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SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, dplyr, knitr, magrittr, microbiome, phyloseq, rmarkdown, testthat, tidyr, tidyverse License: Artistic-2.0 MD5sum: 08d41c692683186fcfc784d458d2bfde NeedsCompilation: no Package: ANF Version: 1.31.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 567051d39c6aced75f9c37163edec83c NeedsCompilation: no Package: animalcules Version: 1.25.0 Depends: R (>= 4.3.0) Imports: ape, assertthat, caret, covr, DESeq2, dplyr, DT, forcats, ggforce, ggplot2, GUniFrac, lattice, limma, magrittr, Matrix, methods, MultiAssayExperiment, plotly, rentrez, reshape2, ROCit, S4Vectors (>= 0.23.19), scales, shiny, shinyjs, stats, SummarizedExperiment, tibble, tidyr, tsne, umap, utils, vegan, XML Suggests: BiocStyle, biomformat, devtools, glmnet, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: 7efad7dd71bedb9975e8c5a69718d820 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NeedsCompilation: no Package: AnnotationDbi Version: 1.71.0 Depends: R (>= 2.7.0), methods, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges Imports: DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST Suggests: utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 MD5sum: d7a0a9774811525c4b0710a3fb424a25 NeedsCompilation: no Package: AnnotationFilter Version: 1.33.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown License: Artistic-2.0 MD5sum: 92d9a9c383746484f38f7df612159176 NeedsCompilation: no Package: AnnotationForge Version: 1.51.0 Depends: R (>= 3.5.0), methods, utils, BiocGenerics (>= 0.15.10), Biobase (>= 1.17.0), AnnotationDbi (>= 1.33.14) Imports: DBI, RSQLite, XML, S4Vectors, RCurl Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, rmarkdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit License: Artistic-2.0 MD5sum: bde656100a825a44b52f15cc60c09a64 NeedsCompilation: no Package: AnnotationHub Version: 3.17.0 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr, yaml, dplyr Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 4bcf5eabbddaa3cd8ffe47a4fba7720d NeedsCompilation: yes Package: AnnotationHubData Version: 1.39.0 Depends: R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges 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License: GPL-3 MD5sum: db293b16a127339e61919a36b6b13164 NeedsCompilation: no Package: antiProfiles Version: 1.49.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: 9784e6e21bfd5fdb9ad22ce040540627 NeedsCompilation: no Package: AnVIL Version: 1.21.0 Depends: R (>= 4.1.0), dplyr, AnVILBase Imports: stats, utils, methods, futile.logger, jsonlite, httr, rapiclient (>= 0.1.3), yaml, tibble, tidyselect, tidyr, rlang, shiny, DT, miniUI, htmltools, BiocBaseUtils Suggests: parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools, AnVILAz, AnVILGCP, lifecycle License: Artistic-2.0 MD5sum: a096de2c4bca5bda6540a862b582efa3 NeedsCompilation: no Package: AnVILAz Version: 1.3.0 Depends: R (>= 4.1.0) Imports: AnVILBase, BiocBaseUtils, curl, httr2, jsonlite, methods, rjsoncons, tibble, utils Suggests: BiocStyle, dplyr, knitr, readr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: eac2411c63526037cac9e75a374522b7 NeedsCompilation: no Package: AnVILBase Version: 1.3.0 Depends: R (>= 4.1.0) Imports: httr, httr2, dplyr, jsonlite, methods, tibble Suggests: AnVIL, AnVILAz, AnVILGCP, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), tinytest License: Artistic-2.0 MD5sum: cca108058a3cd5108373418bb1ba15e1 NeedsCompilation: no Package: AnVILBilling Version: 1.19.0 Depends: R (>= 4.1) Imports: methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr, dplyr, lubridate, plotly, ggplot2 Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 39e9899ad9ccb204ee5837167d256838 NeedsCompilation: no Package: AnVILGCP Version: 1.3.0 Depends: R (>= 4.2.0) Imports: AnVILBase, BiocBaseUtils, dplyr, httr, jsonlite, methods, rlang, stats, tibble, tidyr, utils Suggests: AnVIL, BiocStyle, knitr, rmarkdown, testthat, withr License: Artistic-2.0 MD5sum: d13a33b0d82800457ed87c1578a91139 NeedsCompilation: no Package: AnVILPublish Version: 1.19.0 Imports: AnVIL, AnVILGCP, BiocBaseUtils, BiocManager, httr, jsonlite, rmarkdown, yaml, readr, whisker, tools, utils, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 784d7c15371fdd203baf6ca6ffd58e05 NeedsCompilation: no Package: AnVILWorkflow Version: 1.9.0 Depends: R (>= 4.4.0), AnVILGCP, AnVILBase, httr Imports: AnVIL, dplyr, jsonlite, rlang, tibble, tidyr, utils, methods, plyr, stringr Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: f651fa1adc715db608aed75ea7cf80d3 NeedsCompilation: no Package: APAlyzer Version: 1.23.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq2, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, VariantAnnotation, dplyr, tidyr, repmis, Rsamtools, HybridMTest Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset License: LGPL-3 MD5sum: 743d588b9e798ea23c0fcdcbd45ff407 NeedsCompilation: no Package: apComplex 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2.19.0 Depends: methods, grDevices, stats, utils, parallel, edgeR, limma, AnnotationDbi Imports: GenomicRanges, GenomicFeatures, BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, Rsamtools, BiocStyle, igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid, graphics, pbmcapply, txdbmaker License: GPL MD5sum: dbb61862e695fa1478b41a4761abbac4 NeedsCompilation: no Package: AssessORF Version: 1.27.0 Depends: R (>= 3.5.0), DECIPHER (>= 2.10.0) Imports: Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown, RSQLite (>= 1.1) License: GPL-3 MD5sum: 0fd6fcfa85ca1b0a8b25efe09119c842 NeedsCompilation: no Package: ASSET Version: 2.27.0 Depends: R (>= 3.5.0), stats, graphics Imports: MASS, msm, rmeta Suggests: RUnit, BiocGenerics, knitr License: GPL-2 + file LICENSE MD5sum: be021cbc92fcf1233b17a5c77e2f6744 NeedsCompilation: no Package: ASSIGN Version: 1.45.0 Depends: R (>= 3.4) Imports: gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown License: MIT + file LICENSE MD5sum: eb7a89c377c171d39ad006878bd0cf7a NeedsCompilation: no Package: assorthead Version: 1.3.0 Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: d8d1aa7bcea4928df3947de305b46621 NeedsCompilation: no Package: ASURAT Version: 1.13.0 Depends: R (>= 4.0.0) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp (>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize, grid, grDevices, graphics LinkingTo: Rcpp Suggests: ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: ad2a7de0cd79140704a0a149afc9ba76 NeedsCompilation: yes Package: ATACseqTFEA Version: 1.11.0 Depends: R (>= 4.2) Imports: BiocGenerics, S4Vectors, IRanges, Matrix, GenomicRanges, GenomicAlignments, GenomeInfoDb, SummarizedExperiment, Rsamtools, motifmatchr, TFBSTools, stats, pracma, ggplot2, ggrepel, dplyr, limma, methods, rtracklayer Suggests: BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle License: GPL-3 MD5sum: 6264fc5f2e8e3244931bd28446ea3f2c NeedsCompilation: no Package: atena Version: 1.15.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, MatrixGenerics, BiocParallel, S4Vectors, IRanges, GenomicFeatures, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats, cli Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer License: Artistic-2.0 MD5sum: b7d4fe798ab6d15dc7aa4e1e37077b68 NeedsCompilation: no Package: atSNP Version: 1.25.0 Depends: R (>= 3.6) Imports: BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testthat, utils, lifecycle 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multtest, igraph, orthogene, stabledist, circlize (>= 0.4.14), ComplexHeatmap (>= 2.0.0), stats, scales, RANN, SpatialExperiment, SummarizedExperiment, tools Suggests: knitr, markdown, rmarkdown, STexampleData, testthat (>= 3.0.0), codetools, Matrix, lattice, cluster, survival, MASS, nlme License: CeCILL | file LICENSE MD5sum: 9738366d9ffa71a6ead9135bfdbfe232 NeedsCompilation: no Package: BUMHMM Version: 1.33.0 Depends: R (>= 3.5.0) Imports: devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges Suggests: testthat, knitr, BiocStyle License: GPL-3 MD5sum: b64eadcd11df9cbdd9640631830dcf9f NeedsCompilation: no Package: bumphunter Version: 1.51.0 Depends: R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), GenomeInfoDb, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats Suggests: testthat, RUnit, doParallel, txdbmaker, org.Hs.eg.db, 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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, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: BSD_2_clause + file LICENSE MD5sum: 0fd39eb78148aa7e30e851a1e0eea2b7 NeedsCompilation: yes Package: BUSseq Version: 1.15.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots, grDevices, methods, stats, utils Suggests: BiocStyle, knitr, BiocGenerics License: Artistic-2.0 MD5sum: 4a49b267a5ade09d8a325578b74efe1e NeedsCompilation: yes Package: CaDrA Version: 1.7.0 Depends: R (>= 4.4.0) Imports: doParallel, ggplot2, gplots, graphics, grid, gtable, knnmi, MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats, SummarizedExperiment Suggests: BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat (>= 3.1.6) License: GPL-3 + file LICENSE MD5sum: 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scales, som, stringdist, stringi, SummarizedExperiment, utils, vegan, VGAM Suggests: BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, DESeq2, FANTOM3and4CAGE, ggseqlogo, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 58f8020f048ac3a73e9a6adb1ebd3f7e NeedsCompilation: no Package: calm Version: 1.23.0 Imports: mgcv, stats, graphics Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: b3fd3bf381235646c8c0e8430b4a5d41 NeedsCompilation: no Package: CAMERA Version: 1.65.0 Depends: R (>= 3.5.0), methods, Biobase, xcms (>= 1.13.5) Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph Suggests: faahKO, RUnit, BiocGenerics, multtest Enhances: Rmpi, snow License: GPL (>= 2) MD5sum: 781ba67db73dcebc8ccceedafe44e687 NeedsCompilation: yes Package: canceR Version: 1.43.0 Depends: R (>= 4.3), tcltk, cBioPortalData Imports: GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart, survival, Biobase, phenoTest, circlize, plyr, tidyr, dplyr, graphics, stats, utils, grDevices, R.oo, R.methodsS3 Suggests: testthat (>= 3.1), knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 4b08237a63947e57514c39e4139b3c70 NeedsCompilation: no Package: cancerclass Version: 1.53.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 MD5sum: 383612fc96841b8f32bbb5743dea4e63 NeedsCompilation: yes Package: Cardinal Version: 3.11.0 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: 7f5b93ea751bbd6c573b4460efa60d85 NeedsCompilation: no Package: CardinalIO Version: 1.7.0 Depends: R (>= 4.4), BiocParallel, matter, ontologyIndex Imports: methods, S4Vectors, stats, utils, tools Suggests: 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2.43.0 Depends: R (>= 3.6.0), Biobase, IRanges, methods, GenomicRanges Imports: BiocGenerics (>= 0.31.6), coda, EBarrays, gaga, gtools, GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors (>= 0.9.25), sqldf, survival, VGAM Enhances: parallel License: GPL (>= 2) MD5sum: 2f49faa6c233164b7b1e8083d71b1859 NeedsCompilation: yes Package: CATALYST Version: 1.33.0 Depends: R (>= 4.4), SingleCellExperiment Imports: circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot, data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel, ggridges, graphics, grDevices, grid, gridExtra, Matrix, matrixStats, methods, nnls, purrr, RColorBrewer, reshape2, Rtsne, SummarizedExperiment, S4Vectors, scales, scater, stats Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot License: GPL (>= 2) MD5sum: 4727a235172b4964f002bf3db20f57ed NeedsCompilation: no Package: Category Version: 2.75.0 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: 57656536b1c04fc16ae6287e20ac75ba NeedsCompilation: no Package: categoryCompare Version: 1.53.0 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: f756932ca28456e4f4554fba7f8ba8f8 NeedsCompilation: no Package: CatsCradle Version: 1.3.0 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: 60812c5ea2882b5f396c03fdcf6bf60e NeedsCompilation: no Package: CausalR Version: 1.41.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 49845860ba63938fd23a0e3b42108ace NeedsCompilation: no Package: cbaf Version: 1.31.0 Depends: R (>= 4.1) Imports: BiocFileCache, RColorBrewer, cBioPortalData, genefilter, gplots, grDevices, stats, utils, openxlsx, zip Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 1858c659e297fa19d9329b0314b267e7 NeedsCompilation: no Package: cBioPortalData Version: 2.21.0 Depends: R (>= 4.5.0), AnVIL (>= 1.19.5), MultiAssayExperiment Imports: BiocBaseUtils, BiocFileCache (>= 1.5.3), digest, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment, RTCGAToolbox (>= 2.19.7), S4Vectors, 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rmarkdown, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 99d19c8ec941741f2064654686f3a0e8 NeedsCompilation: no Package: CCAFE Version: 1.1.0 Depends: R (>= 4.4.0) Imports: dplyr, VariantAnnotation Suggests: testthat (>= 3.0.0), rmarkdown, markdown, knitr, tidyverse, DescTools, cowplot, BiocStyle, GenomicRanges, SummarizedExperiment, S4Vectors, IRanges License: GPL-3 MD5sum: 2cfda232e4dd852a4645c07254b5fc87 NeedsCompilation: no Package: ccfindR Version: 1.29.0 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: f4315f7b6d46bb9d220e4c93337a4f8a NeedsCompilation: yes Package: ccImpute Version: 1.11.0 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: 6b4a92918288fcf6e2bf2263dd186b3f NeedsCompilation: yes Package: ccmap Version: 1.35.0 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: cf1fdfb93876c2b69c41a7ddcebbf3cd NeedsCompilation: no Package: CCPlotR Version: 1.7.0 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: cfe43c35339c802087358b8a3dd854ca NeedsCompilation: no Package: 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Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, scater (>= 1.14.4), scran, dbscan, DelayedArray, stringr, ComplexHeatmap, gridExtra, circlize, dendextend, ggdendro, pROC LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData License: MIT + file LICENSE MD5sum: 4eb64678fd6278582f9a71efef8c0e94 NeedsCompilation: yes Package: CellBarcode Version: 1.15.0 Depends: R (>= 4.1.0) Imports: methods, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr, ggplot2, stringr, magrittr, ShortRead (>= 1.48.0), Biostrings (>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors, seqinr, Rsamtools LinkingTo: Rcpp, BH Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: Artistic-2.0 MD5sum: ccfe30b41619fcd76590bd431b134324 NeedsCompilation: yes Package: cellbaseR Version: 1.33.0 Depends: R(>= 3.4) Imports: methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils, Rsamtools, BiocParallel, foreach, utils, parallel, doParallel Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation License: Apache License (== 2.0) MD5sum: 40430b19da165798bf6f2ce07723ae97 NeedsCompilation: no Package: CellBench Version: 1.25.0 Depends: R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils Imports: assertthat, BiocGenerics, BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, tidyselect, lubridate Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 License: GPL-3 MD5sum: 5b9c9ee30f4208185607abee4dd97686 NeedsCompilation: no Package: CelliD Version: 1.17.0 Depends: R (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment Imports: Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater, stringr, irlba, data.table, glue, pbapply, umap, Rtsne, reticulate, fastmatch, matrixStats, ggplot2, BiocParallel, SummarizedExperiment, fgsea LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel License: GPL-3 + file LICENSE MD5sum: 6da9dc97538c9520c8e621d345557a90 NeedsCompilation: yes Package: CellMapper Version: 1.35.