artistic-2.0 MD5sum: 9c8dd928dd2b7900ff453ddc590ad6e4 NeedsCompilation: yes Package: banocc Version: 1.26.0 Depends: R (>= 3.5.1), rstan (>= 2.17.4) Imports: coda (>= 0.18.1), mvtnorm, stringr Suggests: knitr, rmarkdown, methods, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 5a73975945814e725991bd67552349e6 NeedsCompilation: no Package: barcodetrackR Version: 1.10.0 Depends: R (>= 4.1) Imports: cowplot, circlize, dplyr, ggplot2, ggdendro, ggridges, graphics, grDevices, magrittr, plyr, proxy, RColorBrewer, rlang, scales, shiny, stats, SummarizedExperiment, S4Vectors, tibble, tidyr, vegan, viridis, utils Suggests: BiocStyle, knitr, magick, rmarkdown, testthat License: file LICENSE MD5sum: 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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: 1252fa180b0da21a4a22e3400550ab93 NeedsCompilation: yes Package: BASiCStan Version: 1.4.0 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 (>= 2.1.1) 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: testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 MD5sum: b7179ffcf510240c0c3cc6e8e31b60d7 NeedsCompilation: yes Package: BasicSTARRseq Version: 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RcppProgress Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, dplyr, viridis, patchwork, RColorBrewer, Seurat License: MIT + file LICENSE MD5sum: 5505178450768dc45884632e3e0a3baf NeedsCompilation: yes Package: bayNorm Version: 1.20.0 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: fda25f54086787e9a038cc59f0660a58 NeedsCompilation: yes Package: baySeq Version: 2.36.2 Depends: R (>= 2.3.0), methods Imports: edgeR, GenomicRanges, abind, parallel, graphics, stats, utils Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: 95c2d2bfca90a7dd113211761aac9ba7 NeedsCompilation: no Package: BBCAnalyzer Version: 1.32.0 Imports: SummarizedExperiment, VariantAnnotation, Rsamtools, 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testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling License: MIT + file LICENSE MD5sum: c8e6192a3f9bd04b62ed564c8164ba00 NeedsCompilation: no Package: benchdamic Version: 1.8.2 Depends: R (>= 4.3.0) Imports: stats, stats4, utils, methods, phyloseq, TreeSummarizedExperiment, BiocParallel, zinbwave, edgeR, DESeq2, limma, ALDEx2, SummarizedExperiment, MAST, Seurat, ANCOMBC, mixOmics, lme4, NOISeq, dearseq, MicrobiomeStat, Maaslin2, GUniFrac, metagenomeSeq, MGLM, ggplot2, RColorBrewer, plyr, reshape2, ggdendro, ggridges, graphics, cowplot, grDevices, tidytext Suggests: knitr, rmarkdown, kableExtra, BiocStyle, magick, SPsimSeq, testthat License: Artistic-2.0 MD5sum: 3e181e9df4a701c33b61a184a26f0a59 NeedsCompilation: no Package: BG2 Version: 1.2.0 Depends: R (>= 4.2.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), MASS (>= 7.3-58.1), stats (>= 4.2.2) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>= 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Suggests: BiocGenerics, RUnit, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter License: GPL-3 MD5sum: 1c6944989ec4f16b1903143a34296bf0 NeedsCompilation: no Package: BindingSiteFinder Version: 2.0.0 Depends: GenomicRanges, R (>= 4.2) Imports: tidyr, tibble, plyr, 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 License: Artistic-2.0 MD5sum: b54f11a27c1f6f55b4cc60ad8986e029 NeedsCompilation: no Package: bioassayR Version: 1.40.0 Depends: R (>= 3.5.0), DBI (>= 0.3.1), RSQLite (>= 1.0.0), methods, Matrix, rjson, BiocGenerics (>= 0.13.8) Imports: XML, ChemmineR Suggests: 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magrittr, kernlab, ggplot2, cowplot, BiocStyle LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 8229c7c5175e3888c86a5a3a42eb7a8c NeedsCompilation: yes Package: BRAIN Version: 1.48.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 MD5sum: 575b879f058d01202c3bc33b0ff8e3f1 NeedsCompilation: no Package: brainflowprobes Version: 1.16.0 Depends: R (>= 3.6.0) Imports: Biostrings (>= 2.52.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), bumphunter (>= 1.26.0), cowplot (>= 1.0.0), derfinder (>= 1.18.1), derfinderPlot (>= 1.18.1), GenomicRanges (>= 1.36.0), ggplot2 (>= 3.1.1), RColorBrewer (>= 1.1), utils, grDevices, GenomicState (>= 0.99.7) Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr License: Artistic-2.0 MD5sum: eb9efebe165aeeae35ccc6b115836937 NeedsCompilation: no Package: branchpointer Version: 1.28.0 Depends: caret, R(>= 3.4) Imports: plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt, Biostrings, parallel, utils, stats, BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges, GenomeInfoDb, IRanges, S4Vectors, data.table Suggests: knitr, BiocStyle License: BSD_3_clause + file LICENSE MD5sum: 7a62abd020843736b7ea125ffc4a56e0 NeedsCompilation: no Package: breakpointR Version: 1.20.0 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: 96dddc1e7bbd8b880a89f8f1be145e66 NeedsCompilation: no Package: brendaDb Version: 1.16.0 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: 35e521feef3f87b0122ac00ad0deae5b NeedsCompilation: 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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: 6ab4a9ce40637244377f77b7baaecc38 NeedsCompilation: yes Package: compcodeR Version: 1.38.0 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: b1ec77496e614cf3399843b8c34e6ab2 NeedsCompilation: no 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testthat, rmarkdown, knitr, edgeR, limma, glmnet, BiocStyle, flowStats License: GPL-3 MD5sum: b804632cc0742b1e2f9910353a6ed75d NeedsCompilation: yes Package: CytoDx Version: 1.22.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 86d2f225be6ebdaecd3aa4960e443796 NeedsCompilation: no Package: CyTOFpower Version: 1.8.0 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: ea70d698bf8ba363250de04f634c5f74 NeedsCompilation: no Package: cytofQC Version: 1.2.0 Imports: CATALYST, flowCore, e1071, EZtune, gbm, ggplot2, hrbrthemes, matrixStats, randomForest, rmarkdown, SingleCellExperiment, stats, SummarizedExperiment, ssc, S4Vectors, graphics, methods Suggests: gridExtra, knitr, RColorBrewer, testthat, uwot License: Artistic-2.0 MD5sum: 7a4e866c0e57f639b41828c211aff31f NeedsCompilation: no Package: CytoGLMM Version: 1.10.0 Imports: stats, methods, BiocParallel, RColorBrewer, cowplot, doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr, mbest, pheatmap, stringr, strucchange, tibble, ggrepel, MASS, logging, Matrix, tidyr, caret, rlang, grDevices Suggests: knitr, rmarkdown, testthat, BiocStyle License: LGPL-3 MD5sum: 3a4b95062a82da6afe217f20ef905460 NeedsCompilation: no Package: cytoKernel Version: 1.8.0 Depends: R (>= 4.1) Imports: Rcpp, SummarizedExperiment, utils, methods, ComplexHeatmap, circlize, ashr, data.table, BiocParallel, dplyr, stats, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 2e1e2b8d2c545a69a0cec180964f2fd9 NeedsCompilation: yes Package: cytolib Version: 2.14.1 Depends: R (>= 3.4) Imports: RProtoBufLib LinkingTo: BH(>= 1.84.0.0), RProtoBufLib(>= 2.13.1),Rhdf5lib Suggests: 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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: 64986e7db314ddba69d156b35f974680 NeedsCompilation: no Package: DAPAR Version: 1.34.6 Depends: R (>= 4.3.0) Imports: Biobase, MSnbase, DAPARdata (>= 1.27.3), utils, highcharter, foreach, 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, lme4, dplyr, limma, preprocessCore, stringr, tidyr, impute, gplots, grDevices, reshape2, graphics, stats, methods, ggplot2, RColorBrewer, Matrix, org.Sc.sgd.db Suggests: testthat, BiocStyle License: Artistic-2.0 MD5sum: 24ecc0e3b05c61098ccc42488ec3b6ba 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stats, methods, assertthat, graph, pcalg, purrr, tidyverse, Matrix, ggraph, tidygraph, ggplot2, rlang, expm, MASS, edgeR, epiNEM, igraph, metap, mnem, naturalsort, ppcor, glm2, graphite, reshape2, dplyr, magrittr, glue, Rgraphviz, harmonicmeanp, org.Hs.eg.db, logger, shadowtext Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, cowplot, ggplotify, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment, RcppParallel, docopt, CARNIVAL License: GPL-3 MD5sum: dbebdd246ea193f92c1a466a84617876 NeedsCompilation: no Package: dcGSA Version: 1.30.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: f824cffdf3d7c4f41b44d2cc46b69998 NeedsCompilation: no Package: ddCt Version: 1.58.0 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: 560588380b356d55a4e11811ae9100e6 NeedsCompilation: no Package: ddPCRclust Version: 1.22.0 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: 63c29b24786957fcb604e73a61066e47 NeedsCompilation: no Package: dearseq Version: 1.14.0 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: 40f5669b310e7d2142836e3b1592bdd6 NeedsCompilation: no Package: debCAM Version: 1.20.0 Depends: R (>= 3.5) Imports: methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR2, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 MD5sum: 87d118edcaf90e70fd6aafc865ac5c6a NeedsCompilation: no Package: debrowser Version: 1.30.2 Depends: R (>= 3.5.0), Imports: shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT, ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE, igraph, grDevices, graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, 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: 002358e4e24146d0afaf63397b974ec8 NeedsCompilation: no Package: DECIPHER Version: 2.30.0 Depends: R (>= 3.5.0), Biostrings (>= 2.59.1), RSQLite (>= 1.1), stats, parallel Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector License: GPL-3 MD5sum: 0a32c782d61a604dc3594c684daa8c75 NeedsCompilation: yes Package: 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tximportData, testthat (>= 3.0.0) License: GPL-2 MD5sum: 5992ff2692afb665a65bc9755175de5c NeedsCompilation: yes Package: eegc Version: 1.28.0 Depends: R (>= 3.4.0) Imports: R.utils, gplots, sna, wordcloud, igraph, pheatmap, edgeR, DESeq2, clusterProfiler, S4Vectors, ggplot2, org.Hs.eg.db, org.Mm.eg.db, limma, DOSE, AnnotationDbi Suggests: knitr License: GPL-2 MD5sum: b454926a77b06904f3560f0c28ee1299 NeedsCompilation: no Package: EGAD Version: 1.30.0 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: 9a76ae26d942a1e8b8c8764b80c69927 NeedsCompilation: no Package: EGSEA Version: 1.30.1 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: 6df5ddde1ce67014d637e6196177c11b NeedsCompilation: no Package: eiR Version: 1.42.0 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 License: Artistic-2.0 MD5sum: 71e5c96821411e053b417fb15618e1cb NeedsCompilation: yes Package: eisaR Version: 1.14.1 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, 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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: 6cb394ba6d86f9ead0b4cb48e837a2bf NeedsCompilation: yes Package: EnMCB Version: 1.14.0 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: f9fee363d9285ffdf2895062fc0cf26b NeedsCompilation: no Package: ENmix Version: 1.38.01 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: 3ac8861e8c3ad067b1baa266958227cd NeedsCompilation: no Package: EnrichedHeatmap Version: 1.32.0 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: 269aeb6d749072508069805663216dc4 NeedsCompilation: yes Package: EnrichmentBrowser Version: 2.32.0 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: fa4ec5a19513178896d60057a26ec6ce NeedsCompilation: no Package: enrichplot Version: 1.22.0 Depends: R (>= 3.5.0) Imports: aplot (>= 0.2.1), DOSE (>= 3.16.0), ggfun (>= 0.1.3), ggnewscale, ggplot2, ggraph, graphics, grid, igraph, methods, plyr, purrr, RColorBrewer, reshape2, rlang, stats, utils, scatterpie, shadowtext, GOSemSim, magrittr, ggtree, yulab.utils (>= 0.0.8) Suggests: clusterProfiler, dplyr, europepmc, ggupset, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggrepel (>= 0.9.0), ggstar, scales, ggtreeExtra, tidydr License: Artistic-2.0 MD5sum: 4accfec43292c11ec0165092f3266ac2 NeedsCompilation: no Package: enrichTF Version: 1.18.0 Depends: pipeFrame Imports: BSgenome, rtracklayer, motifmatchr, TFBSTools, R.utils, methods, JASPAR2018, GenomeInfoDb, GenomicRanges, IRanges, BiocGenerics, S4Vectors, utils, parallel, stats, ggpubr, heatmap3, ggplot2, clusterProfiler, rmarkdown, grDevices, magrittr Suggests: knitr, testthat, webshot License: GPL-3 MD5sum: a88296c9418e41a8e66fccc276925471 NeedsCompilation: no Package: enrichViewNet Version: 1.0.0 Depends: R (>= 4.2.0) Imports: gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, methods Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 5b2eb51ee4f57abd3b77da182e7e5d1a NeedsCompilation: no Package: ensembldb Version: 2.26.