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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: b44169ab3c45d8d56cd9409a9e8e34ba NeedsCompilation: yes Package: ANF Version: 1.29.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 29bdbbbfac526413f9b46da404d69136 NeedsCompilation: no Package: animalcules Version: 1.23.0 Depends: R (>= 4.3.0) Imports: ape, assertthat, caret, covr, DESeq2, dplyr, DT, forcats, ggforce, ggplot2, GUniFrac, lattice, limma, magrittr, Matrix, methods, MultiAssayExperiment, plotly, rentrez, reshape2, ROCit, S4Vectors (>= 0.23.19), scales, shiny, shinyjs, stats, SummarizedExperiment, tibble, tidyr, tsne, umap, utils, vegan, XML Suggests: BiocStyle, biomformat, 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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: 8dbf2451372b8c87c754210855ce6a16 NeedsCompilation: yes Package: ATACseqQC Version: 1.31.0 Depends: R (>= 3.5.0), BiocGenerics, S4Vectors Imports: BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats, motifStack, preseqR, utils, KernSmooth, edgeR, BiocParallel Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown License: GPL (>= 2) MD5sum: 9c1a54d63fb3e172f3cc7bebbe403f6e NeedsCompilation: no 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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: 6656fa02ff06add1a723bde24144336e NeedsCompilation: yes Package: attract Version: 1.59.0 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: 264fdbcea205735ab3a1381afdb3454e NeedsCompilation: no Package: AUCell Version: 1.29.0 Imports: DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats, SummarizedExperiment, BiocGenerics, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: 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GPL-3 MD5sum: 7d78f5fe5d87f22936de446d6b40f00e NeedsCompilation: no Package: AWFisher Version: 1.21.0 Depends: R (>= 3.6) Imports: edgeR, limma, stats Suggests: knitr, tightClust License: GPL-3 MD5sum: 0602334dbc6589da5167f454a8b0c648 NeedsCompilation: yes Package: awst Version: 1.15.0 Imports: stats, methods, SummarizedExperiment Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown License: MIT + file LICENSE MD5sum: 0d6a16c233e2cf9864f31c3541db9641 NeedsCompilation: no Package: BaalChIP Version: 1.33.0 Depends: R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools, Imports: GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy, reshape2, scales, coda, foreach, ggplot2, methods, utils, graphics, stats Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: b6079c678f35e00f366764f6d8bea167 NeedsCompilation: no Package: bacon Version: 1.35.0 Depends: R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 License: GPL (>= 2) MD5sum: 06f4df3cdb3d32f4e4208ac8e422e6cc NeedsCompilation: yes Package: BADER Version: 1.45.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 MD5sum: 920547d8385d607bd44ab521b2194a7d NeedsCompilation: yes Package: BadRegionFinder Version: 1.35.0 Imports: VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 1336ea45fb9b6fc1f2e7d4e93ff78e90 NeedsCompilation: no Package: BAGS Version: 2.47.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 MD5sum: 0518901a34fd1ce02204c70610a24643 NeedsCompilation: yes Package: ballgown Version: 2.39.0 Depends: R (>= 3.5.0), methods Imports: GenomicRanges (>= 1.17.25), IRanges (>= 1.99.22), S4Vectors (>= 0.9.39), RColorBrewer, splines, sva, limma, rtracklayer (>= 1.29.25), Biobase (>= 2.25.0), GenomeInfoDb Suggests: testthat, knitr, markdown License: Artistic-2.0 MD5sum: 5a7b7ddfe9719786ea7426b55d35004a NeedsCompilation: no Package: bambu Version: 3.9.0 Depends: R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>= 0.22.1), BSgenome, IRanges Imports: BiocGenerics, BiocParallel, data.table, dplyr, tidyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost LinkingTo: Rcpp, RcppArmadillo Suggests: AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq Enhances: parallel License: GPL-3 + file LICENSE MD5sum: 704a50ba91399f59332f7a60002cf36b NeedsCompilation: yes Package: bamsignals Version: 1.39.0 Depends: R (>= 3.5.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: 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RColorBrewer, rlang, scales, shiny, stats, SummarizedExperiment, S4Vectors, tibble, tidyr, vegan, viridis, utils Suggests: BiocStyle, knitr, magick, rmarkdown, testthat License: file LICENSE MD5sum: 30804183e779bef73e3f0ffa6dc834c3 NeedsCompilation: no Package: basecallQC Version: 1.31.0 Depends: R (>= 3.4), stats, utils, methods, rmarkdown, knitr, prettydoc, yaml Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead Suggests: testthat, BiocStyle License: GPL (>= 3) MD5sum: 9f94546a5874cd0dd73ea7e27e4a05e8 NeedsCompilation: no Package: BaseSpaceR Version: 1.51.0 Depends: R (>= 2.15.0), RCurl, RJSONIO Imports: methods Suggests: RUnit, IRanges, Rsamtools License: Apache License 2.0 MD5sum: 60a85ce955f7f16cd0ba3877739ec5f1 NeedsCompilation: no Package: Basic4Cseq Version: 1.43.0 Depends: R (>= 3.4), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805 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BiocGenerics, Rcpp, stats, methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix, SparseArray, DelayedArray (>= 0.31.5), DelayedMatrixStats, BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq License: GPL-3 MD5sum: 4459733830062d871a5f380496b0a88f NeedsCompilation: yes Package: BatchQC Version: 2.3.0 Depends: R (>= 4.4.0) Imports: data.table, DESeq2, dplyr, EBSeq, ggdendro, ggnewscale, ggplot2, limma, matrixStats, pheatmap, RColorBrewer, reader, reshape2, scran, shiny, shinyjs, shinythemes, stats, SummarizedExperiment, sva, S4Vectors, tibble, tidyr, tidyverse, utils Suggests: BiocManager, BiocStyle, bladderbatch, devtools, knitr, lintr, plotly, rmarkdown, spelling, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 7945c5c6aa72a5f03070a0a1ff9ecb55 NeedsCompilation: no Package: BayesKnockdown Version: 1.33.0 Depends: R (>= 3.3) Imports: stats, Biobase License: GPL-3 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Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat License: GPL (>= 2) MD5sum: 23021fdb29ca4125b43ef68365859b66 NeedsCompilation: yes Package: baySeq Version: 2.41.0 Depends: R (>= 2.3.0), methods Imports: edgeR, GenomicRanges, abind, parallel, graphics, stats, utils Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: a96b38865d70d03e6168939f728da2d9 NeedsCompilation: no Package: BBCAnalyzer Version: 1.37.0 Imports: SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices, GenomicRanges, IRanges, Biostrings Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 9779167737fbabaa62a3f5b0bb2fa146 NeedsCompilation: no Package: BCRANK Version: 1.69.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 MD5sum: 11000adaf73797a7e630b4d625555877 NeedsCompilation: yes Package: bcSeq Version: 1.29.0 Depends: R (>= 3.4.0) Imports: Rcpp (>= 0.12.12), Matrix, Biostrings LinkingTo: Rcpp, Matrix Suggests: knitr License: GPL (>= 2) MD5sum: 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TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr License: MIT + file LICENSE MD5sum: 02956ab2acc1faa0badbca5bd8551e59 NeedsCompilation: yes Package: BeadDataPackR Version: 1.59.0 Imports: stats, utils Suggests: BiocStyle, knitr License: GPL-2 MD5sum: 5a8b747f2f49e7de530875c8317317a0 NeedsCompilation: yes Package: BEAT Version: 1.45.0 Depends: R (>= 2.13.0) Imports: GenomicRanges, ShortRead, Biostrings, BSgenome License: LGPL (>= 3.0) MD5sum: 2f497cd941fbe43419b072852d902603 NeedsCompilation: no Package: BEclear Version: 2.23.0 Depends: BiocParallel (>= 1.14.2) Imports: futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp, abind, stats, graphics, utils, methods, dixonTest, ids LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, pander, seewave License: GPL-3 MD5sum: 5849131ee57651736825fcdda68ef89e NeedsCompilation: yes Package: beer Version: 1.11.0 Depends: R (>= 4.2.0), PhIPData (>= 1.1.1), rjags Imports: cli, edgeR, BiocParallel, methods, progressr, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling License: MIT + file LICENSE MD5sum: 264840163396abbe89cc55d4dc26e671 NeedsCompilation: no Package: BERT Version: 1.3.3 Depends: R (>= 4.3.0) Imports: cluster, comprehenr, foreach (>= 1.5.2), invgamma, iterators (>= 1.0.14), janitor (>= 2.2.0), limma (>= 3.46.0), logging (>= 0.10-108), sva (>= 3.38.0), SummarizedExperiment, methods, BiocParallel Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: ac7d88402ecfeef96b497ec5397725fb NeedsCompilation: no Package: betaHMM Version: 1.3.1 Depends: R (>= 4.3.0), SummarizedExperiment, S4Vectors, GenomicRanges Imports: stats, ggplot2, scales, methods, pROC, foreach, doParallel, parallel, cowplot, dplyr, tidyr, tidyselect, stringr, utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: 24f94326460ff3888ef708cc385be7e0 NeedsCompilation: no Package: 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knitr, testthat, rmarkdown, AnnotationHub, httr License: GPL-3 + file LICENSE MD5sum: 8da90e529bd64c17c33576be7dc45561 NeedsCompilation: no Package: BgeeDB Version: 2.33.0 Depends: R (>= 3.6.0), topGO, tidyr Imports: R.utils, data.table, curl, RCurl, digest, methods, stats, utils, dplyr, RSQLite, graph, Biobase, zellkonverter, anndata, HDF5Array, bread Suggests: knitr, BiocStyle, testthat, rmarkdown, markdown License: GPL-3 + file LICENSE MD5sum: 7f1c95bcf8dc4719a6a047de1f46dc3f NeedsCompilation: no Package: BicARE Version: 1.65.0 Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase, GO.db Imports: methods Suggests: hgu95av2 License: GPL-2 MD5sum: eac5a310d8a0fc33b9987f2a3dc5dc8d NeedsCompilation: yes Package: BiFET Version: 1.27.0 Depends: R (>= 3.5.0) Imports: stats, poibin, GenomicRanges Suggests: rmarkdown, testthat, knitr License: GPL-3 MD5sum: c3dd5495961c83e465ef09090940abe1 NeedsCompilation: no Package: BiGGR Version: 1.43.0 Depends: R (>= 2.14.0), rsbml, hyperdraw, LIM,stringr Imports: hypergraph, limSolve License: file LICENSE MD5sum: eda2ca1b253d1ebdf99aa8220d34cf0f NeedsCompilation: no Package: bigmelon Version: 1.33.0 Depends: R (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4), methods, minfi (>= 1.21.0), Biobase, methylumi Imports: stats, utils, GEOquery, graphics, BiocGenerics, illuminaio Suggests: BiocGenerics, RUnit, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter License: GPL-3 MD5sum: 34b6cebd14e45318d7eb5b1c8e4e07b0 NeedsCompilation: no Package: BindingSiteFinder Version: 2.5.2 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, 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Rsamtools, AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase, annotate, RUnit License: Artistic-2.0 MD5sum: 3d35210a258114d23c74084c4401b47c NeedsCompilation: no Package: biocGraph Version: 1.69.0 Depends: Rgraphviz, graph Imports: Rgraphviz, geneplotter, graph, BiocGenerics, methods Suggests: fibroEset, geneplotter, hgu95av2.db License: Artistic-2.0 MD5sum: a574b9d9496b25fbe3b7e824762b3cb0 NeedsCompilation: no Package: BiocHail Version: 1.7.1 Depends: R (>= 4.3.0), graphics, stats, utils Imports: reticulate, basilisk, BiocFileCache, methods, dplyr, BiocGenerics Suggests: knitr, testthat, BiocStyle, ggplot2, DT License: Artistic-2.0 MD5sum: e87088a34de49f92f991cd95c85d7b23 NeedsCompilation: no Package: BiocHubsShiny Version: 1.7.2 Depends: R (>= 4.3.0), shiny Imports: AnnotationHub, ExperimentHub, DT, htmlwidgets, rclipboard, S4Vectors, shinyAce, shinyjs, shinythemes, shinytoastr, utils Suggests: BiocManager, BiocStyle, knitr, rmarkdown, sessioninfo, shinytest2 License: 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S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage, utils, HiCBricks LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, RUnit, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: d9537db99ad482734e1d8caf242a61f5 NeedsCompilation: yes Package: bnem Version: 1.15.0 Depends: R (>= 4.1) Imports: CellNOptR, matrixStats, snowfall, Rgraphviz, cluster, flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods, utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown Suggests: knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit License: GPL-3 MD5sum: da0e2f4a7c24868dae9b147bf4f83f72 NeedsCompilation: no Package: BOBaFIT Version: 1.11.0 Depends: R (>= 2.10) Imports: dplyr, NbClust, ggplot2, ggbio, grDevices, stats, tidyr, GenomicRanges, ggforce, stringr, plyranges, methods, utils, magrittr Suggests: rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0), utils, testthat License: GPL (>= 3) MD5sum: d48a94d844122e83472cc50ccbffe68f NeedsCompilation: no 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methods, plyranges, Rcpp, S4Vectors, stats, stringr, tibble, tidyr, utils, zeallot LinkingTo: Rcpp, RcppArmadillo, RcppProgress, BH Suggests: knitr, rmarkdown, testthat, BiocStyle, txdbmaker, TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene, txdbmaker, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: BSD_2_clause + file LICENSE MD5sum: b1f4571234413c981dd2e10c8200cc70 NeedsCompilation: yes Package: BUSseq Version: 1.13.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots, grDevices, methods, stats, utils Suggests: BiocStyle, knitr, BiocGenerics License: Artistic-2.0 MD5sum: ac230a447b9df708273967590baad515 NeedsCompilation: yes Package: CaDrA Version: 1.5.0 Depends: R (>= 4.4.0) Imports: doParallel, ggplot2, gplots, graphics, grid, gtable, knnmi, MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats, SummarizedExperiment Suggests: BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat (>= 3.1.6) License: GPL-3 + file LICENSE 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vcfR Suggests: BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat, VGAM Enhances: doMC License: GPL-3 MD5sum: 8185c2a2a54c7337598cb46df5af2560 NeedsCompilation: yes Package: Cardinal Version: 3.9.0 Depends: R (>= 4.4), BiocParallel, BiocGenerics, ProtGenerics, S4Vectors, methods, stats, stats4 Imports: CardinalIO, Biobase, EBImage, graphics, grDevices, irlba, Matrix, matter (>= 2.7.10), nlme, parallel, utils Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: b81231f3abf7fed1186511c77fb6e0af NeedsCompilation: no Package: CardinalIO Version: 1.5.0 Depends: R (>= 4.4), BiocParallel, matter, ontologyIndex Imports: methods, S4Vectors, stats, utils, tools Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: 24d27af8711f95c79bb491a4d0c1c463 NeedsCompilation: yes Package: CARNIVAL Version: 2.17.0 Depends: R (>= 4.0) Imports: readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson, rmarkdown Suggests: 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License: GPL (>= 2) MD5sum: 593f65337dc9985eb2cf90cac8f6ae0c NeedsCompilation: no Package: Category Version: 2.73.0 Depends: methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix Imports: utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db License: Artistic-2.0 MD5sum: 0c16729015a364a2bc797c3fded93722 NeedsCompilation: no Package: categoryCompare Version: 1.51.0 Depends: R (>= 2.10), Biobase, BiocGenerics (>= 0.13.8), Imports: AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1), GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29), methods, grDevices, utils Suggests: knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter, rmarkdown License: GPL-2 MD5sum: 72c8c2eddca7f53c761eef32aa62692a NeedsCompilation: no Package: CatsCradle Version: 1.1.0 Depends: R (>= 4.4.0) Imports: Seurat (>= 5.0.1), ggplot2, networkD3, stringr, pracma, reshape2, rdist, igraph, geometry, Rfast, data.table, abind, pheatmap, EBImage, S4Vectors, SeuratObject, SingleCellExperiment, SpatialExperiment, Matrix, methods, SummarizedExperiment, msigdbr Suggests: fossil, interp, knitr, BiocStyle, tictoc License: MIT + file LICENSE MD5sum: 664491efc8de03a84822e90cf43b45a8 NeedsCompilation: no Package: CausalR Version: 1.39.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: bf244fa8787cc9dececec2abb351c8ba NeedsCompilation: no Package: cbaf Version: 1.29.0 Depends: R (>= 4.1) Imports: BiocFileCache, RColorBrewer, cBioPortalData, genefilter, gplots, grDevices, stats, utils, openxlsx, zip Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 1d5fd634d496cc654aed208ec315f350 NeedsCompilation: no Package: cBioPortalData Version: 2.19.4 Depends: R (>= 4.2.0), AnVIL (>= 1.7.1), MultiAssayExperiment Imports: BiocBaseUtils, BiocFileCache (>= 1.5.3), digest, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment, RTCGAToolbox (>= 2.19.7), S4Vectors, SummarizedExperiment, stats, tibble, tidyr, TCGAutils (>= 1.9.4), utils Suggests: BiocStyle, knitr, survival, survminer, rmarkdown, testthat License: AGPL-3 MD5sum: 5f3effab51e507b7b2f9ce22c5f02d92 NeedsCompilation: no Package: CBNplot Version: 1.7.0 Depends: R (>= 4.3.0) Imports: ggplot2, magrittr, graphite, ggraph, igraph, bnlearn (>= 4.7), patchwork, org.Hs.eg.db, clusterProfiler, utils, enrichplot, reshape2, ggforce, dplyr, tidyr, stringr, depmap, ExperimentHub, Rmpfr, graphlayouts, BiocFileCache, ggdist, purrr, pvclust, stats, rlang Suggests: knitr, arules, concaveman, ReactomePA, bnviewer, rmarkdown, withr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 32889a2dd375ebbefbbb69323024fa5e NeedsCompilation: no Package: cbpManager Version: 1.15.0 Depends: shiny, shinydashboard Imports: utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite, rapportools, basilisk, reticulate, shinyBS, shinycssloaders, rintrojs, rlang, markdown Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 6580ed7b3e0bfe90a16f4ae66b2e49f4 NeedsCompilation: no Package: ccfindR Version: 1.27.0 Depends: R (>= 3.6.0) Imports: stats, S4Vectors, utils, methods, Matrix, SummarizedExperiment, SingleCellExperiment, Rtsne, graphics, grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp, Rdpack (>= 0.7) LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 976fbc36a6f78b10a00296780d68b2f0 NeedsCompilation: yes Package: ccImpute Version: 1.9.0 Imports: Rcpp, sparseMatrixStats, stats, BiocParallel, irlba, SingleCellExperiment, Matrix, SummarizedExperiment LinkingTo: Rcpp, RcppEigen Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, mclust, testthat (>= 3.0.0), splatter License: GPL-3 MD5sum: e9dbeeb9bab1f5880eba31680b89b879 NeedsCompilation: yes Package: ccmap Version: 1.33.0 Imports: AnnotationDbi (>= 1.36.2), BiocManager (>= 1.30.4), ccdata (>= 1.1.2), doParallel (>= 1.0.10), data.table (>= 1.10.4), foreach (>= 1.4.3), parallel (>= 3.3.3), xgboost (>= 0.6.4), lsa (>= 0.73.1) Suggests: crossmeta, knitr, rmarkdown, testthat, lydata License: MIT + file LICENSE MD5sum: 282fad9f0e9ea248e78b7a64c78d4ca1 NeedsCompilation: no Package: CCPlotR Version: 1.5.0 Imports: plyr, tidyr, dplyr, ggplot2, forcats, ggraph, igraph, scatterpie, circlize, ComplexHeatmap, tibble, grid, ggbump, stringr, ggtext, ggh4x, patchwork, RColorBrewer, scales, viridis, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: c60aa852df6f1e4bec5b2ef92f860da4 NeedsCompilation: no Package: CCPROMISE Version: 1.33.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: 5648a2e22e45edc3ecc8dee5d7a94f54 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SingleCellExperiment, Matrix Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, reshape2, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, scater (>= 1.14.4), scran, dbscan, DelayedArray, stringr, ComplexHeatmap, gridExtra, circlize LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData License: MIT + file LICENSE MD5sum: 251f04b5857b7945db8e5d6c8b4b6a70 NeedsCompilation: yes Package: CellBarcode Version: 1.13.1 Depends: R (>= 4.1.0) Imports: methods, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr, ggplot2, stringr, magrittr, ShortRead (>= 1.48.0), Biostrings (>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors, seqinr, Rsamtools LinkingTo: Rcpp, BH Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: Artistic-2.0 MD5sum: 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data.table, glue, pbapply, umap, Rtsne, reticulate, fastmatch, matrixStats, ggplot2, BiocParallel, SummarizedExperiment, fgsea LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel License: GPL-3 + file LICENSE MD5sum: 8f30993883fc40954f998e189f5e31a2 NeedsCompilation: yes Package: cellity Version: 1.35.0 Depends: R (>= 3.3) Imports: AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid, mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats, topGO, utils Suggests: BiocStyle, caret, knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: bef43724dd0edf1636ca6ad6f1cea0b6 NeedsCompilation: no Package: CellMapper Version: 1.33.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 MD5sum: fe5dab5461e3585f50d53bbb6470a492 NeedsCompilation: no Package: cellmigRation Version: 1.15.0 Depends: R (>= 4.1), methods, foreach Imports: tiff, graphics, stats, utils, reshape2, parallel, doParallel, grDevices, matrixStats, FME, SpatialTools, sp, vioplot, FactoMineR, Hmisc Suggests: knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl License: GPL-2 MD5sum: 871eaa3d8450f20a1901eb12c9a7f6b5 NeedsCompilation: no Package: CellMixS Version: 1.23.0 Depends: kSamples, R (>= 4.0) Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne License: GPL (>= 2) MD5sum: 6afeca36732eaefa9ff7dc97c945651a NeedsCompilation: no Package: CellNOptR Version: 1.53.0 Depends: R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML, ggplot2, rmarkdown Imports: igraph, stringi, stringr Suggests: data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics, Enhances: doParallel, foreach License: GPL-3 MD5sum: 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Depends: R (>= 4.0), diffcyt Imports: BiocParallel, broom.mixed, dirmult, dplyr, edgeR, fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp, purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment, survival, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 License: MIT + file LICENSE MD5sum: e5461b6d2f9a4598ea9bde932891c747 NeedsCompilation: no Package: Cepo Version: 1.13.0 Depends: GSEABase, R (>= 4.1) Imports: DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors, methods, SingleCellExperiment, SummarizedExperiment, ggplot2, rlang, grDevices, patchwork, reshape2, BiocParallel, stats, dplyr, purrr Suggests: knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap License: MIT + file LICENSE MD5sum: 9d149c1c4b3d3d15fe020c4c6f9f350a NeedsCompilation: no Package: ceRNAnetsim Version: 1.19.0 Depends: R (>= 4.0.0), dplyr, tidygraph Imports: furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, 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utils, pbapply Suggests: RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2 License: GPL-2 MD5sum: 6e017319dae1668f1e65b807e1d54d49 NeedsCompilation: no Package: clustComp Version: 1.35.0 Depends: R (>= 3.3) Imports: sm, stats, graphics, grDevices Suggests: Biobase, colonCA, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: fbb81ed42b70cb0f4bd1fed7f2f0d11f NeedsCompilation: no Package: clusterExperiment Version: 2.27.0 Depends: R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>= 1.15.4), BiocGenerics Imports: methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, locfdr, matrixStats, graphics, parallel, BiocSingular, kernlab, stringr, S4Vectors, grDevices, DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma, mbkmeans LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown License: Artistic-2.0 MD5sum: d462c13a3acc5ea801a70ed8f72943d5 NeedsCompilation: yes Package: 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BiocManager, testthat License: Artistic-2.0 MD5sum: 201bcb9bd63b9b5280cb806eb98e89ca NeedsCompilation: no Package: clusterSeq Version: 1.31.0 Depends: R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats, utils Imports: BiocGenerics Suggests: BiocStyle License: GPL-3 MD5sum: 9606fb8e65f7f4295efa130ad7991888 NeedsCompilation: no Package: ClusterSignificance Version: 1.35.0 Depends: R (>= 3.3.0) Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr License: GPL-3 MD5sum: 180828de5b8e7302fa5d0f303328413a NeedsCompilation: no Package: clusterStab Version: 1.79.