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 MD5sum: e4ed0d3682f8f92bfc729a30c564b223 NeedsCompilation: no Package: cellmigRation Version: 1.17.0 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: b8488f3967329c709ae3569335d80dab NeedsCompilation: no Package: CellMixS Version: 1.25.0 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: 025b19033d4889ab556b6ce8af8ad230 NeedsCompilation: no Package: CellNOptR Version: 1.55.0 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: 2958f774436fb8f7c550a5b375ea8cf1 NeedsCompilation: yes Package: cellscape Version: 1.33.0 Depends: R (>= 3.3) Imports: dplyr (>= 0.4.3), gtools (>= 3.5.0), htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: cae74c6e1f9b71da122ff8c488a74de1 NeedsCompilation: no Package: CellTrails Version: 1.27.0 Depends: R (>= 3.5), SingleCellExperiment Imports: BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats, ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv, reshape2, Rtsne, stats, splines, SummarizedExperiment, utils Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown License: Artistic-2.0 MD5sum: 2c35616e08f332f6b15beb2575a16b2f NeedsCompilation: no Package: cellxgenedp Version: 1.13.0 Depends: R (>= 4.1.0), dplyr Imports: httr, curl, utils, tools, cli, shiny, DT, rjsoncons Suggests: zellkonverter, SingleCellExperiment, HDF5Array, tidyr, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery License: Artistic-2.0 MD5sum: 4bb5e1a44bb320ccdab2c858ff279f3b NeedsCompilation: no Package: CEMiTool Version: 1.33.0 Depends: R (>= 4.0) Imports: methods, scales, dplyr, data.table (>= 1.9.4), WGCNA, grid, ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler, fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools, pracma, intergraph, grDevices, utils, network, matrixStats, ggdendro, gridExtra, gtable, fastcluster Suggests: testthat, BiocManager License: GPL-3 MD5sum: 630fd045ec5beca22d6fde25f2e74fd5 NeedsCompilation: no Package: censcyt Version: 1.17.0 Depends: R (>= 4.0), diffcyt Imports: BiocParallel, broom.mixed, dirmult, dplyr, edgeR, fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp, purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment, survival, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 License: MIT + file LICENSE MD5sum: e01a008f6e943bf6ae581ddfa201535d NeedsCompilation: no Package: Cepo Version: 1.15.0 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: 772fd0b26fb566603d7aa4efb7921a68 NeedsCompilation: no Package: ceRNAnetsim Version: 1.21.0 Depends: R (>= 4.0.0), dplyr, tidygraph Imports: furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, stats Suggests: knitr, png, rmarkdown, testthat, covr License: GPL (>= 3.0) MD5sum: 52c9678f6cd68f7c57a10c5b44b209d2 NeedsCompilation: no Package: CeTF Version: 1.21.0 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, clusterProfiler, DESeq2, dplyr, GenomicTools.fileHandler, GGally, ggnetwork, ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3, stats, SummarizedExperiment, S4Vectors, utils, methods LinkingTo: Rcpp, RcppArmadillo Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat License: GPL-3 MD5sum: 3bafab47e5df487dd0a7aaece23244cd NeedsCompilation: yes Package: CexoR Version: 1.47.0 Depends: R (>= 4.2.0), S4Vectors, IRanges Imports: Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | GPL-2 + file LICENSE MD5sum: ab7a42fc88657c4aa65b5fdae49c3317 NeedsCompilation: no Package: CFAssay Version: 1.43.0 Depends: R (>= 2.10.0) License: LGPL MD5sum: cdb98c7689be7ec1727ca9294067c008 NeedsCompilation: no Package: cfDNAPro Version: 1.15.0 Depends: R (>= 4.1.0), magrittr (>= 1.5.0) Imports: tibble, GenomicAlignments, IRanges, plyranges, GenomeInfoDb, GenomicRanges, BiocGenerics, stats, utils, dplyr (>= 0.8.3), stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1), Rsamtools (>= 2.4.0), rlang (>= 0.4.0), BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.NCBI.GRCh38 Suggests: scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat License: GPL-3 MD5sum: 0322363bea78cf11886fd9b32620c52a NeedsCompilation: no Package: cfTools Version: 1.9.0 Imports: Rcpp, utils, GenomicRanges, basilisk, R.utils, stats, cfToolsData, grDevices, graphics LinkingTo: Rcpp, BH Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: file LICENSE MD5sum: 3e07128fe1ca31353253e1e351d18836 NeedsCompilation: yes Package: CGEN Version: 3.45.0 Depends: R (>= 4.0), survival, mvtnorm Imports: stats, graphics, utils, grDevices Suggests: cluster License: GPL-2 + file LICENSE MD5sum: fb07184a144846af3e585efa148d536f NeedsCompilation: yes Package: CGHbase Version: 1.69.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL MD5sum: d9e1dfef6083b69a0877d916e7b1f334 NeedsCompilation: no Package: CGHcall Version: 2.71.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall MD5sum: cca8cfa13ab59cc32076b14650620f55 NeedsCompilation: no Package: cghMCR Version: 1.67.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL MD5sum: 3cba27b5c700faca1523e2db39b2b8bd NeedsCompilation: no Package: CGHnormaliter Version: 1.63.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL 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testthat, vdiffr License: file LICENSE MD5sum: 82c39e219746928700b81cbd1fdd7d6d NeedsCompilation: no Package: chevreulPlot Version: 1.1.0 Depends: R (>= 4.5.0), SingleCellExperiment, chevreulProcess Imports: base, cluster, clustree, ComplexHeatmap (>= 2.5.4), circlize, dplyr, EnsDb.Hsapiens.v86, forcats, fs, ggplot2, grid, plotly, purrr, S4Vectors, scales, scater, scran, scuttle, stats, stringr, tibble, tidyr, utils, wiggleplotr (>= 1.13.1), tidyselect, patchwork Suggests: BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 9da5ea71b21264e58dd42990aa380c31 NeedsCompilation: no Package: chevreulProcess Version: 1.1.0 Depends: R (>= 4.5.0), SingleCellExperiment, scater Imports: batchelor, bluster, circlize, cluster, DBI, dplyr, EnsDb.Hsapiens.v86, ensembldb, fs, GenomicFeatures, glue, megadepth, methods, purrr, RSQLite, S4Vectors, scran, scuttle, stringr, tibble, tidyr, tidyselect, utils Suggests: BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 4ed8a5b66e0fa3ba9bfcddffe3bbf25f NeedsCompilation: no Package: chevreulShiny Version: 1.1.0 Depends: R (>= 4.5.0), SingleCellExperiment, shiny (>= 1.6.0), shinydashboard, chevreulProcess, chevreulPlot Imports: alabaster.base, clustree, ComplexHeatmap, DataEditR (>= 0.0.9), DBI, dplyr, DT, EnhancedVolcano, fs, future, ggplot2, ggplotify, grDevices, methods, patchwork, plotly, purrr, rappdirs, readr, RSQLite, S4Vectors, scales, shinyFiles, shinyhelper, shinyjs, shinyWidgets, stats, stringr, tibble, tidyr, tidyselect, utils, waiter, wiggleplotr Suggests: BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0), EnsDb.Mmusculus.v79, EnsDb.Hsapiens.v86 License: MIT + file LICENSE MD5sum: 5f77a03aae25f618928ba1e9be4a015e NeedsCompilation: no Package: Chicago Version: 1.37.0 Depends: R (>= 3.3.1), data.table Imports: matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub License: Artistic-2.0 MD5sum: 4f97161ec5172daada7932a0089248d3 NeedsCompilation: no Package: chihaya Version: 1.9.0 Depends: DelayedArray Imports: methods, Matrix, rhdf5, Rcpp, HDF5Array LinkingTo: Rcpp, Rhdf5lib Suggests: BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix, BiocStyle, testthat, rmarkdown, knitr License: GPL-3 MD5sum: 6ca7587f3387d82b06081c8173c63e4f NeedsCompilation: yes Package: chimeraviz Version: 1.35.0 Depends: Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, AnnotationFilter, data.table Imports: methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, checkmate, gtools, magick Suggests: testthat, roxygen2, devtools, knitr, lintr License: Artistic-2.0 MD5sum: e0ebbb6816db285c42cf6620f5511b86 NeedsCompilation: no 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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: 2f61b5299a70ed43b4fbd186ab98cb25 NeedsCompilation: no Package: ClustIRR Version: 1.7.1 Depends: R (>= 4.3.0) Imports: blaster, future, future.apply, grDevices, igraph, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils, posterior, visNetwork, dplyr, tidyr, ggplot2, ggforce, scales LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork License: GPL-3 + file LICENSE MD5sum: 32c8b936908731b7f32fb01dc279e050 NeedsCompilation: yes Package: clustSIGNAL Version: 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GenomicRanges Imports: BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb, S4Vectors Suggests: DNAcopy License: LGPL (>= 2.0) MD5sum: 9211774b408c430f3ffe4b2485c85eaa NeedsCompilation: yes Package: CNAnorm Version: 1.55.0 Depends: R (>= 2.10.1), methods Imports: DNAcopy License: GPL-2 MD5sum: 8f2cec9380383b8eb3bec000b15d9947 NeedsCompilation: yes Package: CNORdt Version: 1.51.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 MD5sum: 6b5356b89cec8d8e4b57bae3cd477d95 NeedsCompilation: yes Package: CNORfeeder Version: 1.49.0 Depends: R (>= 4.0.0), graph Imports: CellNOptR (>= 1.4.0) Suggests: minet, Rgraphviz, RUnit, BiocGenerics, igraph Enhances: MEIGOR License: GPL-3 MD5sum: b19fbb9c6a9b06f8e06646e14ef26efb NeedsCompilation: no Package: CNORfuzzy Version: 1.51.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 MD5sum: 890ca82032a6e0b259ac0caf5292c66d NeedsCompilation: yes Package: 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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: 7f0e5732a4111022e035bf49c52bd45e NeedsCompilation: no Package: CNVRanger Version: 1.25.0 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: 5517f1d4cf3ec35e49d620508d8675eb NeedsCompilation: no Package: CNVrd2 Version: 1.47.0 Depends: R (>= 3.0.0), methods, 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License: LGPL-3 MD5sum: 339a6e6d68ff6ce850bc5ef3909bcb6d NeedsCompilation: no Package: cogeqc Version: 1.13.0 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: cd3d73d0b1893c69b4beb1019be166dc NeedsCompilation: no Package: Cogito Version: 1.15.0 Depends: R (>= 4.1), GenomicRanges, jsonlite, GenomicFeatures, entropy Imports: BiocManager, rmarkdown, GenomeInfoDb, S4Vectors, AnnotationDbi, graphics, stats, utils, methods, magrittr, ggplot2, TxDb.Mmusculus.UCSC.mm9.knownGene Suggests: BiocStyle, knitr, markdown, testthat (>= 3.0.0) License: LGPL-3 MD5sum: bceac1d345c7c2b30a94c0019c4982b8 NeedsCompilation: no Package: coGPS Version: 1.53.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 MD5sum: b5b91dabe4ec77e6a53f5f736f5eef4f NeedsCompilation: no 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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: 28bf9c015a3be516ce0f0fbaf815c5cd NeedsCompilation: no Package: combi Version: 1.21.0 Depends: R (>= 4.0), DBI Imports: ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix (>= 1.6.0), BB, reshape2, alabama, cobs, Biobase, vegan, grDevices, graphics, methods, SummarizedExperiment Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 65c6cdfdddc2645e9895ce0d475a43a9 NeedsCompilation: no Package: coMethDMR Version: 1.13.0 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: 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statmod, covr, sva, tcltk Enhances: rpanel, DSS License: GPL (>= 2) MD5sum: 7f8ea72506fa2df300c6cf308e17a3a0 NeedsCompilation: no Package: ComplexHeatmap Version: 2.25.0 Depends: R (>= 4.0.0), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.14), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges, matrixStats, foreach, doParallel, codetools Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo, magick License: MIT + file LICENSE MD5sum: be0a95688ed82a8b576eb5bf32ba9887 NeedsCompilation: no Package: CompoundDb Version: 1.13.0 Depends: R (>= 4.1), methods, AnnotationFilter, S4Vectors Imports: BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges, Spectra (>= 1.15.10), MsCoreUtils, 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rlang, SingleCellExperiment, sparseMatrixStats, SpatialExperiment, SummarizedExperiment Suggests: BiocManager, BiocStyle, ggplot2, glue, knitr, mbkmeans, patchwork, rmarkdown, scater, SFEData, SpatialFeatureExperiment, TENxPBMCData, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: fdbe0a541f0ed5b171debb724ee68f88 NeedsCompilation: no Package: condiments Version: 1.17.0 Depends: R (>= 4.0) Imports: slingshot (>= 1.9), mgcv, RANN, stats, SingleCellExperiment, SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume (>= 0.9.1), methods, pbapply, matrixStats, BiocParallel, TrajectoryUtils, igraph, distinct Suggests: knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN, DelayedMatrixStats License: MIT + file LICENSE MD5sum: d5de718fe40335883dccb589c692a9fb NeedsCompilation: no Package: CONFESS Version: 1.37.0 Depends: R (>= 3.3),grDevices,utils,stats,graphics Imports: methods,changepoint,cluster,contrast,data.table(>= 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org.Hs.eg.db, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice, MASS, tensorflow, BSgenome.Hsapiens.UCSC.hg38, BiocFileCache, TxDb.Hsapiens.UCSC.hg38.knownGene, testthat, knitr License: file LICENSE MD5sum: 534d3fd66600f0857ca48c965affc2df NeedsCompilation: no Package: crisprShiny Version: 1.5.0 Depends: R (>= 4.4.0), shiny Imports: BiocGenerics, Biostrings, BSgenome, crisprBase, crisprDesign, crisprScore, crisprViz, DT, GenomeInfoDb, htmlwidgets, methods, pwalign, S4Vectors, shinyBS, shinyjs, utils, waiter Suggests: BiocStyle, knitr, rmarkdown, shinyFeedback, testthat (>= 3.0.0), BSgenome.Hsapiens.UCSC.hg38 License: MIT + file LICENSE MD5sum: a6b6a72ab0fcc8b02d3fce35a3cfa9f1 NeedsCompilation: no Package: CrispRVariants Version: 1.37.0 Depends: R (>= 4.3.0), ggplot2 (>= 2.2.0) Imports: AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, 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randomForest, rmarkdown, SingleCellExperiment, stats, SummarizedExperiment, ssc, S4Vectors, graphics, methods Suggests: gridExtra, knitr, RColorBrewer, testthat, uwot License: Artistic-2.0 MD5sum: a5bc98ff88e6cf5b642ad681404af5b4 NeedsCompilation: no Package: CytoGLMM Version: 1.17.0 Imports: stats, methods, BiocParallel, RColorBrewer, cowplot, dplyr, factoextra, flexmix, ggplot2, magrittr, pheatmap, stringr, strucchange, tibble, ggrepel, MASS, Matrix, tidyr, caret, rlang, grDevices Suggests: knitr, rmarkdown, testthat, BiocStyle License: LGPL-3 MD5sum: 9ce1cb8f49fdad6a9badd8fe2763ae47 NeedsCompilation: no Package: cytoKernel Version: 1.15.0 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: b618fb86198a4e37b5bb8f4c2e060ac5 NeedsCompilation: yes Package: cytolib Version: 2.21.0 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knitr, rmarkdown, BiocStyle, HDCytoData License: GPL-3 MD5sum: 9f9d0a8b5edcc41efe11c15f9973fe2d NeedsCompilation: no Package: cytoMEM Version: 1.13.0 Depends: R (>= 4.2.0) Imports: gplots, tools, flowCore, grDevices, stats, utils, matrixStats, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 5002819427cfa2880f68d48d92af33bc NeedsCompilation: no Package: CytoML Version: 2.21.0 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: 84f478d1b2bf9e6625080647f05b3e4a NeedsCompilation: yes Package: CytoPipeline Version: 1.9.0 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: f649f653a08282926e3e4c422aaefcc0 NeedsCompilation: no Package: CytoPipelineGUI Version: 1.7.0 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: 1fabc07e3a0e5828056c2a8590c78583 NeedsCompilation: no Package: cytoviewer Version: 1.9.0 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: be3fbea97df719745183b4fcbf569b2b NeedsCompilation: no Package: dada2 Version: 1.37.0 Depends: R (>= 4.1.0), Rcpp (>= 0.12.0), methods (>= 3.4.0) Imports: Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), ShortRead (>= 1.32.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0), IRanges (>= 2.6.0), XVector (>= 0.16.0), BiocGenerics (>= 0.22.0) LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, knitr, rmarkdown License: LGPL-2 MD5sum: 67fb2eac2c683b4103124fb1080ef332 NeedsCompilation: yes Package: dagLogo Version: 1.47.0 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: 5d845cc2783de958d6813ce9f5bb276e NeedsCompilation: no Package: daMA Version: 1.81.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: 3cdcd8917e9b58a2e167454ebb83e269 NeedsCompilation: no Package: DAMEfinder Version: 1.21.0 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: 4c97d235039be697abd6164f2503423f NeedsCompilation: no Package: DaMiRseq Version: 2.21.0 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: aba59fa57896173efb6c8f15cf4995ab NeedsCompilation: no Package: Damsel Version: 1.5.0 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: 8d91fcc36ab6e9cba1aa3da837edaa25 NeedsCompilation: no Package: dandelionR Version: 1.1.0 Depends: R (>= 4.4.0) Imports: BiocGenerics, bluster, destiny, igraph, MASS, Matrix, methods, miloR, purrr, rlang, S4Vectors, SingleCellExperiment, spam, stats, SummarizedExperiment, uwot Suggests: BiocStyle, knitr, rmarkdown, RColorBrewer, scater, scRepertoire, testthat License: MIT + file LICENSE MD5sum: efc37649a1f4de23374a906021ecf55b NeedsCompilation: no Package: DAPAR Version: 1.41.0 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: 6a04c945218035a98088e04858267838 NeedsCompilation: no Package: dar Version: 1.5.0 Depends: R (>= 4.5.0) Imports: cli, ComplexHeatmap, crayon, dplyr, generics, ggplot2, glue, gplots, heatmaply, magrittr, methods, mia, phyloseq, purrr, readr, rlang (>= 0.4.11), scales, stringr, tibble, tidyr, UpSetR, waldo Suggests: ALDEx2, ANCOMBC, apeglm, ashr, Biobase, corncob, covr, DESeq2, devtools, furrr, future, knitr, lefser, limma, Maaslin2, metagenomeSeq, microbiome, rmarkdown, roxygen2, roxyglobals, roxytest, rstatix, SummarizedExperiment, TreeSummarizedExperiment, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 35cc29aef72d0d984def7e2d77e65b93 NeedsCompilation: no Package: DART Version: 1.57.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: 5eb47523397fbfc03363b799006deb3d NeedsCompilation: no Package: dcanr Version: 1.25.0 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: 4e7fbff8ad59ec3c060bc47f59114c19 NeedsCompilation: no Package: DCATS Version: 1.7.0 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: 32ad8fb523434c0e7d1042b2755ac7ee NeedsCompilation: no Package: dcGSA Version: 1.37.