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.31.18), GenomicFeatures (>= 1.49.6), AnnotationFilter (>= 1.5.2) Imports: methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb, AnnotationDbi (>= 1.31.19), rtracklayer, S4Vectors (>= 0.23.10), Rsamtools, IRanges (>= 2.13.24), ProtGenerics, Biostrings (>= 2.47.9), curl Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), rmarkdown, AnnotationHub Enhances: RMariaDB, shiny License: LGPL MD5sum: 0ad7a33ad9592f54e39d647195aa4c91 NeedsCompilation: no Package: ensemblVEP Version: 1.44.0 Depends: methods, BiocGenerics, GenomicRanges, VariantAnnotation Imports: S4Vectors (>= 0.9.25), Biostrings, SummarizedExperiment, GenomeInfoDb, stats Suggests: RUnit License: Artistic-2.0 MD5sum: 378569d68f5d4973a7b16eb7cc2b9327 NeedsCompilation: no Package: epialleleR Version: 1.10.0 Depends: R (>= 4.1) Imports: stats, methods, utils, GenomicRanges, BiocGenerics, GenomeInfoDb, SummarizedExperiment, VariantAnnotation, data.table, Rcpp LinkingTo: Rcpp, BH, Rhtslib, zlibbioc Suggests: RUnit, knitr, rmarkdown, ggplot2, ggstance, gridExtra License: Artistic-2.0 MD5sum: cbe73c32dc61dac41266279db72e4bee NeedsCompilation: yes Package: EpiCompare Version: 1.6.7 Depends: R (>= 4.2.0) Imports: AnnotationHub, BRGenomics, ChIPseeker, data.table, genomation, GenomicRanges, IRanges, GenomeInfoDb, 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: fb532a96da67b0b190c76b6036ed3968 NeedsCompilation: no Package: epidecodeR Version: 1.10.0 Depends: R (>= 3.1.0) Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 409ed7c959818b7400944e1d20653f68 NeedsCompilation: no Package: EpiDISH Version: 2.18.0 Depends: R (>= 4.1) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix Suggests: 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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: 73fdaf9db5e5d035601282d6e5d832fd NeedsCompilation: yes Package: epiNEM Version: 1.26.0 Depends: R (>= 4.1) Imports: 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: 03702ef94f047496994ebaf19f750787 NeedsCompilation: no Package: epistack Version: 1.8.0 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: 7d06dbae71f93e2c3cb91ba3d16fa916 NeedsCompilation: no Package: epistasisGA Version: 1.4.0 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: 79635d9683f002813e51fa3c17e49b39 NeedsCompilation: yes Package: EpiTxDb Version: 1.14.1 Depends: R (>= 4.0), AnnotationDbi, Modstrings Imports: methods, utils, httr, xml2, curl, GenomicFeatures, GenomicRanges, GenomeInfoDb, 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S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub License: Artistic-2.0 MD5sum: 076ebf7f9141cb71df0867f480ff960c NeedsCompilation: no Package: epivizrData Version: 1.30.0 Depends: R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase Imports: S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0), OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats License: MIT + file LICENSE MD5sum: aa9cf42fdbb0ad293964de33fc62e27a NeedsCompilation: no Package: epivizrServer Version: 1.30.0 Depends: R (>= 3.2.3), methods Imports: httpuv (>= 1.3.0), R6 (>= 2.0.0), rjson, mime (>= 0.2) Suggests: testthat, knitr, rmarkdown, 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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: 6ea63da6e75365243df878d55d6b39f9 NeedsCompilation: yes Package: escape Version: 1.12.0 Depends: R (>= 4.1) Imports: grDevices, dplyr, ggplot2, GSEABase, GSVA, SingleCellExperiment, ggridges, msigdbr, stats, BiocParallel, Matrix, UCell, broom, reshape2, patchwork, MatrixGenerics, utils, rlang, stringr, data.table, SummarizedExperiment, methods Suggests: Seurat, SeuratObject, knitr, rmarkdown, markdown, BiocStyle, testthat, dittoSeq (>= 1.1.2) License: GPL-2 MD5sum: e3dc22e072190e21938689fc0f3ab112 NeedsCompilation: no Package: escheR Version: 1.2.0 Depends: ggplot2, R (>= 4.3) Imports: SpatialExperiment (>= 1.6.1), SingleCellExperiment, rlang, SummarizedExperiment Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, 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Artistic-2.0 MD5sum: fdf71802bbd5967b163447eda2fe37ef NeedsCompilation: no Package: GDSArray Version: 1.22.0 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: 3ae99d95017d67dd67e17f47436f0301 NeedsCompilation: no Package: gdsfmt Version: 1.38.0 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics License: LGPL-3 MD5sum: 8851c188356c12f7e99488ceb4daeca8 NeedsCompilation: yes Package: GEM Version: 1.28.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown License: Artistic-2.0 MD5sum: 2c2c8e79fda151dee0060411c9610ff4 NeedsCompilation: no Package: gemini Version: 1.16.0 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: e8c26d0e8208f56017c8c83a17582f37 NeedsCompilation: no Package: gemma.R Version: 2.0.0 Imports: magrittr, glue, memoise, jsonlite, data.table, rlang, lubridate, utils, stringr, SummarizedExperiment, Biobase, tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat, digest Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, digest License: Apache License (>= 2) MD5sum: 404ce4fa50032ebf727cfdccece32ba2 NeedsCompilation: no Package: genArise Version: 1.78.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: d81489147ccfe688c07c228b7fcfcf7d NeedsCompilation: no Package: geneAttribution Version: 1.28.0 Imports: utils, GenomicRanges, org.Hs.eg.db, BiocGenerics, GenomeInfoDb, GenomicFeatures, IRanges, rtracklayer Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 62d05af7aabb146fb41a5d91fa460dff NeedsCompilation: no Package: GeneBreak Version: 1.32.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: 32b69bf4150c25c908235217dc805ed3 NeedsCompilation: no Package: geneClassifiers Version: 1.26.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: 79b7de2354913e5a91e6026f3f815a46 NeedsCompilation: no Package: GeneExpressionSignature Version: 1.48.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: ee82254ee781e3cd6657c89d94e052b3 NeedsCompilation: no Package: genefilter Version: 1.84.0 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: 15011d1662a58967aeb3e89f1f660e40 NeedsCompilation: yes Package: genefu Version: 2.34.0 Depends: R (>= 4.1), survcomp, biomaRt, iC10, AIMS Imports: amap, impute, mclust, limma, graphics, stats, utils Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown License: Artistic-2.0 MD5sum: cfaef57b66d09a355ae7df0db21c107d NeedsCompilation: no Package: GeneGA Version: 1.52.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: 3047f864af1845ce91869fc2560733c4 NeedsCompilation: no Package: GeneGeneInteR Version: 1.28.0 Depends: R (>= 4.0) Imports: snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods License: GPL (>= 2) MD5sum: 119efde24626155c173e9b24b5f2c9e6 NeedsCompilation: yes Package: GeneMeta Version: 1.74.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: 9d9d2d3dff0ee8a497ac86b5ef8ddac7 NeedsCompilation: no Package: GeneNetworkBuilder Version: 1.44.0 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db License: GPL (>= 2) MD5sum: aedb0b143d59865acfad5ce4d635ff77 NeedsCompilation: yes Package: GeneOverlap Version: 1.38.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 0b5179a1183a82869935ca6c2c55aab3 NeedsCompilation: no Package: geneplast Version: 1.28.0 Depends: R (>= 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Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) MD5sum: 9b3e0cfd305d2db2aae5cfd4003e56a7 NeedsCompilation: no Package: geneRxCluster Version: 1.38.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 61f7d4c5cd314cf84f8648b3097f65b1 NeedsCompilation: yes Package: GeneSelectMMD Version: 2.46.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: dd6cd07bbe095fca03ce4b134c1507b8 NeedsCompilation: yes Package: GENESIS Version: 2.32.0 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 License: GPL-3 MD5sum: 909c6b6ea17b2de1716f3a5102caa0df NeedsCompilation: yes Package: GeneStructureTools Version: 1.22.0 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: 513385498b639ea6acc724bb3795de38 NeedsCompilation: no Package: geNetClassifier Version: 1.42.0 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: 7fed3e42e9ec93956b71960e271aa090 NeedsCompilation: no Package: GeneticsPed Version: 1.64.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: 7d2a79c363e79459dd3edf3b4571f313 NeedsCompilation: yes Package: GeneTonic Version: 2.6.0 Depends: R (>= 4.0.0) Imports: AnnotationDbi, backbone, bs4Dash (>= 2.0.0), circlize, colorspace, colourpicker, ComplexHeatmap, ComplexUpset, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce, ggplot2, ggrepel, ggridges, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinyAce, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tippy, tools, utils, viridis, visNetwork Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: efbbb39095cb7ff8af87ed47d058d8d8 NeedsCompilation: no Package: geneXtendeR Version: 1.28.0 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: 63ab36f83aa3d05bf932dc3c0e0c173a NeedsCompilation: yes Package: GENIE3 Version: 1.24.