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 MD5sum: 19392e3300dff3428f5a78e0430bd8ae NeedsCompilation: no Package: clustifyr Version: 1.19.0 Depends: R (>= 2.10) Imports: cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, SeuratObject, matrixStats, S4Vectors, proxy, httr, utils Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr, data.table, R.utils License: MIT + file LICENSE MD5sum: cefad5e60f6637a481c2c436c97dab93 NeedsCompilation: no Package: ClustIRR Version: 1.5.19 Depends: R (>= 4.4.0) Imports: blaster, future, future.apply, grDevices, igraph, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils, posterior, visNetwork LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork License: GPL-3 + file LICENSE MD5sum: 1c94eabb5d3b3aad01aa116095dfeae2 NeedsCompilation: yes Package: CMA Version: 1.65.0 Depends: R (>= 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BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3 License: GPL-2 | file LICENSE License_restricts_use: yes MD5sum: 44968c337893c92471616e4c4995a154 NeedsCompilation: yes Package: CNORdt Version: 1.49.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 MD5sum: 19a2f6f9df4eef59c617526dbe1c32f5 NeedsCompilation: yes Package: CNORfeeder Version: 1.47.0 Depends: R (>= 3.6.0), CellNOptR (>= 1.4.0), graph Suggests: minet, Rgraphviz, RUnit, BiocGenerics, igraph Enhances: MEIGOR License: GPL-3 MD5sum: 77260819823417dd703c6727444bb0bf NeedsCompilation: no Package: CNORfuzzy Version: 1.49.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 MD5sum: 115431a9454047b57691ec9a305efc56 NeedsCompilation: yes Package: CNORode Version: 1.49.0 Depends: CellNOptR, genalg Suggests: knitr, rmarkdown Enhances: doParallel, foreach License: GPL-2 MD5sum: ec1d475cbe3074334b7791cc310ed5f8 NeedsCompilation: yes 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scales, graphics Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: d4b0bb354932a774411e4e08511c388f NeedsCompilation: no Package: CNVMetrics Version: 1.11.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, S4Vectors, BiocParallel, methods, magrittr, stats, pheatmap, gridExtra, grDevices, rBeta2009 Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 9b0c28070b9f28f92b89005a252cc4eb NeedsCompilation: no Package: CNVPanelizer Version: 1.39.0 Depends: R (>= 3.2.0), GenomicRanges Imports: BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx Suggests: knitr, RUnit License: GPL-3 MD5sum: 5e071195694f74b7fa1db1a0291f7a33 NeedsCompilation: no Package: CNVRanger Version: 1.23.0 Depends: GenomicRanges, RaggedExperiment Imports: BiocGenerics, BiocParallel, GDSArray, GenomeInfoDb, IRanges, S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR, gdsfmt, grDevices, lattice, limma, methods, plyr, qqman, rappdirs, reshape2, stats, utils Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, curatedTCGAData, ensembldb, grid, knitr, org.Hs.eg.db, regioneR, rmarkdown, statmod License: Artistic-2.0 MD5sum: 8d9acb74bfd7e5c6a717057c99257f87 NeedsCompilation: no Package: CNVrd2 Version: 1.45.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 MD5sum: 46b5295579d7ba61ac80ed920a86bc8d NeedsCompilation: no Package: CoCiteStats Version: 1.79.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL MD5sum: 5e7abfa5f40b15b26d821f87a97d12da NeedsCompilation: no Package: COCOA Version: 2.21.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices, simpleCache, fitdistrplus Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 0b6499cfd3252e7669def3df1dfcf63c NeedsCompilation: no Package: codelink Version: 1.75.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 MD5sum: 91bf478103badb5038f9dc258b7bb76e NeedsCompilation: no Package: CODEX Version: 1.39.0 Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors Suggests: WES.1KG.WUGSC License: GPL-2 MD5sum: e0bde123b3e651d0cf5f3dbfe8651ae1 NeedsCompilation: no Package: CoGAPS Version: 3.27.0 Depends: R (>= 3.5.0) Imports: BiocParallel, cluster, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5, dplyr, fgsea, forcats, ggplot2 LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject, BiocFileCache License: BSD_3_clause + file LICENSE MD5sum: 5b2558d10f8cfd0f1e22116aacf42aa6 NeedsCompilation: yes Package: cogena Version: 1.41.0 Depends: R (>= 3.6), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools Suggests: knitr, rmarkdown (>= 2.1) License: LGPL-3 MD5sum: 138e5acd3f1e63c2efff7257f301a554 NeedsCompilation: no Package: cogeqc Version: 1.11.0 Depends: R (>= 4.2.0) Imports: utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr License: GPL-3 MD5sum: d3a9c65194ccb0a197e3249ff4c253bd NeedsCompilation: no Package: Cogito Version: 1.13.0 Depends: R (>= 4.1), 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mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 License: MIT + file LICENSE MD5sum: 77e1c0e391db425af682aac505fa9ec6 NeedsCompilation: yes Package: comapr Version: 1.11.0 Depends: R (>= 4.1.0) Imports: methods, ggplot2, reshape2, dplyr, gridExtra, plotly, circlize, rlang, GenomicRanges, IRanges, foreach, BiocParallel, GenomeInfoDb, scales, RColorBrewer, tidyr, S4Vectors, utils, Matrix, grid, stats, SummarizedExperiment, plyr, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod License: MIT + file LICENSE MD5sum: 58203ae3e0017da6db666b74258db6a6 NeedsCompilation: no Package: coMethDMR Version: 1.11.0 Depends: R (>= 4.1) Imports: AnnotationHub, BiocParallel, bumphunter, ExperimentHub, GenomicRanges, IRanges, lmerTest, methods, stats, utils Suggests: BiocStyle, corrplot, knitr, rmarkdown, testthat, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: GPL-3 MD5sum: 347d785916496ecade0da58251f7e995 NeedsCompilation: no Package: COMPASS Version: 1.45.0 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach, coda LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress License: Artistic-2.0 MD5sum: 059d957ef76dca48274d0435f90dbaf9 NeedsCompilation: yes Package: compcodeR Version: 1.43.0 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: 17ef7033e2ea2d39d63316951483bc53 NeedsCompilation: no Package: compEpiTools Version: 1.41.0 Depends: R (>= 3.5.0), methods, topGO, GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, GenomeInfoDb Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer License: GPL MD5sum: a99e47d82a953db9f01925fc3abe1ebe NeedsCompilation: no Package: ComplexHeatmap Version: 2.23.0 Depends: R (>= 3.5.0), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.14), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges, matrixStats, foreach, doParallel, codetools Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo, magick License: MIT + file LICENSE MD5sum: 0446da886e3ab7b3d190ab7022c5833e NeedsCompilation: no Package: CompoundDb Version: 1.11.1 Depends: R (>= 4.1), methods, AnnotationFilter, S4Vectors Imports: BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges, Spectra (>= 1.15.10), MsCoreUtils, MetaboCoreUtils, BiocParallel, stringi Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf License: Artistic-2.0 MD5sum: 88e2cdb6b7c7cdf27762c9353e7ff3a4 NeedsCompilation: no Package: ComPrAn Version: 1.15.0 Imports: data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr, rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio, scales, shinydashboard, shinyjs, 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matrixStats, gplots, grDevices, methods, graphics, stats, utils Suggests: knitr, RUnit, rmarkdown, BiocGenerics License: BSD_3_clause + file LICENSE MD5sum: 6dfc91f751969a46ad60ee049bb9ec07 NeedsCompilation: no Package: ConsensusClusterPlus Version: 1.71.0 Imports: Biobase, ALL, graphics, stats, utils, cluster License: GPL-2 MD5sum: 3349265e3f12d49f470447109b61f2fa NeedsCompilation: no Package: consensusDE Version: 1.25.0 Depends: R (>= 3.5), BiocGenerics Imports: airway, AnnotationDbi, BiocParallel, Biobase, Biostrings, data.table, dendextend, DESeq2 (>= 1.20.0), EDASeq, ensembldb, edgeR, EnsDb.Hsapiens.v86, GenomicAlignments, GenomicFeatures, limma, org.Hs.eg.db, pcaMethods, RColorBrewer, Rsamtools, RUVSeq, S4Vectors, stats, SummarizedExperiment, TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 4d001adcc9619a5e927e8626b73fbc51 NeedsCompilation: no Package: consensusOV Version: 1.29.0 Depends: R (>= 3.6) Imports: Biobase, GSVA (>= 1.50.0), 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proto, spelling, knitr, data.table, gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery, sf, torch License: GPL-3 MD5sum: a81be7a2cc5860ea8807a5ede75efa08 NeedsCompilation: no Package: countsimQC Version: 1.25.0 Depends: R (>= 3.5) Imports: rmarkdown (>= 2.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr, ggplot2, grDevices, tools, SummarizedExperiment, genefilter, DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods, ragg Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 376604fc69c241e732589a8e1ce4bac5 NeedsCompilation: no Package: covEB Version: 1.33.0 Depends: R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats, LaplacesDemon, Matrix Suggests: curatedBladderData License: GPL-3 MD5sum: c6fccb6a6b1575a32a15e3c1dba5f14a NeedsCompilation: no Package: CoverageView Version: 1.45.0 Depends: R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer Imports: S4Vectors (>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges, 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BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat License: MIT + file LICENSE MD5sum: ccb317fdeef48fb0ce281c58cf547910 NeedsCompilation: no Package: crisprScore Version: 1.11.0 Depends: R (>= 4.1), crisprScoreData (>= 1.1.3) Imports: basilisk (>= 1.9.2), basilisk.utils (>= 1.9.1), BiocGenerics, Biostrings, IRanges, methods, randomForest, reticulate, stringr, utils, XVector Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 8ad0900366dc4839417cbb4e31c1113b NeedsCompilation: no Package: CRISPRseek Version: 1.47.0 Depends: R (>= 3.5.0), BiocGenerics, Biostrings Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges, BSgenome, hash, methods,reticulate,rhdf5,XVector, DelayedArray, GenomeInfoDb, GenomicRanges, dplyr, keras, mltools Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, 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utils, ChemmineR, methods, stats, rappdirs, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: c69d45b43d8f59f29c2181b8d4055339 NeedsCompilation: no Package: customProDB Version: 1.47.0 Depends: R (>= 3.5.0), IRanges, AnnotationDbi, biomaRt (>= 2.17.1) Imports: S4Vectors (>= 0.9.25), DBI, GenomeInfoDb, GenomicRanges, Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>= 2.26.3), GenomicFeatures (>= 1.32.0), stringr, RCurl, plyr, VariantAnnotation (>= 1.13.44), rtracklayer, RSQLite, txdbmaker, AhoCorasickTrie, methods Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 8f984d30426ec22018c61ed5257593a5 NeedsCompilation: no Package: cyanoFilter Version: 1.15.0 Depends: R(>= 4.1.0) Imports: Biobase, flowCore, flowDensity, flowClust, cytometree, ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats, utils Suggests: magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr License: MIT + file LICENSE MD5sum: ed0c631580079d5e35eb08d724362b66 NeedsCompilation: no Package: cycle Version: 1.61.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 MD5sum: c079f6a45d40d08a9587a25d193ade97 NeedsCompilation: no Package: cydar Version: 1.31.0 Depends: SingleCellExperiment Imports: viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment, flowCore, Biobase, Rcpp, BiocNeighbors LinkingTo: Rcpp Suggests: ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet, BiocStyle, flowStats License: GPL-3 MD5sum: ac1cf0b54fabbf2c5d0e9da41ef3d74d NeedsCompilation: yes Package: cypress Version: 1.3.0 Depends: R(>= 4.4.0) Imports: stats, abind, sirt, MASS,TOAST, tibble, parallel, preprocessCore, SummarizedExperiment, TCA, PROPER, methods,dplyr, utils, RColorBrewer, graphics, edgeR, BiocParallel, checkmate, mvtnorm, DESeq2, rlang, e1071 Suggests: knitr, rmarkdown, MatrixGenerics, htmltools, RUnit, BiocGenerics, BiocManager, BiocStyle, Biobase License: GPL-2 | GPL-3 MD5sum: 0f2d0c3caf6728c436ced1e6eec80710 NeedsCompilation: no Package: CytoDx Version: 1.27.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: a76e2818defebc6ee52d7db89ca05aba NeedsCompilation: no Package: cytofQC Version: 1.7.0 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: eae97fef9f8d5cad360eab08db0efebc NeedsCompilation: no Package: CytoGLMM Version: 1.15.0 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: 9a982cf44a2bf596af4ebf47a05cbd7c NeedsCompilation: no Package: cytoKernel Version: 1.13.0 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: 19ac987980b40a8b3af152f64249d956 NeedsCompilation: yes Package: cytolib Version: 2.19.0 Depends: R (>= 3.4) Imports: RProtoBufLib LinkingTo: BH(>= 1.84.0.0), RProtoBufLib(>= 2.13.1),Rhdf5lib Suggests: knitr, rmarkdown License_restricts_use: no MD5sum: f1ff44367c26145e846cfafb78c60b92 NeedsCompilation: yes Package: cytomapper Version: 1.19.0 Depends: R (>= 4.0), EBImage, SingleCellExperiment, methods Imports: SpatialExperiment, S4Vectors, BiocParallel, HDF5Array, DelayedArray, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5, nnls Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest License: GPL (>= 2) MD5sum: 72bc35f6b440d126a9e33854b8c7671d NeedsCompilation: no Package: CytoMDS Version: 1.3.3 Depends: R (>= 4.4), Biobase Imports: methods, stats, rlang, pracma, withr, flowCore, reshape2, ggplot2, ggrepel, ggforce, patchwork, transport, smacof, BiocParallel, CytoPipeline Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, HDCytoData License: GPL-3 MD5sum: 01a2283c6053f7bb66a452a23c72022b NeedsCompilation: no Package: cytoMEM Version: 1.11.0 Depends: R (>= 4.2.0) Imports: gplots, tools, flowCore, grDevices, stats, utils, matrixStats, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 6b6b20b55ff738e2d72a61333965a930 NeedsCompilation: no Package: CytoML Version: 2.19.0 Depends: R (>= 3.5.0) Imports: cytolib(>= 2.3.10), flowCore (>= 1.99.10), flowWorkspace (>= 4.1.8), openCyto (>= 1.99.2), XML, data.table, jsonlite, RBGL, Rgraphviz, Biobase, methods, graph, graphics, utils, jsonlite, dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, stats, tibble LinkingTo: cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, flowWorkspace Suggests: testthat, flowWorkspaceData , knitr, rmarkdown, parallel License_restricts_use: no MD5sum: f544d1272b12eb55647bb965ecdcb930 NeedsCompilation: yes Package: CytoPipeline Version: 1.7.0 Depends: R (>= 4.4) Imports: methods, stats, utils, withr, rlang, ggplot2 (>= 3.4.1), ggcyto, BiocFileCache, BiocParallel, flowCore, PeacoQC, flowAI, diagram, jsonlite, scales Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, reshape2, dplyr, CytoPipelineGUI License: GPL-3 MD5sum: 9b9c1c2ebaf363445d3211f740a84dea NeedsCompilation: no Package: CytoPipelineGUI Version: 1.5.0 Depends: R (>= 4.4), CytoPipeline Imports: shiny, plotly, ggplot2, flowCore Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, patchwork License: GPL-3 MD5sum: e82fb0ecbb5cb5f48ba97ae619db8923 NeedsCompilation: no Package: cytoviewer Version: 1.7.0 Imports: shiny, shinydashboard, utils, colourpicker, shinycssloaders, svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite, EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 MD5sum: 387a359545f6a1d55d1aceaf1ab1da9d NeedsCompilation: no Package: dada2 Version: 1.35.0 Depends: R (>= 3.4.0), Rcpp (>= 0.12.0), methods (>= 3.4.0) Imports: Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), ShortRead (>= 1.32.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0), IRanges (>= 2.6.0), XVector (>= 0.16.0), BiocGenerics (>= 0.22.0) LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, knitr, rmarkdown License: LGPL-2 MD5sum: d767058a803a99a0088bcdc1b36d0a0b NeedsCompilation: yes Package: dagLogo Version: 1.45.0 Depends: R (>= 3.0.1), methods, grid Imports: pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils, biomaRt, motifStack, httr Suggests: XML, grImport, grImport2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: ca53899791ab56a7ec86040840135b5b NeedsCompilation: no Package: daMA Version: 1.79.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: 6e4f9cd46aede1142190567da6366c7a NeedsCompilation: no Package: DAMEfinder Version: 1.19.0 Depends: R (>= 4.0) Imports: stats, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, readr, SummarizedExperiment, GenomicAlignments, stringr, plyr, VariantAnnotation, parallel, ggplot2, Rsamtools, BiocGenerics, methods, limma, bumphunter, Biostrings, reshape2, cowplot, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: f6b04e6869776783be1f6b7d096b5020 NeedsCompilation: no Package: DaMiRseq Version: 2.19.0 Depends: R (>= 3.5.0), SummarizedExperiment, ggplot2 Imports: DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap, FactoMineR, corrplot, randomForest, e1071, caret, MASS, lubridate, plsVarSel, kknn, FSelector, methods, stats, utils, graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR, plyr Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: a0f37a727c6ec9e1a4da2479ef478c5a NeedsCompilation: no Package: Damsel Version: 1.3.0 Depends: R (>= 4.4.0) Imports: AnnotationDbi, Biostrings, ComplexHeatmap, dplyr, edgeR, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggbio, ggplot2, goseq, magrittr, patchwork, plyranges, reshape2, rlang, Rsamtools, Rsubread, stats, stringr, tidyr, utils Suggests: BiocStyle, biomaRt, biovizBase, BSgenome.Dmelanogaster.UCSC.dm6, knitr, limma, org.Dm.eg.db, rmarkdown, testthat (>= 3.0.0), TxDb.Dmelanogaster.UCSC.dm6.ensGene License: MIT + file LICENSE MD5sum: e70cdd63daa72624366351094f6647bf NeedsCompilation: no Package: DAPAR Version: 1.39.0 Depends: R (>= 4.3.0) Imports: Biobase, MSnbase, DAPARdata (>= 1.30.0), utils, highcharter, foreach Suggests: testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph, diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR, factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster, forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr, norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr, limma, preprocessCore, stringr, tidyr, impute, gplots, grDevices, reshape2, graphics, stats, methods, ggplot2, RColorBrewer, Matrix, org.Sc.sgd.db License: Artistic-2.0 MD5sum: 4a962ed160ce46e3fa72e9d6a9fdf327 NeedsCompilation: no Package: DART Version: 1.55.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: 36a2a2fcff52bb2bf06ce58191b633de NeedsCompilation: no Package: dcanr Version: 1.23.0 Depends: R (>= 3.6.0) Imports: igraph, foreach, plyr, stringr, reshape2, methods, Matrix, graphics, stats, RColorBrewer, circlize, doRNG Suggests: EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 MD5sum: 8d6ed7913505b790d657ee2838168868 NeedsCompilation: no Package: DCATS Version: 1.5.0 Depends: R (>= 4.1.0), stats Imports: MCMCpack, matrixStats, robustbase, aod, e1071 Suggests: testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 1faa56842660f648d975a7435404ab5e NeedsCompilation: no Package: dce Version: 1.13.0 Depends: R (>= 4.1) Imports: 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: a369874285bc5f4d10415002ecdc1f03 NeedsCompilation: no Package: dcGSA Version: 1.35.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: 8b69f62dae97659decd1474bf8dc025a NeedsCompilation: no Package: ddCt Version: 1.63.0 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: 504a29359b77f2c92062c045efc9ccd8 NeedsCompilation: no Package: ddPCRclust Version: 1.27.0 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: fcbab27498957051a01a8cfd2d6bdd08 NeedsCompilation: no Package: dearseq Version: 1.19.0 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: d844621512866203027e15927a6ae97d NeedsCompilation: no Package: debCAM Version: 1.25.0 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: 5a9e48ce4f179d28d875fcf6934a5c8f NeedsCompilation: no Package: debrowser Version: 1.35.0 Depends: R (>= 3.5.0), Imports: shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT, ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE, igraph, grDevices, graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker, plotly, heatmaply, Harman, pathview, apeglm, ashr Suggests: testthat, rmarkdown, knitr License: GPL-3 + file LICENSE MD5sum: a507a1fa8f86e785267477165496caaa NeedsCompilation: no Package: DECIPHER Version: 3.3.2 Depends: R (>= 3.5.0), Biostrings (>= 2.59.1), stats Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector Suggests: RSQLite (>= 1.1) License: GPL-3 MD5sum: d94ea706af8c8ee1ac9ac9db9eba6993 NeedsCompilation: yes Package: decompTumor2Sig Version: 2.23.0 Depends: R(>= 4.0), ggplot2 Imports: methods, Matrix, quadprog(>= 1.5-5), GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table, GenomeInfoDb, readxl Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 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BSgenome.Hsapiens.UCSC.hg38, BiocStyle, magick, knitr, rmarkdown, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 53dd1a5436d63aef7abdbe68af6231ca NeedsCompilation: no Package: DegNorm Version: 1.17.0 Depends: R (>= 4.0.0), methods Imports: Rcpp (>= 1.0.2),GenomicFeatures, txdbmaker, parallel, foreach, S4Vectors, doParallel, Rsamtools (>= 1.31.2), GenomicAlignments, heatmaply, data.table, stats, ggplot2, GenomicRanges, IRanges, plyr, plotly, utils,viridis LinkingTo: Rcpp, RcppArmadillo,S4Vectors,IRanges Suggests: knitr,rmarkdown,formatR License: LGPL (>= 3) MD5sum: a270193c5a572ef23c5e4f5507f920ad NeedsCompilation: yes Package: DEGraph Version: 1.59.0 Depends: R (>= 2.10.0), R.utils Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph License: GPL-3 MD5sum: ffc8b9f4519a263767159b1f9372e139 NeedsCompilation: no 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RcppRoll, betareg, grDevices, graphics, methods, stats, utils Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 819431e473505cab31a0f8f4e70629af NeedsCompilation: no Package: DMRcate Version: 3.3.1 Depends: R (>= 4.3.0) Imports: AnnotationHub, ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment, biomaRt, grDevices Suggests: knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest License: file LICENSE MD5sum: 0a19832d3f5a7d5a07cbe6a2e2f8cc77 NeedsCompilation: no Package: dmrseq Version: 1.27.0 Depends: R (>= 3.5), bsseq Imports: GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer, bumphunter, DelayedMatrixStats (>= 1.1.13), matrixStats, BiocParallel, outliers, methods, locfit, IRanges, grDevices, graphics, stats, utils, annotatr, AnnotationHub, rtracklayer, GenomeInfoDb, splines Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 8b6eff5f6dce9ecc2873c58d938eed38 NeedsCompilation: no Package: DNABarcodeCompatibility Version: 1.23.0 Depends: R (>= 3.6.0) Imports: dplyr, tidyr, numbers, purrr, stringr, stats, utils, methods, Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: file LICENSE MD5sum: 20e9daec0e78088b5d751c8dbb81912f NeedsCompilation: yes Package: DNABarcodes Version: 1.37.0 Depends: Matrix, parallel Imports: Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, BiocStyle, rmarkdown License: GPL-2 MD5sum: cc7e4318d686a7875a8a28486082e4e0 NeedsCompilation: yes Package: DNAcopy Version: 1.81.0 License: GPL (>= 2) MD5sum: fc6cac7f73017c8148f7d12f64f76aaf NeedsCompilation: yes Package: DNAfusion Version: 1.9.0 Depends: R (>= 4.2.0) Imports: 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grDevices, graphics, methods, parallel, stats, utils, IRanges, GenomeInfoDb, S4Vectors, GenomicFeatures, TCGAbiolinks (>= 2.23.7), plyr, Matrix, dplyr, Gviz, ComplexHeatmap, circlize, MultiAssayExperiment, SummarizedExperiment, biomaRt, doParallel, downloader, ggrepel, lattice, magrittr, readr, scales, rvest, xml2, plotly, gridExtra, rmarkdown, stringr, tibble, tidyr, progress, purrr, reshape2, ggpubr, rtracklayer (>= 1.61.2), DelayedArray Suggests: BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData License: GPL-3 MD5sum: eac9ad812c49757fa74ccb07d72ff339 NeedsCompilation: no Package: EMDomics Version: 2.37.0 Depends: R (>= 3.2.1) Imports: emdist, BiocParallel, matrixStats, ggplot2, CDFt, preprocessCore Suggests: knitr License: MIT + file LICENSE MD5sum: 45681860bf8d9c9364cb4ba03999d0b8 NeedsCompilation: no Package: EmpiricalBrownsMethod Version: 1.35.