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: 0510bc001da794aa493e560492c725d8 NeedsCompilation: no Package: ddCt Version: 1.65.0 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: 3d524937140af3c72a05946b5461a658 NeedsCompilation: no Package: ddPCRclust Version: 1.29.0 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: 8202fde0cd9462ca0e6d735430d47762 NeedsCompilation: no Package: dearseq Version: 1.21.0 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: 34c24062bd6e53cef66ed0bf68c5e18c NeedsCompilation: no Package: debCAM Version: 1.27.0 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: 09a53d0116442d060f727fc2244c9b2b NeedsCompilation: no Package: debrowser Version: 1.37.0 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: 71f8e8ba2c982d5ea6949550f9231e5a NeedsCompilation: no Package: DECIPHER Version: 3.5.0 Depends: R (>= 3.5.0), Biostrings (>= 2.59.1), stats Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector Suggests: RSQLite (>= 1.1) License: GPL-3 MD5sum: 1e3332d6e0ec7e339ca70e473a319458 NeedsCompilation: yes Package: decompTumor2Sig Version: 2.25.0 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: be5e1aa3199cc768567ad94a2f3d7e9e NeedsCompilation: no Package: DeconRNASeq Version: 1.51.0 Depends: R (>= 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MD5sum: 12e0d2c3fca8fa930745b64b9aade7b6 NeedsCompilation: yes Package: DeconvoBuddies Version: 1.1.0 Depends: R (>= 4.4.0) Imports: AnnotationHub, BiocFileCache, dplyr, ExperimentHub, ggplot2, graphics, grDevices, matrixStats, methods, purrr, rafalib, reshape2, S4Vectors, scran, SingleCellExperiment, spatialLIBD, stats, stringr, SummarizedExperiment, tibble, utils Suggests: Biobase, BiocStyle, BisqueRNA, covr, HDF5Array, knitr, RColorBrewer, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyr, tidyverse License: Artistic-2.0 MD5sum: 99434b4a9c2e02f70e4070ffd16c03c2 NeedsCompilation: no Package: deconvR Version: 1.15.0 Depends: R (>= 4.1), data.table (>= 1.14.0) Imports: S4Vectors (>= 0.30.0), methylKit (>= 1.18.0), IRanges (>= 2.26.0), GenomicRanges (>= 1.44.0), BiocGenerics (>= 0.38.0), stats, methods, foreach (>= 1.5.1), magrittr (>= 2.0.1), matrixStats (>= 0.61.0), e1071 (>= 1.7.9), quadprog (>= 1.5.8), nnls (>= 1.4), rsq (>= 2.2), MASS, utils, dplyr (>= 1.0.7), tidyr (>= 1.1.3), assertthat, minfi Suggests: testthat (>= 3.0.0), roxygen2 (>= 7.1.2), doParallel (>= 1.0.16), parallel, knitr (>= 1.34), BiocStyle (>= 2.20.2), reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), rmarkdown, devtools (>= 2.4.2), sessioninfo (>= 1.1.1), covr, granulator, RefManageR License: Artistic-2.0 MD5sum: a5961a46822f79b47eab8ab57fe81c98 NeedsCompilation: no Package: decoupleR Version: 2.15.0 Depends: R (>= 4.0) Imports: BiocParallel, broom, dplyr, magrittr, Matrix, parallelly, purrr, rlang, stats, stringr, tibble, tidyr, tidyselect, withr Suggests: glmnet (>= 4.1-7), GSVA, viper, fgsea (>= 1.15.4), AUCell, SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr, pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo, pheatmap, testthat, OmnipathR, Seurat, ggplot2, ggrepel, patchwork, magick License: GPL-3 + file LICENSE MD5sum: abb7bb7854f2b9670f75b85b9d11f8a4 NeedsCompilation: no Package: DeepPINCS Version: 1.17.0 Depends: keras, R (>= 4.1) Imports: tensorflow, CatEncoders, matlab, rcdk, stringdist, tokenizers, webchem, purrr, ttgsea, PRROC, reticulate, stats Suggests: knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: 2ff709e4a6a0eeadf7c88735b81230b3 NeedsCompilation: no Package: deepSNV Version: 1.55.0 Depends: R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.27.6), Imports: Rhtslib LinkingTo: Rhtslib (>= 1.13.1) Suggests: RColorBrewer, knitr, rmarkdown License: GPL-3 MD5sum: 9e271e17b8724ad83ce1d6952b59a01c NeedsCompilation: yes Package: DeepTarget Version: 1.3.0 Depends: R (>= 4.2.0) Imports: fgsea, ggplot2, stringr, ggpubr, BiocParallel, pROC, stats, grDevices, graphics, depmap, readr, dplyr Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 5b48ee9dd5ab2ef4cd79090d55b21930 NeedsCompilation: no Package: DEFormats Version: 1.37.0 Imports: checkmate, data.table, DESeq2, edgeR (>= 3.13.4), GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat License: GPL-3 MD5sum: f72c1881482ba92bcf56e6561257c158 NeedsCompilation: no Package: DegCre Version: 1.5.0 Depends: R (>= 4.4) Imports: GenomicRanges, InteractionSet, plotgardener, S4Vectors, stats, graphics, grDevices, BiocGenerics, GenomeInfoDb, IRanges, BiocParallel, qvalue, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, utils Suggests: BSgenome, BSgenome.Hsapiens.UCSC.hg38, BiocStyle, magick, knitr, rmarkdown, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 11ec785394bb561b9be5b0cf0e09fb1d NeedsCompilation: no Package: DegNorm Version: 1.19.0 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: 6b528871c5817a4ecacb9bfc6c99db66 NeedsCompilation: yes Package: DEGraph Version: 1.61.0 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: da482550614ecf8fd216458ae79ca82c NeedsCompilation: no Package: DEGreport Version: 1.45.0 Depends: R (>= 4.0.0) Imports: utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, dendextend, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, magrittr, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, stringi, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE MD5sum: 44b9c1a8fc4aea9a525d88c8c84cdbe8 NeedsCompilation: no Package: DEGseq Version: 1.63.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: 85e2d176085f147464eeb339087b8bf1 NeedsCompilation: yes Package: DelayedArray Version: 0.35.0 Depends: R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>= 0.53.3), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2), IRanges (>= 2.17.3), S4Arrays (>= 1.5.4), SparseArray (>= 1.7.5) Imports: stats LinkingTo: S4Vectors Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit License: Artistic-2.0 MD5sum: 133f3f6064b9f707fb9ad933803a1470 NeedsCompilation: yes Package: DelayedDataFrame Version: 1.25.0 Depends: R (>= 3.6), S4Vectors (>= 0.23.19), DelayedArray (>= 0.7.5) Imports: methods, stats, BiocGenerics Suggests: testthat, knitr, rmarkdown, BiocStyle, SeqArray, GDSArray License: GPL-3 MD5sum: 6311ea485800e44c0246864ca340e152 NeedsCompilation: no Package: 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rmarkdown, genefilter, RColorBrewer License: MIT + file LICENSE MD5sum: 5f76552d533f85eadb49c0e3b1c63df6 NeedsCompilation: yes Package: EnrichmentBrowser Version: 2.39.0 Depends: SummarizedExperiment, graph Imports: AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR, graphite, hwriter, limma, methods, pathview, safe Suggests: ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools, airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr, rmarkdown, statmod License: Artistic-2.0 MD5sum: 6758e4383bc726f2c57c9564314a400c NeedsCompilation: no Package: enrichplot Version: 1.29.0 Depends: R (>= 4.1.0) Imports: aplot (>= 0.2.1), DOSE (>= 3.31.2), ggfun (>= 0.1.7), ggnewscale, ggplot2, ggrepel (>= 0.9.0), ggtangle (>= 0.0.5), graphics, grid, igraph, methods, plyr, purrr, RColorBrewer, reshape2, rlang, stats, utils, scatterpie, GOSemSim (>= 2.31.2), magrittr, ggtree, yulab.utils (>= 0.1.6) Suggests: clusterProfiler, dplyr, europepmc, ggarchery, ggupset, glue, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, ggHoriPlot, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggstar, scales, ggtreeExtra, tidydr License: Artistic-2.0 MD5sum: fc0a15a44263f8a4ceaa559d908c24b6 NeedsCompilation: no Package: enrichViewNet Version: 1.7.0 Depends: R (>= 4.2.0) Imports: gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, DOSE, methods Suggests: BiocStyle, knitr, rmarkdown, ggplot2, testthat, magick License: Artistic-2.0 MD5sum: 18d7baad3c7de9868701783da3b61075 NeedsCompilation: no Package: ensembldb Version: 2.33.0 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: 4a5e83a21707f79cdeb34e8b37b45727 NeedsCompilation: no Package: epialleleR Version: 1.17.0 Depends: R (>= 4.1) Imports: stats, methods, utils, data.table, BiocGenerics, GenomicRanges, Rcpp LinkingTo: Rcpp, BH, Rhtslib Suggests: GenomeInfoDb, SummarizedExperiment, VariantAnnotation, RUnit, knitr, rmarkdown, ggplot2 License: Artistic-2.0 MD5sum: e87343c12d1cc0c1022bad413ab0d9c3 NeedsCompilation: yes Package: EpiCompare Version: 1.13.0 Depends: R (>= 4.2.0) Imports: AnnotationHub, ChIPseeker, data.table, genomation, GenomicRanges, IRanges (>= 2.41.3), 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: 3a9c38605c189eabca26d718bdb1715d NeedsCompilation: no Package: epidecodeR Version: 1.17.0 Depends: R (>= 3.1.0) Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 65737f01f5eda90b4c64bb4d751cefd5 NeedsCompilation: no Package: EpiDISH Version: 2.25.0 Depends: R (>= 4.1) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat License: GPL-2 MD5sum: 46781e1e38aa764cedba3a9602243f4e NeedsCompilation: no Package: epigenomix Version: 1.49.0 Depends: R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment Imports: BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray License: LGPL-3 MD5sum: ca3886dd236ede100e4b470d0dad06f5 NeedsCompilation: no Package: EpiMix Version: 1.11.0 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, BiocGenerics, multiMiR, miRBaseConverter License: GPL-3 MD5sum: 7ec92803d6c5ddee2faae2232202077e NeedsCompilation: no Package: epimutacions Version: 1.13.0 Depends: R (>= 4.3.0), epimutacionsData Imports: minfi, bumphunter, isotree, robustbase, ggplot2, GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment, stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt, BiocParallel, GenomeInfoDb, Homo.sapiens, purrr, tibble, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, AnnotationDbi, AnnotationHub, ExperimentHub, reshape2, grid, ensembldb, gridExtra, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, ggrepel Suggests: testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices License: MIT + file LICENSE MD5sum: 64ea4655f033a6cd0a46560545d4a891 NeedsCompilation: yes Package: epiNEM Version: 1.33.0 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: f936a1891a0692eba64f10ae56f4b0b7 NeedsCompilation: no Package: EpipwR Version: 1.3.0 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: a4af0976d5b24223b4c85ee3b9b1570f NeedsCompilation: no Package: epiregulon Version: 1.5.0 Depends: R (>= 4.4), SingleCellExperiment Imports: AnnotationHub, BiocParallel, ExperimentHub, Matrix, Rcpp, S4Vectors, SummarizedExperiment, bluster, checkmate, entropy, lifecycle, methods, scran, scuttle, stats, utils, scMultiome, GenomeInfoDb, GenomicRanges, AUCell, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, motifmatchr, IRanges, beachmat LinkingTo: Rcpp, beachmat, assorthead Suggests: knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), coin, scater, beachmat.hdf5 License: MIT + file LICENSE MD5sum: 9c33821bd6454ff42689a6336b9ab5e3 NeedsCompilation: yes Package: epiregulon.extra Version: 1.5.0 Depends: R (>= 4.4), SingleCellExperiment Imports: scran, ComplexHeatmap, Matrix, SummarizedExperiment, checkmate, circlize, clusterProfiler, ggplot2, ggraph, igraph, patchwork, reshape2, scales, scater Suggests: epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), msigdb, GSEABase, dorothea, scMultiome, S4Vectors, scuttle, vdiffr, ggrastr, ggrepel License: MIT + file LICENSE MD5sum: 8977487d7e7178d03f31d29d4f0e4ca9 NeedsCompilation: no Package: epistack Version: 1.15.0 Depends: R (>= 4.1) Imports: GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, graphics, plotrix, grDevices, stats, methods Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick License: MIT + file LICENSE MD5sum: e7e6c723ecb16589d5cb70954dc4b6a0 NeedsCompilation: no Package: epistasisGA Version: 1.11.0 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: 8e68de0fcb268e60d8ac91a5e3c645b8 NeedsCompilation: yes Package: EpiTxDb Version: 1.21.0 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: 4876833a8a5e0e636b94eb573bfc9a6d NeedsCompilation: no Package: epivizr Version: 2.39.0 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: 7512d2910ac09545c5f2150665619730 NeedsCompilation: no Package: epivizrChart Version: 1.31.0 Depends: R (>= 3.5.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub License: Artistic-2.0 MD5sum: 3f93460fc5f0c74370cee9888111b53a NeedsCompilation: no Package: epivizrData Version: 1.37.0 Depends: R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase Imports: S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0), OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats License: MIT + file LICENSE MD5sum: a7054877174a564cabcbcb47849ad42f NeedsCompilation: no Package: epivizrServer Version: 1.37.0 Depends: R (>= 3.2.3), methods Imports: httpuv (>= 1.3.0), R6 (>= 2.0.0), rjson, mime (>= 0.2) Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 6d197310be1d86e8747eff97674e63ca NeedsCompilation: no Package: epivizrStandalone Version: 1.37.0 Depends: R (>= 3.2.3), epivizr (>= 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Version: 1.31.0 Depends: R (>= 4.0.0), Rsamtools, GenomicRanges, ShortRead, pipeFrame Imports: Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer, ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph, rJava, magrittr, digest, BSgenome, AnnotationDbi, GenomicAlignments, GenomicFeatures, R.utils, GenomeInfoDb, BiocGenerics, S4Vectors, IRanges, rmarkdown, tools, VennDiagram, grid, JASPAR2018, TFBSTools, grDevices, graphics, stats, utils, parallel, corrplot, BiocManager, motifmatchr LinkingTo: Rcpp Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat, webshot, prettydoc License: GPL-3 | file LICENSE Archs: x64 MD5sum: 292fee30095dd87905face7a7798bdf6 NeedsCompilation: yes Package: escape Version: 2.5.0 Depends: R (>= 4.1) Imports: AUCell, BiocParallel, grDevices, dplyr, ggdist, ggplot2, ggpointdensity, GSEABase, GSVA, SingleCellExperiment, ggridges, msigdb, stats, reshape2, patchwork, MatrixGenerics, utils, SummarizedExperiment, UCell, stringr, methods, SeuratObject, Matrix Suggests: Seurat, hexbin, scran, knitr, rmarkdown, markdown, BiocStyle, RColorBrewer, rlang, spelling, testthat (>= 3.0.0), vdiffr License: MIT + file LICENSE MD5sum: 903bab34dd13c7f91f1315162eab27bf NeedsCompilation: no Package: escheR Version: 1.9.0 Depends: ggplot2, R (>= 4.3) Imports: SpatialExperiment (>= 1.6.1), SingleCellExperiment, rlang, SummarizedExperiment Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat, hexbin License: MIT + file LICENSE MD5sum: 16e7486d6823eb9b2c68c05451cd0b8d NeedsCompilation: no Package: esetVis Version: 1.35.0 Imports: mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils, grDevices, methods Suggests: ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db License: GPL-3 MD5sum: 9a5dd6594e0be159f53c32ca659a0ad1 NeedsCompilation: no Package: eudysbiome Version: 1.39.0 Depends: R (>= 3.1.0) Imports: plyr, Rsamtools, R.utils, Biostrings License: GPL-2 MD5sum: d7bc96e813cde56e92c510b9f12a9e44 NeedsCompilation: no Package: evaluomeR Version: 1.25.0 Depends: R (>= 3.6), SummarizedExperiment, MultiAssayExperiment, cluster (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14), flexmix (>= 2.3.15), RSKC (>= 2.4.2), sparcl (>= 1.0.4) Imports: corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2, ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class, prabclus, mclust, kableExtra, dplyr, dendextend (>= 1.16.0) Suggests: BiocStyle, knitr, rmarkdown, magrittr License: GPL-3 MD5sum: 1a23e342c38291dc8a361623f3aa0510 NeedsCompilation: no Package: EventPointer Version: 3.17.0 Depends: R (>= 3.5.0), SGSeq, Matrix, SummarizedExperiment Imports: GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls, limma, matrixStats, RBGL, prodlim, graph, methods, utils, stats, doParallel, foreach, affxparser, GenomicRanges, S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome, Biostrings, glmnet, abind, iterators, lpSolve, poibin, speedglm, tximport, fgsea Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra License: Artistic-2.0 MD5sum: 6a7494513a497e36d0d53a1afde7edfc NeedsCompilation: yes Package: EWCE Version: 1.17.0 Depends: R (>= 4.2), RNOmni (>= 1.0) Imports: stats, utils, methods, ewceData (>= 1.7.1), dplyr, ggplot2, reshape2, limma, stringr, HGNChelper, Matrix, parallel, SingleCellExperiment, SummarizedExperiment, DelayedArray, BiocParallel, orthogene (>= 0.99.8), data.table Suggests: rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork License: GPL-3 MD5sum: 0e45e010b034405b2ccd3019b3411ded NeedsCompilation: no Package: ExCluster Version: 1.27.0 Depends: Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges Imports: stats, methods, grDevices, graphics, utils License: GPL-3 MD5sum: ccdee733239a549ae729c1869d06c902 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viridis, ggpointdensity LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown, BiocManager, BSgenome.Hsapiens.UCSC.hg19, DT, rtracklayer, testthat (>= 3.0.0), RBGL License: MIT + file LICENSE MD5sum: c71a17f09cd50305f1a8c3633f8d20e7 NeedsCompilation: yes Package: GA4GHclient Version: 1.33.0 Depends: R (>= 3.5.0), S4Vectors Imports: BiocGenerics, Biostrings, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, methods, VariantAnnotation Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: ff2eb565338414671372a6aea56da105 NeedsCompilation: no Package: GA4GHshiny Version: 1.31.0 Depends: GA4GHclient Imports: AnnotationDbi, BiocGenerics, dplyr, DT, GenomeInfoDb, openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny, shinyjs, tidyr, shinythemes Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 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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: 6b5809a355718e9b05df57b181143501 NeedsCompilation: no Package: geNetClassifier Version: 1.49.0 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: 33b4ef6f38fa0b6a4ffccae8733629d1 NeedsCompilation: no Package: GeneticsPed Version: 1.71.