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle License: GPL (>= 2) MD5sum: fb7d197e0e34175eba7dd31608aa67d6 NeedsCompilation: yes Package: genoCN Version: 1.54.0 Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: ebc7fc5cb3b5c2bcd98718a7bcd95d6a NeedsCompilation: yes Package: genomation Version: 1.34.0 Depends: R (>= 3.5.0), grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 5453f50009f3f7227025431d4d10f4bb NeedsCompilation: yes Package: GenomAutomorphism Version: 1.4.0 Depends: R (>= 4.2), Imports: Biostrings, BiocGenerics, BiocParallel, GenomeInfoDb, GenomicRanges, IRanges, 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: 36ebcd90b454dc7450e875730537811b NeedsCompilation: no Package: GenomeInfoDb Version: 1.38.8 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.25.12), IRanges (>= 2.13.12) Imports: stats, stats4, utils, RCurl, GenomeInfoDbData Suggests: R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome, 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: af0949e2aa2f19dbb1eed4d8487d9928 NeedsCompilation: no Package: genomeIntervals Version: 1.58.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 1.5.8), GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: c47b9bb1293b799a7ac75fef82f45589 NeedsCompilation: no Package: genomes Version: 3.32.0 Depends: readr, curl License: GPL-3 MD5sum: 4c11ca2b7b1d4dfd1ffc178b1d9e87e2 NeedsCompilation: no Package: GenomicAlignments Version: 1.38.2 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.55.7), Rsamtools (>= 1.31.2) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 6b1bbb35176db253124a9e6786104421 NeedsCompilation: yes Package: GenomicDataCommons Version: 1.26.0 Depends: R (>= 3.4.0), magrittr 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: 6c945795f62ce3e0b470b07b892d3357 NeedsCompilation: no Package: GenomicDistributions Version: 1.10.0 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: 0b8c2d9df85f9884bb40e3fcd015c824 NeedsCompilation: no Package: GenomicFeatures Version: 1.54.4 Depends: R (>= 3.5.0), BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29), IRanges (>= 2.13.23), GenomeInfoDb (>= 1.35.8), GenomicRanges (>= 1.31.17), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>= 2.0), XVector (>= 0.19.7), Biostrings (>= 2.47.6), BiocIO, rtracklayer (>= 1.51.5), biomaRt (>= 2.58.2), Biobase (>= 2.15.1) Suggests: RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown License: Artistic-2.0 MD5sum: 9b4b6dcc5a7ad626796f3aad34539d29 NeedsCompilation: no Package: GenomicFiles Version: 1.38.0 Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), MatrixGenerics, GenomicRanges (>= 1.31.16), SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3) Imports: GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25), VariantAnnotation (>= 1.27.9), GenomeInfoDb Suggests: BiocStyle, RUnit, genefilter, deepSNV, snpStats, knitr, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens License: Artistic-2.0 MD5sum: 7a58dc35c19ed34afe95d505d15db3f4 NeedsCompilation: no Package: genomicInstability Version: 1.8.0 Depends: R (>= 4.1.0), checkmate Imports: mixtools, SummarizedExperiment Suggests: SingleCellExperiment, ExperimentHub, pROC License: file LICENSE MD5sum: 0d7c244a904ea9286d4e965cddeaf2d7 NeedsCompilation: no Package: GenomicInteractionNodes Version: 1.6.0 Depends: R (>= 4.2.0), stats Imports: AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, GenomeInfoDb, methods, IRanges, RBGL, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: file LICENSE MD5sum: bacb75bdd25ea06d5102c1ef2648c588 NeedsCompilation: no Package: GenomicInteractions Version: 1.36.0 Depends: R (>= 3.5), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: f4bccdd21d639ba8b9907ced202c0082 NeedsCompilation: no Package: GenomicOZone Version: 1.16.0 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, GenomeInfoDb, Rdpack Suggests: readxl, GEOquery, knitr, rmarkdown License: LGPL (>= 3) MD5sum: c975a4b1c29d471efe90a5bba68247bb NeedsCompilation: no Package: GenomicPlot Version: 1.0.8 Depends: R (>= 4.3.0), GenomicRanges (>= 1.46.1) Imports: methods, Rsamtools, parallel, tidyr, rtracklayer (>= 1.54.0), plyranges (>= 1.14.0), cowplot (>= 1.1.1), VennDiagram, ggplotify, GenomeInfoDb, IRanges, ComplexHeatmap, RCAS (>= 1.20.0), scales (>= 1.2.0), GenomicAlignments (>= 1.30.0), edgeR, circlize, viridis, ggsignif (>= 0.6.3), ggsci (>= 2.9), genomation (>= 1.26.0), ggpubr, grDevices, graphics, stats, utils, GenomicFeatures, ggplot2 (>= 3.3.5), BiocGenerics, dplyr, grid Suggests: knitr, rmarkdown, R.utils, Biobase, BiocStyle, testthat, AnnotationDbi License: GPL-2 MD5sum: 8c4f020e1727a2eba0927bd5e7eb7268 NeedsCompilation: no Package: GenomicRanges Version: 1.54.1 Depends: R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.31.2), GenomeInfoDb (>= 1.15.2) Imports: utils, stats, XVector (>= 0.29.2) LinkingTo: S4Vectors, IRanges Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 19fe37133cae70c1c3a1a164e6c8eaed NeedsCompilation: yes Package: GenomicScores Version: 2.14.3 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, GenomeInfoDb, 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.v3.1.2.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: eabfc2c53e94ac24ef186413e38872fc NeedsCompilation: no Package: GenomicSuperSignature Version: 1.10.0 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: ecb55ebec91620ff435715563d8ba304 NeedsCompilation: no Package: GenomicTuples Version: 1.36.0 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), GenomeInfoDb (>= 1.15.2), S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, covr License: Artistic-2.0 MD5sum: 69e0c80982690604f35d9878f6640f37 NeedsCompilation: yes Package: GenProSeq Version: 1.6.0 Depends: keras, mclust, R (>= 4.2) Imports: tensorflow, word2vec, DeepPINCS, 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graphics, stats, testthat, GeomxTools, NanoStringNCTools LinkingTo: Rcpp, RcppArmadillo, roptim Suggests: knitr, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: f719fddf3486b6aad1f36ca439b55114 NeedsCompilation: yes Package: GEOexplorer Version: 1.8.0 Depends: shiny, limma, Biobase, plotly, enrichR, R (>= 4.1.0) Imports: DT, XML, httr, sva, xfun, edgeR, htmltools, factoextra, heatmaply, pheatmap, scales, shinyHeatmaply, shinybusy, ggplot2, stringr, umap, GEOquery, impute, grDevices, stats, graphics, markdown, knitr, utils, xml2, R.utils, readxl, shinycssloaders, car Suggests: rmarkdown, usethis, testthat (>= 3.0.0) License: GPL-3 MD5sum: 213a1b499ce1d0640b267c8fb41e3204 NeedsCompilation: no Package: GEOfastq Version: 1.10.0 Imports: xml2, rvest, stringr, RCurl, doParallel, foreach, plyr Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 339bd0c2f6a3f505457fc436997965a6 NeedsCompilation: no Package: GEOmetadb Version: 1.64.0 Depends: 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License: GPL (>= 2) MD5sum: 835a74433a1f0235676bf2d1012096af NeedsCompilation: no Package: GeoTcgaData Version: 2.2.0 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: 653a353d37b0bcfbd892dfe12d420100 NeedsCompilation: no Package: gep2pep Version: 1.22.0 Imports: repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators Suggests: WriteXLS, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 0a8f1b44003eba297c44f8115f870df0 NeedsCompilation: no Package: gespeR Version: 1.34.0 Depends: methods, graphics, ggplot2, R(>= 2.10) Imports: Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel, 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BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 119c639126af675cbf7b9daf47122dc4 NeedsCompilation: no Package: ggbio Version: 1.50.0 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.29.14), SummarizedExperiment, Biostrings, Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer (>= 1.25.16), GenomicFeatures (>= 1.29.11), OrganismDbi, GGally, ensembldb (>= 1.99.13), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: de7ec73480f41c35fca2a8a758fbc7d0 NeedsCompilation: no Package: ggcyto Version: 1.30.2 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: 5864b5d39532851c3064e9561a88e863 NeedsCompilation: no Package: ggkegg Version: 1.0.13 Depends: R (>= 4.3.0), ggplot2, ggraph, XML, igraph, tidygraph Imports: BiocFileCache, GetoptLong, data.table, dplyr, magick, patchwork, shadowtext, stringr, tibble, org.Hs.eg.db, methods, utils, stats, AnnotationDbi, grDevices, gtable Suggests: knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 02848c5ed45b1480b71e69cc13607a69 NeedsCompilation: no Package: ggmanh Version: 1.6.0 Depends: methods, ggplot2 Imports: gdsfmt, ggrepel, grDevices, RColorBrewer, rlang, scales, SeqArray (>= 1.32.0), stats Suggests: 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scattermore, stats, Seurat, SingleCellExperiment, SummarizedExperiment, tidydr, tidyr, tibble, utils, yulab.utils LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph, knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater, scuttle, shadowtext, sf, SeuratObject, SpatialExperiment, STexampleData, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 4c0a1656e9943cadf436244c65b18242 NeedsCompilation: yes Package: ggspavis Version: 1.8.1 Depends: ggplot2 Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, methods, stats Suggests: BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 8f1c36e3556ccfd88a1750a8b98e139a NeedsCompilation: no Package: ggtree Version: 3.10.1 Depends: R (>= 3.5.0) Imports: ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.0.9), yulab.utils, tidyr, tidytree 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Rcpp Suggests: Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat License: GPL (>= 2) MD5sum: d1b00ef5711c3012a11f52cc7312d60b NeedsCompilation: yes Package: GOpro Version: 1.28.0 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: c92dbcab08a7cdac3ee8ee6c28c6dc78 NeedsCompilation: yes Package: goProfiles Version: 1.64.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: ff2a664ff7284cf03e9caf932ad86d63 NeedsCompilation: no Package: GOSemSim Version: 2.28.1 Depends: R (>= 3.5.0) Imports: AnnotationDbi, GO.db, methods, rlang, stats, utils, yulab.utils LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, readr, rmarkdown, org.Hs.eg.db, prettydoc, testthat, tidyr, tidyselect, ROCR License: Artistic-2.0 MD5sum: 89d833af368b8fb6592d7acd623e0a45 NeedsCompilation: yes Package: goseq Version: 1.54.