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, testthat, 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magrittr, methods, pheatmap, graphics, utils, purrr, tidyr, stats Suggests: knitr, rmarkdown, org.Hs.eg.db, testthat (>= 3.0.0), BiocStyle License: MIT + file LICENSE MD5sum: 7f906e0b549aa2bfdef20f22c1b27465 NeedsCompilation: no Package: EnrichedHeatmap Version: 1.37.0 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: 4c2c644daf9ec8f4dfa8b53aecc3cf79 NeedsCompilation: yes Package: EnrichmentBrowser Version: 2.37.0 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, 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License: Artistic-2.0 MD5sum: bed8197731a8b8d52b0dd546efdd59eb NeedsCompilation: no Package: ensembldb Version: 2.31.0 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: cc0c3b5af780df595713644ad36a0dcb NeedsCompilation: no Package: epialleleR Version: 1.15.1 Depends: R (>= 4.1) Imports: stats, methods, utils, data.table, BiocGenerics, GenomicRanges, Rcpp LinkingTo: Rcpp, BH, Rhtslib Suggests: GenomeInfoDb, SummarizedExperiment, VariantAnnotation, RUnit, knitr, rmarkdown, ggplot2 License: Artistic-2.0 MD5sum: e28f7acd21d27b9f091d33b1f3a27e16 NeedsCompilation: yes Package: EpiCompare Version: 1.11.0 Depends: R (>= 4.2.0) Imports: AnnotationHub, 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: 5ad7c2754505af5391abba542cdd42b7 NeedsCompilation: no Package: epidecodeR Version: 1.15.0 Depends: R (>= 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bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5, Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap, grDevices LinkingTo: Rcpp, RcppArmadillo, Rhdf5lib Suggests: testthat, knitr, rmarkdown, BiocStyle, BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData License: MIT + file LICENSE MD5sum: 0e85fd394d77a5e1684fd675387d6cc1 NeedsCompilation: yes Package: EpiMix Version: 1.9.0 Depends: R (>= 4.2.0), EpiMix.data (>= 1.2.2) Imports: AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table, doParallel, doSNOW, downloader, dplyr, ELMER.data, ExperimentHub, foreach, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, impute, IRanges, limma, methods, parallel, plyr, progress, R.matlab, RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, utils Suggests: BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, 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Package: epiNEM Version: 1.31.0 Depends: R (>= 4.1) Imports: BoutrosLab.plotting.general, BoolNet, e1071, gtools, stats, igraph, utils, lattice, latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph, mnem, latex2exp Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle License: GPL-3 MD5sum: ecb80a0c5c040677b87a82f5df5b9a99 NeedsCompilation: no Package: EpipwR Version: 1.1.0 Depends: R (>= 4.4.0) Imports: EpipwR.data, ExperimentHub (>= 2.10.0), ggplot2 Suggests: knitr, rmarkdown, testthat (>= 3.0.0), sessioninfo License: Artistic-2.0 MD5sum: e18f3eae20a1c90e2185739208b8bfbd NeedsCompilation: no Package: epiregulon Version: 1.3.2 Depends: R (>= 4.4), SingleCellExperiment Imports: AnnotationHub, BiocParallel, ExperimentHub, Matrix, Rcpp, S4Vectors, SummarizedExperiment, bluster, checkmate, entropy, lifecycle, methods, scran, scuttle, stats, utils, scMultiome (>= 1.7.1), GenomeInfoDb, GenomicRanges, AUCell, 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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: 4fe2007e8a3a5219e937f574ce839987 NeedsCompilation: no Package: epistasisGA Version: 1.9.0 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: eaa51002720a5d4f3b2e4f071a9ed4a8 NeedsCompilation: yes Package: EpiTxDb Version: 1.19.0 Depends: R (>= 4.0), AnnotationDbi, Modstrings Imports: methods, utils, httr, xml2, curl, rex, GenomicFeatures, txdbmaker, GenomicRanges, GenomeInfoDb, BiocGenerics, BiocFileCache, S4Vectors, IRanges, RSQLite, DBI, Biostrings, tRNAdbImport Suggests: BiocStyle, knitr, rmarkdown, testthat, httptest, AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: 37b0707c145961ac3d61bdd9aa073432 NeedsCompilation: no Package: epivizr Version: 2.37.0 Depends: R (>= 3.5.0), methods Imports: epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4), GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown License: Artistic-2.0 MD5sum: 146b736e811b17d71e0877d27069811e NeedsCompilation: no Package: epivizrChart Version: 1.29.0 Depends: R (>= 3.5.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, 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BiocStyle, gDRtestData (>= 1.3.3), gDRstyle (>= 1.3.3), knitr, purrr, qs, testthat License: Artistic-2.0 MD5sum: f62ac29a2a1ea8fcdd7e8832cf5e32ef NeedsCompilation: no Package: gDRstyle Version: 1.5.1 Depends: R (>= 4.2) Imports: BiocCheck, BiocManager, checkmate, desc, git2r, lintr (>= 3.0.0), rcmdcheck, remotes, yaml, rjson, pkgbuild, withr Suggests: BiocStyle, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: cf279af02844745a4e6211f5e1b4895c NeedsCompilation: no Package: gDRutils Version: 1.5.5 Depends: R (>= 4.2) Imports: BiocParallel, BumpyMatrix, checkmate, data.table, drc, jsonlite, jsonvalidate, methods, MultiAssayExperiment, S4Vectors, stats, stringr, SummarizedExperiment Suggests: BiocManager, BiocStyle, futile.logger, gDRstyle (>= 1.1.5), gDRtestData (>= 1.1.10), IRanges, knitr, lintr, purrr, qs, rcmdcheck, rmarkdown, scales, testthat, tools, yaml License: Artistic-2.0 MD5sum: 62892d0c4db02871ebf86da2f61b54bc NeedsCompilation: no Package: GDSArray Version: 1.27.0 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pcaExplorer, AnnotationDbi, macrophage, topGO, biomaRt, ReactomePA, clusterProfiler, BiocStyle, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 5cc01f63020533b4e6eccee1d88b7a2f NeedsCompilation: no Package: GEM Version: 1.33.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown License: Artistic-2.0 MD5sum: f27b9a0b5fd77003d0af5e4943a957ae NeedsCompilation: no Package: gemini Version: 1.21.0 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: 330252ffa777c92b6e0295d5d3df544a NeedsCompilation: no Package: gemma.R Version: 3.3.0 Imports: magrittr, glue, memoise, jsonlite, data.table, rlang, lubridate, utils, stringr, SummarizedExperiment, Biobase, tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat, digest, R.utils, base64enc Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, kableExtra, listviewer, shiny License: Apache License (>= 2) MD5sum: c86375579111b2bf5767268472222a66 NeedsCompilation: no Package: genArise Version: 1.83.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: 453cbd6a5b9e5f1411844da5d3eb2bca NeedsCompilation: no Package: geneAttribution Version: 1.33.0 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: f1ea9e6c0bf1546579c01e0dfcdf3fa1 NeedsCompilation: no Package: GeneBreak Version: 1.37.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: ed08e1367fe12a67c536532cae31a8c1 NeedsCompilation: no Package: geneClassifiers Version: 1.31.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: b3f5b0f806bf0467c2240e66284e538c NeedsCompilation: no Package: GeneExpressionSignature Version: 1.53.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: adb44f8d0655c4d19e0c2163172313da NeedsCompilation: no Package: genefilter Version: 1.89.0 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: c0a7aa5a34dd32fd0e5fd88261c2d009 NeedsCompilation: yes Package: genefu Version: 2.39.1 Depends: R (>= 4.1), survcomp, biomaRt, iC10, AIMS Imports: amap, impute, mclust, limma, graphics, stats, utils, iC10TrainingData Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown License: Artistic-2.0 MD5sum: 084b70ba6d34ccabc01decb6414e8403 NeedsCompilation: no Package: GeneGA Version: 1.57.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: 4f83d6ab6ade79efb21d1570af95ec49 NeedsCompilation: no Package: GeneGeneInteR Version: 1.33.0 Depends: R (>= 4.0) Imports: snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods License: GPL (>= 2) MD5sum: ce52e64c41a3fb0331b7e4338cd27081 NeedsCompilation: yes Package: GeneMeta Version: 1.79.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: 533275774692525b0f6d8b69a0ea281e NeedsCompilation: no Package: GeneNetworkBuilder Version: 1.49.0 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, RCy3, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db License: GPL (>= 2) MD5sum: edfd464618335f78360ca90e4c0064d9 NeedsCompilation: yes Package: GeneOverlap Version: 1.43.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 86d88b9f8468f7baff086509fac46253 NeedsCompilation: no Package: geneplast Version: 1.33.0 Depends: R (>= 4.0), methods Imports: igraph, snow, ape, grDevices, graphics, stats, utils, data.table Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: 2bc0bf20bcc0c9ad776c9a12a041e52a NeedsCompilation: no Package: geneplotter Version: 1.85.0 Depends: R (>= 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Package: GeneSelectMMD Version: 2.51.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: 62e4a9091a54608ce93ab740c6bb32b6 NeedsCompilation: yes Package: GENESIS Version: 2.37.0 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: dc45129f64991877763e2379f72474e7 NeedsCompilation: yes Package: GeneStructureTools Version: 1.27.0 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: 2dc8927a7c3358f42c847d48cfedf8b6 NeedsCompilation: no Package: geNetClassifier Version: 1.47.0 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: dc1abac4f7ed1509a9d4bc0a62024e3b NeedsCompilation: no Package: GeneticsPed Version: 1.69.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: e6abe1c9f8c6713677b635d23d6ee3b8 NeedsCompilation: yes Package: GeneTonic Version: 3.1.1 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 (>= 3.5.0), ggrepel, ggridges, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, mosdef (>= 1.1.0), 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: 4934de7c2b1229b82e62bf612ec49dd0 NeedsCompilation: no Package: geneXtendeR Version: 1.33.0 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: 9626a7a4d239aa4c3dce8fd3864e7432 NeedsCompilation: yes Package: GENIE3 Version: 1.29.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, 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GenomeInfoDb, GenomicRanges, IRanges, matrixStats, XVector, dplyr, data.table, parallel, doParallel, foreach, methods, S4Vectors, stats, numbers, utils Suggests: spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr License: Artistic-2.0 MD5sum: 6375add4544342e94c2daa019db2719d NeedsCompilation: no Package: GenomeInfoDb Version: 1.43.2 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.45.2), IRanges (>= 2.41.1) Imports: stats, stats4, utils, UCSC.utils, 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: 08c11918e2a46803836f4fffbeaa9de4 NeedsCompilation: no Package: genomeIntervals Version: 1.63.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 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License: Artistic-2.0 MD5sum: 2e03f7ccaecb69c76382bcac5d4e3849 NeedsCompilation: yes Package: GenomicDataCommons Version: 1.31.0 Depends: R (>= 4.1.0) Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, tibble, tidyr Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table License: Artistic-2.0 MD5sum: 2614b49ae889fec0028d20c4d4318fa0 NeedsCompilation: no Package: GenomicDistributions Version: 1.15.0 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: a6a9291416dc08b35c7a31187da9240c NeedsCompilation: no Package: GenomicFeatures Version: 1.59.1 Depends: R (>= 3.5.0), BiocGenerics (>= 0.51.2), S4Vectors (>= 0.17.29), IRanges (>= 2.37.1), GenomeInfoDb (>= 1.35.8), GenomicRanges (>= 1.55.2), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, DBI, XVector, Biostrings, rtracklayer Suggests: txdbmaker, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), 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: 7b12f556e66b1cc86f47c3b8fba885f5 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IRanges, RBGL, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: file LICENSE MD5sum: 60a4a61ea60ad5e946cd41a7762a53f5 NeedsCompilation: no Package: GenomicInteractions Version: 1.41.0 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: 72890628f2db2d7333bb6a9188d09fce NeedsCompilation: no Package: GenomicOZone Version: 1.21.0 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: 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VennDiagram, withr License: GPL-3 MD5sum: 1674da34f781b5a36088759e54528683 NeedsCompilation: no Package: GlobalAncova Version: 4.25.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: 95f934dc780d868a0edfa9a535b44cff NeedsCompilation: yes Package: globalSeq Version: 1.35.0 Depends: R (>= 3.0.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 MD5sum: 82503f8353883178ee5503ae12c8b245 NeedsCompilation: no Package: globaltest Version: 5.61.0 Depends: methods, survival Imports: Biobase, AnnotationDbi, annotate, graphics Suggests: vsn, golubEsets, KEGGREST, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart, mstate License: GPL (>= 2) MD5sum: 1b16186bde528acc0ce0766249f8984f NeedsCompilation: no Package: GloScope Version: 1.5.0 Depends: R (>= 4.4.0) Imports: utils, stats, MASS, mclust, ggplot2, RANN, FNN, BiocParallel, mvnfast, SingleCellExperiment, rlang Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown, zellkonverter License: Artistic-2.0 MD5sum: 9fded23ee3a3e47a413f0632ca535a59 NeedsCompilation: no Package: gmapR Version: 1.49.0 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2) Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome, GenomicAlignments (>= 1.15.6), BiocParallel Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines License: Artistic-2.0 MD5sum: b42d9c94e51a80c60b0aac79a8bf42f3 NeedsCompilation: yes Package: GmicR Version: 1.21.0 Imports: AnnotationDbi, ape, bnlearn, Category, DT, doParallel, foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db, org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics, reshape2, stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 + file LICENSE MD5sum: 319ed322a3c55d2a74d8f64a59eba19c NeedsCompilation: no Package: gmoviz Version: 1.19.0 Depends: circlize, GenomicRanges, graphics, R (>= 4.0) Imports: grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics, Biostrings, GenomeInfoDb, methods, GenomicAlignments, GenomicFeatures, IRanges, rtracklayer, pracma, colorspace, S4Vectors Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager License: GPL-3 MD5sum: c4a8540b1a0fa3fd8183ebf07dd150a5 NeedsCompilation: no Package: GMRP Version: 1.35.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: b83e883e39526efa3aacdf3d25c6af25 NeedsCompilation: no Package: GNET2 Version: 1.23.0 Depends: R (>= 3.6) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment,dplyr,igraph, grDevices, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 MD5sum: 75259c0f570ea6ae1e968f8fe552f392 NeedsCompilation: yes Package: GNOSIS Version: 1.5.0 Depends: R (>= 4.3.0), shiny, shinydashboard, shinydashboardPlus, dashboardthemes, shinyWidgets, shinymeta, tidyverse, operator.tools, maftools Imports: DT, fontawesome, shinycssloaders, cBioPortalData, shinyjs, reshape2, RColorBrewer, survival, survminer, stats, compareGroups, rpart, partykit, DescTools, car, rstatix, fabricatr, shinylogs, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 8122dc73fb552a75eccf80fb0d28b747 NeedsCompilation: no Package: GOexpress Version: 1.41.0 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), 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BiocManager, BiocStyle, knitr, rmarkdown, org.At.tair.db, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcSakai.eg.db, org.EcK12.eg.db, org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Pt.eg.db, org.Xl.eg.db License: GPL-3 MD5sum: 26d4c4e929aca5f1f4d36f78b1c9c434 NeedsCompilation: no Package: goSTAG Version: 1.31.0 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: a07925ede5f939382476258e53ad1444 NeedsCompilation: no Package: GOstats Version: 2.73.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.43.2), graph Imports: methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, 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progress, utils, methods, stringr, tools, scales, igraph, S4Vectors, ggplot2, rlang, Biostrings, GenomeInfoDb (>= 1.34.8), SummarizedExperiment, forcats, gridExtra, limma, tidyselect, readr, grid, tidyr (>= 1.3.0), dplyr, stats, grDevices, graphics, magrittr, tibble, viridis, colorspace, biomaRt, topGO, AnnotationHub, ensembldb Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Mmulatta.UCSC.rheMac10, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm39.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, 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840e3d21b837d7a97c068ea2fa2ccd61 NeedsCompilation: no Package: GSEABase Version: 1.69.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.13.8), Biobase (>= 2.17.8), annotate (>= 1.45.3), methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr, RUnit License: Artistic-2.0 MD5sum: da00e58239d65a1a25122685963540d2 NeedsCompilation: no Package: GSEABenchmarkeR Version: 1.27.0 Depends: R (>= 3.5.0), Biobase, SummarizedExperiment Imports: AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, S4Vectors, stats, utils Suggests: BiocStyle, GSE62944, knitr, rappdirs, rmarkdown License: Artistic-2.0 MD5sum: 8d4bbd34303acf44f0614054cdd1aa23 NeedsCompilation: no Package: GSEAlm Version: 1.67.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: 2486c505d9f23474c702e814cef676cf NeedsCompilation: no Package: GSEAmining Version: 1.17.0 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: 687e214c785f18de67516123de3206ea NeedsCompilation: no Package: gsean Version: 1.27.0 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi, knitr, plotly, WGCNA, rmarkdown License: Artistic-2.0 MD5sum: e04286a690b56f7042c21ae4c08c183d NeedsCompilation: yes Package: GSgalgoR Version: 1.17.0 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: 32f43d5754160bf6fb5b6352e92a314c NeedsCompilation: no Package: GSReg Version: 1.41.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi Suggests: GenomicRanges, GSBenchMark License: GPL-2 MD5sum: f29c09b7f03d4bda2b4e1eff2ac7a0a3 NeedsCompilation: yes Package: GSRI Version: 2.55.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 MD5sum: d0c5140cb37bdbfa082741f95884dd5a NeedsCompilation: no Package: GSVA Version: 2.1.4 Depends: R (>= 3.5.0) Imports: methods, stats, utils, graphics, S4Vectors, IRanges, Biobase, SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel, BiocParallel, SingleCellExperiment, SpatialExperiment, sparseMatrixStats, DelayedArray, DelayedMatrixStats, HDF5Array, BiocSingular, cli LinkingTo: cli Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinydashboard, ggplot2, data.table, plotly, future, promises, shinybusy, shinyjs License: GPL (>= 2) MD5sum: aa179e6252e9b9000c9c2b9db137fe10 NeedsCompilation: yes Package: gtrellis Version: 1.39.0 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: b9045b6bb4acfbed12419baa8768681d NeedsCompilation: no Package: GUIDEseq Version: 1.37.0 Depends: R (>= 3.5.0), GenomicRanges, BiocGenerics Imports: Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma,dplyr, GenomicFeatures, rio, tidyr, tools, methods, purrr, ggplot2, openxlsx, patchwork, rlang Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 7ea8ae85c95700b0244a6bdc547235d6 NeedsCompilation: no Package: Guitar Version: 2.23.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges, magrittr, ggplot2, methods, stats,utils ,knitr,dplyr License: GPL-2 MD5sum: 8885c8ad55a7639303addac39369712e NeedsCompilation: no Package: Gviz Version: 1.51.0 Depends: R (>= 4.3), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.17.20), grid Imports: XVector (>= 0.5.7), rtracklayer (>= 1.25.13), lattice, RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5), Biobase (>= 2.15.3), GenomicFeatures (>= 1.17.22), ensembldb (>= 2.11.3), BSgenome (>= 1.33.1), Biostrings (>= 2.33.11), biovizBase (>= 1.13.8), Rsamtools (>= 1.17.28), latticeExtra (>= 0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>= 1.1.16), GenomeInfoDb (>= 1.1.3), BiocGenerics (>= 0.11.3), digest(>= 0.6.8), graphics, grDevices, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 7d5393d2029b0e09f2ad52adb60abc4e NeedsCompilation: no Package: GWAS.BAYES Version: 1.17.0 Depends: R (>= 4.3.