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: a5b83e239f1be58c2e762a5763a0ba6f NeedsCompilation: yes Package: geneXtendeR Version: 1.35.0 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: 6b6e16c97fcd030afdfabd20af98880e NeedsCompilation: yes Package: GENIE3 Version: 1.31.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle License: GPL (>= 2) MD5sum: 3dcf0b84254b7024788fdb39a7a55f5c NeedsCompilation: yes Package: genomation Version: 1.41.0 Depends: R (>= 3.5.0), grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 5734396e6e73e1b0bbb7d88cea451599 NeedsCompilation: yes Package: GenomAutomorphism Version: 1.11.0 Depends: R (>= 4.4.0), Imports: Biostrings, BiocGenerics, BiocParallel, 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: 4c5418c5eeab5a05fba3d1c929794e3e NeedsCompilation: no Package: GenomeInfoDb Version: 1.45.0 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: 6760aed4065c8d7c8bc49aff535a0463 NeedsCompilation: no Package: genomeIntervals Version: 1.65.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 1.5.8), GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: f0b352d51b5685d0d24e31f6cd1e0952 NeedsCompilation: no Package: genomes Version: 3.39.0 Depends: readr, curl License: GPL-3 MD5sum: b97e3e144d684a408377d5b850574740 NeedsCompilation: no Package: GenomicAlignments Version: 1.45.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.55.3), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.55.7), Rsamtools (>= 1.31.2) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, knitr, BiocStyle License: Artistic-2.0 MD5sum: 017cf92839ecb3a1a6cd934c29392456 NeedsCompilation: yes Package: GenomicDataCommons Version: 1.33.0 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: 4f32f137ecb908b328023950c7c120f4 NeedsCompilation: no Package: GenomicDistributions Version: 1.17.0 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: c7d13a0809f992151a81da3fe4e7d59f NeedsCompilation: no Package: GenomicFeatures Version: 1.61.0 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: c3a50de94b48a6c16b022dded83bbbf7 NeedsCompilation: no Package: GenomicFiles Version: 1.45.0 Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), MatrixGenerics, GenomicRanges (>= 1.31.16), SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3) Imports: GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25), VariantAnnotation (>= 1.27.9), GenomeInfoDb Suggests: BiocStyle, RUnit, genefilter, deepSNV, snpStats, knitr, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens License: Artistic-2.0 MD5sum: 041ea38192ce57b213ed93b9cf85a12a NeedsCompilation: no Package: genomicInstability Version: 1.15.0 Depends: R (>= 4.1.0), checkmate Imports: mixtools, SummarizedExperiment Suggests: SingleCellExperiment, ExperimentHub, pROC License: file LICENSE MD5sum: 97a4f392fcea3184f86a68fb77d8b006 NeedsCompilation: no Package: GenomicInteractionNodes Version: 1.13.0 Depends: R (>= 4.2.0), stats Imports: AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, GenomeInfoDb, methods, IRanges, RBGL, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: file LICENSE MD5sum: bc6bf655a1b21cb4d69a4922a04fc3dd NeedsCompilation: no Package: GenomicInteractions Version: 1.43.0 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: 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BiocStyle License: Artistic-2.0 MD5sum: 71a79684dff4b90935f6c100ac4dd963 NeedsCompilation: yes Package: GenomicScores Version: 2.21.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache, IRanges (>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub, rhdf5, DelayedArray, HDF5Array Suggests: RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard, BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38, MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v4.0.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: 5aaac1d7cfb43b863033f226c9204c87 NeedsCompilation: no Package: GenomicSuperSignature Version: 1.17.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils License: Artistic-2.0 MD5sum: 614e54ef00184a2049c3770f74835627 NeedsCompilation: no Package: GenomicTuples Version: 1.43.0 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), GenomeInfoDb (>= 1.15.2), S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, covr, GenomicAlignments, Biostrings License: Artistic-2.0 MD5sum: 8c98eb56f88ddb6c99d19f6f4de3bc59 NeedsCompilation: yes Package: GenProSeq Version: 1.13.0 Depends: keras, mclust, R (>= 4.2) Imports: tensorflow, word2vec, DeepPINCS, ttgsea, CatEncoders, reticulate, stats Suggests: VAExprs, stringdist, knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: f431a13d163376ebe00bb7a8a1cd9ea8 NeedsCompilation: no Package: GEOexplorer Version: 1.15.0 Depends: shiny, limma, Biobase, plotly, enrichR, R (>= 4.1.0) Imports: DT, XML, httr, sva, xfun, edgeR, htmltools, factoextra, heatmaply, pheatmap, scales, shinyHeatmaply, shinybusy, ggplot2, stringr, umap, GEOquery, impute, grDevices, stats, graphics, markdown, knitr, utils, xml2, R.utils, readxl, shinycssloaders, car Suggests: rmarkdown, usethis, testthat (>= 3.0.0) License: GPL-3 MD5sum: 501b23b62e427e90173c630d47909a9b NeedsCompilation: no Package: GEOfastq Version: 1.17.0 Imports: xml2, rvest, stringr, RCurl, doParallel, foreach, plyr Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: e6c41ebb397c2dc93fac38267e9c5181 NeedsCompilation: no Package: GEOmetadb Version: 1.71.0 Depends: R.utils,RSQLite Suggests: knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud License: Artistic-2.0 MD5sum: d1c69cd88ad70fc65f8a4b8bee240da7 NeedsCompilation: no Package: geomeTriD Version: 1.3.0 Depends: R (>= 4.4.0) Imports: BiocGenerics, dbscan, GenomeInfoDb, GenomicRanges, graphics, grDevices, grid, htmlwidgets, igraph, InteractionSet, IRanges, MASS, Matrix, methods, plotrix, RANN, rgl, rjson, S4Vectors, scales, stats, trackViewer Suggests: RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, manipulateWidget, shiny, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: b2221ce1d59d2a5acf9ca780b9e42a5b NeedsCompilation: no Package: GEOquery Version: 2.77.0 Depends: R (>= 4.1.0), methods, Biobase Imports: readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr, limma, curl, rentrez, R.utils, stringr, SummarizedExperiment, S4Vectors, rvest, httr2 Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr, markdown License: MIT + file LICENSE MD5sum: 9e28eb36f4bca3a620766dfbbf7fe8be NeedsCompilation: no Package: GEOsubmission Version: 1.61.0 Imports: affy, Biobase, 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License: GPL-3 MD5sum: 21f042d98c8cb44c6413c49e1cf6efa4 NeedsCompilation: no Package: geva Version: 1.17.0 Depends: R (>= 4.1) Imports: grDevices, graphics, methods, stats, utils, dbscan, fastcluster, matrixStats Suggests: devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat (>= 3.0.0) License: LGPL-3 MD5sum: 66ec71bf3c44110f33aa715989a61603 NeedsCompilation: no Package: GEWIST Version: 1.53.0 Depends: R (>= 2.10), car License: GPL-2 MD5sum: 740a1d6207694ee7687f86e3af973ec8 NeedsCompilation: no Package: geyser Version: 1.1.0 Depends: R (>= 3.5.0) Imports: bslib (>= 0.6.0), BiocStyle, ComplexHeatmap, dplyr, DT, ggbeeswarm, ggplot2, htmltools, magrittr, shiny, SummarizedExperiment, tibble, tidyselect, tidyr Suggests: airway, knitr, DESeq2, recount3, rmarkdown, stringr, testthat (>= 3.0.0) License: CC0 MD5sum: 8455e0eb575c5f3cf829748bb09ef411 NeedsCompilation: no Package: gg4way Version: 1.7.0 Depends: R (>= 4.3.0), ggplot2 Imports: DESeq2, dplyr, edgeR, ggrepel, glue, janitor, limma, magrittr, methods, purrr, rlang, scales, stats, stringr, tibble, tidyr Suggests: airway, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat, vdiffr License: MIT + file LICENSE MD5sum: ea153bbc6a23343761ec763c641c511d NeedsCompilation: no Package: ggbio Version: 1.57.0 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.29.14), SummarizedExperiment, Biostrings, Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer (>= 1.25.16), GenomicFeatures (>= 1.29.11), OrganismDbi, GGally, ensembldb (>= 1.99.13), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: 8bd5920089fe842a1f8bcc73b344146b NeedsCompilation: no Package: ggcyto Version: 1.37.0 Depends: methods, ggplot2(>= 3.5.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 4.3.1) Imports: plyr, scales, hexbin, data.table, RColorBrewer, gridExtra, rlang Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr License: file LICENSE MD5sum: c39beab1437ba551cdb62e4833acac4a NeedsCompilation: no Package: ggkegg Version: 1.7.0 Depends: R (>= 4.3.0), ggplot2, ggraph, XML, igraph, tidygraph Imports: BiocFileCache, data.table, dplyr, magick, patchwork, shadowtext, stringr, tibble, methods, utils, stats, grDevices, gtable Suggests: knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, AnnotationDbi, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 1d8fb3370e1062e661eecb325ee8c7be NeedsCompilation: no Package: ggmanh Version: 1.13.0 Depends: methods, ggplot2 Imports: gdsfmt, ggrepel, grDevices, paletteer, RColorBrewer, rlang, scales, SeqArray (>= 1.32.0), stats, tidyr, dplyr, pals, magrittr Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0), GenomicRanges License: MIT + file LICENSE MD5sum: 0c4021d12878c33aa55ed87af6da06fa NeedsCompilation: no Package: ggmsa Version: 1.15.0 Depends: R (>= 4.1.0) Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot, RColorBrewer, ggalt, ggforce, dplyr, R4RNA, grDevices, seqmagick, grid, methods, statebins, ggtree (>= 1.17.1) Suggests: ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: dee43ec4467ef38c09e9b34af8fb4c0a NeedsCompilation: no Package: GGPA Version: 1.21.0 Depends: R (>= 4.0.0), stats, methods, graphics, GGally, network, sna, scales, matrixStats Imports: Rcpp (>= 0.11.3) LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle License: GPL (>= 2) MD5sum: 263a8c7e2408652f399af616006d6884 NeedsCompilation: yes Package: ggsc Version: 1.7.0 Depends: R (>= 4.1.0) Imports: Rcpp, RcppParallel, cli, dplyr, ggfun (>= 0.1.5), ggplot2, grDevices, grid, methods, rlang, scattermore, stats, Seurat, SingleCellExperiment, SummarizedExperiment, tidydr, tidyr, tibble, utils, RColorBrewer, yulab.utils, scales LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph, knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater, scatterpie (>= 0.2.4), scuttle, shadowtext, sf, SeuratObject, SpatialExperiment, STexampleData, testthat (>= 3.0.0), MASS License: Artistic-2.0 MD5sum: f823d883a8082bcbf2448955d7f7988e NeedsCompilation: yes Package: ggseqalign Version: 1.3.0 Depends: R (>= 4.4.0) Imports: pwalign, dplyr, ggplot2 Suggests: Biostrings, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: cf5efc1144b62169e793b84a108b94f5 NeedsCompilation: no Package: ggspavis Version: 1.15.0 Depends: ggplot2 Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, ggrepel, RColorBrewer, scales, grDevices, methods, stats Suggests: BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork License: MIT + file LICENSE MD5sum: ae8f817fe548b79b649dd1e6c1e8a33f NeedsCompilation: no Package: ggtree Version: 3.17.0 Depends: R (>= 3.5.0) Imports: ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.1.7), yulab.utils (>= 0.1.6), tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0), utils, scales, stats, cli Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue License: Artistic-2.0 MD5sum: dbd40d1c2a56a1eff4a246021c721400 NeedsCompilation: no Package: ggtreeDendro Version: 1.11.0 Depends: ggtree (>= 3.5.3) Imports: ggplot2, stats, tidytree, utils Suggests: aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust, rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils License: Artistic-2.0 MD5sum: 4fe2ccb996e976a0b8e1ca3797944763 NeedsCompilation: no Package: ggtreeExtra Version: 1.19.0 Imports: ggplot2, utils, rlang, ggnewscale, stats, ggtree, tidytree (>= 0.3.9), cli, magrittr Suggests: treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown, testthat (>= 3.0.0), pillar License: GPL (>= 3) MD5sum: ab05bad85e9211751b5020e4518f46cf NeedsCompilation: no Package: ggtreeSpace Version: 1.5.0 Depends: R (>= 4.1.0) Imports: interp, ape, dplyr, GGally, ggplot2, grid, ggtree, phytools, rlang, tibble, tidyr, tidyselect, stats Suggests: knitr, prettydoc, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 5d85280b92134e7749348a670bc24e4e NeedsCompilation: no Package: GIGSEA Version: 1.27.0 Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils Suggests: knitr, rmarkdown License: LGPL-3 MD5sum: 5fd3edda271db1afa7f4ba396ee4fbf0 NeedsCompilation: no Package: ginmappeR Version: 1.5.0 Imports: KEGGREST, UniProt.ws, XML, rentrez, httr, utils, memoise, cachem, jsonlite, rvest Suggests: RUnit, BiocGenerics, markdown, knitr License: GPL-3 + file LICENSE MD5sum: 5e31d225cd46914eb218ba4f130bbcd3 NeedsCompilation: no Package: gINTomics Version: 1.5.0 Depends: R (>= 4.4.0) Imports: BiocParallel, biomaRt, OmnipathR, edgeR, ggplot2, ggridges, gtools, MultiAssayExperiment, plyr, stringi, stringr, SummarizedExperiment, methods, stats, reshape2, randomForest, limma, org.Hs.eg.db, org.Mm.eg.db, BiocGenerics, GenomicFeatures, ReactomePA, clusterProfiler, dplyr, AnnotationDbi, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, shiny, GenomicRanges, ggtree, shinydashboard, plotly, DT, MASS, InteractiveComplexHeatmap, ComplexHeatmap, visNetwork, shiny.gosling, ggvenn, RColorBrewer, utils, grDevices, callr, circlize, MethylMix, shinyjs Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 MD5sum: c9830e5d8d159563432c8d2377892808 NeedsCompilation: no Package: GLAD Version: 2.73.0 Depends: R (>= 2.10) Imports: aws License: GPL-2 MD5sum: 5486d727b0640e98dd0997d2c6afba92 NeedsCompilation: yes Package: GladiaTOX Version: 1.25.0 Depends: R (>= 3.6.0), data.table (>= 1.9.4) Imports: DBI, RMariaDB, RSQLite, numDeriv, RColorBrewer, parallel, stats, methods, graphics, grDevices, xtable, tools, brew, stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: 8f74843ad8505550fe65e39710955644 NeedsCompilation: no Package: Glimma Version: 2.19.0 Depends: R (>= 4.0.0) Imports: htmlwidgets, edgeR, DESeq2, limma, SummarizedExperiment, stats, jsonlite, methods, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran, scRNAseq, License: GPL-3 MD5sum: 520b206d37b6d4075f8afae8dd4b7098 NeedsCompilation: no Package: glmGamPoi Version: 1.21.0 Depends: R (>= 4.1.0) Imports: Rcpp, beachmat, DelayedMatrixStats, matrixStats, MatrixGenerics, SparseArray (>= 1.5.21), S4Vectors, DelayedArray, HDF5Array, Matrix, SummarizedExperiment, SingleCellExperiment, BiocGenerics, methods, stats, utils, splines, rlang, vctrs LinkingTo: Rcpp, RcppArmadillo, beachmat, assorthead Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, dplyr License: GPL-3 MD5sum: f0d990e5fcb99dbc79eafafd168e8fe0 NeedsCompilation: yes Package: glmSparseNet Version: 1.27.0 Depends: R (>= 4.3.0) Imports: biomaRt, checkmate, dplyr, forcats, futile.logger, ggplot2, glue, httr, lifecycle, methods, parallel, readr, rlang, glmnet, Matrix, MultiAssayExperiment, SummarizedExperiment, survminer, TCGAutils, utils Suggests: BiocStyle, curatedTCGAData, knitr, magrittr, reshape2, pROC, rmarkdown, survival, testthat, VennDiagram, withr License: GPL-3 MD5sum: 0aeffda4ffd53b34044131a7369e5f46 NeedsCompilation: no Package: GlobalAncova Version: 4.27.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: 138213950389b12dee2b603ae8b81d21 NeedsCompilation: yes Package: globalSeq Version: 1.37.0 Depends: R (>= 3.0.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 MD5sum: 0aa0eb12ad54d27dd0fbb4781d283b34 NeedsCompilation: no Package: globaltest Version: 5.63.0 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: 91312bbc9324513812f1cee5fe64401d NeedsCompilation: no Package: GloScope Version: 1.7.0 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: 3eff533a976497c371a24872cfefbaa0 NeedsCompilation: no Package: gmapR Version: 1.51.0 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, BiocIO 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: 02b1f2274b57f19ecaed013e422e9e13 NeedsCompilation: yes Package: GmicR Version: 1.23.0 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: 41f03e1f4e8d9164997f397ef3b65595 NeedsCompilation: no Package: gmoviz Version: 1.21.0 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: e1821984fc0d3a151dcd24dbf568465e NeedsCompilation: no Package: GMRP Version: 1.37.