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2) Imports: mgcv, graphics, stats, utils, AnnotationDbi, GO.db,BiocGenerics Suggests: edgeR, org.Hs.eg.db, rtracklayer License: LGPL (>= 2) MD5sum: 4c39d7fbb51594a70dd3e54b1bc10375 NeedsCompilation: no Package: GOSim Version: 1.40.0 Depends: GO.db, annotate Imports: org.Hs.eg.db, AnnotationDbi, topGO, cluster, flexmix, RBGL, graph, Matrix, corpcor, Rcpp LinkingTo: Rcpp Enhances: igraph License: GPL (>= 2) MD5sum: 2fb07a8f5ac4b386b5063f52486bb82b NeedsCompilation: yes Package: goSorensen Version: 1.4.0 Depends: R (>= 4.3.0) Imports: GO.db, org.Hs.eg.db, goProfiles, stats, clusterProfiler, parallel, stringr Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 8fa5cc982341291dd857ab340abe4c73 NeedsCompilation: no Package: goSTAG Version: 1.26.0 Depends: R (>= 3.4) Imports: AnnotationDbi, 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methods Imports: AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats, utils, graphics, rlang, purrr Suggests: checkmate, a4Preproc, ALL, BiocStyle, 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: 532e304cdb96a828c4b764bfd36cce85 NeedsCompilation: no Package: GraphPAC Version: 1.44.0 Depends: R(>= 2.15),iPAC, igraph, TSP, RMallow Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 68794a35ae528c5cde68e7915611ace8 NeedsCompilation: no Package: GRENITS Version: 1.54.0 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: fd00e191f8c57c6ef54146263d21a089 NeedsCompilation: yes Package: GreyListChIP Version: 1.34.0 Depends: R (>= 4.0), methods, GenomicRanges Imports: GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, RUnit, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 42fa9dbbc56cc2c4fdf511ce67ee234e NeedsCompilation: no Package: GRmetrics Version: 1.28.0 Depends: R (>= 4.0), SummarizedExperiment Imports: drc, plotly, ggplot2, S4Vectors, stats Suggests: knitr, rmarkdown, BiocStyle, tinytex License: GPL-3 MD5sum: 16b27cb79eafe9dbdbb84f0626c5f8da NeedsCompilation: no Package: groHMM Version: 1.36.0 Depends: R (>= 3.0.2), MASS, parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), rtracklayer (>= 1.39.7) Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 0b1077948ddc9895c57188ca2560bc10 NeedsCompilation: yes Package: GSALightning Version: 1.30.0 Depends: R (>= 3.3.0) Imports: Matrix, data.table, stats Suggests: knitr, rmarkdown 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no Package: GSEAmining Version: 1.12.0 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: 703f12fed97e95761b2cd41894da0645 NeedsCompilation: no Package: gsean Version: 1.22.0 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi, knitr, plotly, WGCNA, rmarkdown License: Artistic-2.0 MD5sum: 501dfe30896b53197345abe9d1600247 NeedsCompilation: yes Package: GSgalgoR Version: 1.12.0 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: 09d5b90490f44ee7384c71762228244d NeedsCompilation: no Package: GSReg 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License: GPL (>= 2) MD5sum: afc67121775cc0fd6ea9d20d0df2a7b8 NeedsCompilation: yes Package: gtrellis Version: 1.34.0 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: 795b74d96310e3cd9a5771bd8695cf64 NeedsCompilation: no Package: GUIDEseq Version: 1.32.0 Depends: R (>= 3.5.0), GenomicRanges, BiocGenerics Imports: Biostrings, 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 (>= 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stats4 LinkingTo: S4Vectors Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 87618d2e5ee94d7ab81d2e1c4d847120 NeedsCompilation: yes Package: ISAnalytics Version: 1.12.0 Depends: R (>= 4.3) Imports: utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs, lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools, grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib, DT Suggests: testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown, roxygen2, vegan, withr, extraDistr, ggalluvial, scales, gridExtra, R.utils, RefManageR, flexdashboard, circlize, plotly, gtools, eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr, future, doFuture, foreach, psych, data.table, Rcapture License: CC BY 4.0 MD5sum: d1962980b18dd3ff8fdcc1bb0c855eaf NeedsCompilation: no Package: iSEE Version: 2.14.0 Depends: SummarizedExperiment, SingleCellExperiment 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SingleMoleculeFootprintingData, spatialDmelxsim, STexampleData, TabulaMurisData, TabulaMurisSenisData, TENxVisiumData, tissueTreg, VectraPolarisData, xcoredata License: Artistic-2.0 MD5sum: 6ebb32da66242f608b83522fca1d9a62 NeedsCompilation: no Package: iSEEindex Version: 1.0.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: BiocFileCache, DT, iSEE, methods, paws.storage, rintrojs, shiny, shinydashboard, shinyjs, stringr, urltools, utils Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), yaml License: Artistic-2.0 MD5sum: 98a9141431a3206fd242b5b0b4056c41 NeedsCompilation: no Package: iSEEpathways Version: 1.0.0 Depends: iSEE Imports: ggplot2, methods, S4Vectors, shiny, shinyWidgets, stats, SummarizedExperiment Suggests: airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr, org.Hs.eg.db, RefManageR, rmarkdown, scater, scuttle, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 52b84dcbd5e5ab0a6bbdc27120d7e86a 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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: 7bdda59fc802fc09d10ca9a4916cfe94 NeedsCompilation: no Package: MethTargetedNGS Version: 1.34.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings License: Artistic-2.0 MD5sum: 0bce9edc9682a9ca23653409301d7225 NeedsCompilation: no Package: MethylAid Version: 1.36.0 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: 8e5139726d6384208be410a794ba6388 NeedsCompilation: no 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miaViz, colourvalues, philentropy License: Artistic-2.0 | file LICENSE MD5sum: 0867c6e7b7cae5acbfd6154b8af06d41 NeedsCompilation: no Package: miaViz Version: 1.10.0 Depends: R (>= 4.0), SummarizedExperiment, TreeSummarizedExperiment, mia (>= 0.99), ggplot2, ggraph (>= 2.0) Imports: methods, stats, S4Vectors, BiocGenerics, BiocParallel, DelayedArray, scater, ggtree, ggnewscale, viridis, tibble, tidytree, tidygraph, rlang, purrr, tidyr, dplyr, ape, DirichletMultinomial, ggrepel, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, microbiomeDataSets, bluster License: Artistic-2.0 | file LICENSE MD5sum: 8388770fbcfce7b95040dc84f02938bc NeedsCompilation: no Package: MiChip Version: 1.56.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: 28daafdf6588314a9fad7a75b1671c10 NeedsCompilation: no Package: microbiome Version: 1.24.0 Depends: R (>= 3.6.0), phyloseq, ggplot2 Imports: Biostrings, compositions, dplyr, reshape2, Rtsne, 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MD5sum: c1e966728a968697ad53fd6405c156c5 NeedsCompilation: no Package: microbiomeMarker Version: 1.8.0 Depends: R (>= 4.1.0) Imports: dplyr, phyloseq, magrittr, purrr, MASS, utils, ggplot2, tibble, rlang, stats, coin, ggtree, tidytree, methods, IRanges, tidyr, patchwork, ggsignif, metagenomeSeq, DESeq2, edgeR, BiocGenerics, Biostrings, yaml, biomformat, S4Vectors, Biobase, ComplexHeatmap, ANCOMBC, caret, limma, ALDEx2, multtest, plotROC, vegan, pROC, BiocParallel Suggests: testthat, covr, glmnet, Matrix, kernlab, e1071, ranger, knitr, rmarkdown, BiocStyle, withr License: GPL-3 MD5sum: facf2f8071da6049b688fe3d16efb0e2 NeedsCompilation: no Package: MicrobiomeProfiler Version: 1.8.0 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 Suggests: rmarkdown, knitr, testthat (>= 3.0.0), prettydoc License: GPL-2 MD5sum: 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(>= 1.21), magrittr (>= 1.5), methods, stringi (>= 1.2.4), rlang (>= 0.3.1), S4Vectors (>= 0.20.1), stats, SummarizedExperiment (>= 1.12.0), tibble (>= 2.0.1), utils, qdapTools (>= 1.3.3) Suggests: broom.mixed (>= 0.2.4), cowplot (>= 1.0.0), devtools (>= 2.0.1), ggplot2 (>= 3.1.0), ggpubr (>= 0.2.5), rmarkdown, seqinr (>= 3.4-5), survival (>= 2.43-3), testthat (>= 2.0.1), tidyr (>= 1.1.2) License: MIT + file LICENCE MD5sum: 7d77f1bda1bff8d67de91e02cb985519 NeedsCompilation: no Package: miloR Version: 1.10.0 Depends: R (>= 4.0.0), edgeR Imports: BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>= 1.3-0), S4Vectors, stats, stringr, methods, igraph, irlba, cowplot, BiocParallel, BiocSingular, limma, ggplot2, tibble, matrixStats, ggraph, gtools, SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices Suggests: testthat, MASS, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, curl, graphics License: GPL-3 + file LICENSE MD5sum: 9ab9a4a2fe26786cd8fef69354bfa08f NeedsCompilation: no Package: mimager Version: 1.26.0 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: 2a9eaf36345d24dc2d44a65c1f8640a0 NeedsCompilation: no Package: mina Version: 1.10.0 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: d6578736bef864eef8f89958a849137b NeedsCompilation: yes Package: MineICA Version: 1.42.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, 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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: 3c1998eee0aabbfab3c3796c82339a18 NeedsCompilation: no Package: MinimumDistance Version: 1.46.0 Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1) Imports: methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: ab96e788a4152b80b7a685f3fc8fcd9c NeedsCompilation: no Package: MiPP Version: 1.74.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: ce412e2a72891fcc7969faee078b2be3 NeedsCompilation: no Package: miQC Version: 1.10.0 Depends: R (>= 3.5.0) Imports: SingleCellExperiment, flexmix, ggplot2, splines Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: e1246c2b5dcb83059d6887b35db543a0 NeedsCompilation: no Package: MIRA Version: 1.24.0 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: 670cb42f275d260b28e0e2d140cacda2 NeedsCompilation: no Package: MiRaGE Version: 1.44.0 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: c86c12c042052eb4d558bdff55e8c47a NeedsCompilation: no Package: miRBaseConverter Version: 1.26.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown License: GPL (>= 2) MD5sum: c823ce909e1ae3a584fb5790fecf6b54 NeedsCompilation: no Package: miRcomp Version: 1.32.0 Depends: R (>= 3.2), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: 06b97d8829ca13b60dd4869a48b684ab NeedsCompilation: no Package: mirIntegrator Version: 1.32.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: 9ec5789f159dfc3880ce8369af20c27a NeedsCompilation: no Package: miRLAB Version: 1.32.0 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: 3347a99a17fc2caade03a35471a79ad0 NeedsCompilation: no Package: miRmine Version: 1.24.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, DESeq2 License: GPL (>= 3) MD5sum: a49fb63deed3bc3361263701c8f1ae52 NeedsCompilation: no Package: miRNAmeConverter Version: 1.30.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: cfc6563f669ecbc03292cccba919fe05 NeedsCompilation: no Package: miRNApath Version: 1.62.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: 94aad8a3b57b070cb5c559d9d1f14726 NeedsCompilation: no Package: miRNAtap 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License: GPL-3 MD5sum: 145c70b6246eb437d83d3257b5eda98a NeedsCompilation: yes Package: mirTarRnaSeq Version: 1.10.0 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: b8cac8c363bddb02eb97e6009bb91f4e NeedsCompilation: no Package: missMethyl Version: 1.36.0 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub License: GPL-2 MD5sum: 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rmarkdown, ggplot2, gplots, beeswarm, echarts4r, kableExtra Suggests: stringi, testthat (>= 2.1.0) License: CC BY-SA 4.0 + file LICENSE MD5sum: c21044d7d878482677fcb758acf0a650 NeedsCompilation: no Package: mitoClone2 Version: 1.8.1 Depends: R (>= 4.1.0) Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2 LinkingTo: Rhtslib (>= 1.13.1) Suggests: knitr, rmarkdown, Biostrings, testthat License: GPL-3 MD5sum: 22c58ba6ed0a51f10714551935477355 NeedsCompilation: yes Package: mixOmics Version: 6.26.0 Depends: R (>= 3.5.