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), limma (>= 3.54.0), stats (>= 4.2.2), MASS (>= 7.3-58.1) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP License: GPL-3 + file LICENSE MD5sum: 8240beed7ffee9b583e661db57e4b2c1 NeedsCompilation: no Package: gwascat Version: 2.39.0 Depends: R (>= 3.5.0), methods Imports: S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges (>= 1.29.6), GenomicFeatures, readr, Biostrings, AnnotationDbi, BiocFileCache, snpStats, VariantAnnotation, AnnotationHub Suggests: DO.db, DT, knitr, RBGL, testthat, rmarkdown, dplyr, Gviz, Rsamtools, rtracklayer, graph, ggbio, DelayedArray, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BiocStyle Enhances: SNPlocs.Hsapiens.dbSNP144.GRCh37 License: Artistic-2.0 MD5sum: 15f505e9dc87b627305eb2214c09a938 NeedsCompilation: no Package: GWASTools Version: 1.53.0 Depends: Biobase Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr License: Artistic-2.0 MD5sum: 35e335f32b53b5ead5085039a768010a NeedsCompilation: no Package: gwasurvivr Version: 1.25.0 Depends: R (>= 3.4.0) Imports: GWASTools, survival, VariantAnnotation, parallel, matrixStats, SummarizedExperiment, stats, utils, SNPRelate Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 1d5f28130207c5065e692cc7545e2201 NeedsCompilation: no Package: GWENA Version: 1.17.0 Depends: R (>= 4.1) Imports: WGCNA (>= 1.67), dplyr (>= 0.8.3), 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d3435039c6516e3674560cebe524fc18 NeedsCompilation: no Package: heatmaps Version: 1.31.0 Depends: R (>= 3.5.0) Imports: methods, grDevices, graphics, stats, Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage, RColorBrewer, BiocGenerics, GenomeInfoDb Suggests: BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 64872a90e60068f12c49744a64153dfc NeedsCompilation: no Package: Heatplus Version: 3.15.0 Imports: graphics, grDevices, stats, RColorBrewer Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) MD5sum: d63b8115d5202e58f7c7d0d74c96ec0e NeedsCompilation: no Package: HelloRanges Version: 1.33.0 Depends: methods, BiocGenerics, S4Vectors (>= 0.17.39), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.10), Biostrings (>= 2.41.3), BSgenome, GenomicFeatures (>= 1.31.5), VariantAnnotation (>= 1.19.3), Rsamtools, GenomicAlignments (>= 1.15.7), rtracklayer (>= 1.33.8), GenomeInfoDb, SummarizedExperiment, BiocIO Imports: docopt, stats, 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httr, knitr, rmarkdown, statmod, testthat (>= 2.0), vdiffr License: Apache License 2.0 MD5sum: c8f8b92195ef5810566a0ae77a0d3237 NeedsCompilation: no Package: HERON Version: 1.5.0 Depends: R (>= 4.4.0), SummarizedExperiment (>= 1.1.6), GenomicRanges, IRanges, S4Vectors Imports: matrixStats, stats, data.table, harmonicmeanp, metap, cluster, spdep, Matrix, limma, methods Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: ae204cb642f6466762c668d62efd237c NeedsCompilation: no Package: Herper Version: 1.17.0 Depends: R (>= 4.0), reticulate Imports: utils, rjson, withr, stats Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 02eff3bb7ec941338edb44b7643560f1 NeedsCompilation: no Package: HGC Version: 1.15.0 Depends: R (>= 4.1.0) Imports: Rcpp (>= 1.0.0), RcppEigen(>= 0.3.2.0), Matrix, RANN, ape, dendextend, ggplot2, mclust, patchwork, dplyr, grDevices, methods, stats LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 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checkmate, purrr, withr Suggests: covr, tools, kableExtra (>= 1.3.4), knitr (>= 1.45), rmarkdown, testthat (>= 3.0.0), BiocFileCache (>= 2.6.1) License: MIT + file LICENSE MD5sum: c7aff2e8cc6294b28fdb05f649e4835a NeedsCompilation: no Package: HiCBricks Version: 1.25.0 Depends: R (>= 3.6), utils, curl, rhdf5, R6, grid Imports: ggplot2, viridis, RColorBrewer, scales, reshape2, stringr, data.table, GenomeInfoDb, GenomicRanges, stats, IRanges, grDevices, S4Vectors, digest, tibble, jsonlite, BiocParallel, R.utils, readr, methods Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: b60ff97b743516c921e2951ac87b5649 NeedsCompilation: no Package: HiCcompare Version: 1.29.0 Depends: R (>= 3.5.0), dplyr Imports: data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5 Suggests: knitr, rmarkdown, testthat, multiHiCcompare License: MIT + file LICENSE MD5sum: e0630fb56464ecd9ca04fdbfc2d2fd76 NeedsCompilation: no Package: HiCDCPlus Version: 1.15.0 Imports: Rcpp,InteractionSet,GenomicInteractions,bbmle,pscl,BSgenome,data.table,dplyr,tidyr,GenomeInfoDb,rlang,splines,MASS,GenomicRanges,IRanges,tibble,R.utils,Biostrings,rtracklayer,methods,S4Vectors LinkingTo: Rcpp Suggests: BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, RUnit, BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix, BiocFileCache, rappdirs Enhances: parallel License: GPL-3 MD5sum: 2003eaa7ca546056ee12e1723c122f44 NeedsCompilation: yes Package: HiCDOC Version: 1.9.2 Depends: InteractionSet, GenomicRanges, SummarizedExperiment, R (>= 4.1.0) Imports: methods, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools, pbapply, BiocParallel, BiocGenerics, grid, cowplot, gridExtra, data.table, multiHiCcompare, GenomeInfoDb LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5 License: LGPL-3 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EnsDb.Mmusculus.v79, knitr, markdown, rmarkdown, rtracklayer, RUnit, grDevices, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL (>= 2) MD5sum: e680923d19d9422deb4571fcbbd9cbeb NeedsCompilation: no Package: INPower Version: 1.43.0 Depends: R (>= 3.1.0), mvtnorm Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE MD5sum: b2f4eff27b4ae59e30ae717033d44855 NeedsCompilation: no Package: INSPEcT Version: 1.37.0 Depends: R (>= 3.6), methods, Biobase, BiocParallel Imports: pROC, deSolve, rootSolve, KernSmooth, readxl, GenomicFeatures, GenomicRanges, IRanges, BiocGenerics, GenomicAlignments, Rsamtools, S4Vectors, GenomeInfoDb, DESeq2, plgem, rtracklayer, SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 3beb5f79b402e70a485ee2a59d46b376 NeedsCompilation: no Package: INTACT Version: 1.7.0 Depends: R (>= 4.3.0) Imports: SQUAREM, bdsmatrix, numDeriv, stats, tidyr, ggplot2 Suggests: 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shinyalert, tibble, umap, visNetwork, wordcloud2, readxl, htmlwidgets, colorspace, signal, scales, htmltools, ComplexHeatmap, grDevices, stats, tools, utils, biomaRt, rlang, fmsb, igraph Suggests: testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, httr License: MIT + file LICENSE MD5sum: d1b9955aa5cf68a7918d4e0c98fc98b5 NeedsCompilation: no Package: IntramiRExploreR Version: 1.29.0 Depends: R (>= 3.4) Imports: igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats, utils, grDevices, graphics Suggests: gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat License: GPL-2 MD5sum: fac728779bc94f8f14de8e647d0a6ca9 NeedsCompilation: no Package: IONiseR Version: 2.31.0 Depends: R (>= 3.4) Imports: rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2, methods, BiocGenerics, XVector, tibble, stats, BiocParallel, bit64, stringr, utils Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData License: MIT + file LICENSE MD5sum: 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Depends: R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.45.2) Imports: stats4 LinkingTo: S4Vectors Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle License: Artistic-2.0 MD5sum: b493af234823db286ace8748d98659f0 NeedsCompilation: yes Package: ISAnalytics Version: 1.17.1 Depends: R (>= 4.5) Imports: utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs, lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools, grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib, 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: f2ea0fe3781775d78651e5dfa321a745 NeedsCompilation: no Package: iSEE Version: 2.19.2 Depends: SummarizedExperiment, SingleCellExperiment Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, listviewer, ComplexHeatmap, circlize, grid Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools, GenomicRanges License: MIT + file LICENSE MD5sum: 3d7969d2bfff368d660271cf1e7e10d9 NeedsCompilation: no Package: iSEEde Version: 1.5.0 Depends: iSEE Imports: DESeq2, edgeR, methods, S4Vectors, shiny, SummarizedExperiment Suggests: airway, BiocStyle, covr, knitr, limma, org.Hs.eg.db, RefManageR, rmarkdown, scuttle, sessioninfo, statmod, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 66cee6294aaafe1527e971b0c9232239 NeedsCompilation: no Package: iSEEfier Version: 1.3.0 Imports: iSEE, 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OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS License: LGPL-2 MD5sum: 189dac6af3815bd6ff377963ad60aaa1 NeedsCompilation: no Package: IsoBayes Version: 1.5.0 Depends: R (>= 4.3.0) Imports: methods, Rcpp, data.table, glue, stats, doParallel, parallel, doRNG, foreach, iterators, ggplot2, HDInterval, SummarizedExperiment, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: fad672779e9b38732bba0f108eafd75d NeedsCompilation: yes Package: IsoCorrectoR Version: 1.25.0 Depends: R (>= 3.5) Imports: dplyr, magrittr, methods, quadprog, readr, readxl, stringr, tibble, tools, utils, pracma, WriteXLS Suggests: IsoCorrectoRGUI, knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: b29c72535e281d6f39e3950f3bcd9b9b NeedsCompilation: no Package: IsoCorrectoRGUI Version: 1.23.0 Depends: R (>= 3.6) Imports: IsoCorrectoR, readxl, tcltk2, tcltk, utils Suggests: knitr, rmarkdown, testthat, BiocStyle 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AnnotationHub Suggests: testthat, knitr, rmarkdown, BiocStyle, MACSdata License: BSD_3_clause + file LICENSE MD5sum: 2a76a759c9641a3fc76c0f9e2bdc9cae NeedsCompilation: no Package: made4 Version: 1.81.0 Depends: RColorBrewer,gplots,scatterplot3d, Biobase, SummarizedExperiment Imports: ade4 Suggests: affy, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 299454c9160173d1875c7957cdc1c520 NeedsCompilation: no Package: MADSEQ Version: 1.33.0 Depends: R (>= 3.5.0), rjags (>= 4.6) Imports: VGAM, coda, BSgenome, BSgenome.Hsapiens.UCSC.hg19, S4Vectors, methods, preprocessCore, GenomicAlignments, Rsamtools, Biostrings, GenomicRanges, IRanges, VariantAnnotation, SummarizedExperiment, GenomeInfoDb, rtracklayer, graphics, stats, grDevices, utils, zlibbioc, vcfR Suggests: knitr License: GPL (>= 2) MD5sum: 1bea13413919a5ca6773026477217be2 NeedsCompilation: no Package: maftools Version: 2.23.0 Depends: R (>= 3.3) Imports: data.table, grDevices, methods, RColorBrewer, Rhtslib, survival, DNAcopy, pheatmap LinkingTo: Rhtslib, zlibbioc Suggests: berryFunctions, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors, curl License: MIT + file LICENSE MD5sum: 18a09feeacc5f123dd0bfadf466fbd29 NeedsCompilation: yes Package: MAGAR Version: 1.15.1 Depends: R (>= 4.1), HDF5Array, RnBeads, snpStats, crlmm Imports: doParallel, igraph, bigstatsr, rjson, plyr, data.table, UpSetR, reshape2, jsonlite, methods, ff, argparse, impute, RnBeads.hg19, RnBeads.hg38, utils, stats Suggests: gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager License: GPL-3 MD5sum: 0b432e4b4c4696aab3b071981144ecef NeedsCompilation: no Package: magpie Version: 1.7.0 Depends: R (>= 4.3.0) Imports: utils, rtracklayer, Matrix, matrixStats, stats, S4Vectors, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi, aod, BiocParallel, DESeq2, openxlsx, RColorBrewer, reshape2, TRESS Suggests: knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset, BiocGenerics, BiocStyle License: MIT + file LICENSE MD5sum: ddbf635aebbf9eb2adc5ca4d196282a7 NeedsCompilation: no Package: magrene Version: 1.9.0 Depends: R (>= 4.2.0) Imports: utils, stats, BiocParallel Suggests: BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo, testthat (>= 3.0.0) License: GPL-3 MD5sum: f2d799330e076b034554601ca78a7e16 NeedsCompilation: no Package: MAI Version: 1.13.0 Depends: R (>= 3.5.0) Imports: caret, parallel, doParallel, foreach, e1071, future.apply, future, missForest, pcaMethods, tidyverse, stats, utils, methods, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: d6c551de5de0d3ef93bdbb99bbe46aae NeedsCompilation: no Package: MAIT Version: 1.41.0 Depends: R (>= 2.10), CAMERA, Rcpp, pls Imports: gplots,e1071,class,MASS,plsgenomics,agricolae,xcms,methods,caret Suggests: faahKO Enhances: rgl License: GPL-2 MD5sum: cf000a22ce3df1611fd5baa5df66347d NeedsCompilation: no Package: makecdfenv Version: 1.83.0 Depends: R (>= 2.6.0), affyio Imports: Biobase, affy, methods, stats, utils, zlibbioc License: GPL (>= 2) MD5sum: 68ae66482d2a629691bc4c394d722c5b NeedsCompilation: yes Package: MANOR Version: 1.79.0 Depends: R (>= 2.10) Imports: GLAD, graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, bookdown License: GPL-2 MD5sum: ae88a458aeb7a3c5f8126ece30b161cf NeedsCompilation: yes Package: MantelCorr Version: 1.77.0 Depends: R (>= 2.10) Imports: stats License: GPL (>= 2) MD5sum: 1340722a0b75db9b6e0e7cc933b5a886 NeedsCompilation: no Package: MAPFX Version: 1.3.0 Depends: R (>= 4.4.0) Imports: flowCore, Biobase, stringr, uwot, iCellR, igraph, ggplot2, RColorBrewer, Rfast, ComplexHeatmap, circlize, glmnetUtils, e1071, xgboost, parallel, pbapply, reshape2, gtools, utils, stats, cowplot, methods, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 3de62c929db78d0e5eee7a6f9987ff80 NeedsCompilation: no Package: maPredictDSC Version: 1.45.0 Depends: R (>= 2.15.0), MASS,affy,limma,gcrma,ROC,class,e1071,caret,hgu133plus2.db,ROCR,AnnotationDbi,LungCancerACvsSCCGEO Suggests: parallel License: GPL-2 MD5sum: 23436536a1c669e8bae065e6d8a14c0e NeedsCompilation: no Package: mapscape Version: 1.31.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), base64enc (>= 0.1-3), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 7d22d916214ef55aea2d28e48805b932 NeedsCompilation: no Package: mariner Version: 1.7.0 Depends: R (>= 4.2.0) Imports: methods, S4Vectors, BiocGenerics, BiocManager, GenomicRanges, InteractionSet, data.table, stats, rlang, glue, assertthat, plyranges, magrittr, dbscan, purrr, progress, GenomeInfoDb, strawr (>= 0.0.91), DelayedArray, HDF5Array, abind, BiocParallel, IRanges, SummarizedExperiment, rhdf5, plotgardener, RColorBrewer, colourvalues, utils, grDevices, graphics, grid Suggests: knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub, marinerData License: GPL-3 MD5sum: cf9eb7c62347bee10b72f2c94b965573 NeedsCompilation: no Package: marr Version: 1.17.0 Depends: R (>= 4.0) Imports: Rcpp, SummarizedExperiment, utils, methods, ggplot2, dplyr, magrittr, rlang, S4Vectors LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, covr License: GPL (>= 3) MD5sum: 4a75724c83dd168bddd9d8e5992cd476 NeedsCompilation: yes Package: marray Version: 1.85.0 Depends: R (>= 2.10.0), limma, methods Suggests: tkWidgets License: LGPL MD5sum: e49a983ac059de43679075ec7db44546 NeedsCompilation: no Package: martini Version: 1.27.0 Depends: R (>= 4.0) Imports: igraph (>= 1.0.1), Matrix, memoise (>= 2.0.0), methods (>= 3.3.2), Rcpp (>= 0.12.8), snpStats (>= 1.20.0), stats, utils, LinkingTo: Rcpp, RcppEigen (>= 0.3.3.5.0) Suggests: biomaRt (>= 2.34.1), circlize (>= 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Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, stats, utils License: GPL (>= 2) MD5sum: b98aead862bab7acec1cff74f78a9710 NeedsCompilation: no Package: massiR Version: 1.43.0 Depends: cluster, gplots, diptest, Biobase, R (>= 3.0.2) Suggests: biomaRt, RUnit, BiocGenerics License: GPL-3 MD5sum: ddba7ec47ba72d95cb843fd873946f33 NeedsCompilation: no Package: MassSpecWavelet Version: 1.73.1 Suggests: signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench License: LGPL (>= 2) MD5sum: 47619cc9cbfaa9dd542f3bfc6a300088 NeedsCompilation: yes Package: MAST Version: 1.33.0 Depends: SingleCellExperiment (>= 1.2.0), R(>= 3.5) Imports: Biobase, BiocGenerics, S4Vectors, data.table, ggplot2, plyr, stringr, abind, methods, parallel, reshape2, stats, stats4, graphics, utils, SummarizedExperiment(>= 1.5.3), progress, Matrix Suggests: knitr, rmarkdown, testthat, lme4(>= 1.0), blme, roxygen2(> 6.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF, TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer, BiocStyle, scater, DelayedArray, HDF5Array, zinbwave, dplyr License: GPL (>= 2) MD5sum: 32f6eba6564fd970099df0d9e2beaa44 NeedsCompilation: no Package: mastR Version: 1.7.0 Depends: R (>= 4.3.0) Imports: AnnotationDbi, Biobase, dplyr, edgeR, ggplot2, ggpubr, graphics, grDevices, GSEABase, limma, Matrix, methods, msigdb, org.Hs.eg.db, patchwork, SeuratObject, SingleCellExperiment, stats, SummarizedExperiment, tidyr, utils Suggests: BiocManager, BiocStyle, BisqueRNA, clusterProfiler, ComplexHeatmap, depmap, enrichplot, ggrepel, ggvenn, gridExtra, jsonlite, knitr, rmarkdown, RobustRankAggreg, rvest, scuttle, singscore, splatter, testthat (>= 3.0.0), UpSetR License: MIT + file LICENSE MD5sum: 252eee1ddc99ee4911e84c7a0135e774 NeedsCompilation: no Package: matchBox Version: 1.49.0 Depends: R (>= 2.8.0) License: Artistic-2.0 MD5sum: 7504469c7453fac03c630e09963ca421 NeedsCompilation: no Package: MatrixGenerics Version: 1.19.0 Depends: matrixStats (>= 1.4.1) Imports: 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graphics, utils, stats, AnnotationDbi, GO.db, org.Hs.eg.db, GGally, ggplot2, scales, cluster, WGCNA Suggests: gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr, pander, devtools, testthat, GSVA License: GPL-2 MD5sum: 4659db6642e5713b4d7bf8a7e9f3ac48 NeedsCompilation: no Package: mCSEA Version: 1.27.2 Depends: R (>= 3.5), mCSEAdata, Homo.sapiens Imports: biomaRt, fgsea, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, Gviz, IRanges, limma, methods, parallel, S4Vectors, stats, SummarizedExperiment, utils Suggests: Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k, knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit License: GPL-2 MD5sum: 3d0465dc8bfd663a894bf4f52e21753e NeedsCompilation: no Package: mdp Version: 1.27.0 Depends: R (>= 4.0) Imports: ggplot2, gridExtra, grid, stats, utils Suggests: testthat, knitr, rmarkdown, fgsea, BiocManager License: GPL-3 MD5sum: 588ab4d7442accae88bd5e9d980ec566 NeedsCompilation: no Package: mdqc Version: 1.69.0 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Wrench Suggests: annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW License: Artistic-2.0 MD5sum: 45962347184bd5bf032f51f1b76d1661 NeedsCompilation: no Package: metahdep Version: 1.65.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 MD5sum: e77a3bf50c2297d6876c9f58552166d9 NeedsCompilation: yes Package: metaMS Version: 1.43.0 Depends: R (>= 4.0), methods, CAMERA, xcms (>= 1.35) Imports: Matrix, tools, robustbase, BiocGenerics, graphics, stats, utils Suggests: metaMSdata, RUnit License: GPL (>= 2) MD5sum: 0502c32326efc36cd9dbbfcff2291688 NeedsCompilation: no Package: MetaNeighbor Version: 1.27.0 Depends: R(>= 3.5) Imports: grDevices, graphics, methods, stats (>= 3.4), utils (>= 3.4), Matrix (>= 1.2), matrixStats (>= 0.54), beanplot (>= 1.2), gplots (>= 3.0.1), RColorBrewer (>= 1.1.2), SummarizedExperiment (>= 1.12), SingleCellExperiment, igraph, dplyr, tidyr, tibble, ggplot2 Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), 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parallel, methods, ggplot2, S4Vectors, matrixStats, graphics, stats, utils, GenomicRanges, IRanges Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 951d21b904aafafc8e8d367f5d3b0e42 NeedsCompilation: no Package: MethTargetedNGS Version: 1.39.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign Imports: utils, graphics, stats License: Artistic-2.0 MD5sum: 5afeaea1d57c8a230f658e49b5a3b97b NeedsCompilation: no Package: MethylAid Version: 1.41.0 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 (>= 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NeedsCompilation: yes Package: methylGSA Version: 1.25.0 Depends: R (>= 3.5) Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, shiny, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr, rmarkdown, testthat, enrichplot License: GPL-2 MD5sum: ee554c9854b75d29eb846989d4ecf7ae NeedsCompilation: no Package: methyLImp2 Version: 1.3.0 Depends: R (>= 4.3.0), ChAMPdata Imports: BiocParallel, parallel, stats, methods, corpcor, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: 5c7b3cd77349f038770508aa536085d3 NeedsCompilation: no Package: methylInheritance Version: 1.31.0 Depends: R (>= 3.5) Imports: methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors, methods, parallel, ggplot2, gridExtra, rebus Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim 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biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2, BiocStyle, miaViz, vegan, scater, phyloseq, magick License: Artistic-2.0 | file LICENSE MD5sum: 0babca2499c753a778cd83618a0533ac NeedsCompilation: no Package: mgsa Version: 1.55.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: 5fc28fbf350fc811940cde8bb5c85bde NeedsCompilation: yes Package: mia Version: 1.15.6 Depends: R (>= 4.0), MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment (>= 1.99.3) Imports: ape, BiocGenerics, BiocParallel, Biostrings, bluster, DECIPHER, decontam, DelayedArray, DelayedMatrixStats, DirichletMultinomial, dplyr, IRanges, MASS, MatrixGenerics, mediation, methods, rbiom, rlang, S4Vectors, scater, scuttle, stats, tibble, tidyr, utils, vegan Suggests: ade4, BiocStyle, biomformat, dada2, knitr, miaViz, microbiomeDataSets, NMF, patchwork, phyloseq, reldist, rhdf5, rmarkdown, 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bluster, circlize, ComplexHeatmap, ggh4x, knitr, patchwork, rmarkdown, testthat, vegan License: Artistic-2.0 | file LICENSE MD5sum: 8ac1b3ed5b1babc2491920f7a642ca27 NeedsCompilation: no Package: MiChip Version: 1.61.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: 4cbbe78f97364667ee4dc2ebb4bc549b NeedsCompilation: no Package: microbiomeExplorer Version: 1.17.0 Depends: shiny, magrittr, metagenomeSeq, Biobase Imports: shinyjs (>= 2.0.0), shinydashboard, shinycssloaders, shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer, dplyr, tidyr, purrr, rlang, knitr, readr, DT (>= 0.12.0), biomformat, tools, stringr, vegan, matrixStats, heatmaply, car, broom, limma, reshape2, tibble, forcats, lubridate, methods, plotly (>= 4.9.1) Suggests: V8, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 106a659d2b3affb302d44b3417b9bb02 NeedsCompilation: no Package: MicrobiomeProfiler Version: 1.13.0 Depends: R (>= 4.2.0) Imports: clusterProfiler (>= 4.5.2), config, DT, enrichplot, golem, gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader, htmltools, ggplot2, graphics, stats, utils, yulab.utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), prettydoc License: GPL-2 MD5sum: 3ff817046593001a77935a80cca99b6d NeedsCompilation: no Package: MicrobiotaProcess Version: 1.19.0 Depends: R (>= 4.0.0) Imports: ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>= 1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table, ggfun (>= 0.1.1) Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, 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ggplot2, tibble, matrixStats, ggraph, gtools, SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices, Rcpp, pracma, numDeriv LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppML Suggests: testthat, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, MASS, curl, scRNAseq, graphics, sparseMatrixStats License: GPL-3 + file LICENSE MD5sum: c790f0f45dc67696dbabf619b2205035 NeedsCompilation: yes Package: mimager Version: 1.31.0 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: 7e367bff081b072678f5a2b536d73c2c NeedsCompilation: no Package: mina Version: 1.15.0 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: 8f10396e8d39186158bb3c75315c649d NeedsCompilation: yes Package: MineICA Version: 1.47.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply Enhances: doMC License: GPL-2 MD5sum: bf39ae61deb73fffdda3a3a8b7a335ea NeedsCompilation: no Package: minet Version: 3.65.0 Imports: infotheo License: Artistic-2.0 MD5sum: 99e8824bddd66161401595f5b9e1fdb4 NeedsCompilation: yes Package: 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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: 6c446d351a854c25de7b9cd7848bf916 NeedsCompilation: no Package: MiPP Version: 1.79.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: 00a2e2ed6c1148ed40aa7ad33ce803f2 NeedsCompilation: no Package: miQC Version: 1.15.0 Depends: R (>= 3.5.0) Imports: SingleCellExperiment, flexmix, ggplot2, splines Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: ca67888bba35670b75acf030ff0af54f NeedsCompilation: no Package: MIRA Version: 1.29.0 Depends: R (>= 3.5) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, 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RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: fc5d44e1b95b91ffcdf4aec16bc7f2e3 NeedsCompilation: no Package: mirIntegrator Version: 1.37.