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: 80eb67f3cd6a5ea3e8640e387aa0e358 NeedsCompilation: no Package: GNET2 Version: 1.25.0 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: 820b48989cc378c05e47c8d63082d4ca NeedsCompilation: yes Package: GOexpress Version: 1.43.0 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), randomForest (>= 4.6), RCurl (>= 1.95) Suggests: BiocStyle License: GPL (>= 3) MD5sum: 24ef62a5cf41adb40b3d1d15bc75797e NeedsCompilation: no Package: GOfuncR Version: 1.29.0 Depends: R (>= 3.4), vioplot (>= 0.2), Imports: Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils, grDevices, graphics, stats, LinkingTo: Rcpp Suggests: Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat License: GPL (>= 2) MD5sum: fbd452abb816561f70866b076065cdcc NeedsCompilation: yes Package: GOpro Version: 1.35.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, dendextend, doParallel, foreach, parallel, org.Hs.eg.db, GO.db, Rcpp, stats, graphics, MultiAssayExperiment, IRanges, S4Vectors LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat License: GPL-3 MD5sum: d6baa383c2d45e4402c0a049efa35715 NeedsCompilation: yes Package: goProfiles Version: 1.71.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: a4614fd6c3db81d926c505d50f3b37aa NeedsCompilation: no Package: GOSemSim Version: 2.35.0 Depends: R (>= 4.2.0) Imports: AnnotationDbi, DBI, digest, GO.db, methods, rlang, R.utils, stats, utils, yulab.utils (>= 0.1.6) LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, rappdirs, readr, rmarkdown, testthat, tidyr, tidyselect, ROCR License: Artistic-2.0 MD5sum: b86ebd47132d1148aacdc1911c323a5e NeedsCompilation: yes Package: goseq Version: 1.61.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2) Imports: mgcv, graphics, stats, utils, AnnotationDbi, GO.db, BiocGenerics, methods, rtracklayer, GenomicFeatures, GenomeInfoDb Suggests: edgeR, org.Hs.eg.db License: LGPL (>= 2) MD5sum: 51edee484fe0b7e0542aac999e4b3522 NeedsCompilation: no Package: goSorensen Version: 1.11.0 Depends: R (>= 4.4) Imports: clusterProfiler, goProfiles, org.Hs.eg.db, parallel, stats, stringr Suggests: BiocManager, BiocStyle, knitr, rmarkdown, org.At.tair.db, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcSakai.eg.db, org.EcK12.eg.db, org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Pt.eg.db, org.Xl.eg.db, GO.db, ggplot2, ggrepel, DT, magick License: GPL-3 MD5sum: abdacc5fe583eba518b93d111ff04701 NeedsCompilation: no Package: goSTAG Version: 1.33.0 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 8587a456061bff617a36c84f5b42fdcc NeedsCompilation: no Package: GOstats Version: 2.75.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.43.2), graph Imports: methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr License: Artistic-2.0 MD5sum: 990ce852000d1169eed2d70d4dd2d456 NeedsCompilation: no Package: GOTHiC Version: 1.45.0 Depends: R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome, data.table Imports: BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils, stats, GenomeInfoDb Suggests: HiCDataLymphoblast Enhances: parallel License: GPL-3 MD5sum: 77e9bf57968fb92a083831f2d625e344 NeedsCompilation: no Package: goTools Version: 1.83.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 MD5sum: f6470d8bb8bc8382d76919b0a3f9e6ff NeedsCompilation: no Package: GPA Version: 1.21.0 Depends: R (>= 4.0.0), methods, graphics, Rcpp Imports: parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS, stats, utils, grDevices LinkingTo: Rcpp Suggests: gpaExample License: GPL (>= 2) MD5sum: 9bf175fd52e5e385c443148fa530d42a NeedsCompilation: yes Package: gpls Version: 1.81.0 Imports: stats Suggests: MASS License: Artistic-2.0 MD5sum: 60d8196a53b68cc523e4f1f44a3d7ad2 NeedsCompilation: no Package: GrafGen Version: 1.5.0 Depends: R (>= 4.3.0) Imports: stats, utils, graphics, ggplot2, plotly, scales, RColorBrewer, dplyr, grDevices, GenomicRanges, shiny, cowplot, ggpubr, stringr, rlang Suggests: knitr, rmarkdown, RUnit, BiocManager, BiocGenerics, BiocStyle, devtools License: GPL-2 MD5sum: 122a7f81b448d7c4844558aa3bb71287 NeedsCompilation: yes Package: granulator Version: 1.17.0 Depends: R (>= 4.1) Imports: cowplot, e1071, epiR, dplyr, dtangle, ggplot2, ggplotify, grDevices, limSolve, magrittr, MASS, nnls, parallel, pheatmap, purrr, rlang, stats, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 88441b5cd05a1148233a8863331dce07 NeedsCompilation: no Package: graph Version: 1.87.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.11) Imports: stats, stats4, utils Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle, knitr Enhances: Rgraphviz License: Artistic-2.0 MD5sum: 58a4fb0b2ba1ef36ee3d47ff15265edb NeedsCompilation: yes Package: GraphAlignment Version: 1.73.0 License: file LICENSE License_restricts_use: yes MD5sum: af85aee7ec76c6d93ad48280e4b13d2c NeedsCompilation: yes Package: GraphAT Version: 1.81.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL MD5sum: 766c8e0c1fa8113efcc40658a6c147ce NeedsCompilation: no Package: graphite Version: 1.55.0 Depends: R (>= 4.2), methods Imports: AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats, utils, graphics, rlang, purrr Suggests: checkmate, a4Preproc, ALL, BiocStyle, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) License: AGPL-3 MD5sum: c28b14cf8e0ebce3f420cf1ab6aaa248 NeedsCompilation: no Package: GRENITS Version: 1.61.0 Depends: R (>= 2.12.0), Rcpp (>= 0.8.6), RcppArmadillo (>= 0.2.8), ggplot2 (>= 0.9.0) Imports: graphics, grDevices, reshape2, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: network License: GPL (>= 2) MD5sum: 993df93fd14d190f3616679f35f7ee1b NeedsCompilation: yes Package: GreyListChIP Version: 1.41.0 Depends: R (>= 4.0), methods, GenomicRanges Imports: GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, RUnit, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 4ca6999d56011ae615ebd4b76f2407b8 NeedsCompilation: no Package: GRmetrics Version: 1.35.0 Depends: R (>= 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hgu95av2.db, edgeR, BiocStyle License: GPL (>= 2) MD5sum: c6c6569beb54f8601cfa0af68aa6dc40 NeedsCompilation: no Package: GSCA Version: 2.39.0 Depends: shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5, R(>= 2.10.0) Imports: graphics Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr License: GPL (>= 2) MD5sum: 89898f2d821e62668c4a590ef2ab0c84 NeedsCompilation: no Package: gscreend Version: 1.23.0 Depends: R (>= 3.6) Imports: SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics Suggests: knitr, testthat, rmarkdown, BiocStyle License: GPL-3 MD5sum: f51abcc33d01de74948201106e916b68 NeedsCompilation: no Package: GSEABase Version: 1.71.0 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: d78a7bc89f5d27a2b57315b900e10e16 NeedsCompilation: no Package: GSEABenchmarkeR Version: 1.29.0 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: b2b8195714a448eece29fa9019c1479a NeedsCompilation: no Package: GSEAlm Version: 1.69.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: c735c69f71d67c6bb7b6b2ae78111eaa NeedsCompilation: no Package: GSEAmining Version: 1.19.0 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: 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Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 MD5sum: 0e4d2d1e9e1c1902d3149ae26e19c210 NeedsCompilation: no Package: GSVA Version: 2.3.0 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, sva, shiny, shinydashboard, ggplot2, data.table, plotly, future, promises, shinybusy, shinyjs License: GPL (>= 2) MD5sum: 1c248fc90e608818abbd72b469cd962a NeedsCompilation: yes Package: gtrellis Version: 1.41.0 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: fd7482c93e431018069df2b36fab22a7 NeedsCompilation: no Package: Guitar Version: 2.25.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges, magrittr, ggplot2, methods, stats,utils ,knitr,dplyr License: GPL-2 MD5sum: 10687a4dc6183766711ed1a696580449 NeedsCompilation: no Package: Gviz Version: 1.53.0 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: dfe5d5e81733bdd97c5cfe57cd4aad80 NeedsCompilation: no Package: GWAS.BAYES Version: 1.19.0 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: 088ae99c451131f893efc61d923b4005 NeedsCompilation: no Package: GWASTools Version: 1.55.0 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: 475767a53bf86ec91c2e496c33c7e9c4 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BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown License: GPL (>= 3) MD5sum: 881e10b39718910e4156eae079a849db NeedsCompilation: yes Package: hapFabia Version: 1.51.0 Depends: R (>= 3.6.0), Biobase, fabia (>= 2.3.1) Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: df26efa01ee88a203d5238f8ac32b336 NeedsCompilation: yes Package: Harman Version: 1.37.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel, methods, matrixStats LinkingTo: Rcpp Suggests: HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva License: GPL-3 + file LICENCE MD5sum: dac94739524b4b46602a3c43c11ba712 NeedsCompilation: yes Package: HarmonizR Version: 1.7.0 Depends: R (>= 4.2.0) Imports: doParallel (>= 1.0.16), foreach (>= 1.5.1), janitor (>= 2.1.0), plyr (>= 1.8.6), sva (>= 3.36.0), seriation (>= 1.3.5), limma 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RUnit, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 00b5afb859ef537f4b8ec8902bab030e NeedsCompilation: no Package: HDTD Version: 1.43.0 Depends: R (>= 4.1) Imports: stats, Rcpp (>= 1.0.1) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 34b96673f328bdeb70e2b92e4272490f NeedsCompilation: yes Package: hdxmsqc Version: 1.5.0 Depends: R(>= 4.3), QFeatures, S4Vectors, Spectra Imports: dplyr, tidyr, ggplot2, BiocStyle, knitr, methods, grDevices, stats, MsCoreUtils Suggests: RColorBrewer, pheatmap, MASS, patchwork, testthat License: file LICENSE MD5sum: db09da1ea3927f6f3d6b5e4a48226a5a NeedsCompilation: no Package: heatmaps Version: 1.33.0 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: fec5e6bef54267b5a4fd27521c988fed 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GenomeInfoDb, GenomicRanges, stats, IRanges, grDevices, S4Vectors, digest, tibble, jsonlite, BiocParallel, R.utils, readr, methods Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 54c4bbad7faff65309742b8c06cfb252 NeedsCompilation: no Package: HiCcompare Version: 1.31.0 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: dd6e8c77743c7517287f11a6a37700f2 NeedsCompilation: no Package: HiCDCPlus Version: 1.17.0 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: 662de0bda1b73b28b77481e626c14593 NeedsCompilation: yes Package: HiCDOC Version: 1.11.0 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 MD5sum: a31e02e57cfb8b64010a968820788af8 NeedsCompilation: yes Package: HiCExperiment Version: 1.9.0 Depends: R (>= 4.2) Imports: InteractionSet, strawr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5, Matrix, vroom, dplyr, stats Suggests: HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: 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grDevices, protr, MCL Suggests: rmarkdown, colorspace, e1071, kernlab, ranger, SummarizedExperiment, Biostrings, randomForest, gprofiler2, gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools, knitr License: MIT + file LICENSE MD5sum: 7058baac75578e186a212b745d0c539a NeedsCompilation: no Package: HTqPCR Version: 1.63.0 Depends: Biobase, RColorBrewer, limma Imports: affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils Suggests: statmod License: Artistic-2.0 MD5sum: d2e1e71c3fbe4b3368aa199bfd807a67 NeedsCompilation: no Package: HTSFilter Version: 1.49.0 Depends: R (>= 4.0.0) Imports: edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices, graphics, methods Suggests: EDASeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 8a3d7fe0eb1d7c8d5983498673aaf3be NeedsCompilation: no Package: HuBMAPR Version: 1.3.0 Depends: R (>= 4.4.0) Imports: httr2, dplyr, tidyr, tibble, rjsoncons, rlang, utils, stringr, whisker, purrr 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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: 18e48419c9e7fef6f7035dca9bbd1680 NeedsCompilation: no Package: iSEE Version: 2.21.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, listviewer, ComplexHeatmap, circlize, grid Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools, GenomicRanges License: MIT + file LICENSE MD5sum: ef2c1d1e0da266e01237b7fb96dfdcd4 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Suggests: BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 5f80b73cd4e6e7c7638b5ef8efde71a7 NeedsCompilation: no Package: LinkHD Version: 1.23.0 Depends: R(>= 3.6.0), methods, ggplot2, stats Imports: scales, cluster, graphics, ggpubr, gridExtra, vegan, rio, MultiAssayExperiment, emmeans, reshape2, data.table Suggests: MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: b3cb44c6f97d707997b6d6f4a4f27248 NeedsCompilation: no Package: Linnorm Version: 2.33.0 Depends: R(>= 4.1.0) Imports: Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan, mclust, apcluster, ggplot2, ellipse, limma, utils, statmod, MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo, stats, amap, Rtsne, gmodels LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer, moments, testthat, matrixStats License: MIT + file LICENSE MD5sum: 26ead88b196fe59ed3b806d9e3c3599d NeedsCompilation: yes Package: 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ggrepel, pracma, ggridges, AnnotationDbi, IRanges, circlize, cowplot, mclust, phangorn, ComplexHeatmap (>= 1.9.3), ggplot2, RColorBrewer, grDevices, stats, utils, S4Vectors Suggests: shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), org.Hs.eg.db, clusterProfiler, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: d39ebce59c8d2a7d80358dc0e0f0eadb NeedsCompilation: no Package: messina Version: 1.45.0 Depends: R (>= 3.1.0), survival (>= 2.37-4), methods Imports: Rcpp (>= 0.11.1), plyr (>= 1.8), ggplot2 (>= 0.9.3.1), grid (>= 3.1.0), foreach (>= 1.4.1), graphics LinkingTo: Rcpp Suggests: knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>= 2.22.0), BiocStyle Enhances: doMC (>= 1.3.3) License: EPL (>= 1.0) MD5sum: bd3efa3e4ee0cc4f6004e8114f4626eb NeedsCompilation: yes Package: metabCombiner Version: 1.19.0 Depends: R (>= 4.0) Imports: dplyr (>= 1.0), methods, mgcv, caret, S4Vectors, stats, utils, rlang, graphics, matrixStats, tidyr Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 768a5fe6124b9828e1cfff543934e692 NeedsCompilation: yes Package: metabinR Version: 1.11.0 Depends: R (>= 4.3) Imports: methods, rJava Suggests: BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: cfdb5672955a8cd9e265ace04fd9db06 NeedsCompilation: no Package: MetaboAnnotation Version: 1.13.0 Depends: R (>= 4.0.0) Imports: BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics, methods, S4Vectors, Spectra (>= 1.13.2), BiocParallel, SummarizedExperiment, QFeatures, AnnotationHub, graphics, CompoundDb Suggests: testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, microbenchmark, mzR Enhances: RMariaDB, RSQLite License: Artistic-2.0 MD5sum: 7034ec42592b319c7919dfa9040e682b NeedsCompilation: no Package: MetaboCoreUtils Version: 1.17.0 Depends: R (>= 4.0) Imports: utils, MsCoreUtils, BiocParallel, methods, stats Suggests: BiocStyle, 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KEGGREST, EnsDb.Hsapiens.v75, stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi, MWASTools, mygene Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: b4d9ab550557002c3319816d90525b4e NeedsCompilation: no Package: metaCCA Version: 1.37.0 Suggests: knitr License: MIT + file LICENSE MD5sum: 4ad010074403b20f9e431f3a98741a62 NeedsCompilation: no Package: MetaCyto Version: 1.31.0 Depends: R (>= 3.4) Imports: flowCore (>= 1.4),tidyr (>= 0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices, graphics, stats, utils Suggests: knitr, dplyr, rmarkdown License: GPL (>= 2) MD5sum: dd3dcbded6cd973bc7172048ea47327f NeedsCompilation: no Package: metagene2 Version: 1.25.0 Depends: R (>= 4.0), R6 (>= 2.0), GenomicRanges, BiocParallel Imports: rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges, ggplot2, Rsamtools, purrr, data.table, methods, dplyr, magrittr, reshape2 Suggests: BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown License: Artistic-2.0 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utils (>= 3.4), Matrix (>= 1.2), matrixStats (>= 0.54), beanplot (>= 1.2), gplots (>= 3.0.1), RColorBrewer (>= 1.1.2), SummarizedExperiment (>= 1.12), SingleCellExperiment, igraph, dplyr, tidyr, tibble, ggplot2 Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2), UpSetR License: MIT + file LICENSE MD5sum: 929703cb23fd8213aea940dc16afc946 NeedsCompilation: no Package: MetaPhOR Version: 1.11.0 Depends: R (>= 4.2.0) Imports: utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats, clusterProfiler, RecordLinkage, RCy3 Suggests: BiocStyle, knitr, rmarkdown, kableExtra License: Artistic-2.0 MD5sum: eeec6078050e1808f0164df4c2011a79 NeedsCompilation: no Package: metapod Version: 1.17.0 Imports: Rcpp LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 9665804f31300abb716fa658af4a1fb8 NeedsCompilation: yes Package: metapone Version: 1.15.0 Depends: R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea, ggplot2, ggrepel Imports: 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BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: a9312afa1a4c92bfc4c772c7fc7dbe06 NeedsCompilation: no Package: methylCC Version: 1.23.