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, ggrepel, BiocParallel, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rgl License: GPL (>= 2) MD5sum: d735d1aec6a3576238256244e87031ff NeedsCompilation: no Package: MLInterfaces Version: 1.82.0 Depends: R (>= 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cowplot, ExperimentHub, iCOBRA, knitr, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, testthat, UpSetR License: GPL-3 MD5sum: ee69286717f8d129ce59fb554c1c0994 NeedsCompilation: no Package: muscle Version: 3.44.0 Depends: Biostrings License: Unlimited MD5sum: 159745260e624c7aeb3d2e0deeef99ab NeedsCompilation: yes Package: musicatk Version: 1.12.0 Depends: R (>= 4.0.0), 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, deconstructSigs, decompTumor2Sig, topicmodels, ggrepel, plotly, utils, factoextra, cluster, ComplexHeatmap, philentropy, maftools, shiny, stringi, tidyverse, ggpubr Suggests: TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard, shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr, shinyWidgets, cowplot, withr License: LGPL-3 MD5sum: 50869915aff9dd79823e05b4ae163bc6 NeedsCompilation: no Package: MutationalPatterns Version: 3.12.0 Depends: R (>= 4.2.0), GenomicRanges (>= 1.24.0), NMF (>= 0.20.6) Imports: stats, S4Vectors, BiocGenerics (>= 0.18.0), BSgenome (>= 1.40.0), VariantAnnotation (>= 1.18.1), dplyr (>= 0.8.3), tibble(>= 2.1.3), purrr (>= 0.3.2), tidyr (>= 1.0.0), stringr (>= 1.4.0), magrittr (>= 1.5), ggplot2 (>= 2.1.0), pracma (>= 1.8.8), IRanges (>= 2.6.0), GenomeInfoDb (>= 1.12.0), Biostrings (>= 2.40.0), ggdendro (>= 0.1-20), cowplot (>= 0.9.2), ggalluvial (>= 0.12.2), RColorBrewer, methods Suggests: BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 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NeedsCompilation: no Package: nearBynding Version: 1.12.0 Depends: R (>= 4.0) Imports: R.utils, matrixStats, plyranges, transport, Rsamtools, S4Vectors, grDevices, graphics, rtracklayer, dplyr, GenomeInfoDb, methods, GenomicRanges, utils, stats, magrittr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, ggplot2, gplots, BiocGenerics, rlang Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 2bcc4459fa78c6327ee2708f06da54db NeedsCompilation: no Package: Nebulosa Version: 1.12.1 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: daedaeb79ec239323487565bce3f7ca2 NeedsCompilation: no Package: nempi Version: 1.10.0 Depends: R (>= 4.1), mnem Imports: e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats, epiNEM 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OS_type: unix MD5sum: d21f645a3fe85c35ff9b9127bce1fbca NeedsCompilation: yes Package: netDx Version: 1.14.0 Depends: R (>= 3.6) Imports: ROCR,pracma,ggplot2,glmnet,igraph,reshape2, parallel,stats,utils,MultiAssayExperiment,graphics,grDevices, methods,BiocFileCache,GenomicRanges, bigmemory,doParallel,foreach, combinat,rappdirs,GenomeInfoDb,S4Vectors, IRanges,RColorBrewer,Rtsne,httr,plotrix Suggests: curatedTCGAData, rmarkdown, testthat, knitr, BiocStyle, RCy3, clusterExperiment, netSmooth, scater License: MIT + file LICENSE MD5sum: 6fdc48ce518c74e0261acee84948ce26 NeedsCompilation: no Package: nethet Version: 1.34.0 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: 35bc35cf08904b721563aa54e486cc95 NeedsCompilation: yes Package: netOmics Version: 1.8.0 Depends: R (>= 4.1) Imports: dplyr, ggplot2, igraph, magrittr, minet, purrr, tibble, tidyr, AnnotationDbi, GO.db, RandomWalkRestartMH, gprofiler2, methods, stats Suggests: mixOmics, timeOmics, tidyverse, BiocStyle, testthat, covr, rmarkdown, knitr License: GPL-3 MD5sum: 8ab3cf60546da2beea2e9c3630340c12 NeedsCompilation: no Package: NetPathMiner Version: 1.38.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 91cc0601961f682fcf1a2bed61eb6438 NeedsCompilation: yes Package: netprioR Version: 1.28.0 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: 7e4023edbe230057c85ae74d90f59fd1 NeedsCompilation: no Package: netresponse Version: 1.62.0 Depends: R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods, minet, mclust, reshape2 Imports: ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer Suggests: 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SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, SharedObject, stats Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr License: GPL-3 MD5sum: ed222f643c357c84a7eb8534aa7b3a91 NeedsCompilation: no Package: ngsReports Version: 2.4.0 Depends: R (>= 4.2.0), BiocGenerics, ggplot2 (>= 3.4.0), patchwork (>= 1.1.1), tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 1.1.0), DT, forcats, ggdendro, grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate, methods, pander, plotly (>= 4.9.4), readr, reshape2, rlang, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo Suggests: BiocStyle, Cairo, knitr, testthat, truncnorm License: file LICENSE MD5sum: c2d8c1f7a1869275420e05125fb1b420 NeedsCompilation: no Package: nipalsMCIA Version: 1.0.0 Depends: R (>= 4.3.0) Imports: ComplexHeatmap, dplyr, fgsea, ggplot2 (>= 3.0.0), graphics, grid, methods, MultiAssayExperiment, SummarizedExperiment, pracma, rlang, 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org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics, org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, methods,markdown License: MIT + file LICENSE MD5sum: 8e3a1a53f9c68bc68ab881bd49e28ecb NeedsCompilation: no Package: normalize450K Version: 1.30.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: f5ea0fdcbdd43103b5ee941c96fe43fa NeedsCompilation: no Package: NormalyzerDE Version: 1.20.0 Depends: R (>= 4.1.0) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, Biobase, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 MD5sum: e55d57346b59dbd8b317a263e4b413b0 NeedsCompilation: no Package: NormqPCR Version: 1.48.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: 379e7395ad03c0d57dffa7331748e253 NeedsCompilation: no Package: normr Version: 1.28.0 Depends: R (>= 3.3.0) Imports: methods, stats, utils, grDevices, parallel, GenomeInfoDb, GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2), bamsignals (>= 1.4), rtracklayer (>= 1.32) LinkingTo: Rcpp Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown Enhances: BiocParallel License: GPL-2 MD5sum: 06d294d5935656789cc44341eca46620 NeedsCompilation: yes Package: NPARC Version: 1.14.0 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: b49f408fb60e58d3c62cfd2d5d4809cb NeedsCompilation: no Package: npGSEA Version: 1.38.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: 82d2208fe4478a1d5423940daa7128be NeedsCompilation: no Package: NTW Version: 1.52.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: 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InteractionSet, ggplot2, grDevices, plyranges, data.table, progress, ggridges Suggests: testthat, knitr, rmarkdown, ks, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, nullrangesData, excluderanges, ensembldb, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38, patchwork, plotgardener, dplyr, purrr, magrittr, tidyr, cobalt, DiagrammeR, tidySummarizedExperiment License: GPL-3 MD5sum: 6ee32a46c332cfeefa89ebc2b32608bf NeedsCompilation: no Package: NuPoP Version: 2.10.0 Depends: R (>= 4.0) Imports: graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 65372d828848fa588584e42324762643 NeedsCompilation: yes Package: occugene Version: 1.62.0 Depends: R (>= 2.0.0) License: GPL (>= 2) MD5sum: 264da1422714d735ac474b414e57a2a9 NeedsCompilation: no Package: OCplus Version: 1.76.0 Depends: R (>= 2.1.0) Imports: multtest (>= 1.7.3), graphics, grDevices, stats, interp License: LGPL MD5sum: 8093ec3c635bc4ba57d27f42c6c85c48 NeedsCompilation: no Package: octad Version: 1.4.0 Depends: R (>= 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oligo Version: 1.66.0 Depends: R (>= 3.2.0), BiocGenerics (>= 0.13.11), oligoClasses (>= 1.29.6), Biobase (>= 2.27.3), Biostrings (>= 2.35.12) Imports: affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, zlibbioc LinkingTo: preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl Enhances: doMC, doMPI License: LGPL (>= 2) MD5sum: 3ba99dedbe0ebca2fcaa81a400777469 NeedsCompilation: yes Package: oligoClasses Version: 1.64.0 Depends: R (>= 2.14) Imports: BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods, graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>= 1.23.2), foreach, BiocManager, 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Rcpp (>= 1.0.7), diceR (>= 0.6.0), ggplot2 (>= 3.3.5), reshape (>= 0.8.8), genieclust (>= 1.1.3), clValid (>= 0.7), glmnet (>= 4.1.3), dplyr(>= 1.0.7), stats (>= 4.1.2), clValid(>= 0.7) Suggests: rmarkdown, knitr, testthat License: GPL-3 MD5sum: d214fdb20c51cbce86bf1d34c59cb84b NeedsCompilation: no Package: OmaDB Version: 2.18.0 Depends: R (>= 3.5), httr (>= 1.2.1), plyr(>= 1.8.4) Imports: utils, ape, Biostrings, GenomicRanges, IRanges, methods, topGO, jsonlite Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 4bfced261f7429c6e881e05dc45ec0d3 NeedsCompilation: no Package: omicade4 Version: 1.42.0 Depends: R (>= 3.0.0), ade4 Imports: made4, Biobase Suggests: BiocStyle License: GPL-2 MD5sum: ed6de2f603d54a9ad262ff62784818a2 NeedsCompilation: no Package: OmicCircos Version: 1.40.0 Depends: R (>= 2.14.0), methods,GenomicRanges License: GPL-2 MD5sum: 7d77b9a00853d3e6fec869012ce33daf NeedsCompilation: no Package: omicplotR Version: 1.22.0 Depends: R (>= 3.6), ALDEx2 (>= 1.18.0) Imports: compositions, DT, grDevices, knitr, jsonlite, matrixStats, rmarkdown, shiny, stats, vegan, zCompositions License: MIT + file LICENSE MD5sum: 1ab1c2e82c98f8086b4dba4f65a613e7 NeedsCompilation: no Package: omicRexposome Version: 1.24.3 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: 5504120962d682e799611cb01e10c603 NeedsCompilation: no Package: OMICsPCA Version: 1.20.0 Depends: R (>= 3.5.0), OMICsPCAdata Imports: HelloRanges, fpc, stats, MultiAssayExperiment, pdftools, methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown, kableExtra, rtracklayer, IRanges, GenomeInfoDb, reshape2, ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR, PerformanceAnalytics, tidyr, data.table, cluster, magick Suggests: 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License: GPL-2 MD5sum: 7d650ff242a133610199a574a29abfde NeedsCompilation: no Package: Omixer Version: 1.12.0 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: 6360569495c662f2c34c86dbd7387f4a NeedsCompilation: no Package: OmnipathR Version: 3.10.1 Depends: R(>= 4.0) Imports: checkmate, crayon, curl, digest, dplyr(>= 1.1.0), httr, igraph, jsonlite, later, logger, lubridate, magrittr, progress, purrr, rappdirs, readr(>= 2.0.0), readxl, rlang, rmarkdown, rvest, stats, stringi, stringr, tibble, tidyr, tidyselect, tools, utils, withr, xml2, yaml Suggests: BiocStyle, biomaRt, bookdown, dnet, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, sigmajs, smoof, supraHex, testthat License: MIT + file LICENSE MD5sum: c51296b40e8d580f14dc3ff6839495f6 NeedsCompilation: no Package: ompBAM Version: 1.6.0 Imports: utils, Rcpp, zlibbioc Suggests: RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 9e9d31ddcad0b4bb4acb30ad970a0cd5 NeedsCompilation: no Package: oncomix Version: 1.24.