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: 743b6444050b42ee24034c9c9549767f NeedsCompilation: no Package: MIRit Version: 1.3.0 Depends: MultiAssayExperiment, R (>= 4.4.0) Imports: AnnotationDbi, BiocFileCache, BiocParallel, DESeq2, edgeR, fgsea, genekitr, geneset, ggplot2, ggpubr, graph, graphics, graphite, grDevices, httr, limma, methods, Rcpp, Rgraphviz (>= 2.44.0), rlang, stats, utils LinkingTo: Rcpp Suggests: BiocStyle, biomaRt, BSgenome.Hsapiens.UCSC.hg38, GenomicRanges, ggrepel, ggridges, Gviz, gwasrapidd, knitr, MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 79b5da64cf134ce0232c4c6873b094e7 NeedsCompilation: yes Package: miRLAB Version: 1.37.0 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: 480edb6ab8ee3290d8b96efb20418223 NeedsCompilation: no Package: miRNAmeConverter Version: 1.35.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: fdc01469baf2925d054a4d02ecad0b93 NeedsCompilation: no Package: miRNApath Version: 1.67.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: 763f8cf122ffc9d261bc827e60f77d34 NeedsCompilation: no Package: miRNAtap Version: 1.41.0 Depends: R (>= 3.3.0), AnnotationDbi Imports: DBI, RSQLite, stringr, sqldf, plyr, methods Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat License: GPL-2 MD5sum: 63262de4887759a5cae1ffbf02f2c939 NeedsCompilation: no Package: miRSM Version: 2.3.0 Depends: R (>= 4.4.0) Imports: WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL, fabia, NMF, biclust, iBBiG, BicARE, isa2, s4vd, BiBitR, rqubic, Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero, ppclust, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE, MatrixCorrelation, energy Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: cd76f3ef01f5d2a392b8b476f68e648f NeedsCompilation: yes Package: miRspongeR Version: 2.11.0 Depends: R (>= 4.4.0) Imports: corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, linkcomm, utils, Rcpp, org.Hs.eg.db, foreach, doParallel Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 0f1b678ed813c4c15ef45e35c02c79e4 NeedsCompilation: yes Package: mirTarRnaSeq Version: 1.15.0 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: 971c94fc259fce478aec52cbb7b75bde NeedsCompilation: no Package: missMethyl Version: 1.41.0 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICv2manifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub License: GPL-2 MD5sum: d54daf2292df496b0b30973b8aaa27a8 NeedsCompilation: no Package: missRows Version: 1.27.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, 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BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4, tools, grDevices, graphics, stats, magrittr, SummarizedExperiment Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, BiocStyle, knitr, testthat Enhances: parallel License: LGPL MD5sum: 0ff110bf271f614007d2da209f554f57 NeedsCompilation: no Package: MLP Version: 1.55.0 Imports: AnnotationDbi, gplots, graphics, stats, utils Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, org.Mmu.eg.db, KEGGREST, annotate, Rgraphviz, GOstats, graph, limma, mouse4302.db, reactome.db License: GPL-3 MD5sum: a47af6ec8389d393f63eb638b6f065ae NeedsCompilation: no Package: MLSeq Version: 2.25.0 Depends: caret, ggplot2 Imports: testthat, VennDiagram, pamr, methods, 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cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071, ggplot2, wesanderson LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle License: GPL-3 MD5sum: e2246018c10efeaef8ce1c30a031c07b NeedsCompilation: yes Package: moanin Version: 1.15.0 Depends: R (>= 4.0), SummarizedExperiment, topGO, stats Imports: S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics, methods, grDevices, reshape2, NMI, zoo, ClusterR, splines, matrixStats Suggests: testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: 9dd4b481d1521d2db2c558b427bf9a31 NeedsCompilation: no Package: mobileRNA Version: 1.3.0 Depends: R (>= 4.3.0) Imports: dplyr, tidyr, ggplot2, BiocGenerics, DESeq2, edgeR, ggrepel, grDevices, pheatmap, utils, tidyselect, progress, RColorBrewer, GenomicRanges, rtracklayer, data.table, SimDesign, scales, IRanges, stats, methods, Biostrings, reticulate, S4Vectors, GenomeInfoDb, SummarizedExperiment, rlang, bioseq, grid Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 907d073bcfa05a20e658fbc20b5c5124 NeedsCompilation: no Package: MODA Version: 1.33.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 0dd0d8530b1692218fd70975f3c0f459 NeedsCompilation: no Package: ModCon Version: 1.15.0 Depends: data.table, parallel, utils, stats, R (>= 4.1) Suggests: testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny, shinyFiles, shinydashboard, shinyjs License: GPL-3 + file LICENSE MD5sum: efddabe88c0a481318b2e408fb9111d9 NeedsCompilation: no Package: Modstrings Version: 1.23.0 Depends: R (>= 3.6), Biostrings (>= 2.51.5) Imports: methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 3d33a97a2cffb1100e508c979acca450 NeedsCompilation: no Package: MOFA2 Version: 1.17.0 Depends: R (>= 4.0) Imports: rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods, RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array, grDevices, stats, magrittr, forcats, utils, corrplot, DelayedArray, Rtsne, uwot, basilisk, stringi Suggests: knitr, testthat, Seurat, SeuratObject, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown License: file LICENSE MD5sum: 1e79cc54a97aaa0f33e40ee21a84802b NeedsCompilation: yes Package: MOGAMUN Version: 1.17.0 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: knitr, markdown License: GPL-3 + file LICENSE MD5sum: 5aef2862885955f563882c8b85c4578b NeedsCompilation: no Package: mogsa Version: 1.41.0 Depends: R (>= 3.4.0) Imports: methods, graphite, genefilter, BiocGenerics, gplots, GSEABase, Biobase, parallel, corpcor, svd, cluster, grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, org.Hs.eg.db License: GPL-2 MD5sum: 5511debeb0e35d73f3eb9b0aba832576 NeedsCompilation: no Package: MoleculeExperiment Version: 1.7.0 Depends: R (>= 2.10) Imports: SpatialExperiment, Matrix, purrr, data.table, dplyr (>= 1.1.1), magrittr, rjson, utils, methods, terra, ggplot2, rlang, cli, EBImage, rhdf5, BiocParallel, S4Vectors, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 7172a79d20705d6a44b8a527b7f48b4c NeedsCompilation: no Package: MOMA Version: 1.19.0 Depends: R (>= 4.0) Imports: circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics, grid, grDevices, magrittr, methods, MKmisc, MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr, reshape2, rlang, stats, stringr, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, viper License: GPL-3 MD5sum: 6ecda9e59b439a8d406630c820c53ef8 NeedsCompilation: no Package: monaLisa Version: 1.13.0 Depends: R (>= 4.1) Imports: methods, stats, utils, grDevices, graphics, BiocGenerics, GenomicRanges, TFBSTools, Biostrings, IRanges, stabs, BSgenome, glmnet, S4Vectors, SummarizedExperiment, BiocParallel, grid, circlize, ComplexHeatmap (>= 2.11.1), XVector, GenomeInfoDb, tools, vioplot, RSQLite Suggests: JASPAR2020, JASPAR2024, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat, BiocStyle, gridExtra License: GPL (>= 3) MD5sum: 66b2b0ce14185fcf4455c0a4dad74c7c NeedsCompilation: no Package: monocle Version: 2.35.0 Depends: R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-6), DDRTree (>= 0.1.4), Imports: parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, Rtsne, MASS, reshape2, leidenbase (>= 0.1.9), limma, tibble, dplyr, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0) LinkingTo: Rcpp Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat License: Artistic-2.0 MD5sum: c086fffdc67fac83696c419f2c65b470 NeedsCompilation: yes Package: Moonlight2R Version: 1.5.2 Depends: R (>= 4.4), doParallel, foreach Imports: parmigene, randomForest, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, grDevices, graphics, GEOquery, stats, purrr, RISmed, grid, utils, ComplexHeatmap, GenomicRanges, dplyr, fuzzyjoin, rtracklayer, magrittr, qpdf, readr, seqminer, stringr, tibble, tidyHeatmap, tidyr, AnnotationHub, easyPubMed, org.Hs.eg.db, EpiMix, BiocGenerics, ggplot2, ExperimentHub, rlang, withr, data.table Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), devtools, roxygen2, png License: GPL-3 MD5sum: f26ab07ff6e32c7cc013e0e74ce1e641 NeedsCompilation: no Package: MoonlightR Version: 1.33.0 Depends: R (>= 3.5), doParallel, foreach Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png, edgeR License: GPL (>= 3) MD5sum: f241d49777f3c3056102beff18f3edc7 NeedsCompilation: no Package: mosaics Version: 2.45.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: dd506943324f7d75456f812653505e15 NeedsCompilation: yes Package: mosbi Version: 1.13.0 Depends: R (>= 4.1) Imports: Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust, isa2, QUBIC, akmbiclust, RColorBrewer LinkingTo: Rcpp, BH, RcppParallel Suggests: knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 58b3ebff2c6f295d02bc4345a37c893a NeedsCompilation: yes Package: MOSClip Version: 1.1.0 Depends: R (>= 4.4.0) Imports: MultiAssayExperiment, methods, survminer, graph, graphite, AnnotationDbi, checkmate, ggplot2, gridExtra, igraph, pheatmap, survival, RColorBrewer, SuperExactTest, reshape, NbClust, S4Vectors, grDevices, graphics, stats, utils, ComplexHeatmap, FactoMineR, circlize, corpcor, coxrobust, elasticnet, gRbase, ggplotify, qpgraph, org.Hs.eg.db, Matrix Suggests: RUnit, BiocGenerics, MASS, BiocStyle, knitr, EDASeq, rmarkdown, kableExtra, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 1fbf147a8d3216b22125600ec23fe926 NeedsCompilation: no Package: mosdef Version: 1.3.1 Depends: R (>= 4.4.0) Imports: DT, ggplot2, ggforce, ggrepel, graphics, grDevices, htmltools, methods, AnnotationDbi, topGO, GO.db, clusterProfiler, goseq, utils, RColorBrewer, rlang, DESeq2, scales, SummarizedExperiment, S4Vectors, stats Suggests: knitr, rmarkdown, macrophage, org.Hs.eg.db, GeneTonic, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene, BiocStyle License: MIT + file LICENSE MD5sum: 9598b0e72678a992178c8fa58e91c3a4 NeedsCompilation: no Package: MOSim Version: 2.3.0 Depends: R (>= 4.2.0) Imports: HiddenMarkov, zoo, IRanges, S4Vectors, dplyr, ggplot2, lazyeval, matrixStats, methods, rlang, stringi, stringr, scran, Seurat, Signac, edgeR, Rcpp LinkingTo: cpp11, Rcpp Suggests: testthat, knitr, rmarkdown, codetools, BiocStyle, stats, utils, purrr, scales, tibble, tidyr, Biobase, scater, SingleCellExperiment, decor, markdown, Rsamtools, igraph, leiden, bluster License: GPL-3 MD5sum: 2f58b2bf23b7a3bfe11716c6b3944ad6 NeedsCompilation: yes Package: Motif2Site Version: 1.11.0 Depends: R (>= 4.1) Imports: S4Vectors, stats, utils, methods, grDevices, graphics, BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges, GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools Suggests: BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805 License: GPL-2 MD5sum: 2b9d46dad244176b365c4d8d79f31594 NeedsCompilation: no Package: motifbreakR Version: 2.21.0 Depends: R (>= 4.4.0), grid, MotifDb Imports: methods, grDevices, stringr, parallel, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment, pwalign, DT, bsicons, BiocFileCache, biomaRt, bslib, shiny, vroom Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Hsapiens.UCSC.hg38 License: GPL-2 MD5sum: 9fdf33eaa1dd098155fa573a39abcc82 NeedsCompilation: no Package: motifcounter Version: 1.31.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: 0d381bd7135b436646920100113f46f0 NeedsCompilation: yes Package: MotifDb Version: 1.49.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes MD5sum: e480594498cb1bcae2cd9e57f4427eef NeedsCompilation: no Package: motifmatchr Version: 1.29.0 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, GenomeInfoDb LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 + file LICENSE MD5sum: df20eee2c1360463a4fa803ba4a16a69 NeedsCompilation: yes Package: MotifPeeker Version: 0.99.13 Depends: R (>= 4.4.0) Imports: BiocFileCache, BiocParallel, DT, ggplot2, plotly, universalmotif, GenomicRanges, IRanges, rtracklayer, tools, htmltools, rmarkdown, viridis, SummarizedExperiment, htmlwidgets, Rsamtools, GenomicAlignments, GenomeInfoDb, Biostrings, BSgenome, memes, S4Vectors, dplyr, purrr, tidyr, heatmaply, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, downloadthis, knitr, markdown, methods, remotes, rworkflows, testthat (>= 3.0.0), withr, emoji, curl, jsonlite License: GPL (>= 3) MD5sum: b9d03f93a4050c340a95b945c0628ce2 NeedsCompilation: no Package: motifStack Version: 1.51.0 Depends: R (>= 2.15.1), methods, grid Imports: ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets, stats, stats4, utils, XML, TFBSTools Suggests: Cairo, grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020 License: GPL (>= 2) MD5sum: 669ed040f9178c17ba06411cf70c622e NeedsCompilation: no Package: motifTestR Version: 1.3.1 Depends: Biostrings, GenomicRanges, ggplot2 (>= 3.5.0), R (>= 4.3.0), Imports: GenomeInfoDb, graphics, harmonicmeanp, IRanges, matrixStats, methods, parallel, patchwork, rlang, S4Vectors, stats, universalmotif Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, extraChIPs, ggdendro, knitr, MotifDb, rmarkdown, rtracklayer, testthat (>= 3.0.0) License: GPL-3 MD5sum: 159d32b8823e3f122d9aeed982053e6d NeedsCompilation: no Package: MouseFM Version: 1.17.0 Depends: R (>= 4.0.0) Imports: httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales, gtools, tidyr, data.table, jsonlite, rlist, GenomeInfoDb, methods, biomaRt, stats, IRanges Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 6837b92bc761521efaa75c2d2a75372f NeedsCompilation: no Package: MPAC Version: 1.1.0 Depends: R (>= 4.4.0) Imports: data.table (>= 1.14.2), SummarizedExperiment (>= 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NeedsCompilation: no Package: msa Version: 1.39.0 Depends: R (>= 3.3.0), methods, Biostrings (>= 2.40.0) Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors, tools LinkingTo: Rcpp Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign License: GPL (>= 2) MD5sum: bb2e03698c501ce0adde620dd0b94574 NeedsCompilation: yes Package: MSA2dist Version: 1.11.1 Depends: R (>= 4.4.0) Imports: Rcpp, Biostrings, GenomicRanges, IRanges, ape, doParallel, dplyr, foreach, methods, parallel, pwalign, rlang, seqinr, stats, stringi, stringr, tibble, tidyr, utils LinkingTo: Rcpp, RcppThread Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle License: GPL-3 + file LICENSE MD5sum: f42df85858d4c2d3a5fda4b48bdf21c2 NeedsCompilation: yes Package: MsBackendMassbank Version: 1.15.0 Depends: R (>= 4.0), Spectra (>= 1.15.10) Imports: BiocParallel, S4Vectors, IRanges, methods, ProtGenerics (>= 1.35.3), MsCoreUtils, DBI, utils Suggests: testthat, knitr (>= 1.1.0), roxygen2, 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glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, rlang, S4Vectors, scales, scater, scuttle, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition, viridis Suggests: BiocStyle, countsimQC, ExperimentHub, iCOBRA, knitr, patchwork, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, stageR, testthat, UpSetR License: GPL-3 MD5sum: b12eed2af5c7172844ea91e2b61b9d61 NeedsCompilation: no Package: muscle Version: 3.49.0 Depends: Biostrings License: Unlimited MD5sum: 144d601eea9a36461e1c4c31db78a254 NeedsCompilation: yes Package: musicatk Version: 2.1.0 Depends: R (>= 4.4.0), NMF Imports: SummarizedExperiment, VariantAnnotation, Biostrings, base, methods, magrittr, tibble, tidyr, gtools, gridExtra, MCMCprecision, MASS, matrixTests, data.table, dplyr, rlang, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, S4Vectors, uwot, ggplot2, stringr, TxDb.Hsapiens.UCSC.hg19.knownGene, 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Package: mygene Version: 1.43.0 Depends: R (>= 3.2.1), GenomicFeatures, txdbmaker Imports: methods, utils, stats, httr (>= 0.3), jsonlite (>= 0.9.7), Hmisc, sqldf, plyr, S4Vectors Suggests: BiocStyle License: Artistic-2.0 MD5sum: 6949c47dba9ad742603226325aa74f70 NeedsCompilation: no Package: myvariant Version: 1.37.0 Depends: R (>= 3.2.1), VariantAnnotation Imports: httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, GenomeInfoDb Suggests: BiocStyle License: Artistic-2.0 MD5sum: 87210f6ba43340b0f6946a05edba0514 NeedsCompilation: no Package: mzID Version: 1.45.0 Depends: methods Imports: XML, plyr, parallel, doParallel, foreach, iterators, ProtGenerics Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 4fed8b4cc7058bb0fd5a0863c1b28ecb NeedsCompilation: no Package: mzR Version: 2.41.1 Depends: R (>= 4.0.0), Rcpp (>= 0.10.1), methods, utils Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3), ncdf4 LinkingTo: Rcpp, Rhdf5lib (>= 1.1.4) Suggests: msdata (>= 0.15.1), RUnit, 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Rsamtools, scales (>= 1.2.0), stats, stringr, tibble, tidyr, utils, withr, zlibbioc LinkingTo: Rcpp Suggests: BiocStyle, DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm39.refGene, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr License: Apache License (>= 2.0) MD5sum: e23392fc80d7c7d293146c0821421322 NeedsCompilation: yes Package: NanoStringDiff Version: 1.37.0 Depends: Biobase Imports: matrixStats, methods, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle License: GPL MD5sum: fd9c7ddb654eab15b7b39e125d3c5edd NeedsCompilation: yes Package: NanoStringNCTools Version: 1.15.0 Depends: R (>= 3.6), Biobase, S4Vectors, ggplot2 Imports: BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes, grDevices, IRanges, methods, pheatmap, RColorBrewer, stats, utils Suggests: biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf 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MultiAssayExperiment, SummarizedExperiment, pracma, rlang, RSpectra, scales, stats Suggests: BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0) License: GPL-3 MD5sum: 925f0aa76576e476324821beb91e142a NeedsCompilation: no Package: nnNorm Version: 2.71.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: 4c1fd87352174e61b49cc88ed980223b NeedsCompilation: no Package: nnSVG Version: 1.11.0 Depends: R (>= 4.2) Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat License: MIT + file LICENSE MD5sum: 218b6c64f04970dd34a2a965981a3f2b NeedsCompilation: no Package: NOISeq Version: 2.51.0 Depends: R (>= 2.13.0), methods, Biobase (>= 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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: 5d1e895194461fc917a0dbe2cc58ea77 NeedsCompilation: yes Package: oligoClasses Version: 1.69.0 Depends: R (>= 2.14) Imports: BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods, graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>= 1.23.2), foreach, BiocManager, utils, S4Vectors (>= 0.9.25), RSQLite, DBI, ff Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm 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methods, shinyjs, curl, flatxml, ggplot2, S4Vectors, SummarizedExperiment, RSQLite, Matrix, shinycssloaders, ROCR, drc Suggests: BiocStyle, knitr, rmarkdown, unittest License: GPL-2 MD5sum: b12d1e5ddfb7b060e23706530bbc13cf NeedsCompilation: no Package: Omixer Version: 1.17.0 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: cbc36a3ac0bee6ebcb1fc14fb995316d NeedsCompilation: no Package: OmnipathR Version: 3.15.0 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, RSQLite, R.utils, rvest, stats, stringi, stringr, tibble, tidyr, tidyselect, tools, utils, vctrs, withr, XML, xml2, yaml, zip Suggests: BiocStyle, bookdown, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, R.matlab, sigmajs, smoof, supraHex, testthat License: MIT + file LICENSE MD5sum: 4424da5802837e2b0ba6bf1d3ab7f4a6 NeedsCompilation: no Package: ompBAM Version: 1.11.0 Imports: utils, Rcpp Suggests: RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 08954273a47228a1a4f3b9f52faaff79 NeedsCompilation: no Package: omXplore Version: 1.1.0 Depends: R (>= 4.4.0), methods Imports: shiny, MSnbase, PSMatch, SummarizedExperiment, MultiAssayExperiment, shinyBS, shinyjs, shinyjqui, DT, RColorBrewer, gplots, highcharter, visNetwork, tibble, grDevices, stats, utils, htmlwidgets, vioplot, graphics, FactoMineR, dendextend, dplyr, factoextra, tidyr Suggests: knitr, rmarkdown, BiocStyle, testthat, Matrix, graph License: Artistic-2.0 MD5sum: cbe09f47688846c8becd1c92636c84b4 NeedsCompilation: no Package: oncomix Version: 1.29.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, 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basilisk, BiocParallel, colorspace, cowplot, DelayedArray, dplyr, ExperimentHub, ggplot2, ggpubr, ggrepel, ggsci, grDevices, grid, HDF5Array, keras, methods, orthosData, parallel, plyr, reticulate, rlang, S4Vectors, stats, tensorflow, tidyr Suggests: BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 99ae7fcc71a95598350c2b220de55f25 NeedsCompilation: no Package: OSAT Version: 1.55.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 MD5sum: 636c6226ebcfb56bd45541e7b6b6d81c NeedsCompilation: no Package: Oscope Version: 1.37.0 Depends: EBSeq, cluster, testthat, BiocParallel Suggests: BiocStyle License: Artistic-2.0 MD5sum: 0c7dacec4fbdf82d5870e4747f5667f0 NeedsCompilation: no Package: OTUbase Version: 1.57.0 Depends: R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>= 1.23.15), Biobase, vegan Imports: Biostrings License: Artistic-2.0 MD5sum: ba08a023ed03b520f05579ce106622c4 NeedsCompilation: no Package: 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BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: bc725943a2aba04b2c96c30856e8679d NeedsCompilation: no Package: OVESEG Version: 1.23.0 Depends: R (>= 3.6) Imports: stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales License: GPL-2 MD5sum: 915166a7f654b4fa6e079f7ad7b14bb5 NeedsCompilation: yes Package: PAA Version: 1.41.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.6) Imports: e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR, sva LinkingTo: Rcpp Suggests: BiocStyle, RUnit, BiocGenerics, vsn License: BSD_3_clause + file LICENSE MD5sum: 6098d128913b6756d61e858d2d20929b NeedsCompilation: yes Package: packFinder Version: 1.19.0 Depends: R (>= 4.1.0) Imports: Biostrings, GenomicRanges, kmer, ape, methods, IRanges, S4Vectors Suggests: biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle License: GPL-2 MD5sum: 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AnnotationDbi, BiocStyle, biomaRt, covr, DESeq2, jsonlite, knitr, org.Hs.eg.db, rmarkdown, scales, testthat (>= 3.0.0), vdiffr License: GPL-3 + file LICENSE MD5sum: 8e424cec4c6b56495701aaeef179bcff NeedsCompilation: no Package: PathNet Version: 1.47.0 Suggests: PathNetData, RUnit, BiocGenerics License: GPL-3 MD5sum: 3f844bd364cd35018e489dfb7ac5271f NeedsCompilation: no Package: pathRender Version: 1.75.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods, stats4 Suggests: ALL, hgu95av2.db License: LGPL MD5sum: 0cbc76fe9cdd7c646cd32db07efd931a NeedsCompilation: no Package: pathview Version: 1.47.0 Depends: R (>= 3.5.0) Imports: KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils Suggests: gage, org.Mm.eg.db, org.EcK12.