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: GPL-3 MD5sum: b536cf97d59edab11b4d24e50f4f28c1 NeedsCompilation: no Package: methylclock Version: 1.15.0 Depends: R (>= 4.1.0), methylclockData, devtools, quadprog Imports: Rcpp (>= 1.0.6), ExperimentHub, dplyr, impute, PerformanceAnalytics, Biobase, ggpmisc, tidyverse, ggplot2, ggpubr, minfi, tibble, RPMM, stats, graphics, tidyr, gridExtra, preprocessCore, dynamicTreeCut, planet LinkingTo: Rcpp Suggests: BiocStyle, knitr, GEOquery, rmarkdown License: MIT + file LICENSE MD5sum: a7c7671461eb1761b7869c68dc142f0f NeedsCompilation: yes Package: methylGSA Version: 1.27.0 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: b20ee7d09fe879f33af0284a46adfe4d NeedsCompilation: no Package: methyLImp2 Version: 1.5.0 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: 91b6fd6fdd3018e8d42fb7488f7e8a34 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(>= 1.1.4), mia, rintrojs, scater, shinydashboard, shinyjs, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, utils, vegan Suggests: BiocStyle, knitr, philr, remotes, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 3ff642ab0dd37cf215a96594ec0b5274 NeedsCompilation: no Package: miaSim Version: 1.15.0 Depends: TreeSummarizedExperiment Imports: SummarizedExperiment, deSolve, stats, poweRlaw, MatrixGenerics, S4Vectors Suggests: ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy License: Artistic-2.0 | file LICENSE MD5sum: a211fb01287b633e090a489443c250c0 NeedsCompilation: no Package: miaViz Version: 1.17.0 Depends: R (>= 4.1.0), ggplot2, ggraph (>= 2.0), mia (>= 1.13.0), SummarizedExperiment, TreeSummarizedExperiment Imports: ape, BiocGenerics, BiocParallel, DelayedArray, DirichletMultinomial, dplyr, ggnewscale, ggrepel, ggtree, methods, rlang, S4Vectors, scales, scater, SingleCellExperiment, stats, tibble, tidygraph, tidyr, tidytext, tidytree, viridis Suggests: BiocStyle, bluster, circlize, ComplexHeatmap, ggh4x, knitr, patchwork, rmarkdown, shadowtext, testthat, vegan License: Artistic-2.0 | file LICENSE MD5sum: 678ed09fdea4631da5d5d587f3315476 NeedsCompilation: no Package: MiChip Version: 1.63.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: 49f88846937d39aea1dfe3af0122d310 NeedsCompilation: no Package: microbiome Version: 1.31.0 Depends: R (>= 3.6.0), phyloseq, ggplot2 Imports: Biostrings, compositions, dplyr, reshape2, Rtsne, scales, stats, tibble, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE MD5sum: 9473cef5c06bc910fd718e9af00b53a8 NeedsCompilation: no Package: microbiomeDASim Version: 1.23.0 Depends: R (>= 3.6.0) Imports: graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase Suggests: testthat (>= 2.1.0), knitr, devtools License: MIT + file LICENSE MD5sum: 6f9c05f332b4a3d8334c3b0b0f6c7859 NeedsCompilation: no Package: microbiomeExplorer Version: 1.19.0 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: 24d4e61cd1f5334eb7a53f29ff2766c5 NeedsCompilation: no Package: MicrobiomeProfiler Version: 1.15.0 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: eabc83c3c281152580cd0c639e796455 NeedsCompilation: no Package: MicrobiotaProcess Version: 1.21.0 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, DirichletMultinomial, ggpp, BiocManager License: GPL (>= 3.0) MD5sum: f7a7f44e374ccd956b0dd037cc82ba21 NeedsCompilation: no Package: microRNA Version: 1.67.0 Depends: R 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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: 03d4a52d302241a9ad20b3c2292eaddc NeedsCompilation: yes Package: mimager Version: 1.33.0 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: 45bccfaac6fcd7d3c29fa977b7b335ad NeedsCompilation: no Package: mina Version: 1.17.0 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: 18ad4f373e0b17075f629419e186cc6e NeedsCompilation: yes Package: MineICA Version: 1.49.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply Enhances: doMC License: GPL-2 MD5sum: 2dbb4eab9b4063520a7749799d2bf61f NeedsCompilation: no Package: minet Version: 3.67.0 Imports: infotheo License: Artistic-2.0 MD5sum: 1a36f54e29823fff5d8a97ac2b4a5fed NeedsCompilation: yes Package: minfi Version: 1.55.0 Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges, SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>= 1.1.9) Imports: S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray (>= 0.15.16), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools License: Artistic-2.0 MD5sum: c81d6f47cf9b0adf1809c0acf9e948d7 NeedsCompilation: no Package: MinimumDistance Version: 1.53.0 Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1) Imports: methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: 2d50788246bceb99f57a8d853b07798f NeedsCompilation: no Package: MiPP Version: 1.81.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: 64b7a295b891c50def66637721b841e1 NeedsCompilation: no Package: miQC Version: 1.17.0 Depends: R (>= 3.5.0) Imports: SingleCellExperiment, flexmix, ggplot2, splines Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 6868a05bbf9c6ffe06284fd0039a21b7 NeedsCompilation: no Package: MIRA Version: 1.31.0 Depends: R (>= 3.5) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 9cd809b213a45a73ad71ea98763746b5 NeedsCompilation: no Package: MiRaGE Version: 1.51.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: BiocGenerics, S4Vectors, AnnotationDbi, BiocManager Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL MD5sum: 36b0cca2d744a29fdefabbe6ab2c7d1d NeedsCompilation: no Package: miRBaseConverter Version: 1.33.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown License: GPL (>= 2) MD5sum: 936347ad138eedcade1b3554ef08dd5c NeedsCompilation: no Package: miRcomp Version: 1.39.0 Depends: R (>= 3.2), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: 4bbd2a1b73591e582a8d111f2dd4567f NeedsCompilation: no Package: mirIntegrator Version: 1.39.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: 8ba22ba10a4695fc8f3cb5917a5106a4 NeedsCompilation: no Package: MIRit Version: 1.5.0 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: 4382ffdbd35d7741dadc5b7e73b5d415 NeedsCompilation: yes Package: miRLAB Version: 1.39.0 Imports: methods, stats, utils, RCurl, httr, stringr, Hmisc, energy, entropy, gplots, glmnet, impute, limma, pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc, InvariantCausalPrediction, 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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: 617e032f9bfc3bbfabdab2e25cb109e7 NeedsCompilation: yes Package: miRspongeR Version: 2.13.0 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: c27daa79ab41b3f294397285f30743ff NeedsCompilation: yes Package: mirTarRnaSeq Version: 1.17.0 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: 87bb8fb4febfdfb0644348e375e3fb6d NeedsCompilation: no Package: missMethyl Version: 1.43.0 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: 714c35e817ea25e8fb0d8194fbe67a24 NeedsCompilation: no Package: missRows Version: 1.29.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: daa816b2d4265788c189ea32abc5dbf0 NeedsCompilation: 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GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r, kableExtra, dplyr, network Suggests: stringi, testthat (>= 2.1.0), HGNChelper, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: CC BY-SA 4.0 + file LICENSE MD5sum: c750bb3277f02d519755ff78f27560e4 NeedsCompilation: no Package: mitoClone2 Version: 1.15.0 Depends: R (>= 4.4.0) Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2 LinkingTo: Rhtslib (>= 1.13.1) Suggests: knitr, rmarkdown, Biostrings, testthat License: GPL-3 MD5sum: 4ca1ddd101fd0e2367f2df29970e1bc4 NeedsCompilation: yes Package: mitology Version: 1.1.0 Depends: R (>= 4.5.0) Imports: AnnotationDbi, ape, circlize, ComplexHeatmap, ggplot2, ggtree, magrittr, org.Hs.eg.db, scales Suggests: Biobase, BiocStyle, clusterProfiler, GSVA, methods, rmarkdown, knitr, SummarizedExperiment, testthat License: AGPL-3 MD5sum: 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keggorthology, kernlab, mboost, party, klaR, BiocStyle, knitr, testthat Enhances: parallel License: LGPL MD5sum: 819f977318494a603a4ac8bb85708f37 NeedsCompilation: no Package: MLP Version: 1.57.0 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: 77b2dd6f1cf4f139c06a79f3dd87ee3a NeedsCompilation: no Package: MLSeq Version: 2.27.0 Depends: caret, ggplot2 Imports: testthat, VennDiagram, pamr, methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, e1071, kernlab License: GPL (>= 2) MD5sum: 43b048ff06cf39a8c8863d60caff0878 NeedsCompilation: no Package: MMDiff2 Version: 1.37.0 Depends: R (>= 3.5.0), Rsamtools, Biobase Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 MD5sum: f07c5e708a7fef738689c28ff10fe788 NeedsCompilation: no Package: MMUPHin Version: 1.23.0 Depends: R (>= 3.6) Imports: Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr, stringr, cowplot, utils, stats, grDevices Suggests: testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter License: MIT + file LICENSE MD5sum: 310d7ae7e56c212beb2bc1d984c37be0 NeedsCompilation: no Package: mnem Version: 1.25.0 Depends: R (>= 4.1) Imports: cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071, ggplot2, wesanderson LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle License: GPL-3 MD5sum: 20a298bf513f49e335ae9bf3fd92034d NeedsCompilation: yes Package: mobileRNA Version: 1.5.0 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: 1523e736337781b4c067fc11c697312e NeedsCompilation: no Package: MODA Version: 1.35.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 4c4083f02cd73c1a57b1c90cc118632d NeedsCompilation: no Package: ModCon Version: 1.17.0 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: 9409cf13710ac2e00dcd34f27c886df5 NeedsCompilation: no Package: Modstrings Version: 1.25.0 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: d717df9b3af95837ebf6cd3bdefed257 NeedsCompilation: no Package: MOFA2 Version: 1.19.0 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: 1d6e95595098eb2cef0cd62bf0184c8c NeedsCompilation: yes Package: MOGAMUN Version: 1.19.0 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: knitr, markdown License: GPL-3 + file LICENSE MD5sum: c9b1597eb16471e1bc52b7a62242dd71 NeedsCompilation: no Package: mogsa Version: 1.43.0 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: b3c64a31d0357182f90a1765d7368333 NeedsCompilation: no Package: MoleculeExperiment Version: 1.9.0 Depends: R (>= 4.1.0) Imports: SpatialExperiment, Matrix, purrr, data.table, dplyr (>= 1.1.1), magrittr, rjson, utils, methods, terra, ggplot2, rlang, cli, EBImage, rhdf5, BiocParallel, S4Vectors, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 93e83b281329c72fca07b345112e2aa1 NeedsCompilation: no Package: MOMA Version: 1.21.0 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: db906b9596a56c439cdcb8273dea0a91 NeedsCompilation: no Package: monaLisa Version: 1.15.0 Depends: R (>= 4.1) Imports: BiocGenerics, BiocParallel, Biostrings, BSgenome, circlize, ComplexHeatmap (>= 2.11.1), GenomeInfoDb, GenomicRanges, cli, ggplot2, glmnet, grDevices, grid, IRanges, methods, rlang, RSQLite, stabs, stats, SummarizedExperiment, S4Vectors, TFBSTools, tidyr, tools, utils, XVector Suggests: BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, ggrepel, gridExtra, JASPAR2020, JASPAR2024, knitr, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL (>= 3) MD5sum: 559d26d1e4756d1e94d45f9821a6651c NeedsCompilation: no Package: monocle Version: 2.37.0 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: 0e765af35c085a225c67060662df183d NeedsCompilation: yes Package: Moonlight2R Version: 1.7.0 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: 6ad2ff4cf62ec42b9d4353fa8f2f5edb NeedsCompilation: no Package: MoonlightR Version: 1.35.0 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: 01aa91a594755e6d2d7d712845e61df4 NeedsCompilation: no Package: mosaics Version: 2.47.0 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: d93eb050d2428faa9fca291873d0a5a4 NeedsCompilation: yes Package: mosbi Version: 1.15.0 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: 79e9a6fb253e2ff06ae1e3c715833c85 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: 51b6b91f7495ed93e00894c9811a4768 NeedsCompilation: no Package: MOSim Version: 2.5.0 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: 8427f9997499cdaf9005b67924725726 NeedsCompilation: yes Package: Motif2Site Version: 1.13.0 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: 4fd35c7bae16079ca56e59d16b8b634b NeedsCompilation: no Package: motifbreakR Version: 2.23.0 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: cea4232a7a3977b37222f52a13a08bae NeedsCompilation: no Package: motifcounter Version: 1.33.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: ed4d9a95881d69aeb8740a606c8a4d1e NeedsCompilation: yes Package: MotifDb Version: 1.51.0 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: 3fc50ede76dde21019ae1ee439d0640f NeedsCompilation: no Package: motifmatchr Version: 1.31.0 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: f121cc882d235b5f8c23d84d0ed9729e NeedsCompilation: yes Package: MotifPeeker Version: 1.1.0 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: f230dca096106c6ca095622b38de845f NeedsCompilation: no Package: motifStack Version: 1.53.0 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: d85d788c3b53f53edc5a98584ef762b6 NeedsCompilation: no Package: motifTestR Version: 1.5.0 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, ComplexUpset, extraChIPs, ggdendro, knitr, MASS, MotifDb, rmarkdown, rtracklayer, testthat (>= 3.0.0), VGAM License: GPL-3 MD5sum: 0d8eaa6a00e56facdc51406532f2c125 NeedsCompilation: no Package: MouseFM Version: 1.19.0 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: 19bedb27e9b6e973de059f40c3bd07ec NeedsCompilation: no Package: MPAC Version: 1.3.0 Depends: R (>= 4.4.0) Imports: data.table (>= 1.14.2), SummarizedExperiment (>= 1.30.2), BiocParallel (>= 1.28.3), fitdistrplus (>= 1.1), igraph (>= 1.4.3), BiocSingular (>= 1.10.0), S4Vectors (>= 0.32.3), SingleCellExperiment (>= 1.16.0), bluster (>= 1.4.0), fgsea (>= 1.20.0), scran (>= 1.22.1), ComplexHeatmap (>= 2.16.0), circlize (>= 0.4.16), scales (>= 1.3.0), stringr (>= 1.5.1), 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LinkingTo: Rcpp, RcppParallel Suggests: knitr, rmarkdown License: GPL-3 OS_type: unix MD5sum: dc27f827ada2e64c29f245f8dc5cdaab NeedsCompilation: yes Package: nethet Version: 1.41.0 Imports: glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network, ggplot2, grDevices, graphics, stats, utils Suggests: knitr, xtable, BiocStyle, testthat License: GPL-2 MD5sum: ee640acd3b74b0ba8cb6ae19e6b50ae0 NeedsCompilation: yes Package: NetPathMiner Version: 1.45.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: b49964e2d8ddd721b1828243011962d6 NeedsCompilation: yes Package: netprioR Version: 1.35.0 Depends: methods, graphics, R(>= 3.3) Imports: stats, Matrix, dplyr, doParallel, foreach, parallel, sparseMVN, ggplot2, gridExtra, pROC Suggests: knitr, BiocStyle, pander License: GPL-3 MD5sum: ad18eaa0b67ec2cc2f33a068a3590c53 NeedsCompilation: no Package: 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SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods, DelayedArray, HDF5Array (>= 1.15.13) Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot License: GPL-3 MD5sum: 5fe2d3b6add920e0b23b29996fe11c45 NeedsCompilation: no Package: NewWave Version: 1.19.0 Depends: R (>= 4.0), SummarizedExperiment Imports: methods, SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, SharedObject, stats Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr License: GPL-3 MD5sum: 0158bd832b2a680d8206f38ae4443856 NeedsCompilation: no Package: ngsReports Version: 2.11.0 Depends: R (>= 4.2.0), BiocGenerics, ggplot2 (>= 3.5.0), patchwork (>= 1.1.1), tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro, grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate, methods, plotly (>= 4.9.4), reshape2, rlang, rmarkdown, 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SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat License: MIT + file LICENSE MD5sum: d6d11c8328ae93e7336fef1e5f44a4ef NeedsCompilation: no Package: NOISeq Version: 2.53.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 MD5sum: 096af7f6dc16e4331f95bf5900766801 NeedsCompilation: no Package: normalize450K Version: 1.37.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 36f869328e1f54673ef962a527b31127 NeedsCompilation: no Package: NormalyzerDE Version: 1.27.0 Depends: R (>= 4.1.0) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 MD5sum: 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waiter, thematic, MSnbase, PSMatch, SummarizedExperiment, MultiAssayExperiment, shinyBS, shinyjs, shinyjqui, RColorBrewer, gplots, highcharter, visNetwork, tibble, grDevices, stats, utils, htmlwidgets, vioplot, graphics, FactoMineR, dendextend, dplyr, factoextra, tidyr, nipals Suggests: knitr, rmarkdown, BiocStyle, testthat, Matrix, graph License: Artistic-2.0 MD5sum: 70f0c8b0a7a3bbceb2b1c986fd971790 NeedsCompilation: no Package: oncomix Version: 1.31.