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: dd6381604152d7cb96f7c592e8f82ab7 NeedsCompilation: no Package: oncoscanR Version: 1.4.0 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: 48aee6850c94c299417e75cf74418b01 NeedsCompilation: no Package: OncoScore Version: 1.30.0 Depends: R (>= 4.1.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: 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Organism.dplyr Version: 1.30.1 Depends: R (>= 3.4), dplyr (>= 0.7.0), AnnotationFilter (>= 1.1.3) Imports: RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges, GenomicFeatures, AnnotationDbi, rlang, methods, tools, utils, BiocFileCache, DBI, dbplyr, tibble Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, magick, BiocStyle, ggplot2 License: Artistic-2.0 MD5sum: b16c25c3ee5abafa1007a9c7bd731801 NeedsCompilation: no Package: OrganismDbi Version: 1.44.0 Depends: R (>= 2.14.0), methods, BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.39.4) Imports: Biobase, BiocManager, GenomicRanges (>= 1.31.13), graph, IRanges, RBGL, DBI, S4Vectors (>= 0.9.25), stats Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr License: Artistic-2.0 MD5sum: 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splines, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr License: MIT + file LICENSE MD5sum: 92609d3ce486cdf55004d26887a9494d NeedsCompilation: yes Package: OutSplice Version: 1.2.0 Depends: R(>= 4.3) Imports: AnnotationDbi (>= 1.60.0), GenomicRanges (>= 1.49.0), GenomicFeatures (>= 1.50.2), IRanges (>= 2.32.0), org.Hs.eg.db (>= 3.16.0), Repitools (>= 1.44.0), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.16.0), S4Vectors (>= 0.36.0) Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 7a55735983a79681a2bbcd567c9f0c53 NeedsCompilation: no Package: OVESEG Version: 1.18.0 Depends: R (>= 3.6) Imports: stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales License: GPL-2 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NeedsCompilation: no Package: pathwayPCA Version: 1.18.0 Depends: R (>= 3.1) Imports: lars, methods, parallel, stats, survival, utils Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse License: GPL-3 MD5sum: 100ae90b68c015f8e344da1d3a2a4863 NeedsCompilation: no Package: paxtoolsr Version: 1.36.0 Depends: R (>= 3.2), rJava (>= 0.9-8), methods, XML Imports: utils, httr, igraph, plyr, rjson, R.utils, jsonlite, readr, rappdirs Suggests: testthat, knitr, BiocStyle, formatR, rmarkdown, RColorBrewer, foreach, doSNOW, parallel, org.Hs.eg.db, clusterProfiler License: LGPL-3 MD5sum: 2ed785fb7d7859ff53d143baba8ff73d NeedsCompilation: no Package: pcaExplorer Version: 2.28.0 Imports: DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, genefilter, ggplot2 (>= 2.0.0), heatmaply, plotly, scales, NMF, plyr, topGO, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, ggrepel, DT, shinyAce, threejs, biomaRt, pheatmap, knitr, rmarkdown, base64enc, tidyr, grDevices, methods Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, htmltools License: MIT + file LICENSE MD5sum: 622f43cef60e783c51d59ed8624019d8 NeedsCompilation: no Package: pcaMethods Version: 1.94.0 Depends: Biobase, methods Imports: BiocGenerics, Rcpp (>= 0.11.3), MASS LinkingTo: Rcpp Suggests: matrixStats, lattice, ggplot2 License: GPL (>= 3) MD5sum: a989ad925a9852f55eb5e4d16d1529d0 NeedsCompilation: yes Package: PCAN Version: 1.30.0 Depends: R (>= 3.3), BiocParallel Imports: grDevices, stats Suggests: BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb License: CC BY-NC-ND 4.0 MD5sum: 94596d43854d98aee2e6da198147772b NeedsCompilation: no Package: PCAtools Version: 2.14.0 Depends: ggplot2, ggrepel Imports: lattice, grDevices, cowplot, methods, reshape2, stats, Matrix, DelayedMatrixStats, DelayedArray, BiocSingular, BiocParallel, Rcpp, dqrng LinkingTo: Rcpp, beachmat, BH, dqrng Suggests: testthat, scran, BiocGenerics, knitr, Biobase, GEOquery, hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2, airway, org.Hs.eg.db, magrittr, rmarkdown License: GPL-3 MD5sum: 316c693617402890169745a37dfaead6 NeedsCompilation: yes Package: pcxn Version: 2.24.0 Depends: R (>= 3.4), pcxnData Imports: methods, grDevices, utils, pheatmap Suggests: igraph, annotate, org.Hs.eg.db License: MIT + file LICENSE MD5sum: bc66fe53111b80e8978344ddc59eff6f NeedsCompilation: no Package: PDATK Version: 1.10.0 Depends: R (>= 4.1), SummarizedExperiment Imports: data.table, MultiAssayExperiment, ConsensusClusterPlus, igraph, ggplotify, matrixStats, RColorBrewer, clusterRepro, CoreGx, caret, survminer, methods, S4Vectors, BiocGenerics, survival, stats, plyr, dplyr, MatrixGenerics, BiocParallel, rlang, piano, scales, survcomp, genefu, ggplot2, switchBox, reportROC, pROC, verification, utils Suggests: testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr, HDF5Array License: MIT + file LICENSE MD5sum: 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NeedsCompilation: no Package: pgca Version: 1.26.0 Imports: utils, stats Suggests: knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: 43c58c5b347ebf060a9e6afdc8aa8e93 NeedsCompilation: no Package: phantasus Version: 1.22.2 Depends: R (>= 3.5) Imports: ggplot2, protolite, Biobase, GEOquery, Rook, htmltools, httpuv, jsonlite, limma, edgeR, opencpu, assertthat, methods, httr, rhdf5, utils, parallel, stringr, fgsea (>= 1.9.4), svglite, gtable, stats, Matrix, pheatmap, scales, ccaPP, grid, grDevices, AnnotationDbi, DESeq2, data.table, curl Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 84c6e2dce18e76a3268130cdd236ba59 NeedsCompilation: no Package: phantasusLite Version: 1.0.0 Depends: R (>= 4.3) Imports: data.table, rhdf5client(>= 1.21.5), httr, stringr, stats, utils, Biobase, methods Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5, GEOquery License: MIT + file LICENSE MD5sum: 5fe0e101ac53a89dd49e077d5fb4c07d NeedsCompilation: no Package: PharmacoGx Version: 3.6.0 Depends: R (>= 3.6), CoreGx Imports: BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, magicaxis, RColorBrewer, 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: a786bf3c0ace641195cfb3b00823cda3 NeedsCompilation: yes Package: phemd Version: 1.18.0 Depends: R (>= 4.0), monocle, Seurat Imports: SingleCellExperiment, RColorBrewer, igraph, transport, pracma, cluster, Rtsne, destiny, RANN, ggplot2, maptree, pheatmap, scatterplot3d, VGAM, methods, grDevices, graphics, stats, utils, cowplot, S4Vectors, BiocGenerics, SummarizedExperiment, Biobase, phateR, reticulate Suggests: knitr, BiocStyle License: GPL-2 MD5sum: 8cefd4ddfea1dd2deb007acb6cebfb7a NeedsCompilation: no Package: PhenoGeneRanker Version: 1.10.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 International License MD5sum: a6530ed180fae6b4250bc56d3de24e19 NeedsCompilation: no Package: phenomis Version: 1.4.0 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: 6fc3be4aed9fead1f2038fb3d2837854 NeedsCompilation: no Package: phenopath Version: 1.26.0 Imports: Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr, tibble, ggplot2, tidyr LinkingTo: Rcpp Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment License: Apache License (== 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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: 49f34b9174257536ac2a912530d69d10 NeedsCompilation: no Package: PhyloProfile Version: 1.16.5 Depends: R (>= 4.3.0) Imports: ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, DT, energy, ExperimentHub, ggplot2, gridExtra, pbapply, RColorBrewer, RCurl, shiny, shinyBS, shinycssloaders, shinyFiles, shinyjs, stringr, OmaDB, plyr, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 83d80cf3910941baf5423978764a25b8 NeedsCompilation: no Package: phyloseq Version: 1.46.0 Depends: R (>= 3.3.0) Imports: ade4 (>= 1.7-4), ape (>= 5.0), Biobase (>= 2.36.2), BiocGenerics (>= 0.22.0), biomformat (>= 1.0.0), Biostrings (>= 2.40.0), cluster (>= 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cb989f0e8a3a1ab90a4a319c860ef602 NeedsCompilation: no Package: piano Version: 2.18.0 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: 84b0ce2cca9fb11110bd82113e066e82 NeedsCompilation: no Package: pickgene Version: 1.74.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: 250b3649eff783447f1d2c34f67bf3ca NeedsCompilation: no Package: PICS Version: 2.46.0 Depends: R (>= 3.0.0) Imports: utils, stats, graphics, grDevices, methods, IRanges, GenomicRanges, Rsamtools, GenomicAlignments Suggests: rtracklayer, parallel, knitr License: Artistic-2.0 MD5sum: 04ed3fdb7f1db15654e9974438495e43 NeedsCompilation: yes Package: Pigengene Version: 1.28.0 Depends: 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RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, limma, testthat, rmarkdown License: GPL (>= 3) + file LICENSE MD5sum: 0e8192f66f9ba7110763755200edee3a NeedsCompilation: no Package: rifi Version: 1.6.0 Depends: R (>= 4.2) Imports: car, cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, graphics, grDevices, grid, methods, nls2, nnet, rlang, S4Vectors, scales, stats, stringr, SummarizedExperiment, tibble, rtracklayer, reshape2, utils Suggests: DescTools, devtools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: 5d070b26ca40e04e4e3f9851853caa48 NeedsCompilation: no Package: rifiComparative Version: 1.2.0 Depends: R (>= 4.2) Imports: cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, ggrepel, graphics, grDevices, grid, methods, nnet, rlang, S4Vectors, scales, stats, stringr, tibble, rtracklayer, utils, writexl, DTA, LSD, reshape2, devtools, SummarizedExperiment Suggests: DescTools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: 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RUnit, knitr, markdown, rmarkdown, BiocStyle License: GPL-3 MD5sum: dfa447cd634a432486a982a719e27451 NeedsCompilation: no Package: SCATE Version: 1.12.0 Depends: parallel, preprocessCore, splines, splines2, xgboost, SCATEData, Rtsne, mclust Imports: utils, stats, GenomicAlignments, GenomicRanges Suggests: rmarkdown, ggplot2, knitr License: MIT + file LICENSE MD5sum: 877e80a925c1b76cc1a759dd7df2c788 NeedsCompilation: no Package: scater Version: 1.30.1 Depends: SingleCellExperiment, scuttle, ggplot2 Imports: stats, utils, methods, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, DelayedArray, MatrixGenerics, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer, RcppML, uwot, pheatmap, ggrepel, ggrastr Suggests: BiocStyle, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore License: GPL-3 MD5sum: c161043392323318c01792e2de828ad5 NeedsCompilation: no Package: scatterHatch Version: 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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: 5d11fe3a4af0d56d3028d97c6090ccfb NeedsCompilation: yes Package: schex Version: 1.16.1 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: f57d8e86734da9d7e2b645c5871fa7a1 NeedsCompilation: no Package: scHOT Version: 1.14.0 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: 75f460d2a6c2d8bee223b64a05eb6224 NeedsCompilation: no Package: scider Version: 1.0.0 Depends: R (>= 4.3) Imports: SpatialExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, sf, lwgeom, ggplot2, stats, pheatmap, plotly, shiny, igraph, janitor, knitr, methods, utils, rlang, isoband, S4Vectors, grDevices Suggests: edgeR, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: d20e0e846be7368da2613650b3834957 NeedsCompilation: no Package: scifer Version: 1.4.0 Imports: dplyr, rmarkdown, data.table, Biostrings, parallel, stats, plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra, tibble, scales, rlang, flowCore, methods Suggests: fs, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 82fb184bec0c09d5f7067baf81f8fee1 NeedsCompilation: no Package: scmap Version: 1.24.0 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: de159d16de109a02a1c7cb3c85418b58 NeedsCompilation: yes Package: scMerge Version: 1.18.0 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: d5b285890500ad5c781d33ab45282aca NeedsCompilation: no Package: scMET Version: 1.4.0 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: 6420a2af7464f67eb676f06d20f9d5a6 NeedsCompilation: yes Package: scmeth Version: 1.22.0 Depends: R (>= 3.5.0) Imports: knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes License: GPL-2 MD5sum: 52beac81d58da27e01cc5e1a0b6584b2 NeedsCompilation: no Package: SCnorm Version: 1.24.0 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: cfac086eb57336e865c999c4c0b42a0c NeedsCompilation: no Package: scone Version: 1.26.0 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 Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData License: Artistic-2.0 MD5sum: 0e7dd77999fc8cbf842fee6452c82a1b NeedsCompilation: no Package: Sconify Version: 1.22.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 61762bc5d7e8560ae818942a21da33a5 NeedsCompilation: no Package: SCOPE Version: 1.14.0 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: b8e4ce76717f217322282d378de1b3bd NeedsCompilation: no Package: scoreInvHap Version: 1.24.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: 7505f8161571dcc7b9b752fc62dedce5 NeedsCompilation: no Package: scp Version: 1.12.0 Depends: R (>= 4.2.0), QFeatures (>= 1.3.5) Imports: methods, stats, utils, SingleCellExperiment, SummarizedExperiment, MultiAssayExperiment, MsCoreUtils, matrixStats, S4Vectors, dplyr, magrittr Suggests: scpdata, testthat, knitr, BiocStyle, rmarkdown, ggplot2, patchwork, impute, scater, sva, preprocessCore, vsn, uwot License: Artistic-2.0 MD5sum: c4f759cfb996e6150ecec65b7de3e343 NeedsCompilation: no Package: scPCA Version: 1.16.0 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: e7058ad8f079f25d21ae55911652d01d NeedsCompilation: no Package: scPipe Version: 2.2.0 Depends: R (>= 4.2.0), SingleCellExperiment Imports: AnnotationDbi, basilisk, 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edgeR, limma, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, bluster, metapod, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, monocle, Biobase, pheatmap, scater License: GPL-3 MD5sum: 36f9f69d4699d050a95d6f6f971d2387 NeedsCompilation: yes Package: scReClassify Version: 1.8.0 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: 722bce944db1f380df35d68a47c4bef7 NeedsCompilation: no Package: scRecover Version: 1.18.0 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 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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: 7fcf2fd9ff8c1d34aaa64399fa876f3a NeedsCompilation: no Package: scTHI Version: 1.14.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: c90e49b0aaed73dd76437e5236607e06 NeedsCompilation: no Package: scTreeViz Version: 1.8.0 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: 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ggplot2, matlab, reshape, sigclust Suggests: org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle License: GPL-3 MD5sum: cb03ecb39c2df4b4f5e1b49f8ba5d594 NeedsCompilation: no Package: siggenes Version: 1.76.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: ae9899f2a3587a423169a27502868709 NeedsCompilation: no Package: sights Version: 1.28.0 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: 566e869c884c7b12f1a42a9dbaeec05a NeedsCompilation: no Package: signatureSearch Version: 1.16.0 Depends: R(>= 4.2.0), Rcpp, SummarizedExperiment, org.Hs.eg.db Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, 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rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne License: GPL-3 MD5sum: ef057b77f40efba992f311486e83448b NeedsCompilation: no Package: SingleCellSignalR Version: 1.14.0 Depends: R (>= 4.0) Imports: BiocManager, circlize, limma, igraph, gplots, grDevices, edgeR, data.table, pheatmap, stats, Rtsne, graphics, stringr, foreach, multtest, scran, utils, Suggests: knitr, rmarkdown License: GPL-3 MD5sum: d00060a859db9cd8c87ce9673cc9d886 NeedsCompilation: no Package: singleCellTK Version: 2.12.2 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, GSVA (>= 1.26.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix (>= 1.5-3), matrixStats, methods, msigdbr, multtest, plotly, plyr, ROCR, Rtsne, S4Vectors, scater, scMerge (>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, SoupX, sva, reshape2, shinyalert, circlize, enrichR (>= 3.2), celda, shinycssloaders, DropletUtils, scds (>= 1.2.0), reticulate (>= 1.14), tools, tximport, 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 Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, stringr, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony, SeuratObject, optparse License: MIT + file LICENSE MD5sum: b4d542c9326864f485b6c6e6ddb55e1e NeedsCompilation: no Package: SingleMoleculeFootprinting Version: 1.10.0 Depends: R (>= 4.1.0) Imports: BiocGenerics, Biostrings, BSgenome, GenomeInfoDb, GenomicRanges, data.table, grDevices, plyr, IRanges, RColorBrewer, stats, QuasR Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, parallel, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0) License: GPL-3 MD5sum: dcdbbace0f6394ce22397640da1dd03f NeedsCompilation: no Package: SingleR Version: 2.4.1 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocSingular, stats, utils, Rcpp, beachmat, parallel LinkingTo: Rcpp, beachmat, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scater, scran, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 + file LICENSE MD5sum: ff17f8c8804598bb80a27bba33216919 NeedsCompilation: yes Package: singscore Version: 1.22.0 Depends: R (>= 3.6) Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, reshape2, 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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: 556fe5835a602547c3475065eb5c11d0 NeedsCompilation: no Package: SLqPCR Version: 1.68.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) MD5sum: 72759fb6b62f3852f458e695318c0f6f NeedsCompilation: no Package: SMAD Version: 1.18.0 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: 65f0eba6ed0bf086797b95b2c9da6dd6 NeedsCompilation: yes Package: SMAP Version: 1.66.0 Depends: R (>= 2.10), methods License: GPL-2 MD5sum: f29ffdead8f34c2f531dd7ea764febe0 NeedsCompilation: yes Package: SMITE Version: 1.30.0 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: 47c578785a426c3c7850880ed58033e8 NeedsCompilation: no Package: SNAGEE Version: 1.42.0 Depends: R (>= 2.6.0), SNAGEEdata Suggests: ALL, hgu95av2.db Enhances: parallel License: Artistic-2.0 MD5sum: faadcab23b170f71a29ac7fd67b2a5d8 NeedsCompilation: no Package: snapCGH Version: 1.72.0 Depends: R (>= 3.5.0) Imports: aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma, methods, stats, tilingArray, utils License: GPL MD5sum: d21dbae207756cb76e04cadbcfa8b086 NeedsCompilation: yes Package: snapcount Version: 1.14.0 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: 8efa036bfe73acf9c31a279b3c365ae7 NeedsCompilation: no Package: snifter Version: 1.12.0 Depends: R (>= 4.0.0) Imports: basilisk, reticulate, irlba, stats, assertthat Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) License: GPL-3 MD5sum: a6cfc8a05013cd2d050a1adba2b3fe4d NeedsCompilation: no Package: snm Version: 1.50.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL MD5sum: 103ab8eb4cca35d12c53c48615ebd5da NeedsCompilation: no Package: SNPediaR Version: 1.28.0 Depends: R (>= 3.0.0) Imports: RCurl, jsonlite Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 25d5eec5081ccfac687eba26102eb826 NeedsCompilation: no Package: SNPhood Version: 1.32.0 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: f5a30ae405bebdb97e51cb2782debcbf NeedsCompilation: no Package: SNPRelate Version: 1.36.1 Depends: R (>= 2.15), gdsfmt (>= 1.8.3) Imports: methods LinkingTo: gdsfmt Suggests: parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics Enhances: SeqArray (>= 1.12.0) License: GPL-3 MD5sum: 19ded26ae346dc74ae7b6f8258b2afb0 NeedsCompilation: yes Package: snpStats Version: 1.52.0 Depends: R(>= 2.10.0), survival, Matrix, methods Imports: graphics, grDevices, stats, utils, BiocGenerics, zlibbioc Suggests: hexbin License: GPL-3 MD5sum: 0625c920470937a31fd278cf8bd8982a NeedsCompilation: yes Package: soGGi Version: 1.34.0 Depends: R (>= 3.5.0), BiocGenerics, SummarizedExperiment Imports: methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, preprocessCore, chipseq, BiocParallel Suggests: testthat, BiocStyle, knitr License: GPL (>= 3) MD5sum: 6b8a823ad7812fdda198d38b28c00f6f NeedsCompilation: no Package: SomaticSignatures Version: 2.38.0 Depends: R (>= 3.5.0), VariantAnnotation, GenomicRanges, NMF Imports: S4Vectors, IRanges, GenomeInfoDb, Biostrings, ggplot2, ggbio, reshape2, NMF, pcaMethods, Biobase, methods, proxy Suggests: testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva License: MIT + file LICENSE MD5sum: 46d14334be0098323bc956bade5d5e9e NeedsCompilation: no Package: SOMNiBUS Version: 1.10.0 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: 0865c015122f915127302bf751a10812 NeedsCompilation: no Package: SpacePAC Version: 1.40.0 Depends: R(>= 2.15),iPAC Suggests: RUnit, BiocGenerics, rgl License: GPL-2 MD5sum: aa35450e9ef0b3cd7ca3d90262d36ddf NeedsCompilation: no Package: Spaniel Version: 1.16.0 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: fb29666756a1db567f16b5c72420de4c NeedsCompilation: no Package: sparrow Version: 1.8.0 Depends: R (>= 4.0) Imports: babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet, checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>= 1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>= 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matrixStats (>= 0.60.0), methods LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 4319e6fb04b91467bd08cc4ce2ad609c NeedsCompilation: yes Package: sparsenetgls Version: 1.20.0 