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) MD5sum: 9e8d5717bad51eff47f15437bf5f7b31 NeedsCompilation: no Package: pathwayPCA Version: 1.23.0 Depends: R (>= 3.1) Imports: lars, methods, parallel, stats, 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graphics, methods, parallel, scater, SingleCellExperiment, SummarizedExperiment, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 3) MD5sum: a8432650393b347d3fe0ef977082af7b NeedsCompilation: no Package: Pedixplorer Version: 1.3.0 Depends: R (>= 4.3.0) Imports: graphics, stats, methods, ggplot2, utils, grDevices, stringr, plyr, dplyr, tidyr, quadprog, Matrix, S4Vectors, shiny, readxl, shinyWidgets, htmlwidgets, DT, gridExtra, data.table, plotly, colourpicker, shinytoastr, scales, shinycssloaders Suggests: diffviewer, testthat (>= 3.0.0), vdiffr, rmarkdown, BiocStyle, knitr, withr, qpdf, shinytest2, covr, devtools, R.devices, usethis, magick License: Artistic-2.0 MD5sum: 1d72f0b86401255f086e3804b98a32a3 NeedsCompilation: no Package: pengls Version: 1.13.0 Depends: R (>= 4.2.0) Imports: glmnet, nlme, stats, BiocParallel Suggests: knitr,rmarkdown,testthat License: GPL-2 MD5sum: 9c0e1a94eae933b8a586de201837ee4c NeedsCompilation: no Package: PepSetTest Version: 1.1.0 Imports: dplyr, 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Depends: R (>= 4.2) Imports: utils, methods, grDevices, graphics, circlize, httr, dplyr, attempt, lubridate, survival, survminer, ggplot2, GenomicRanges, SummarizedExperiment, S4Vectors, yaml, parallel, future, future.apply Suggests: BiocStyle, rmarkdown, knitr, testthat License: Artistic-2.0 MD5sum: 16e6c4632b6789d73740f03eec6ab32d NeedsCompilation: no Package: phantasus Version: 1.27.0 Depends: R (>= 4.3) 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, apeglm, tidyr, config (>= 0.3.2), rhdf5client (>= 1.25.1), yaml, fs, phantasusLite, XML Suggests: testthat, BiocStyle, knitr, rmarkdown, org.Hs.eg.db, org.Mm.eg.db License: MIT + file LICENSE MD5sum: 251ef56c68e9b599d3f5a3471ba8714a NeedsCompilation: no Package: phantasusLite Version: 1.5.0 Depends: R (>= 4.2) Imports: data.table, rhdf5client(>= 1.25.1), httr, stringr, stats, utils, Biobase, methods Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5, GEOquery License: MIT + file LICENSE MD5sum: fd8d806e071afd34e789ec317d6eacf2 NeedsCompilation: no Package: PharmacoGx Version: 3.11.0 Depends: R (>= 3.6), CoreGx Imports: BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, RColorBrewer, magicaxis, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, checkmate, boot, coop LinkingTo: Rcpp Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils License: GPL (>= 3) MD5sum: 77c099ec07fef81cbf07d6067ec38843 NeedsCompilation: yes Package: PhenoGeneRanker Version: 1.15.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 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BMA, ggplot2, Hmisc Imports: survival, limma, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, hgu133a.db, ellipse Suggests: GSEABase, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) MD5sum: ad7433b2a2569ca5236d13dfdd842412 NeedsCompilation: no Package: PhenStat Version: 2.43.0 Depends: R (>= 3.5.0) Imports: SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf, knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4, graphics, grDevices, utils, stats Suggests: RUnit, BiocGenerics License: file LICENSE MD5sum: c670458808ee1712479274c77d7fcc45 NeedsCompilation: no Package: philr Version: 1.33.0 Imports: ape, phangorn, tidyr, ggplot2, ggtree, methods Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia License: GPL-3 MD5sum: ae358b71a0587942eb951bfa5aef03a1 NeedsCompilation: no Package: PhIPData Version: 1.15.0 Depends: R (>= 4.1.0), SummarizedExperiment (>= 1.3.81) Imports: BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors, edgeR, cli, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr License: MIT + file LICENSE MD5sum: 736836e503fa9bf41b12d19dcf0fe4a3 NeedsCompilation: no Package: phosphonormalizer Version: 1.31.0 Depends: R (>= 4.0) Imports: plyr, stats, graphics, matrixStats, methods Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) MD5sum: e953f26c9a6c2b642be2d7dea0c7c8e9 NeedsCompilation: no Package: PhosR Version: 1.17.0 Depends: R (>= 4.2.0) Imports: ruv, e1071, dendextend, limma, pcaMethods, stats, RColorBrewer, circlize, dplyr, igraph, pheatmap, preprocessCore, tidyr, rlang, graphics, grDevices, utils, SummarizedExperiment, methods, S4Vectors, BiocGenerics, ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext, stringi Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate License: GPL-3 + file LICENSE MD5sum: 8c51a271394cc0f3a2baa7c6bafd887f NeedsCompilation: no Package: PhyloProfile Version: 1.99.1 Depends: R (>= 4.4.0) Imports: ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, dplyr, DT, energy, ExperimentHub, extrafont, fastcluster, ggplot2, gridExtra, pbapply, plotly, RColorBrewer, RCurl, Rfast, scattermore, shiny, shinyBS, shinycssloaders, shinyFiles, shinyjs, stringr, tsne, umap, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat, OmaDB License: MIT + file LICENSE MD5sum: 00e32418764eb1aba2bb7f5261d0a71a NeedsCompilation: no Package: piano Version: 2.23.0 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: 727d3e0215591903753a9c0a496a1b42 NeedsCompilation: no Package: pickgene Version: 1.79.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: 6bbda0aa1e802ed3c0edea51085e4675 NeedsCompilation: no Package: PICS Version: 2.51.0 Depends: R (>= 3.0.0) Imports: utils, stats, graphics, grDevices, methods, IRanges, GenomicRanges, Rsamtools, GenomicAlignments Suggests: rtracklayer, parallel, knitr License: Artistic-2.0 MD5sum: b49c50d8c987aad52b362f8d3f1aaf63 NeedsCompilation: yes Package: Pigengene Version: 1.33.0 Depends: R (>= 4.0.3), graph, BiocStyle (>= 2.28.0) Imports: bnlearn (>= 4.7), C50 (>= 0.1.2), MASS, matrixStats, partykit, Rgraphviz, WGCNA, GO.db, impute, preprocessCore, grDevices, graphics, stats, utils, parallel, pheatmap (>= 1.0.8), dplyr, gdata, clusterProfiler, ReactomePA, ggplot2, openxlsx, DBI, DOSE Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), 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digest, visNetwork, magrittr, methods, Biostrings, GenomeInfoDb, parallel, stats, utils, rmarkdown Suggests: BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: 78dfa5108d8ab4bec68e3689ea0e46b8 NeedsCompilation: no Package: PIPETS Version: 1.3.0 Depends: R (>= 4.4.0) Imports: dplyr, utils, stats, GenomicRanges, BiocGenerics, methods Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: b62e90e81f9d8dfe85e90174e1923a57 NeedsCompilation: no Package: Pirat Version: 1.1.0 Depends: R (>= 4.4.0) Imports: basilisk, reticulate, progress, ggplot2, MASS, invgamma, grDevices, stats, graphics, SummarizedExperiment, S4Vectors Suggests: knitr, BiocStyle License: GPL-2 MD5sum: e553be7913a5dec9229358fbecae7d97 NeedsCompilation: no Package: PIUMA Version: 1.3.0 Depends: R (>= 4.3), ggplot2 Imports: cluster, umap, tsne, kernlab, vegan, dbscan, igraph, scales, Hmisc, patchwork, grDevices, stats, methods, SummarizedExperiment Suggests: 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ggplot2 (>= 3.0.0), dplyr (>= 0.7.6), tidyr (>= 0.2.0), tibble (>= 1.4.2), stringr (>= 1.3.1), readr (>= 1.1.1), readxl (>= 1.1.0), scales (>= 1.0.0), stats, grid, gridExtra (>= 2.3), egg (>= 0.4.0), gtable (>= 0.2.0), ggpubr (>= 0.1.8), shiny (>= 1.1.0), shinythemes (>= 1.1.1), colourpicker (>= 1.0), magrittr (>= 1.5), Hmisc (>= 4.1.1), rlang (>= 0.2.2) Suggests: knitr, htmltools, BiocStyle, rmarkdown, testthat License: GPL-3 MD5sum: adf99f4b400e11c66ba6cc495b60bd90 NeedsCompilation: no Package: PLPE Version: 1.67.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) MD5sum: c4145d9517d53e227f50c2c4be01a6bf NeedsCompilation: no Package: PLSDAbatch Version: 1.3.0 Depends: R (>= 4.3.0) Imports: mixOmics, scales, Rdpack, ggplot2, gridExtra, ggpubr, lmerTest, performance, grid, stats, pheatmap, vegan, Biobase, BiocStyle, TreeSummarizedExperiment Suggests: knitr, rmarkdown, testthat, badger License: GPL-3 MD5sum: 5904dd74ec8c6f1632c6bbcca6d3a371 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biomaRt, BiocFileCache, broom, Seurat, SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0) License: Apache License (== 2.0) | file LICENSE MD5sum: ef34f73577f32f56e639edbd94662f35 NeedsCompilation: no Package: projectR Version: 1.23.0 Depends: R (>= 4.0.0) Imports: methods, cluster, stats, limma, NMF, ROCR, ggalluvial, RColorBrewer, dplyr, fgsea, reshape2, viridis, scales, Matrix, MatrixModels, msigdbr, ggplot2, cowplot, ggrepel, umap, tsne Suggests: BiocStyle, CoGAPS, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap, gplots, SeuratObject License: GPL (== 2) MD5sum: 465358714c25c92f66a1b00378a77cff NeedsCompilation: no Package: pRoloc Version: 1.47.1 Depends: R (>= 3.5), MSnbase (>= 1.19.20), MLInterfaces (>= 1.67.10), methods, Rcpp (>= 0.10.3), BiocParallel Imports: stats4, Biobase, mclust (>= 4.3), caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS, knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools, plyr, ggplot2, biomaRt, utils, grDevices, graphics LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, rmarkdown, pRolocdata (>= 1.43.2), roxygen2, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape, magick License: GPL-2 MD5sum: 41e5754efc5d3c5daca38cefc86fe698 NeedsCompilation: yes Package: pRolocGUI Version: 2.17.0 Depends: methods, R (>= 3.1.0), pRoloc (>= 1.27.6), Biobase, MSnbase (>= 2.1.11) Imports: shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics, utils, ggplot2, shinydashboardPlus (>= 2.0.0), colourpicker, shinyhelper, shinyWidgets, shinyjs, colorspace, stats, grDevices, grid, BiocGenerics, shinydashboard Suggests: pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown, testthat (>= 3.0.0) License: GPL-2 MD5sum: 639d599de1a6e98701f23bec3f33de2b NeedsCompilation: no Package: PROMISE 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Imports: gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats, graphics Suggests: BiocStyle, knitr, rmarkdown License: MIT MD5sum: b96b2bb4857aa4c65545fdd66ac728ff NeedsCompilation: no Package: protGear Version: 1.11.0 Depends: R (>= 4.2), dplyr (>= 0.8.0) , limma (>= 3.40.2) ,vsn (>= 3.54.0) Imports: magrittr (>= 1.5) , stats (>= 3.6) , ggplot2 (>= 3.3.0) , tidyr (>= 1.1.3) , data.table (>= 1.14.0), ggpubr (>= 0.4.0), gtools (>= 3.8.2) , tibble (>= 3.1.0) , rmarkdown (>= 2.9) , knitr (>= 1.33), utils (>= 3.6), genefilter (>= 1.74.0), readr (>= 2.0.1) , Biobase (>= 2.52.0), plyr (>= 1.8.6) , Kendall (>= 2.2) , shiny (>= 1.0.0) , purrr (>= 0.3.4), plotly (>= 4.9.0) , MASS (>= 7.3) , htmltools (>= 0.4.0) , flexdashboard (>= 0.5.2) , shinydashboard (>= 0.7.1) , GGally (>= 2.1.2) , pheatmap (>= 1.0.12) , grid(>= 4.1.1), styler (>= 1.6.1) , factoextra (>= 1.0.7) ,FactoMineR (>= 2.4) , rlang (>= 0.4.11), remotes (>= 2.4.0) Suggests: gridExtra (>= 2.3), png (>= 0.1-7) , magick (>= 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parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling License: MIT + file LICENSE MD5sum: 0ff34f114e25954b958b0a181bcd8454 NeedsCompilation: yes Package: PSMatch Version: 1.11.0 Depends: S4Vectors Imports: utils, stats, igraph, methods, Matrix, BiocParallel, BiocGenerics, ProtGenerics (>= 1.27.1), QFeatures, MsCoreUtils Suggests: msdata, rpx, mzID, mzR, Spectra, SummarizedExperiment, BiocStyle, rmarkdown, knitr, factoextra, testthat License: Artistic-2.0 MD5sum: b54aaf81037c7ee6841d382974f940e8 NeedsCompilation: no Package: ptairMS Version: 1.15.0 Imports: Biobase, bit64, chron, data.table, doParallel, DT, enviPat, foreach, ggplot2, graphics, grDevices, ggpubr, gridExtra, Hmisc, methods, minpack.lm, MSnbase, parallel, plotly, rhdf5, rlang, Rcpp, shiny, shinyscreenshot, signal, scales, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData, ropls License: GPL-3 MD5sum: 8ff7a8ef9e447ce26604f01d75893990 NeedsCompilation: yes 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SingleCellExperiment, MsDataHub (>= 1.3.3), Matrix, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap License: Artistic-2.0 MD5sum: 8f208ea61f23edb332b5de639719b1a7 NeedsCompilation: no Package: qmtools Version: 1.11.0 Depends: R (>= 4.2.0), SummarizedExperiment Imports: rlang, ggplot2, patchwork, heatmaply, methods, MsCoreUtils, stats, igraph, VIM, scales, grDevices, graphics, limma Suggests: Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute, imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: eda7ca7629203de48d56e0b34254e62b NeedsCompilation: no Package: qpcrNorm Version: 1.65.0 Depends: methods, Biobase, limma, affy License: LGPL (>= 2) MD5sum: 966b13adfe8bf2a60ca8e5492a8a8051 NeedsCompilation: no Package: qpgraph Version: 2.41.0 Depends: R (>= 3.5) Imports: methods, parallel, Matrix 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License: GPL-3 MD5sum: ef4bdb9123538637df083941686b3237 NeedsCompilation: no Package: quantro Version: 1.41.0 Depends: R (>= 4.0) Imports: Biobase, minfi, doParallel, foreach, iterators, ggplot2, methods, RColorBrewer Suggests: rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 46bad2499177025d4db46886efc27fcc NeedsCompilation: no Package: quantsmooth Version: 1.73.0 Depends: R(>= 2.10.0), quantreg, grid License: GPL-2 MD5sum: 1b2cf6d3435441c532c9722da025636d NeedsCompilation: no Package: QuasR Version: 1.47.2 Depends: R (>= 4.4), parallel, GenomicRanges, Rbowtie Imports: methods, grDevices, graphics, utils, stats, tools, BiocGenerics, S4Vectors, IRanges, Biobase, Biostrings, BSgenome, Rsamtools (>= 2.13.1), GenomicFeatures, txdbmaker, ShortRead, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, AnnotationDbi LinkingTo: Rhtslib (>= 1.99.1) Suggests: Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat License: GPL-2 Archs: x64 MD5sum: 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License: GPL-2 MD5sum: e535ef177169ff43cabf060201d21261 NeedsCompilation: yes Package: rnaEditr Version: 1.17.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, BiocGenerics, GenomeInfoDb, bumphunter, S4Vectors, stats, survival, logistf, plyr, corrplot Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: ca3e9611b6bdad96750076d5e6d19ba9 NeedsCompilation: no Package: RNAmodR Version: 1.21.0 Depends: R (>= 4.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomicRanges, Modstrings Imports: methods, stats, grDevices, matrixStats, BiocGenerics, Biostrings (>= 2.57.2), BiocParallel, txdbmaker, GenomicFeatures, GenomicAlignments, GenomeInfoDb, rtracklayer, Rsamtools, BSgenome, RColorBrewer, colorRamps, ggplot2, Gviz (>= 1.31.0), reshape2, graphics, ROCR Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data License: Artistic-2.0 MD5sum: e09dee3b914edbe5c7d6a1f6a017a2b3 NeedsCompilation: no Package: RNAmodR.AlkAnilineSeq Version: 1.21.0 Depends: R (>= 4.0), RNAmodR (>= 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stats, Rcpp (>= 0.11.2),recount,ggpubr,SummarizedExperiment,tidyr,dplyr,tidyselect,utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 34c58dfc73b93fc753e81ffdac678954 NeedsCompilation: yes Package: RnBeads Version: 2.25.0 Depends: R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25), GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, grid, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr Imports: IRanges Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, RnBeads.hg38, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame License: GPL-3 MD5sum: dec334a172fd9aa648e1eadcc41b07cb 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msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom, tidyr, AUCell, BiocParallel, rmarkdown, methods, stats, cli, SingleCellSignalR, MatrixGenerics, Seurat, DT Suggests: knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler License: GPL-3 MD5sum: 2c6d43d9dff58491e83780ce49a5f167 NeedsCompilation: no Package: scGPS Version: 1.21.0 Depends: R (>= 3.6), SummarizedExperiment, dynamicTreeCut, SingleCellExperiment Imports: glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1), fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel, grDevices, graphics, stats, utils, DESeq2, locfit LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE License: GPL-3 MD5sum: 6d8d86cde9b2ee1ed82819967ccbf37b NeedsCompilation: yes Package: schex Version: 1.21.0 Depends: SingleCellExperiment (>= 1.7.4), ggplot2 (>= 3.2.1) Imports: hexbin, stats, methods, cluster, dplyr, entropy, ggforce, grid, rlang, concaveman Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, Seurat, shinydashboard, iSEE, igraph, scran, tibble, scuttle License: GPL-3 MD5sum: 044df0cb0bbe69fe40429dd858b2238d NeedsCompilation: no Package: scHOT Version: 1.19.0 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: 49f5b07b0f96b076772af584a8a02ce2 NeedsCompilation: no Package: scider Version: 1.5.0 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: f58ec649c8e2dadf2c182fac32cf39aa NeedsCompilation: no Package: scifer Version: 1.9.0 Imports: dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra, tibble, scales, rlang, flowCore, methods, basilisk, reticulate, here, utils, basilisk.utils Suggests: BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0) Enhances: parallel License: MIT + file LICENSE MD5sum: 6a43fd8241705a2b7a5dc8c4a66c255e NeedsCompilation: no Package: scmap Version: 1.29.0 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: 9a8d6bb902f0fbbfd400e2b8ee5af2d0 NeedsCompilation: yes Package: scMerge Version: 1.23.0 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: e7a0023da7a2fbb704ed0d162d419a6c NeedsCompilation: no Package: scMET Version: 1.9.0 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: a833076ef534b5fe2f6aa4dd17ee2263 NeedsCompilation: yes Package: scmeth Version: 1.27.0 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: 7cb1722a8f19208aa152b7c7f596625c NeedsCompilation: no Package: scMitoMut Version: 1.3.1 Depends: R (>= 4.3.0) Imports: data.table, Rcpp, magrittr, plyr, stringr, utils, stats, methods, ggplot2, pheatmap, RColorBrewer, rhdf5, readr, parallel, grDevices LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils License: Artistic-2.0 MD5sum: a4ba77792586a892ce8c9394eb286dfe NeedsCompilation: yes Package: scMultiSim Version: 1.3.0 Depends: R (>= 4.4.0) Imports: foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats, phytools, KernelKnn, gplots, zeallot, crayon, assertthat, igraph, methods, grDevices, graphics, stats, utils, markdown, SummarizedExperiment, BiocParallel Suggests: knitr, rmarkdown, roxygen2, shiny, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 5b8532b29e531eb8ea1bbc1068baeda0 NeedsCompilation: no Package: SCnorm Version: 1.29.0 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: 91701ccf6ba680496222e68c17368ddc NeedsCompilation: no Package: scone Version: 1.31.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment, DelayedMatrixStats, sparseMatrixStats 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: 751c18d0742b04c85224ca8b4c42671f NeedsCompilation: no Package: Sconify Version: 1.27.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 3d10923ef2e5d24dfbbaa1bb70ab47b6 NeedsCompilation: no Package: SCOPE Version: 1.19.0 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: 410561e9ddb7d42d90f04fcc30497657 NeedsCompilation: no Package: scoreInvHap Version: 1.29.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: 6ac61ec8a2f2613d2bb579579d06104e NeedsCompilation: no Package: scoup Version: 1.1.1 Depends: R (>= 4.4), Matrix Imports: Biostrings, methods Suggests: BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat (>= 3.0.0), yaml License: GPL (>= 2) MD5sum: 61b1b128ceb2c309c93bd6da92913ca6 NeedsCompilation: no Package: scp Version: 1.17.0 Depends: R (>= 4.3.0), QFeatures (>= 1.13.5) Imports: IHW, ggplot2, ggrepel, matrixStats, metapod, methods, MsCoreUtils, MultiAssayExperiment, nipals, RColorBrewer, S4Vectors, SingleCellExperiment, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, MsDataHub (>= 1.3.3), impute, knitr, patchwork, preprocessCore, rmarkdown, scater, scpdata, sva, testthat, vdiffr, vsn, uwot License: Artistic-2.0 MD5sum: 8f7e74352660b480831a9106adc12405 NeedsCompilation: no Package: scPCA Version: 1.21.0 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: 3b2ece9f0b747f98e32655d3daf78efd NeedsCompilation: no Package: scPipe Version: 2.7.1 Depends: R (>= 4.2.0), SingleCellExperiment Imports: AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings, data.table, dplyr, DropletUtils, flexmix, GenomicRanges, GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grDevices, graphics, hash, IRanges, magrittr, MASS, Matrix (>= 1.5.0), mclust, methods, MultiAssayExperiment, org.Hs.eg.db, org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate, Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer, SummarizedExperiment, S4Vectors, scales, stats, stringr, tibble, tidyr, tools, utils, vctrs (>= 0.5.2) LinkingTo: Rcpp, Rhtslib (>= 1.13.1), testthat Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap License: GPL (>= 2) MD5sum: 408c9f014761019b16875f53782b86d0 NeedsCompilation: yes Package: scran Version: 1.35.0 Depends: SingleCellExperiment, scuttle Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, MatrixGenerics, S4Arrays, DelayedArray, BiocSingular, bluster, metapod, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, DelayedMatrixStats, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, pheatmap, scater License: GPL-3 MD5sum: b50399d58c2d37c06c5ac5788f8fe733 NeedsCompilation: yes Package: scrapper Version: 1.1.7 Imports: methods, Rcpp, beachmat (>= 2.21.6), DelayedArray, BiocNeighbors (>= 1.99.0), igraph, parallel LinkingTo: Rcpp, assorthead, beachmat, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, MatrixGenerics, sparseMatrixStats, Matrix, scRNAseq License: MIT + file LICENSE MD5sum: 864ac11a6c480f5a78f958dc8232691d NeedsCompilation: yes Package: scReClassify Version: 1.13.0 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: 2f647d2eaabd77bb0c240072065d3dc6 NeedsCompilation: no Package: scRecover Version: 1.23.0 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL MD5sum: 80b84472e0274c37e7684ff512c635b1 NeedsCompilation: no Package: screenCounter Version: 1.7.1 Depends: S4Vectors, SummarizedExperiment Imports: Rcpp, BiocParallel LinkingTo: Rcpp Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: cbd9ea1f8565dce67b0815fb53c43af4 NeedsCompilation: yes Package: ScreenR Version: 1.9.0 Depends: R (>= 4.2) Imports: methods (>= 4.0), rlang (>= 0.4), stringr (>= 1.4), limma (>= 3.46), patchwork (>= 1.1), tibble (>= 3.1.6), scales (>= 1.1.1), ggvenn (>= 0.1.9), purrr (>= 0.3.4), ggplot2 (>= 3.3), stats, tidyr (>= 1.2), magrittr (>= 1.0), dplyr (>= 1.0), edgeR (>= 3.32), tidyselect (>= 1.1.2) Suggests: rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0), BiocStyle (>= 2.22.0), covr (>= 3.5) License: MIT + file LICENSE MD5sum: ca3886ae9ad5f3978ba359129d8341ee NeedsCompilation: no Package: scRepertoire Version: 2.3.1 Depends: ggplot2, R (>= 4.0) Imports: assertthat, cubature, dplyr, evmix, ggalluvial, ggdendro, ggraph, grDevices, igraph, iNEXT, methods, plyr, quantreg, Rcpp, reshape2, rjson, rlang, S4Vectors, SeuratObject, SingleCellExperiment, stats, stringr, stringdist, SummarizedExperiment, tidygraph, truncdist, utils, VGAM, hash, purrr, lifecycle LinkingTo: Rcpp Suggests: BiocManager, BiocStyle, circlize, knitr, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0), vdiffr License: MIT + file LICENSE MD5sum: cea06b34e3edc7b3fce386b8ebf03ae9 NeedsCompilation: yes Package: scRNAseqApp Version: 1.7.6 Depends: R (>= 4.3.0) Imports: bibtex, bslib, circlize, ComplexHeatmap, colourpicker, data.table, DBI, DT, fs, GenomicRanges, GenomeInfoDb, ggdendro, ggforce, ggplot2, ggrepel, ggridges, grDevices, grid, gridExtra, htmltools, IRanges, jsonlite, Matrix, magrittr, methods, patchwork, plotly, RColorBrewer, RefManageR, rhdf5, Rsamtools, RSQLite, rtracklayer, S4Vectors, scales, scrypt, Seurat, SeuratObject, shiny, shinyhelper, shinymanager, slingshot, SingleCellExperiment, sortable, stats, tools, xfun, xml2, utils Suggests: rmarkdown, knitr, testthat, BiocStyle Enhances: celldex, future, SingleR, SummarizedExperiment, tricycle License: GPL-3 MD5sum: 1d99aea5fdcd328f595c98e1f082f444 NeedsCompilation: no Package: scruff Version: 1.25.0 Depends: R (>= 4.0) Imports: data.table, GenomicAlignments, GenomicFeatures, txdbmaker, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread, parallelly Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 5afa0d01b10845165684f0755423a600 NeedsCompilation: no Package: scry Version: 1.19.0 Depends: R (>= 4.0), stats, methods Imports: DelayedArray, glmpca (>= 0.2.0), Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array, knitr, markdown, rmarkdown, TENxPBMCData, testthat License: Artistic-2.0 MD5sum: 82cc98ef235ccf53dabe0f6189b93e0c NeedsCompilation: no Package: scShapes Version: 1.13.0 Depends: R (>= 4.1) Imports: Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS, emdbook, magrittr, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 5b2f3c03832d37f3879b3cbf60f502cf NeedsCompilation: yes Package: scTensor Version: 2.17.0 Depends: R (>= 4.1.