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: eee6629df45f4fbcc808132ba0b046ea NeedsCompilation: no Package: oncoscanR Version: 1.11.0 Depends: R (>= 4.2), IRanges (>= 2.30.0), GenomicRanges (>= 1.48.0), magrittr Imports: readr, S4Vectors, methods, utils Suggests: testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 215c189401fa53eac09777c7803df521 NeedsCompilation: no 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BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph, AnnotationHub, SummarizedExperiment, reticulate, R.utils, httr, basilisk Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown, AnnotationDbi, magick License: Artistic-2.0 MD5sum: 631bd9961524b9c62fefec167823dfa9 NeedsCompilation: no Package: openCyto Version: 2.21.0 Depends: R (>= 3.5.0) Imports: methods, Biobase, BiocGenerics, flowCore(>= 1.99.17), flowViz, ncdfFlow(>= 2.11.34), flowWorkspace(>= 3.99.1), flowClust(>= 3.11.4), RBGL, graph, data.table, RColorBrewer, grDevices LinkingTo: cpp11, BH(>= 1.62.0-1) Suggests: flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS MD5sum: 5a7fdff2bcb66f0e105c19037c5bd34b NeedsCompilation: yes Package: OpenStats Version: 1.21.0 Depends: nlme Imports: MASS, jsonlite, Hmisc, methods, knitr, AICcmodavg, car, rlist, summarytools, graphics, stats, 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NeedsCompilation: no Package: OPWeight Version: 1.31.0 Depends: R (>= 3.4.0), Imports: graphics, qvalue, MASS, tibble, stats, Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat License: Artistic-2.0 MD5sum: 63f744fc98ae270e64058a09c6f78eb5 NeedsCompilation: no Package: OrderedList Version: 1.81.0 Depends: R (>= 3.6.1), Biobase, twilight Imports: methods License: GPL (>= 2) MD5sum: 97399261c1e5e6f78c9de5e554bca501 NeedsCompilation: no Package: ORFhunteR Version: 1.17.0 Depends: Biostrings, rtracklayer, Peptides Imports: Rcpp (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg38, data.table, stringr, randomForest, xfun, stats, utils, parallel, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown License: MIT License MD5sum: c5340be6d65b966b4612bee9ef18888a NeedsCompilation: yes Package: ORFik Version: 1.29.0 Depends: R (>= 4.1.0), IRanges (>= 2.17.1), GenomicRanges (>= 1.35.1), GenomicAlignments (>= 1.19.0) Imports: AnnotationDbi (>= 1.45.0), Biostrings (>= 2.51.1), biomaRt, biomartr (>= 1.0.7), BiocFileCache, BiocGenerics (>= 0.29.1), BiocParallel (>= 1.19.0), BSgenome, cowplot (>= 1.0.0), data.table (>= 1.11.8), DESeq2 (>= 1.24.0), fst (>= 0.9.2), GenomeInfoDb (>= 1.15.5), GenomicFeatures (>= 1.31.10), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), httr (>= 1.3.0), jsonlite, methods (>= 3.6.0), R.utils, Rcpp (>= 1.0.0), Rsamtools (>= 1.35.0), rtracklayer (>= 1.43.0), stats, SummarizedExperiment (>= 1.14.0), S4Vectors (>= 0.21.3), tools, txdbmaker, utils, XML, xml2 (>= 1.2.0), withr LinkingTo: Rcpp Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 84abe4f364eb3c59a9c8f163c47b28f4 NeedsCompilation: yes Package: Organism.dplyr Version: 1.37.0 Depends: R (>= 4.1.0), dplyr (>= 0.7.0), AnnotationFilter (>= 1.1.3) Imports: RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges, GenomicFeatures, AnnotationDbi, rlang, methods, tools, utils, BiocFileCache, DBI, dbplyr, tibble Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, magick, BiocStyle, ggplot2 License: Artistic-2.0 MD5sum: 2a2674823dc071fcfeb11d09c6843a2d NeedsCompilation: no Package: OrganismDbi Version: 1.51.0 Depends: R (>= 2.14.0), BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.39.4) Imports: methods, utils, stats, DBI, BiocManager, Biobase, graph, RBGL, S4Vectors, IRanges, GenomicRanges (>= 1.31.13), txdbmaker Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr License: Artistic-2.0 MD5sum: 2b3010f2494b4112725aaf43b8efb8e7 NeedsCompilation: no Package: orthogene Version: 1.15.0 Depends: R (>= 4.1) Imports: dplyr, methods, stats, utils, Matrix, jsonlite, homologene, gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr, 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NeedsCompilation: no Package: pathwayPCA Version: 1.25.0 Depends: R (>= 3.1) Imports: lars, methods, parallel, stats, survival, utils Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse License: GPL-3 MD5sum: 373a5fedff1c69350e15566254a774bd NeedsCompilation: no Package: pcaMethods Version: 2.1.0 Depends: Biobase, methods Imports: BiocGenerics, Rcpp (>= 0.11.3), MASS LinkingTo: Rcpp Suggests: matrixStats, lattice, ggplot2 License: GPL (>= 3) MD5sum: 2c3132d269309abdd979960b49bc816a NeedsCompilation: yes Package: PCAN Version: 1.37.0 Depends: R (>= 3.3), BiocParallel Imports: grDevices, stats Suggests: BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb License: CC BY-NC-ND 4.0 MD5sum: dc608c9eabfd739d13642f032e9e444a NeedsCompilation: no Package: PCAtools Version: 2.21.0 Depends: ggplot2, ggrepel Imports: lattice, grDevices, cowplot, methods, reshape2, stats, Matrix, DelayedMatrixStats, DelayedArray, BiocSingular, BiocParallel, Rcpp, dqrng LinkingTo: Rcpp, beachmat, BH, dqrng Suggests: testthat, scran, BiocGenerics, knitr, Biobase, GEOquery, hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2, airway, org.Hs.eg.db, magrittr, rmarkdown License: GPL-3 MD5sum: 541a6d3a40b865de655fc0e9f8e46ed8 NeedsCompilation: yes Package: PDATK Version: 1.17.0 Depends: R (>= 4.1), SummarizedExperiment Imports: data.table, MultiAssayExperiment, ConsensusClusterPlus, igraph, ggplotify, matrixStats, RColorBrewer, clusterRepro, CoreGx, caret, survminer, methods, S4Vectors, BiocGenerics, survival, stats, plyr, dplyr, MatrixGenerics, BiocParallel, rlang, piano, scales, survcomp, genefu, ggplot2, switchBox, reportROC, pROC, verification, utils Suggests: testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr, HDF5Array License: MIT + file LICENSE MD5sum: 369c98128ad07f92acf1f89e0df688c5 NeedsCompilation: no Package: pdInfoBuilder Version: 1.73.0 Depends: R (>= 3.2.0), methods, Biobase (>= 2.27.3), RSQLite (>= 1.0.0), affxparser (>= 1.39.4), oligo (>= 1.31.5) Imports: Biostrings (>= 2.35.12), BiocGenerics (>= 0.13.11), DBI (>= 0.3.1), IRanges (>= 2.1.43), oligoClasses (>= 1.29.6), S4Vectors (>= 0.5.22) License: Artistic-2.0 MD5sum: e95f26fcd995ab0c47e93038374a7895 NeedsCompilation: yes Package: PeacoQC Version: 1.19.0 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, flowCore, flowWorkspace, ggplot2, grDevices, grid, gridExtra, methods, plyr, stats, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL (>= 3) MD5sum: 16f176e2f9c36ea0f314c1831010d3e4 NeedsCompilation: no Package: peakPantheR Version: 1.23.0 Depends: R (>= 4.2) Imports: foreach (>= 1.4.4), doParallel (>= 1.0.11), ggplot2 (>= 3.5.0), gridExtra (>= 2.3), MSnbase (>= 2.4.0), mzR (>= 2.12.0), stringr (>= 1.2.0), methods (>= 3.4.0), XML (>= 3.98.1.10), minpack.lm (>= 1.2.1), scales(>= 0.5.0), shiny (>= 1.0.5), bslib, shinycssloaders (>= 1.0.0), DT (>= 0.15), pracma (>= 2.2.3), utils, lubridate, svglite (>= 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colourpicker, shinytoastr, scales, shinycssloaders Suggests: diffviewer, testthat (>= 3.0.0), vdiffr, rmarkdown, BiocStyle, knitr, withr, qpdf, shinytest2, devtools, R.devices, usethis, rlang, magick, cyclocomp License: Artistic-2.0 MD5sum: 1f98ff6952a67f268bddf4af2117c64c NeedsCompilation: no Package: pengls Version: 1.15.0 Depends: R (>= 4.2.0) Imports: glmnet, nlme, stats, BiocParallel Suggests: knitr,rmarkdown,testthat License: GPL-2 MD5sum: 31817b29ac0119772253936e2d276719 NeedsCompilation: no Package: PepSetTest Version: 1.3.0 Depends: R (>= 4.1.0) Imports: dplyr, limma, lme4, MASS, matrixStats, reshape2, stats, tibble, SummarizedExperiment, methods Suggests: statmod, BiocStyle, knitr, rmarkdown, tidyr License: GPL (>= 3) MD5sum: 11fafc678063946270e7a7f60588f23e NeedsCompilation: no Package: PepsNMR Version: 1.27.0 Depends: R (>= 3.6) Imports: Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2, methods, graphics, stats Suggests: knitr, markdown, rmarkdown, BiocStyle, 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Depends: R (>= 3.6.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2, Hmisc Imports: survival, limma, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, hgu133a.db, ellipse Suggests: GSEABase, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) MD5sum: 58e9522f205be7f56d81ef2ebe6d1775 NeedsCompilation: no Package: PhenStat Version: 2.45.0 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: e9d1ad114cc0f650f9bfd9fd4bfe3dda NeedsCompilation: no Package: philr Version: 1.35.0 Imports: ape, phangorn, tidyr, ggplot2, ggtree, methods Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia License: GPL-3 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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: 8deb97ff737b55952af0484ee22a2991 NeedsCompilation: no Package: PhyloProfile Version: 2.1.0 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, svglite, umap, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat, OmaDB License: MIT + file LICENSE MD5sum: 3153f6fa83ccc94d01d3d7c9fed43072 NeedsCompilation: no Package: phyloseq Version: 1.53.0 Depends: R (>= 3.3.0) Imports: ade4 (>= 1.7-4), ape (>= 5.0), Biobase (>= 2.36.2), BiocGenerics (>= 0.22.0), biomformat (>= 1.0.0), Biostrings (>= 2.40.0), cluster (>= 2.0.4), data.table (>= 1.10.4), foreach (>= 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Biostrings, Rsamtools, data.table, IRanges, seqinr, stats, openxlsx, dplyr, S4Vectors, methods Suggests: knitr, rtracklayer, testthat, BiocStyle, prettydoc, BSgenome, BSgenome.Dmelanogaster.UCSC.dm6, BiocManager, rmarkdown, ggplot2 License: CC0 MD5sum: 8f670045252a2ce8d22978fb559bb8c0 NeedsCompilation: no Package: pickgene Version: 1.81.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: 8ca3169c505663308b2da14767992b5d NeedsCompilation: no Package: Pigengene Version: 1.35.0 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), biomaRt (>= 2.30.0), knitr, AnnotationDbi, energy License: GPL (>= 2) MD5sum: 966f7cdca29e54c88bce0d07507f1471 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GenomicRanges, glue, grDevices, grid, ggplotify, IRanges, methods, plyranges, purrr, Rcpp, RColorBrewer, rhdf5, rlang, stats, strawr, tools, utils, withr LinkingTo: Rcpp Suggests: AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene License: MIT + file LICENSE MD5sum: 6a1313d7453d52118bc16f4e58c198fa NeedsCompilation: yes Package: plotGrouper Version: 1.27.0 Depends: R (>= 3.5) Imports: ggplot2 (>= 3.0.0), dplyr (>= 0.7.6), tidyr (>= 0.2.0), tibble (>= 1.4.2), stringr (>= 1.3.1), readr (>= 1.1.1), readxl (>= 1.1.0), scales (>= 1.0.0), stats, grid, gridExtra (>= 2.3), egg (>= 0.4.0), gtable (>= 0.2.0), ggpubr (>= 0.1.8), shiny (>= 1.1.0), shinythemes (>= 1.1.1), colourpicker (>= 1.0), magrittr (>= 1.5), Hmisc (>= 4.1.1), rlang (>= 0.2.2) Suggests: knitr, htmltools, BiocStyle, rmarkdown, testthat License: GPL-3 MD5sum: 2e8af7d1ee11cca34db28f0e37ec9681 NeedsCompilation: no Package: PLPE Version: 1.69.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) MD5sum: 14d7eabd25de1a26077ef631bf629a8e NeedsCompilation: no Package: PLSDAbatch Version: 1.5.0 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: 84c2593eb4b2c91c45176e7de9950f2b NeedsCompilation: no Package: plyinteractions Version: 1.7.0 Depends: R (>= 4.3.0) Imports: InteractionSet, GenomeInfoDb, BiocGenerics, GenomicRanges, plyranges, IRanges, S4Vectors, rlang, dplyr, tibble, tidyselect, methods, utils Suggests: tidyverse, BSgenome.Mmusculus.UCSC.mm10, Biostrings, BiocParallel, scales, HiContactsData, rtracklayer, BiocStyle, covr, knitr, rmarkdown, sessioninfo, 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regionalpcs Version: 1.7.0 Depends: R (>= 4.3.0) Imports: dplyr, PCAtools, tibble, GenomicRanges Suggests: knitr, rmarkdown, RMTstat, testthat (>= 3.0.0), BiocStyle, tidyr, minfiData, TxDb.Hsapiens.UCSC.hg19.knownGene, IRanges License: MIT + file LICENSE MD5sum: c99605f4b153661c19f6a021140cd738 NeedsCompilation: no Package: regionReport Version: 1.43.0 Depends: R(>= 3.2) Imports: BiocStyle (>= 2.5.19), derfinder (>= 1.25.3), DEFormats, DESeq2, GenomeInfoDb, GenomicRanges, knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR, rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment, utils Suggests: BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot (>= 1.29.1), sessioninfo, DT, edgeR, ggbio (>= 1.35.2), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker License: Artistic-2.0 MD5sum: 655ad9e7bab4e6e8c1a31e978d53cef6 NeedsCompilation: no Package: regsplice Version: 1.35.0 Imports: glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats, pbapply, utils, methods Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 0c93c11db5ee8efeebcc1218fcff2140 NeedsCompilation: no Package: regutools Version: 1.21.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, Biostrings, DBI, GenomicRanges, Gviz, IRanges, RCy3, RSQLite, S4Vectors, methods, stats, utils, BiocFileCache Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr License: Artistic-2.0 MD5sum: 5418c2bb5c8e77eeba61ad01d08b36ac NeedsCompilation: no Package: REMP Version: 1.33.0 Depends: R (>= 3.6), SummarizedExperiment(>= 1.1.6), minfi (>= 1.22.0) Imports: readr, rtracklayer, graphics, stats, utils, methods, settings, BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel, doParallel, parallel, foreach, caret, kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db, impute, iterators Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC License: GPL-3 MD5sum: 27ba16a643b9fb020f75f1f14d2b69dd NeedsCompilation: no Package: Repitools Version: 1.55.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.8.0) Imports: parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, BSgenome (>= 1.47.3), gplots, grid, MASS, gsmoothr, edgeR (>= 3.4.0), DNAcopy, Rsolnp, cluster Suggests: ShortRead, BSgenome.Hsapiens.UCSC.hg18 License: LGPL (>= 2) MD5sum: d8a3a8dd34aef4510a37ae4d20951b6f NeedsCompilation: yes Package: ReportingTools Version: 2.49.0 Depends: methods, knitr, utils Imports: Biobase,hwriter,Category,GOstats,limma(>= 3.17.5),lattice,AnnotationDbi,edgeR, annotate,PFAM.db, GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils, DESeq2(>= 1.3.41), ggplot2, ggbio, IRanges Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db, rmarkdown, markdown License: Artistic-2.0 MD5sum: 5a44e3649aa81b6c358ed0010680c10d NeedsCompilation: no Package: RepViz Version: 1.25.0 Depends: R (>= 3.5.1), GenomicRanges (>= 1.30.0), Rsamtools (>= 1.34.1), IRanges (>= 2.14.0), biomaRt (>= 2.36.0), S4Vectors (>= 0.18.0), graphics, grDevices, utils Suggests: rmarkdown, knitr, testthat License: GPL-3 MD5sum: 6061838b3dc970dbae5410f8c0d894c8 NeedsCompilation: no Package: ResidualMatrix Version: 1.19.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular License: GPL-3 MD5sum: e5b21b3a30669b58966045250cde7402 NeedsCompilation: no Package: RESOLVE Version: 1.11.0 Depends: R (>= 4.1.0) Imports: Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5, cluster, data.table, GenomeInfoDb, GenomicRanges, glmnet, ggplot2, gridExtra, IRanges, lsa, MutationalPatterns, nnls, parallel, reshape2, S4Vectors, RhpcBLASctl, survival Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: d62f7e0b5a244de22aba8a9e176056f0 NeedsCompilation: no Package: retrofit Version: 1.9.0 Depends: R (>= 4.2), Rcpp LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2, corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl License: GPL-3 MD5sum: 5902cf106fd3d058003968ecd3103d21 NeedsCompilation: yes Package: ReUseData Version: 1.9.0 Imports: Rcwl, RcwlPipelines, BiocFileCache, S4Vectors, stats, tools, utils, methods, jsonlite, yaml, basilisk Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: bcaee07a36ddf3b5359b02d0663bc014 NeedsCompilation: no Package: rexposome Version: 1.31.0 Depends: R (>= 3.5), Biobase Imports: methods, utils, stats, lsr, FactoMineR, stringr, circlize, corrplot, ggplot2, ggridges, reshape2, pryr, S4Vectors, imputeLCMD, scatterplot3d, glmnet, gridExtra, grid, Hmisc, gplots, gtools, scales, lme4, grDevices, graphics, ggrepel, mice Suggests: mclust, flexmix, testthat, BiocStyle, knitr, formatR, rmarkdown License: MIT + file LICENSE MD5sum: 7a410361efa05e63e117502be8c20db5 NeedsCompilation: no Package: rfaRm Version: 1.19.0 Imports: httr, stringi, rsvg, magick, data.table, Biostrings, utils, rvest, xml2, IRanges, S4Vectors, jsonlite Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics, RUnit License: GPL-3 MD5sum: ca3905e2b439794076b90f6d13cd7979 NeedsCompilation: no Package: RFLOMICS Version: 1.1.0 Depends: R (>= 4.4.0), SummarizedExperiment, MultiAssayExperiment, shinyBS, dplyr, ggplot2, htmltools, knitr, coseq Imports: vroom, org.At.tair.db, AnnotationDbi, circlize, clusterProfiler, ComplexHeatmap, data.table, DT, edgeR, EnhancedVolcano, enrichplot, FactoMineR, ggpubr, ggrepel, grDevices, grid, httr, limma, magrittr, methods, mixOmics, MOFA2, purrr, RColorBrewer, reshape2, reticulate, rmarkdown, S4Vectors, shiny, shinydashboard, shinyWidgets, stats, stringr, tidyr, tibble, tidyselect, UpSetR, Suggests: testthat, shinytest2, BiocStyle, org.Hs.eg.db License: Artistic-2.0 MD5sum: 7bc9b0f038a680d49a7e7a60a0c5c252 NeedsCompilation: no Package: rfPred Version: 1.47.0 Depends: R (>= 3.5.0), methods Imports: utils, GenomeInfoDb, data.table, IRanges, GenomicRanges, parallel, Rsamtools Suggests: BiocStyle License: GPL (>= 2) MD5sum: cd6f61c27a0f4b57f90531aa8a1c8c43 NeedsCompilation: yes Package: rGenomeTracks Version: 