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: 32b8f3b9fe86b40386aee23ac4ea55fd NeedsCompilation: no Package: SparseSignatures Version: 2.12.0 Depends: R (>= 4.1.0), NMF Imports: nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2, gridExtra, reshape2 Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr, License: file LICENSE MD5sum: 832b206679a06252fa3b76f2700a70e9 NeedsCompilation: no Package: spaSim Version: 1.4.0 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: d69e70975aaaa9bffc5e52f95885e59c NeedsCompilation: no Package: SpatialCPie Version: 1.18.0 Depends: R (>= 3.6) Imports: colorspace (>= 1.3-2), data.table (>= 1.12.2), digest (>= 0.6.21), dplyr (>= 0.7.6), ggforce (>= 0.3.0), ggiraph (>= 0.5.0), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), grid (>= 3.5.1), igraph (>= 1.2.2), lpSolve (>= 5.6.13), methods (>= 3.5.0), purrr (>= 0.2.5), readr (>= 1.1.1), rlang (>= 0.2.2), shiny (>= 1.1.0), shinycssloaders (>= 0.2.0), shinyjs (>= 1.0), shinyWidgets (>= 0.4.8), stats (>= 3.6.0), SummarizedExperiment (>= 1.10.1), tibble (>= 1.4.2), tidyr (>= 0.8.1), tidyselect (>= 0.2.4), tools (>= 3.6.0), utils (>= 3.5.0), zeallot (>= 0.1.0) Suggests: BiocStyle (>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0) License: MIT + file LICENSE MD5sum: 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License: GPL-3 MD5sum: 7dbd7938c005104df763ecf3d016154f NeedsCompilation: no Package: SpatialFeatureExperiment Version: 1.4.0 Depends: R (>= 4.2.0) Imports: BiocGenerics, BiocNeighbors, BiocParallel, grDevices, Matrix, methods, rjson, rlang, S4Vectors, sf, SingleCellExperiment, SpatialExperiment, spdep (>= 1.1-7), SummarizedExperiment, stats, terra, utils Suggests: BiocStyle, dplyr, DropletUtils, knitr, rhdf5, rmarkdown, sfarrow, SFEData, vroom, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 56d4ad5144861bea16c2f677e096ac75 NeedsCompilation: no Package: spatialHeatmap Version: 2.8.5 Depends: R (>= 3.5.0) Imports: data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid, gridExtra, gplots, igraph, methods, Matrix, rsvg, shiny, grDevices, graphics, ggplotify, parallel, reshape2, scater, scuttle, scran, 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, 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, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, yaml License: Artistic-2.0 MD5sum: 2c5ee52628039f8293fd20bdd2874004 NeedsCompilation: no Package: SpatialOmicsOverlay Version: 1.2.1 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, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf License: MIT MD5sum: 149a968f19aa22b57caca243b3480378 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1.26.0 Depends: R (>= 3.6.0) Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, tibble, tidytree (>= 0.4.5), utils, stats Suggests: Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml, purrr, cli License: Artistic-2.0 MD5sum: 583758f88bf0d8efa0749407f4183567 NeedsCompilation: no Package: treekoR Version: 1.10.0 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: c1b9ce26aa6252f5cb1fe9cd07c3245f NeedsCompilation: no Package: TreeSummarizedExperiment Version: 2.10.0 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: 595842345af9cb4136aea17bdfdceb3f NeedsCompilation: no Package: TREG Version: 1.6.0 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: d76ba3f3707e1810e6491d04013d6e7b NeedsCompilation: no Package: trena Version: 1.24.0 Depends: R (>= 3.5.0), utils, glmnet (>= 2.0.3), MotifDb (>= 1.19.17) Imports: RSQLite, RMySQL, lassopv, randomForest, xgboost, RPostgreSQL, methods, DBI, BSgenome, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, SNPlocs.Hsapiens.dbSNP150.GRCh38, org.Hs.eg.db, Biostrings, GenomicRanges, biomaRt, AnnotationDbi, WGCNA Suggests: RUnit, plyr, knitr, BiocGenerics, rmarkdown, formatR, markdown, BiocParallel, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Athaliana.TAIR.TAIR9 License: GPL-3 MD5sum: 427f71434aa331a134672ca1746a28ae NeedsCompilation: no Package: Trendy Version: 1.24.1 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: 00e5de9c46c116f4adc3caf3708608df NeedsCompilation: no Package: TRESS Version: 1.8.0 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: f0a0a2bbb1b989970231d8ac23ecfaaa NeedsCompilation: no Package: tricycle Version: 1.10.0 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: 6a6a35c0a2cd9f279395e046b98a79f6 NeedsCompilation: no Package: trigger Version: 1.48.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 MD5sum: d8cb2a76223f510ff08d9dcbf1d6210c NeedsCompilation: yes Package: trio Version: 3.40.0 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1) Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 MD5sum: cd87ad1a66fe181df937dd7a8edfda56 NeedsCompilation: no Package: triplex Version: 1.42.0 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: c66a6990486e7a4873b256d08eff9933 NeedsCompilation: yes Package: tripr Version: 1.8.0 Depends: 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 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: 6682fcae99b44178612cdf8ebc48d045 NeedsCompilation: no Package: tRNA Version: 1.20.1 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE MD5sum: e44e072f320f35d6cf6210074fbdf665 NeedsCompilation: no Package: tRNAdbImport Version: 1.20.1 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: 800f0115cf3ffcfb1fd2dd45b3574f30 NeedsCompilation: no Package: tRNAscanImport Version: 1.22.0 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, stringr, BiocGenerics, Biostrings, Structstrings, S4Vectors, IRanges, XVector, GenomeInfoDb, rtracklayer, BSgenome, Rsamtools Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 + file LICENSE MD5sum: 49f872c7de9b6cba139c7758330efa8c NeedsCompilation: no Package: TRONCO Version: 2.34.0 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: 0e137e734d0e5552bdcaa25ccdd4df08 NeedsCompilation: no Package: TSAR Version: 1.0.0 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: 7cc8589151c5b03e247590bbd7dc04dd NeedsCompilation: no Package: TSCAN Version: 1.40.1 Depends: SingleCellExperiment, TrajectoryUtils Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, DelayedArray, S4Vectors Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor License: GPL (>= 2) MD5sum: 8ab1f3f5a68c4aa03e7e7ed10c61a20f NeedsCompilation: no Package: ttgsea Version: 1.10.0 Depends: keras Imports: tm, text2vec, tokenizers, textstem, stopwords, data.table, purrr, DiagrammeR, stats Suggests: fgsea, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: 0b38c9baea88905217b9ed667c80c26f NeedsCompilation: no Package: TTMap Version: 1.24.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 MD5sum: 9fb52b78486eff55cc91ef0f8116633b NeedsCompilation: no Package: TurboNorm Version: 1.50.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata, hgu95av2cdf License: LGPL MD5sum: 6df6da83bc36e4ce202d91888feaafa7 NeedsCompilation: yes Package: TVTB Version: 1.28.0 Depends: R (>= 3.4), methods, utils, stats Imports: AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel, Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges (>= 2.21.6), reshape2, Rsamtools, S4Vectors (>= 0.25.14), SummarizedExperiment, VariantAnnotation (>= 1.19.9) Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander License: Artistic-2.0 MD5sum: 64da00f3c21bf3f9a82dc32e451395a1 NeedsCompilation: no Package: tweeDEseq Version: 1.48.0 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: 1a919ba1b3c5709068bc126336b77826 NeedsCompilation: yes Package: twilight Version: 1.78.0 Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, grDevices, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) MD5sum: fa6b01126ace9423edfc04757f6392b1 NeedsCompilation: yes Package: twoddpcr Version: 1.26.0 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: bbdb2cd12a3bd6f756b700d1216043ee NeedsCompilation: no Package: txcutr Version: 1.8.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, GenomicFeatures, 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 License: GPL-3 MD5sum: 10d81d02156a45cebc08845455180010 NeedsCompilation: no Package: tximeta Version: 1.20.3 Imports: SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, tools, utils, methods, Matrix Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools License: GPL-2 MD5sum: 2d53855f3d4afe1e6785ac21f97a8c50 NeedsCompilation: no Package: tximport Version: 1.30.0 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: 8bbe549dafbf5b0dfe626f327910a893 NeedsCompilation: no Package: TypeInfo Version: 1.68.0 Depends: methods Suggests: Biobase License: BSD_2_clause MD5sum: a2c4ab8a27a1d9c5a463a18cd0e37356 NeedsCompilation: no Package: UCell Version: 2.6.2 Depends: R(>= 4.2.0) Imports: methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel, BiocNeighbors, SingleCellExperiment, SummarizedExperiment Suggests: Seurat, scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: c02318fc6a9ac12b0d902460be5204d4 NeedsCompilation: no Package: Ularcirc Version: 1.20.0 Depends: R (>= 3.4.0) Imports: AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments, Organism.dplyr, 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: dee64401e02d9e5884a6399d7ab122b2 NeedsCompilation: no Package: UMI4Cats Version: 1.12.0 Depends: R (>= 4.0.0), SummarizedExperiment Imports: magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, magrittr, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats, org.Hs.eg.db, annotate, TxDb.Hsapiens.UCSC.hg19.knownGene, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat License: Artistic-2.0 MD5sum: bfadc67d7452919fe1e4a63684692442 NeedsCompilation: no Package: uncoverappLib Version: 1.12.0 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: 2aa395f92e95d5ff7e67612c6a2c0021 NeedsCompilation: no Package: UNDO Version: 1.44.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: a94665c036a09fbf3728f0a1ad220dfa NeedsCompilation: no Package: unifiedWMWqPCR Version: 1.38.0 Depends: methods Imports: BiocGenerics, stats, graphics, HTqPCR License: GPL (>= 2) MD5sum: d9a09d196f72dc2246328247851dd24a NeedsCompilation: no Package: UniProt.ws Version: 2.42.0 Depends: BiocGenerics, methods, RSQLite, utils Imports: AnnotationDbi, BiocFileCache, BiocBaseUtils, httr, httpcache, jsonlite, progress, rjsoncons Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 47d9ee4038c5dcaf66229e4e1e07c052 NeedsCompilation: no Package: Uniquorn Version: 2.22.0 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: 63658e23af6991784cdd4b038f2d1268 NeedsCompilation: no Package: universalmotif Version: 1.20.0 Depends: R (>= 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BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 MD5sum: 0c89e7d86bb2f37b99ce32989b121110 NeedsCompilation: no Package: VAExprs Version: 1.8.0 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: 6f9ed6eba476abd7908d6849381b545c NeedsCompilation: no Package: VanillaICE Version: 1.64.1 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: 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