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8), abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics, stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2 Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens, AnnotationHub License: Artistic-2.0 MD5sum: 79d13a34d33f8d6455b536946d971186 NeedsCompilation: no Package: scTGIF Version: 1.21.0 Depends: R (>= 3.6.0) Imports: GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly, tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr, S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor, methods, scales, msigdbr, schex, tibble, ggplot2, igraph Suggests: testthat License: Artistic-2.0 MD5sum: a794200679da0fe705499d3c4633d611 NeedsCompilation: no Package: scTHI Version: 1.19.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 3957fc1b46aa3af828fbf80836c9fba8 NeedsCompilation: no Package: scTreeViz Version: 1.13.0 Depends: R (>= 4.0), methods, epivizr, SummarizedExperiment Imports: data.table, S4Vectors, digest, Matrix, Rtsne, httr, igraph, clustree, scran, sys, epivizrData, epivizrServer, ggraph, scater, Seurat, SingleCellExperiment, ggplot2, stats, utils Suggests: knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb License: Artistic-2.0 MD5sum: 4e6ac436529856199dbeffdfd5d2d189 NeedsCompilation: no Package: scuttle Version: 1.17.0 Depends: SingleCellExperiment Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays, MatrixGenerics, SparseArray, DelayedArray, beachmat LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, sparseMatrixStats, DelayedMatrixStats, scran License: GPL-3 MD5sum: f5b04790204d31085cd289d03cb2f93d NeedsCompilation: yes Package: scviR Version: 1.7.0 Depends: R (>= 4.3), basilisk, shiny, SingleCellExperiment Imports: reticulate, BiocFileCache, utils, pheatmap, SummarizedExperiment, S4Vectors, limma, scater, stats, MatrixGenerics Suggests: knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle License: Artistic-2.0 MD5sum: 28a66b85bb8f3fa4521e6f4e5779c95a NeedsCompilation: no Package: SDAMS Version: 1.27.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: 562c478a75b98fe3f327b642e0c5be20 NeedsCompilation: no Package: seahtrue Version: 1.1.0 Depends: R (>= 4.2.0) Imports: dplyr (>= 1.1.2), readxl (>= 1.4.1), logger (>= 0.2.2), tidyxl (>= 1.0.8), purrr (>= 0.3.5), tidyr (>= 1.3.0), lubridate (>= 1.8.0), stringr (>= 1.4.1), tibble (>= 3.1.8), validate (>= 1.1.1), rlang (>= 1.0.0), glue (>= 1.6.2), cli (>= 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Version: 2.41.1 Depends: R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown License: GPL-3 MD5sum: c10b73b9722f5fd243ad1cf8a95ed55a NeedsCompilation: no Package: selectKSigs Version: 1.19.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: 550c61356561b577f67aeebeb6dc1093 NeedsCompilation: yes Package: SELEX Version: 1.39.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: 5f46a821d9c2b15aee5fb216a3fdabc2 NeedsCompilation: no Package: SemDist Version: 1.41.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) MD5sum: f6b436acfa2ac70606e7d8a933d4ca1f NeedsCompilation: no Package: semisup Version: 1.31.0 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pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, scales, stats, UpSetR Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 491b2f20d99f5cfdc7f180c86a525fd5 NeedsCompilation: no Package: SeqSQC Version: 1.29.0 Depends: R (>= 3.4), ExperimentHub (>= 1.3.7), SNPRelate (>= 1.10.2) Imports: e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, plotly, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: 1452849542e040121d65c6518543b47f NeedsCompilation: no Package: seqTools Version: 1.41.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: c24c4d4c06682e30adb4e7e8e68e50a4 NeedsCompilation: yes Package: SeqVarTools Version: 1.45.0 Depends: SeqArray Imports: grDevices, graphics, stats, methods, Biobase, BiocGenerics, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, data.table, Suggests: BiocStyle, RUnit, stringr License: GPL-3 MD5sum: b9c7c7877ce8dd569f3955d70eb4327f NeedsCompilation: no Package: sesame Version: 1.25.1 Depends: R (>= 4.5.0), sesameData Imports: graphics, BiocParallel, utils, methods, stringr, readr, tibble, MASS, wheatmap (>= 0.2.0), GenomicRanges, IRanges, grid, preprocessCore, S4Vectors, ggplot2, BiocFileCache, GenomeInfoDb, stats, SummarizedExperiment, dplyr, reshape2 Suggests: scales, BiocManager, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals License: MIT + file LICENSE MD5sum: 25c6c5b9befd99f69002826d9a94f813 NeedsCompilation: no Package: SEtools Version: 1.21.0 Depends: R (>= 4.0), SummarizedExperiment, sechm Imports: BiocParallel, Matrix, DESeq2, S4Vectors, data.table, edgeR, openxlsx, pheatmap, stats, circlize, methods, sva Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL MD5sum: 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genefilter, GOstats, RColorBrewer, xtable, Rgraphviz, reshape2, openxlsx, ggridges, DescTools, org.Hs.eg.db, methods, grDevices, stats, RSpectra, graph Suggests: knitr, rmarkdown, BiocManager, devtools, BiocStyle License: GPL-3 MD5sum: 3d5827493aa07ea1ebb580e3f210b77d NeedsCompilation: no Package: SGSeq Version: 1.41.0 Depends: R (>= 4.0), IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), Rsamtools (>= 1.31.2), SummarizedExperiment, methods Imports: AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>= 2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>= 1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19), grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7), stats Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown License: Artistic-2.0 MD5sum: 2ca6dac8c6a3f2daf36e7e520161aac7 NeedsCompilation: no Package: SharedObject Version: 1.21.0 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, 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org.Hs.eg.db Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, utils, reshape2, visNetwork, BiocParallel, fastmatch, reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray, BiocGenerics, tibble LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT License: Artistic-2.0 MD5sum: aa73bd93f9f8ced2122944da404fc2fc NeedsCompilation: yes Package: signeR Version: 2.9.0 Depends: R (>= 3.0.2), VariantAnnotation, NMF Imports: BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat, survivalAnalysis, future, VGAM, MASS, kknn, glmnet, e1071, randomForest, ada, future.apply, ggplot2, pROC, pheatmap, RColorBrewer, listenv, reshape2, scales, survminer, dplyr, ggpubr, cowplot, tibble, readr, shiny, shinydashboard, shinycssloaders, shinyWidgets, bsplus, DT, magrittr, tidyr, BiocFileCache, proxy, rtracklayer, BSgenome LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown License: GPL-3 MD5sum: f13426636d125c443aef56b1c11b2c2b NeedsCompilation: yes Package: SigsPack Version: 1.21.0 Depends: R (>= 3.6) Imports: quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0), VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb, GenomicRanges, rtracklayer, SummarizedExperiment, graphics, stats, utils Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: d6c995d1c3a199501e7407fd1c8a2f2e NeedsCompilation: no Package: sigsquared Version: 1.39.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 969d6031d4182d7acdf7db957b0c7b28 NeedsCompilation: no Package: SIM Version: 1.77.0 Depends: R (>= 3.5), quantreg Imports: graphics, stats, globaltest, 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License: MIT + file LICENSE MD5sum: 8f2ffe18b1339d3792860dbdb7299314 NeedsCompilation: no Package: SingleCellExperiment Version: 1.29.1 Depends: SummarizedExperiment Imports: methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne License: GPL-3 MD5sum: 85ff5758fcae65fb74f9581562ea293a NeedsCompilation: no Package: SingleCellSignalR Version: 1.19.0 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: 0300a9dd57604bec47533b81ae2ddcda NeedsCompilation: no Package: singleCellTK Version: 2.15.2 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, grid, GSVA (>= 1.50.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix (>= 1.6-1), matrixStats, methods, msigdbr, multtest, plotly, plyr, ROCR, Rtsne, S4Vectors, scater, scMerge (>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, stringr, SoupX, sva, reshape2, shinyalert, circlize, enrichR (>= 3.2), celda, shinycssloaders, DropletUtils, scds (>= 1.2.0), reticulate (>= 1.14), tools, tximport, tidyr, eds, withr, GSEABase, R.utils, zinbwave, scRNAseq (>= 2.0.2), TENxPBMCData, yaml, rmarkdown, magrittr, scDblFinder, metap, VAM (>= 0.5.3), tibble, rlang, TSCAN, TrajectoryUtils, scuttle, utils, stats, zellkonverter, tidyr Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony, SeuratObject, optparse License: MIT + file LICENSE MD5sum: 04200ec40b491ccd0895cd26ee8deb0c NeedsCompilation: no Package: SingleMoleculeFootprinting Version: 2.1.0 Depends: R (>= 4.4.1) Imports: BiocGenerics, Biostrings, BSgenome, dplyr, GenomeInfoDb, GenomicRanges, ggpointdensity, ggplot2, ggrepel, grDevices, IRanges, Matrix, parallel, patchwork, plyr, plyranges, QuasR, RColorBrewer, rlang, S4Vectors, stats, stringr, tibble, tidyr, tidyverse, viridis Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, qs, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0) License: GPL-3 MD5sum: 74f94c106d47d05e78d1b197804566c3 NeedsCompilation: no Package: SingleR Version: 2.9.3 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocNeighbors, stats, utils, Rcpp, beachmat (>= 2.23.5) LinkingTo: Rcpp, beachmat, assorthead, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scrapper, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 MD5sum: 2fdbfabe23fbbee0cd42e88975394b8e NeedsCompilation: yes Package: singscore Version: 1.27.0 Depends: R (>= 3.6) Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, reshape2, S4Vectors Suggests: pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: e9c29b198a42e63996f7164215957607 NeedsCompilation: no Package: SiPSiC Version: 1.7.0 Depends: Matrix, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle License: file LICENSE MD5sum: 9adda7dd2b14f02bf11f1d6afe01755f NeedsCompilation: no Package: sitadela Version: 1.15.0 Depends: R (>= 4.1.0) Imports: Biobase, BiocGenerics, biomaRt, Biostrings, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, methods, parallel, Rsamtools, RSQLite, rtracklayer, S4Vectors, 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clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr License: Artistic-2.0 MD5sum: 38908959724cbd9de3a2f88ce401522d NeedsCompilation: no Package: SLqPCR Version: 1.73.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) MD5sum: c3be6921c898cb49024a14a1fb115b73 NeedsCompilation: no Package: SMAD Version: 1.23.0 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: 336445097ef61aab2f372cb230df60f3 NeedsCompilation: yes Package: smartid Version: 1.3.2 Depends: R (>= 4.4) Imports: dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools, sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater, splatter, testthat (>= 3.0.0), tidytext, UpSetR License: MIT + file LICENSE MD5sum: 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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: 3762fb8b748da42deed55778f803d2aa NeedsCompilation: no Package: snifter Version: 1.17.0 Depends: R (>= 4.0.0) Imports: basilisk, reticulate, irlba, stats, assertthat Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) License: GPL-3 MD5sum: 19b8495fececeb77b9146fd6fd99f08a NeedsCompilation: no Package: snm Version: 1.55.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL MD5sum: bcdb31a1913dcb3914c5037bbb546208 NeedsCompilation: no Package: SNPediaR Version: 1.33.0 Depends: R (>= 3.0.0) Imports: RCurl, jsonlite Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 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SummarizedExperiment, S4Vectors, utils Suggests: testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown, covr, BiocStyle, Seurat, patchwork, ggforce, ggnewscale License: GPL (>= 3) MD5sum: 2e7f2b25be5f4d78bca359f666ff04c7 NeedsCompilation: no Package: sparrow Version: 1.13.4 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 (>= 2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix, methods, plotly (>= 4.9.0), stats, utils, viridis Suggests: AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr, PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot License: MIT + file LICENSE MD5sum: 11d635582f8b019e95a9d1b5bb3cd6ae NeedsCompilation: no Package: SparseArray Version: 1.7.2 Depends: R (>= 4.3.0), methods, Matrix, BiocGenerics (>= 0.43.1), MatrixGenerics (>= 1.11.1), S4Vectors (>= 0.43.2), S4Arrays (>= 1.5.11) Imports: utils, stats, matrixStats, IRanges, XVector LinkingTo: S4Vectors, IRanges, XVector Suggests: HDF5Array, ExperimentHub, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 4a7567a6c94090693a9140f98f49f3a3 NeedsCompilation: yes Package: sparseMatrixStats Version: 1.19.0 Depends: MatrixGenerics (>= 1.5.3) Imports: Rcpp, Matrix, matrixStats (>= 0.60.0), methods LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: cf632a40ed06cbe93386a44d4cd2d6ca NeedsCompilation: yes Package: sparsenetgls Version: 1.25.0 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: 255ee95a1d0ccfd3b6ca9968f9465803 NeedsCompilation: no Package: SparseSignatures Version: 2.17.0 Depends: R (>= 4.1.0), NMF Imports: nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2, gridExtra, reshape2, RhpcBLASctl Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr, License: file LICENSE MD5sum: efab10084a7684ebf4bc98feb52371d7 NeedsCompilation: no Package: spaSim Version: 1.9.0 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: d5a55fb013a35697d9205e21baf716cf NeedsCompilation: no Package: SpatialCPie Version: 1.23.0 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 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stats, utils, graphics, SeuratObject, Biobase, GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4) Suggests: testthat, knitr, rmarkdown, qpdf, Seurat License: MIT + file LICENSE MD5sum: ed17ef6dc24428671de58bb56b7facad NeedsCompilation: no Package: SpatialExperiment Version: 1.17.0 Depends: methods, SingleCellExperiment Imports: rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils License: GPL-3 MD5sum: 0edfabf3d5dd25433d329b50efc8a82f NeedsCompilation: no Package: SpatialFeatureExperiment Version: 1.9.6 Depends: R (>= 4.2.0) Imports: Biobase, BiocGenerics, BiocNeighbors, BiocParallel, data.table, DropletUtils, EBImage, grDevices, lifecycle, Matrix, methods, rjson, rlang, S4Vectors, sf, sfheaders, SingleCellExperiment, SpatialExperiment, spatialreg, spdep (>= 1.1-7), SummarizedExperiment, stats, terra, utils, zeallot Suggests: arrow, BiocStyle, dplyr, knitr, RBioFormats, rhdf5, rmarkdown, scater, sfarrow, SFEData (>= 1.5.3), Seurat, SeuratObject, sparseMatrixStats, testthat (>= 3.0.0), tidyr, Voyager (>= 1.7.2), withr, xml2 License: Artistic-2.0 MD5sum: dbd13df1cecebc621ca1ecebde53e98b NeedsCompilation: no Package: spatialHeatmap Version: 2.13.1 Depends: R (>= 3.5.0) Imports: data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid, gridExtra, igraph, methods, Matrix, rsvg, shiny, grDevices, graphics, ggplotify, parallel, reshape2, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2 Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend, DT, dynamicTreeCut, flashClust, gplots, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, scater, scuttle, scran, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, xlsx, yaml License: Artistic-2.0 MD5sum: 92a54977edcdeffe903a60e7c2e13421 NeedsCompilation: no Package: SpatialOmicsOverlay Version: 1.7.0 Depends: R (>= 4.1.0) Imports: S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML, scattermore, dplyr, pbapply, data.table, readxl, magick, grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats, utils, methods, ggtext, tools, RBioFormats Suggests: knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf License: MIT MD5sum: 8136667fe9a92778c0f5c87430610c80 NeedsCompilation: no Package: spatialSimGP Version: 1.1.0 Depends: R (>= 4.4) Imports: SpatialExperiment, MASS, SummarizedExperiment Suggests: testthat (>= 3.0.0), STexampleData, ggplot2, knitr License: MIT + file LICENSE MD5sum: 86b2b027d9461f792ee9bc85613e08de NeedsCompilation: no Package: spatzie Version: 1.13.0 Depends: R (>= 4.3) Imports: BiocGenerics, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicInteractions, GenomicRanges, ggplot2, IRanges, MatrixGenerics, matrixStats, motifmatchr, S4Vectors, stats, SummarizedExperiment, TFBSTools, utils Suggests: BiocManager, Biostrings, knitr, pheatmap, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-3 MD5sum: 1ece21fd1a4f1359369a885fb7f0a76d NeedsCompilation: no Package: speckle Version: 1.7.0 Depends: R (>= 4.2.0) Imports: limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods, stats, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 0655cbab431cb42f5f17dce95b818038 NeedsCompilation: no Package: specL Version: 1.41.0 Depends: R (>= 4.1), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.7), RSQLite (>= 1.1), seqinr (>= 3.3) Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) License: GPL-3 MD5sum: db5737c6df505bebd0523c9c21cae373 NeedsCompilation: no Package: SpeCond Version: 1.61.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) MD5sum: c43f302920b9108aff478d626707dcdf NeedsCompilation: no Package: Spectra Version: 1.17.4 Depends: R (>= 4.0.0), S4Vectors, BiocParallel Imports: ProtGenerics (>= 1.39.1), methods, IRanges, MsCoreUtils (>= 1.7.5), graphics, grDevices, stats, tools, utils, fs, BiocGenerics, MetaboCoreUtils Suggests: testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick License: Artistic-2.0 MD5sum: e7e71af15c46414fa4f68314ac747819 NeedsCompilation: no Package: SpectralTAD Version: 1.23.0 Depends: R (>= 3.6) Imports: dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges, utils Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr License: MIT + file LICENSE MD5sum: 40445c71c62bea40a71269bf8958f96e NeedsCompilation: no Package: SpectraQL Version: 1.1.0 Depends: R (>= 4.4.0), ProtGenerics (>= 1.25.1) Imports: Spectra (>= 1.5.6), MsCoreUtils, methods Suggests: testthat, msdata (>= 0.19.3), roxygen2, rmarkdown, knitr, S4Vectors, BiocStyle, mzR License: Artistic-2.0 MD5sum: 9995c2fa51263a6be0569ce90cc4ef1d NeedsCompilation: no Package: SPEM Version: 1.47.0 Depends: R (>= 2.15.1), Rsolnp, Biobase, methods License: GPL-2 MD5sum: 74484d4559ef0e5875bb55f569c2ee69 NeedsCompilation: no Package: SPIA Version: 2.59.0 Depends: R (>= 2.14.0), graphics, KEGGgraph Imports: graphics Suggests: graph, Rgraphviz, hgu133plus2.db License: file LICENSE License_restricts_use: yes MD5sum: 36721cc46862a634b9651dc5f5b2fda5 NeedsCompilation: no Package: SPIAT Version: 1.9.0 Depends: R (>= 4.2.0), SpatialExperiment (>= 1.8.0) Imports: apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3), gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3), RANN (>= 2.6.1), pracma (>= 2.2.5), dbscan (>= 1.1-5), mmand (>= 1.5.4), tibble (>= 2.1.3), grDevices, stats, utils, vroom, dittoSeq, spatstat.geom, methods, spatstat.explore, raster, sp, SummarizedExperiment, rlang Suggests: BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown, testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap, elsa License: Artistic-2.0 + file LICENSE MD5sum: e4b9ef873d95087098d97b962f780466 NeedsCompilation: no Package: spicyR Version: 1.19.3 Depends: R (>= 4.1) Imports: ggplot2, concaveman, BiocParallel, spatstat.explore, spatstat.geom, lmerTest, S4Vectors, methods, pheatmap, rlang, grDevices, stats, data.table, dplyr, tidyr, scam, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, ggforce, ClassifyR, tibble, magrittr, cli, survival, ggthemes, ggh4x, coxme, ggnewscale, lifecycle, simpleSeg Suggests: SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 920abff009c524959b899a18458c87df NeedsCompilation: no Package: spikeLI Version: 2.67.0 Imports: graphics, grDevices, stats, utils License: GPL-2 MD5sum: 4bc6d193f1f4eef50dea6dc6864187c1 NeedsCompilation: no Package: spiky Version: 1.13.0 Depends: Rsamtools, GenomicRanges, R (>= 3.6.0) Imports: stats, scales, bamlss, methods, tools, IRanges, Biostrings, GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome, S4Vectors, graphics, ggplot2, utils Suggests: covr, testthat, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager License: GPL-2 MD5sum: 26eae640a73b29c3f401ecc03c1e995e NeedsCompilation: no Package: spillR Version: 1.3.0 Depends: R (>= 4.3.0), SummarizedExperiment, CATALYST Imports: dplyr, tibble, tidyselect, stats, ggplot2, tidyr, spatstat.univar, S4Vectors, parallel Suggests: knitr, rmarkdown, cowplot, testthat (>= 3.0.0), BiocStyle, hexbin License: LGPL-3 MD5sum: 4a72ce740460d8087aa7370037944c6b NeedsCompilation: no Package: spkTools Version: 1.63.0 Depends: R (>= 2.7.0), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), graphics, grDevices, gtools, methods, RColorBrewer, stats, utils Suggests: xtable License: GPL (>= 2) MD5sum: 6432311dcd63686234b762091ede4ebd NeedsCompilation: no Package: splatter Version: 1.31.0 Depends: R (>= 4.0), SingleCellExperiment Imports: BiocGenerics, BiocParallel, checkmate (>= 2.0.0), crayon, edgeR, fitdistrplus, grDevices, locfit, matrixStats, methods, rlang, S4Vectors, scuttle, stats, SummarizedExperiment, utils, withr Suggests: BASiCS (>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), igraph, IRanges, knitr, limSolve, lme4, magick, mfa, phenopath, preprocessCore, progress, pscl, rmarkdown, scales, scater (>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave License: GPL-3 + file LICENSE MD5sum: ff50d593ad6c5a09ee541218221add79 NeedsCompilation: no Package: SpliceWiz Version: 1.9.0 Depends: R (>= 3.5.0), NxtIRFdata Imports: ompBAM, methods, stats, utils, tools, parallel, scales, magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2, AnnotationHub, RSQLite, BiocFileCache, BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray, DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges, HDF5Array, htmltools, IRanges, patchwork, pheatmap, progress, plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment, S4Vectors, shiny, shinyFiles, shinyWidgets, shinydashboard, stringi, rhandsontable, DT, grDevices, heatmaply, matrixStats, RColorBrewer, rvest, httr LinkingTo: ompBAM, Rcpp, RcppProgress Suggests: knitr, rmarkdown, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, AnnotationDbi, fgsea, Rsubread License: MIT + file LICENSE MD5sum: 733227bf14f72740e4d82963388f7d67 NeedsCompilation: yes Package: SplicingFactory Version: 1.15.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, methods, stats Suggests: testthat, knitr, rmarkdown, ggplot2, tidyr License: GPL-3 + file LICENSE MD5sum: f09aa2b929faebe5de2e7897567e48c3 NeedsCompilation: no Package: SplicingGraphs Version: 1.47.0 Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22), Rgraphviz (>= 2.3.7) Imports: methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>= 0.17.5), BiocParallel, IRanges (>= 2.21.2), GenomeInfoDb, GenomicRanges (>= 1.23.21), Rsamtools, graph Suggests: igraph, Gviz, txdbmaker, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit License: Artistic-2.0 MD5sum: 7993f0431a742a208da65d9f8e135810 NeedsCompilation: no Package: SplineDV Version: 0.99.11 Depends: R (>= 3.5.0) Imports: plotly, dplyr, scuttle, methods, Biobase, BiocGenerics, S4Vectors, sparseMatrixStats, SingleCellExperiment, SummarizedExperiment, Matrix (>= 1.6.4), utils Suggests: knitr, DelayedMatrixStats, rmarkdown, BiocStyle, ggplot2, ggpubr, MASS, scales, scRNAseq, testthat (>= 3.0.0) License: GPL-2 MD5sum: 15fec493df162e89d6d9a12bd57f74ff NeedsCompilation: no Package: splineTimeR Version: 1.35.0 Depends: R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines, GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs Suggests: knitr License: GPL-3 MD5sum: 0797269530ae8d64453b3716a5c67792 NeedsCompilation: no Package: splots Version: 1.73.0 Imports: grid, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI, dplyr, ggplot2 License: LGPL MD5sum: a0f3e1c40661fc9ad85398615a316024 NeedsCompilation: no Package: SPONGE Version: 1.29.0 Depends: R (>= 3.6) Imports: Biobase, stats, ppcor, logging, foreach, doRNG, data.table, MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse, caret, dplyr, biomaRt, randomForest, ggridges, cvms, ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr, stringr, tidyr Suggests: testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, digest, doParallel, bigmemory, GSVA License: GPL (>= 3) MD5sum: 322ce39486340b36cfd4ad0de1f3ef05 NeedsCompilation: no Package: spoon Version: 1.3.1 Depends: R (>= 4.4) Imports: SpatialExperiment, BRISC, nnSVG, BiocParallel, Matrix, methods, SummarizedExperiment, stats, utils, scuttle Suggests: testthat, STexampleData, knitr License: MIT + file LICENSE MD5sum: 884997a2c0fef09186a120eb7d2b04dd NeedsCompilation: no Package: SpotClean Version: 1.9.0 Depends: R (>= 4.2.0), Imports: stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment, SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap, rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling License: GPL-3 MD5sum: 1f9245363f0f932debb070e44b80bd1d NeedsCompilation: yes Package: SPOTlight Version: 1.11.0 Depends: R (>= 4.1) Imports: ggplot2, NMF, Matrix, matrixStats, nnls, SingleCellExperiment, sparseMatrixStats, stats Suggests: BiocStyle, colorBlindness, DelayedArray, DropletUtils, ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat License: GPL-3 MD5sum: 1fea9bbebe67f856ed0b9a2b18ad3096 NeedsCompilation: no Package: SpotSweeper Version: 1.3.2 Depends: R (>= 4.4.0) Imports: SpatialExperiment, SummarizedExperiment, BiocNeighbors, SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco, grDevices, BiocParallel Suggests: knitr, BiocStyle, rmarkdown, scuttle, STexampleData, ggpubr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: ca3648affab6cb651bfeb9df281d98f7 NeedsCompilation: no Package: spqn Version: 1.19.0 Depends: R (>= 4.0), ggplot2, ggridges, SummarizedExperiment, BiocGenerics Imports: graphics, stats, utils, matrixStats Suggests: BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3), RUnit License: Artistic-2.0 MD5sum: 005fc423b98190db42eb306a909ecb3a NeedsCompilation: no Package: SQLDataFrame Version: 1.21.0 Depends: DelayedArray, S4Vectors Imports: stats, utils, methods, BiocGenerics, RSQLite, duckdb, DBI Suggests: knitr, rmarkdown, BiocStyle, testthat MD5sum: ba914ce1dbf33b80bede3c4af05ca510 NeedsCompilation: no Package: squallms Version: 1.1.0 Depends: R (>= 3.5.0) Imports: xcms, MSnbase, MsExperiment, RaMS, dplyr, tidyr, tibble, ggplot2, shiny, plotly, data.table, caret, stats, graphics, utils, keys Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: cd04d48df6385166f9b5ea1312bc8586 NeedsCompilation: no Package: sRACIPE Version: 1.23.0 Depends: R (>= 3.6.0),SummarizedExperiment, methods, Rcpp Imports: ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork, gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices, stats, utils, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown, tinytest, doFuture License: MIT + file LICENSE MD5sum: 9129e965914d183b60f2281414167a77 NeedsCompilation: yes Package: SRAdb Version: 1.69.2 Depends: RSQLite, graph, RCurl Imports: R.utils Suggests: Rgraphviz License: Artistic-2.0 MD5sum: e867e6fd7ae81c6b519d04950e235072 NeedsCompilation: no Package: sscu Version: 2.37.0 Depends: R (>= 3.3) Imports: Biostrings (>= 2.36.4), seqinr (>= 3.1-3), BiocGenerics (>= 0.16.1) Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 4fe0d55cd906d8f493c7f388f6703789 NeedsCompilation: no Package: sSeq Version: 1.45.0 Depends: R (>= 3.0), caTools, RColorBrewer License: GPL (>= 3) MD5sum: 218fcf7e70cd8329ac7d5696875d5c12 NeedsCompilation: no Package: ssize Version: 1.81.0 Depends: gdata, xtable License: LGPL MD5sum: a48a13552dee83c5724e4ff51396c091 NeedsCompilation: no Package: sSNAPPY Version: 1.11.0 Depends: R (>= 4.3.0), ggplot2 Imports: dplyr (>= 1.1), magrittr, rlang, stats, graphite, tibble, ggraph, igraph, reshape2, org.Hs.eg.db, SummarizedExperiment, edgeR, methods, ggforce, pheatmap, utils, stringr, gtools, tidyr Suggests: BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: 0bfe3c1b9b01530ee6727bd2af663e41 NeedsCompilation: no Package: ssPATHS Version: 1.21.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: ROCR, dml, MESS Suggests: ggplot2, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 5332d79c3cfffd45f2d4e2aa078d9c74 NeedsCompilation: no Package: ssrch Version: 1.23.0 Depends: R (>= 3.6), methods Imports: shiny, DT, utils Suggests: knitr, testthat, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 6313e44aa89edb9779716d9bf319741c NeedsCompilation: no Package: ssviz Version: 1.41.0 Depends: R (>= 3.5.0), methods, Rsamtools, Biostrings, reshape, ggplot2, RColorBrewer, stats Suggests: knitr License: GPL-2 MD5sum: f4ed45f748b1d29ef34d8d7c6198f183 NeedsCompilation: no Package: 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RUVSeq Suggests: knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 403f0baac6620427df8de647ab6feb38 NeedsCompilation: no Package: STATegRa Version: 1.43.0 Depends: R (>= 2.10) Imports: Biobase, gridExtra, ggplot2, methods, stats, grid, MASS, calibrate, gplots, edgeR, limma, foreach, affy Suggests: RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>= 1.3), roxygen2, doSNOW License: GPL-2 MD5sum: 1fb375f51e40f44d5f3e28c6bc2a3796 NeedsCompilation: no Package: Statial Version: 1.9.0 Depends: R (>= 4.1.0) Imports: BiocParallel, spatstat.geom, concaveman, data.table, spatstat.explore, dplyr, tidyr, SingleCellExperiment, tibble, stringr, tidyselect, ggplot2, methods, stats, SummarizedExperiment, S4Vectors, plotly, purrr, ranger, magrittr, limma, SpatialExperiment, cluster, treekoR Suggests: BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR, ggsurvfit, lisaClust, survival License: GPL-3 MD5sum: 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R (>= 3.4), methods Imports: biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 4e46733f8c014de67ac385187ae98635 NeedsCompilation: no Package: transcriptR Version: 1.35.0 Depends: R (>= 3.5.0), methods Imports: BiocGenerics, caret, chipseq, e1071, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2, Rsamtools, rtracklayer, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat License: GPL-3 MD5sum: 9dab2c49e6a659cfa78b558909e3e0dc NeedsCompilation: no Package: transformGamPoi Version: 1.13.0 Imports: glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp LinkingTo: Rcpp Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 2eed1e011c1d8e9cecdf828726c1dd1b NeedsCompilation: yes Package: transite Version: 1.25.0 Depends: R (>= 3.5) Imports: BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils LinkingTo: Rcpp (>= 1.0.4.8) Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: deba913508a7157de83a43cae1f1bb74 NeedsCompilation: yes Package: tRanslatome Version: 1.45.0 Depends: R (>= 2.15.0), methods, limma, anota, DESeq2, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 MD5sum: 39c055eef59270538c2d533c8d553e01 NeedsCompilation: no Package: transmogR Version: 1.3.0 Depends: Biostrings, GenomicRanges Imports: BSgenome, dplyr, GenomeInfoDb, GenomicFeatures, ggplot2 (>= 3.5.0), IRanges, 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NeedsCompilation: no Package: Trendy Version: 1.29.0 Depends: R (>= 3.4) Imports: stats, utils, graphics, grDevices, segmented, gplots, parallel, magrittr, BiocParallel, DT, S4Vectors, SummarizedExperiment, methods, shiny, shinyFiles Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL-3 MD5sum: 257d938733f1bfdb35775061a4fa0160 NeedsCompilation: no Package: TRESS Version: 1.13.0 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: 4aab0f8c710dd33d1f13c335cbe75b43 NeedsCompilation: no Package: tricycle Version: 1.15.0 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: 956ec285d4cf7351db8410fb0deefb0b NeedsCompilation: no Package: trigger Version: 1.53.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 MD5sum: 81d8b5dcc872c3fc9ea73b3f22b8c546 NeedsCompilation: yes Package: trio Version: 3.45.0 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: eb07bd4adc28a307db8dc9fa771c857a NeedsCompilation: no Package: triplex Version: 1.47.0 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: 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NeedsCompilation: no Package: tRNAdbImport Version: 1.25.0 Depends: R (>= 3.6), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, stringr, httr2, xml2, S4Vectors, methods, IRanges, utils Suggests: BiocGenerics, knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE MD5sum: 40097ce34d60a04af468d70d8af48d31 NeedsCompilation: no Package: tRNAscanImport Version: 1.27.0 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: b73f42b07666e33324a70b30fb1b58ad NeedsCompilation: no Package: TRONCO Version: 2.39.0 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: de178955e77754ac3fc6ff9f50a26900 NeedsCompilation: no Package: TSAR Version: 1.5.0 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: 0157e88a25bb052ffcb1dbbe0a174709 NeedsCompilation: no Package: TSCAN Version: 1.45.0 Depends: R (>= 4.4.0), SingleCellExperiment, TrajectoryUtils Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, SparseArray (>= 1.5.23), DelayedArray 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Depends: R (>= 3.4), methods, utils, stats Imports: AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel, Biostrings, ensembldb, 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: 567ae04c945bc0d7d6599c24750e5a24 NeedsCompilation: no Package: tweeDEseq Version: 1.53.0 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: 1021653b4898869fac7e47200e22c466 NeedsCompilation: yes Package: twilight Version: 1.83.0 Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, 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GenomicRanges, GenomicFeatures Imports: methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>= 2.0), IRanges, UCSC.utils, AnnotationDbi, Biobase, BiocIO, rtracklayer, biomaRt (>= 2.59.1) Suggests: RMariaDB, mirbase.db, ensembldb, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 223bba60d510b0f57d6a1c8fb761bb18 NeedsCompilation: no Package: tximeta Version: 1.25.0 Imports: SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, txdbmaker, 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: 0da89c8c21edf03498b37a28f63c5f77 NeedsCompilation: no Package: tximport Version: 1.35.0 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR, DESeq2 (>= 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Version: 2.47.1 Depends: BiocGenerics, methods, RSQLite, utils Imports: AnnotationDbi, BiocFileCache, BiocBaseUtils, httr, httpcache, jsonlite, progress, rjsoncons Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 67e5612afdd5c9584b9f05a8d872ebc4 NeedsCompilation: no Package: Uniquorn Version: 2.27.0 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: fc77181b6bbeb6753d3486b5803d4a68 NeedsCompilation: no Package: universalmotif Version: 1.25.1 Depends: R (>= 3.5.0) Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid, MatrixGenerics LinkingTo: Rcpp, RcppThread Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio Enhances: PWMEnrich, rGADEM License: GPL-3 MD5sum: e91fcc1ca23a5da6e3711417d7e1799d NeedsCompilation: yes Package: updateObject Version: 1.11.0 Depends: R (>= 4.2.0), methods, BiocGenerics (>= 0.51.1), S4Vectors Imports: utils, digest Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, SingleCellExperiment, MultiAssayExperiment, BiSeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 6312bf740fd11a9b1637621d273556c6 NeedsCompilation: no Package: UPDhmm Version: 1.3.0 Depends: R (>= 4.3.0) Imports: HMM, utils, VariantAnnotation, GenomicRanges, S4Vectors, IRanges, stats Suggests: knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown, karyoploteR, regioneR, dplyr License: MIT + file LICENSE MD5sum: 9db56f22f707cda6ebc9ba5bec3950f6 NeedsCompilation: no Package: uSORT Version: 1.33.0 Depends: R (>= 3.3.0), tcltk Imports: igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 MD5sum: e6b73fdd0201a28b925b12332c02d174 NeedsCompilation: no Package: VAExprs Version: 1.13.0 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: cc4fe1e1499b1399710a207769e0e756 NeedsCompilation: no Package: VanillaICE Version: 1.69.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, human610quadv1bCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 MD5sum: 584557cfbe222533f7377edfbe9cae2d NeedsCompilation: yes Package: VarCon Version: 1.15.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 8c82e6389f456bafaf40468f4d511800 NeedsCompilation: no Package: variancePartition Version: 1.37.1 Depends: R (>= 4.3.0), ggplot2, limma, BiocParallel Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack, rlang, lme4 (>= 1.1.33), grDevices, graphics, Biobase, methods, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr License: GPL-2 MD5sum: b6e5a21c596e61c6f174e1afc11ac56d NeedsCompilation: no Package: VariantAnnotation Version: 1.53.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5), Rsamtools (>= 2.19.1) Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.57.2), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome (>= 1.47.3), GenomicFeatures (>= 1.31.3) LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0) Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr, magick, jsonlite, httr, rjsoncons License: Artistic-2.0 MD5sum: 7c457fa8802309f88dea2b4dace263d4 NeedsCompilation: yes Package: VariantExperiment Version: 1.21.0 Depends: R (>= 3.6.0), S4Vectors (>= 0.21.24), SummarizedExperiment (>= 1.13.0), GenomicRanges, Imports: GDSArray (>= 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PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 License: Artistic-2.0 MD5sum: 04b204854a60b51e6d8ba22b2ae113d4 NeedsCompilation: yes Package: VariantTools Version: 1.49.0 Depends: R (>= 3.5.0), S4Vectors (>= 0.17.33), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), VariantAnnotation (>= 1.11.16), methods Imports: Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel, GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7), BiocParallel, GenomeInfoDb, BSgenome, Biobase Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3), TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: Artistic-2.0 MD5sum: 04fc8c9a302c888dc3e55a4d7f376ba2 NeedsCompilation: no Package: VaSP Version: 1.19.0 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 076a3408200d9eb08ebe6bd2ad090678 NeedsCompilation: no Package: vbmp Version: 1.75.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: ffe0330eb972e06eb3bdcabd794ccfa0 NeedsCompilation: no Package: VCFArray Version: 1.23.0 Depends: R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28) Imports: tools, GenomicRanges, VariantAnnotation (>= 1.29.3), GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 02fd6a1339ba27cde9b5835870f372e9 NeedsCompilation: no Package: VDJdive Version: 1.9.0 Depends: R (>= 4.2) Imports: BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix, methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils LinkingTo: Rcpp Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: 401eda6efe28d95a363d7c15d6eccc77 NeedsCompilation: yes Package: VegaMC Version: 3.45.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods License: GPL-2 MD5sum: 8c24e7a935bb9c5e41a602053efcded8 NeedsCompilation: yes Package: velociraptor Version: 1.17.0 Depends: SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors, DelayedArray, basilisk, zellkonverter, scuttle, SingleCellExperiment, BiocParallel, BiocSingular Suggests: BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran, scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot, GGally, patchwork, metR License: MIT + file LICENSE MD5sum: b283ee3a3111445827b14b4d801cdf54 NeedsCompilation: no Package: veloviz Version: 1.13.0 Depends: R (>= 4.1) Imports: Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 31260a7b7152c5b26da7f9500e08efe2 NeedsCompilation: yes Package: VennDetail Version: 1.23.0 Imports: utils, grDevices, stats, methods, dplyr, purrr, tibble, magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger Suggests: knitr, rmarkdown, testthat, markdown License: GPL-2 MD5sum: 742a0b6661552f1d118929c590b1bfad NeedsCompilation: no Package: VERSO Version: 1.17.0 Depends: R (>= 4.1.0) Imports: utils, data.tree, ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 7448adb9f4031da3fabf898c061ca7fc NeedsCompilation: no Package: vidger Version: 1.27.0 Depends: R (>= 3.5) Imports: Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr, RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, testthat License: GPL-3 | file LICENSE MD5sum: f9c2831a0bd8ba1511c7cb6677457e55 NeedsCompilation: no Package: viper Version: 1.41.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: f1b5ae441ebec13d64676e7a8ab978a6 NeedsCompilation: no Package: ViSEAGO Version: 1.21.0 Depends: R (>= 3.6) Imports: data.table, AnnotationDbi, AnnotationForge, biomaRt, dendextend, DiagrammeR, DT, dynamicTreeCut, fgsea, GOSemSim, ggplot2, GO.db, grDevices, heatmaply, htmlwidgets, igraph, methods, plotly, processx, topGO, RColorBrewer, R.utils, scales, stats, UpSetR, utils Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager MD5sum: 26174710a2e1fef209177bdd484f8e55 NeedsCompilation: no Package: VisiumIO Version: 1.3.2 Depends: R (>= 4.4.0), TENxIO Imports: BiocBaseUtils, BiocGenerics, BiocIO (>= 1.15.1), jsonlite, methods, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment Suggests: arrow, BiocStyle, data.table, knitr, readr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: dc6abc6296134b3d337695e833775760 NeedsCompilation: no Package: visiumStitched Version: 0.99.15 Depends: R (>= 4.4), SpatialExperiment Imports: BiocBaseUtils, BiocGenerics, dplyr, DropletUtils, grDevices, imager, Matrix, methods, pkgcond, readr, rjson, S4Vectors, SingleCellExperiment, spatialLIBD (>= 1.17.8), stringr, SummarizedExperiment, tibble, tidyr, xml2 Suggests: BiocFileCache, BiocStyle, ggplot2, knitr, RefManageR, rmarkdown, sessioninfo, Seurat, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 6e7bd087b0a233e0b85755b2057b5568 NeedsCompilation: no Package: vissE Version: 1.15.0 Depends: R (>= 4.1) Imports: igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm, ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb, ggrepel, textstem, tidygraph, stats, scales, ggraph Suggests: testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr License: GPL-3 MD5sum: 6c495062d411be4d6541cb8089fb309c NeedsCompilation: no Package: Voyager Version: 1.9.1 Depends: R (>= 4.2.0), SpatialFeatureExperiment (>= 1.7.3) Imports: BiocParallel, bluster, DelayedArray, ggnewscale, ggplot2 (>= 3.4.0), grDevices, grid, lifecycle, Matrix, matrixStats, memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, spdep, stats, SummarizedExperiment, terra, utils, zeallot Suggests: arrow, automap, BiocSingular, BiocStyle, cowplot, data.table, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, xml2 License: Artistic-2.0 MD5sum: 81cb8330482fffa4931d0ea2dbd4e829 NeedsCompilation: no Package: VplotR Version: 1.17.0 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown License: GPL (>= 3) MD5sum: a118085335952c14511d6a032c3eaf2e NeedsCompilation: no Package: vsclust Version: 1.9.3 Depends: R (>= 4.2.0) Imports: matrixStats, limma, parallel, shiny, qvalue, grDevices, stats, MultiAssayExperiment, graphics LinkingTo: Rcpp Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, clusterProfiler License: GPL-2 MD5sum: 5d874784425df56986b695178fd4d2d2 NeedsCompilation: yes Package: vsn Version: 3.75.0 Depends: R (>= 4.0.0), methods, Biobase Imports: affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat License: Artistic-2.0 MD5sum: e41ee936701ec65753a4efdfb182c124 NeedsCompilation: yes Package: vtpnet Version: 0.47.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: 21fac43230cc46ddd7fb57c3b22c426d NeedsCompilation: no Package: vulcan Version: 1.29.0 Depends: R (>= 4.0), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene, zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit Imports: wordcloud, csaw, gplots, stats, utils, caTools, graphics, DESeq2, Biobase Suggests: vulcandata License: LGPL-3 MD5sum: c90bd2f5735f443085999fd5203a1334 NeedsCompilation: no Package: waddR Version: 1.21.0 Depends: R (>= 3.6.0) Imports: Rcpp (>= 1.0.1), arm (>= 1.10-1), eva, BiocFileCache (>= 2.6.0), BiocParallel, SingleCellExperiment, parallel, methods, stats LinkingTo: Rcpp, RcppArmadillo, Suggests: knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown, scater License: MIT + file LICENSE MD5sum: 52d98d860ddf48368adc02cb0fd32511 NeedsCompilation: yes Package: wateRmelon Version: 2.13.0 Depends: R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi, lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19, illuminaio Imports: Biobase Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore Enhances: minfi License: GPL-3 MD5sum: 89dcfa6a01468c7ad4c1a68f6cfc62b8 NeedsCompilation: no Package: wavClusteR Version: 2.41.0 Depends: R (>= 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DelayedMatrixStats, BiocParallel, BiocGenerics, limma, topconfects, dplyr, purrr, ggplot2, rlang, scales, reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl Suggests: knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0) License: LGPL-2.1 | file LICENSE MD5sum: da901d913905515b178002a1b165bbd1 NeedsCompilation: no Package: widgetTools Version: 1.85.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: 185bae757044573d842fd9c009e83acb NeedsCompilation: no Package: wiggleplotr Version: 1.31.0 Depends: R (>= 3.6) Imports: dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer, cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter License: Apache License 2.0 MD5sum: 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