1.15.0 Depends: R (>= 4.1.0), Imports: imager, reticulate, methods, rGenomeTracksData Suggests: rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 18ae191321dc4373f802debe972a4848 NeedsCompilation: no Package: rgoslin Version: 1.13.0 Imports: Rcpp (>= 1.0.3), dplyr LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra, BiocManager, stringr, stringi, ggplot2, tibble, lipidr License: MIT + file LICENSE MD5sum: 38e6be22427360f542b008e0ad26148d NeedsCompilation: yes Package: RGraph2js 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TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment License: GPL-3 MD5sum: 1e6da9501b60412177319ff5c0108303 NeedsCompilation: no Package: ribor Version: 1.21.0 Depends: R (>= 3.6.0) Imports: dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors, tidyr, tools, yaml Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 6ff491f57b6933ab2d44346be4f86aa8 NeedsCompilation: no Package: riboSeqR Version: 1.43.0 Depends: R (>= 3.0.2), methods, GenomicRanges, abind Imports: Rsamtools, IRanges, S4Vectors, baySeq, GenomeInfoDb, seqLogo Suggests: BiocStyle, RUnit, BiocGenerics License: GPL-3 MD5sum: e44e26a68572b8b800fad7e91a6f49e7 NeedsCompilation: no Package: ribosomeProfilingQC Version: 1.21.0 Depends: R (>= 4.0), GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq, GenomicAlignments, GenomicFeatures, GenomeInfoDb, IRanges, methods, motifStack, rtracklayer, Rsamtools, RUVSeq, Rsubread, S4Vectors, XVector, ggplot2, ggfittext, scales, ggrepel, utils, cluster, stats, graphics, grid, txdbmaker, ggExtra Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, DESeq2, limma, ashr, testthat, rmarkdown, vsn, Biobase License: GPL (>= 3) + file LICENSE MD5sum: c8b73761a5ea516b08e466508774064f NeedsCompilation: no Package: rifi Version: 1.13.0 Depends: R (>= 4.2) Imports: car, cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, graphics, grDevices, grid, methods, nls2, nnet, rlang, S4Vectors, scales, stats, stringr, SummarizedExperiment, tibble, rtracklayer, reshape2, utils Suggests: DescTools, devtools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: de8d4055700da9d5a3950061bbafc811 NeedsCompilation: no Package: rifiComparative Version: 1.9.0 Depends: R (>= 4.2) Imports: cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, ggrepel, graphics, grDevices, grid, methods, nnet, rlang, S4Vectors, scales, stats, stringr, tibble, rtracklayer, utils, writexl, DTA, LSD, reshape2, devtools, SummarizedExperiment Suggests: DescTools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: 0b1eab31ad645ff4bc4ea531bd656828 NeedsCompilation: no Package: Rigraphlib Version: 1.1.0 LinkingTo: biocmake Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: ebe81baec8162678dd20c251df3b2c5f NeedsCompilation: yes Package: rigvf Version: 1.1.0 Depends: R (>= 4.1.0) Imports: methods, httr2, rjsoncons, dplyr, tidyr, rlang, memoise, cachem, whisker, jsonlite, GenomicRanges, IRanges, GenomeInfoDb Suggests: knitr, rmarkdown, testthat (>= 3.0.0), plyranges, plotgardener, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene License: MIT + file LICENSE MD5sum: fc3636186a9fb720965cac6a257ebe03 NeedsCompilation: no Package: RImmPort Version: 1.37.0 Imports: plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools, utils, RSQLite Suggests: knitr License: GPL-3 MD5sum: 852c5d5f7981d83cdb19cfa6f8909092 NeedsCompilation: no Package: RIVER Version: 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rvinecopulib, umap, ggplot2, irlba, viridis, BiocParallel, matrixStats, Matrix, sparseMVN, coop Suggests: mvnfast, igraph, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle License: MIT + file LICENSE MD5sum: 61d08e8cb2699978323416e5687a9bf0 NeedsCompilation: no Package: scDiagnostics Version: 1.3.0 Depends: R (>= 4.4.0) Imports: SingleCellExperiment, methods, isotree, ggplot2, ggridges, SummarizedExperiment, ranger, transport, speedglm, cramer, rlang, bluster, patchwork Suggests: AUCell, BiocStyle, knitr, Matrix, rmarkdown, scran, scRNAseq, SingleR, celldex, scuttle, scater, dplyr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 3d23216ad4fe5489eb9997059d8bd511 NeedsCompilation: no Package: scDotPlot Version: 1.3.0 Depends: R (>= 4.4.0) Imports: aplot, BiocGenerics, cli, dplyr, ggplot2, ggsci, ggtree, grDevices, magrittr, purrr, rlang, scales, scater, Seurat, SingleCellExperiment, stats, stringr, tibble, tidyr Suggests: AnnotationDbi, BiocStyle, knitr, rmarkdown, scran, scRNAseq, scuttle, SeuratObject, testthat, vdiffr License: Artistic-2.0 MD5sum: 571ab872e65ac7617250e58ec27ba452 NeedsCompilation: no Package: scds Version: 1.25.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown License: MIT + file LICENSE MD5sum: c3dd06bc64336b28c7cc2048c70375ad NeedsCompilation: no Package: SCFA Version: 1.19.0 Depends: R (>= 4.0) Imports: matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph, Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival Suggests: knitr, rmarkdown, BiocStyle License: LGPL MD5sum: 160b2449b1aad496c9afe0dae91a4ca6 NeedsCompilation: no Package: scFeatureFilter Version: 1.29.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods Suggests: testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE MD5sum: db4581eb22948455e04088172896c034 NeedsCompilation: no Package: scFeatures Version: 1.9.0 Depends: R (>= 4.2.0) Imports: DelayedArray, DelayedMatrixStats, EnsDb.Hsapiens.v79, EnsDb.Mmusculus.v79, GSVA, ape, glue, dplyr, ensembldb, gtools, 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: 0d8c2a6924b378c7a1a8a99f336e91d8 NeedsCompilation: no Package: scGPS Version: 1.23.0 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: 5bd3fb6530d97e072b03091ee1120265 NeedsCompilation: yes Package: schex Version: 1.23.0 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: 234a7699ec02c91e357723e73501ca55 NeedsCompilation: no Package: scHiCcompare Version: 1.1.0 Depends: R (>= 4.5.0) Imports: grDevices, graphics, stats, utils, dplyr, ggplot2, gtools, HiCcompare, lattice, mclust, mice, miceadds, ranger, rstatix, tidyr, rlang, data.table, BiocParallel Suggests: knitr, rmarkdown, testthat, BiocStyle, DT, gridExtra License: MIT + file LICENSE MD5sum: 198ec094668cbcff7c71c397e65ee3ad NeedsCompilation: no Package: scHOT Version: 1.21.0 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: 3cff16cefaa8e58f03f779c8c1a60b75 NeedsCompilation: no Package: scider Version: 1.7.0 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: e2e431f5d28584a75096025d24c67b60 NeedsCompilation: no Package: scifer Version: 1.11.0 Imports: dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr, ggplot2, 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parallel, grDevices LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils License: Artistic-2.0 MD5sum: 01818074e436ea8cc6f27b1f60b48548 NeedsCompilation: yes Package: scMultiSim Version: 1.5.0 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: b35d36428c52b82667378abeeff8b194 NeedsCompilation: no Package: SCnorm Version: 1.31.0 Depends: R (>= 3.4.0), Imports: SingleCellExperiment, SummarizedExperiment, stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, S4Vectors, ggplot2, forcats, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) MD5sum: 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NeedsCompilation: no Package: SCOPE Version: 1.21.0 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: d8d12ec54f6797308000e6c0eb161863 NeedsCompilation: no Package: scoup Version: 1.3.0 Depends: R (>= 4.4), Matrix Imports: Biostrings, methods Suggests: BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat (>= 3.0.0), yaml License: GPL (>= 2) MD5sum: bfac1500bef374d18917efbcf0e29f8a NeedsCompilation: no Package: scp Version: 1.19.0 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: 2bb31340030800cbe59ab6a9deda021c NeedsCompilation: no Package: scPCA Version: 1.23.0 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: feda5095d39f8c145970d1225ef3b232 NeedsCompilation: no Package: scQTLtools Version: 1.1.0 Depends: R (>= 4.4.1.0) Imports: ggplot2(>= 3.5.1), Matrix (>= 1.7-0), stats (>= 4.4.1), progress(>= 1.2.3), stringr(>= 1.5.1), dplyr(>= 1.1.4), SeuratObject(>= 5.0.2), methods(>= 4.4.1), magrittr(>= 2.0.3), patchwork(>= 1.2.0), DESeq2 (>= 1.45.3), VGAM (>= 1.1-11), limma (>= 3.61.9), biomaRt(>= 2.61.3), gamlss (>= 5.4-22), SingleCellExperiment(>= 1.27.2), SummarizedExperiment(>= 1.32.0), GOSemSim(>= 2.31.2) Suggests: BiocStyle, knitr, rmarkdown, org.Hs.eg.db, org.Mm.eg.db, org.Ce.eg.db, org.At.tair.db, testthat (>= 3.2.1.1) License: MIT + file LICENSE MD5sum: 5b9bdfa4ecf9d3359c585b81272dcbf2 NeedsCompilation: no Package: scran Version: 1.37.0 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: 256092e54d8bc91c550dc91d875eb0dd NeedsCompilation: yes Package: scrapper Version: 1.3.0 Imports: methods, Rcpp, beachmat (>= 2.21.6), DelayedArray, BiocNeighbors (>= 1.99.0), Rigraphlib, parallel LinkingTo: Rcpp, assorthead, beachmat, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, MatrixGenerics, sparseMatrixStats, Matrix, S4Vectors, SummarizedExperiment, SingleCellExperiment, scRNAseq, igraph License: MIT + file LICENSE MD5sum: a93db514ac2e5c4e0f43fb4399bce0b7 NeedsCompilation: yes Package: scReClassify Version: 1.15.0 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: 8c4cb2b926800147042fa27163ab1cf5 NeedsCompilation: no Package: scRecover Version: 1.25.0 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS 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License: MIT + file LICENSE MD5sum: 2ef5b041b1003f69858f88c4439ccc24 NeedsCompilation: no Package: scRepertoire Version: 2.5.0 Depends: ggplot2, R (>= 4.0) Imports: assertthat, cubature, dplyr, evmix, ggalluvial, ggdendro, ggraph, grDevices, igraph, iNEXT, plyr, quantreg, Rcpp, reshape2, rjson, rlang, S4Vectors, SeuratObject, SingleCellExperiment, stringr, stringdist, SummarizedExperiment, tidygraph, truncdist, VGAM, purrr, lifecycle, methods LinkingTo: Rcpp Suggests: BiocManager, BiocStyle, circlize, knitr, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0), vdiffr, withr License: MIT + file LICENSE MD5sum: 0dba9d5550a2d92d619245d34e9c634c NeedsCompilation: yes Package: scRNAseqApp Version: 1.9.0 Depends: R (>= 4.3.0) Imports: bibtex, bslib, circlize, ComplexHeatmap, colourpicker, data.table, DBI, DT, fs, GenomicRanges, GenomeInfoDb, ggdendro, ggforce, ggplot2, ggrepel, ggridges, grDevices, grid, gridExtra, htmltools, IRanges, jsonlite, Matrix, magrittr, methods, patchwork, plotly, RColorBrewer, RefManageR, 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: a9d2f7d9328682ca53464e4635e78956 NeedsCompilation: no Package: scruff Version: 1.27.0 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: 03b6bc9988985b41bfa5baaf47fa40a2 NeedsCompilation: no Package: scry Version: 1.21.0 Depends: R 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NeedsCompilation: no Package: scTHI Version: 1.21.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: b5a6a74abc51181d3c9face90a773506 NeedsCompilation: no Package: scTreeViz Version: 1.15.0 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: c8c885c84cbc7e50ecde955001433f87 NeedsCompilation: no Package: scuttle Version: 1.19.0 Depends: SingleCellExperiment Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays, MatrixGenerics, SparseArray, DelayedArray, beachmat LinkingTo: 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ChIPseeker, cli, clusterProfiler, cowplot, factoextra, GenomeInfoDb, ggplot2, ggimage, graphics, grDevices, gridExtra, heatmaps, magick, methods, RColorBrewer, scales, seqArchR, seqPattern, stats, utils Suggests: BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr (>= 2.0.2), covr, knitr (>= 1.22), org.Dm.eg.db, pdftools, rmarkdown (>= 1.12), slickR, TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun License: GPL-3 MD5sum: 63031f8b3e3cd9779ac454055d602e18 NeedsCompilation: no Package: SeqArray Version: 1.49.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.31.1) Imports: methods, parallel, digest, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, Biostrings LinkingTo: gdsfmt Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation License: GPL-3 MD5sum: 080135e45b13a7914e760b6ba4efa73e NeedsCompilation: yes Package: seqCAT Version: 1.31.0 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE MD5sum: 437221db72ce28c97146817a3b51f449 NeedsCompilation: no Package: seqcombo Version: 1.31.0 Depends: R (>= 3.4.0) Imports: ggplot2, grid, igraph, utils, yulab.utils Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble License: Artistic-2.0 MD5sum: 9501d409c66b77877dc4ad988ad983b7 NeedsCompilation: no Package: SeqGate Version: 1.19.0 Depends: S4Vectors, SummarizedExperiment, GenomicRanges Imports: stats, methods, BiocManager Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown License: GPL (>= 2.0) MD5sum: f4dd5a34325a7de5e5b7c06e425b6ad3 NeedsCompilation: no Package: SeqGSEA Version: 1.49.0 Depends: Biobase, doParallel, DESeq2 Imports: methods, biomaRt Suggests: GenomicRanges License: GPL (>= 3) MD5sum: 075e4dfe9357f3709f7f845c2483947d NeedsCompilation: no Package: seqLogo Version: 1.75.0 Depends: R (>= 4.2), methods, grid Imports: stats4, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: LGPL (>= 2) MD5sum: b1c1d3351137c94d2735209fd499b0a6 NeedsCompilation: no Package: seqPattern Version: 1.41.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 MD5sum: 17c03ca4a240ebabb939e31fcd911e3f NeedsCompilation: no Package: seqsetvis Version: 1.29.0 Depends: R (>= 4.3), ggplot2 Imports: cowplot, data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, ggplotify, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, scales, stats, UpSetR Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 5cdf997c06cd9b8a9168cd8ebd2f9e87 NeedsCompilation: no Package: SeqSQC Version: 1.31.0 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: 7d4e5279ae61088ab1982adf0ed9741b NeedsCompilation: no Package: SeqVarTools Version: 1.47.0 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: b454565ca9432f66c7cd3aec0ee2468b NeedsCompilation: no Package: SEraster Version: 1.1.0 Depends: R (>= 4.5.0) Imports: BiocParallel, ggplot2, Matrix, methods, rearrr, sf, SpatialExperiment, SummarizedExperiment Suggests: CooccurrenceAffinity, nnSVG, 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NeedsCompilation: no Package: sevenbridges Version: 1.39.0 Depends: methods, utils, stats Imports: httr, jsonlite, yaml, objectProperties, stringr, S4Vectors, docopt, curl, uuid, data.table Suggests: knitr, rmarkdown, testthat, readr License: Apache License 2.0 | file LICENSE MD5sum: d4750265a22274675921e276f74f9b9b NeedsCompilation: no Package: sevenC Version: 1.29.0 Depends: R (>= 3.5), InteractionSet (>= 1.2.0) Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), GenomeInfoDb (>= 1.12.2), GenomicRanges (>= 1.28.5), IRanges (>= 2.10.3), S4Vectors (>= 0.14.4), readr (>= 1.1.0), purrr (>= 0.2.2), data.table (>= 1.10.4), boot (>= 1.3-20), methods (>= 3.4.1) Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr License: GPL-3 MD5sum: 2ad74a3c2a8b5120fc5d2ec82e5ffd8e NeedsCompilation: no Package: SGCP Version: 1.9.0 Depends: R (>= 4.2.0) Imports: ggplot2, expm, caret, plyr, dplyr, GO.db, annotate, SummarizedExperiment, 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: 67066972a03c577b29b3e46afce8783e NeedsCompilation: no Package: SGSeq Version: 1.43.0 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: 3814607893535e6dc2c2dc73e5fd01d8 NeedsCompilation: no Package: SharedObject Version: 1.23.0 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, Rcpp Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 04901a304e06a4f33018d2adc847379e NeedsCompilation: yes Package: shiny.gosling Version: 1.5.0 Depends: R (>= 4.1.0) Imports: htmltools, jsonlite, rlang, shiny, shiny.react, fs, digest, rjson Suggests: config, covr, knitr, lintr, mockery (>= 0.4.3), rcmdcheck, rmarkdown, sessioninfo, spelling, testthat (>= 3.0.0), GenomicRanges, VariantAnnotation, StructuralVariantAnnotation, biovizBase, ggbio License: LGPL-3 MD5sum: b45ce859f47e4f51d2394f768d8b7d89 NeedsCompilation: no Package: shinyDSP Version: 1.1.0 Depends: R (>= 4.5) Imports: AnnotationHub, BiocGenerics, bsicons, bslib, circlize, ComplexHeatmap, cowplot, dplyr, DT, edgeR, ExperimentHub, ggplot2, ggpubr, ggrepel, grDevices, grid, htmltools, limma, magrittr, pals, readr, S4Vectors, scales, scater, shiny, shinycssloaders, shinyjs, shinyvalidate, shinyWidgets, SingleCellExperiment, standR, stats, stringr, SummarizedExperiment, tibble, tidyr, utils, withr Suggests: BiocStyle, knitr, rmarkdown, shinytest2, spelling, svglite, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 1981285961c7d4f4096c150232d2e8df NeedsCompilation: no Package: shinyepico Version: 1.17.0 Depends: R (>= 4.3.0) Imports: DT (>= 0.15.0), data.table (>= 1.13.0), doParallel (>= 1.0.0), dplyr (>= 1.0.9), foreach (>= 1.5.0), GenomicRanges (>= 1.38.0), ggplot2 (>= 3.3.0), gplots (>= 3.0.0), heatmaply (>= 1.1.0), limma (>= 3.42.0), minfi (>= 1.32.0), plotly (>= 4.9.2), reshape2 (>= 1.4.0), rlang (>= 1.0.2), rmarkdown (>= 2.3.0), rtracklayer (>= 1.46.0), shiny (>= 1.5.0), shinyWidgets (>= 0.5.0), shinycssloaders (>= 0.3.0), shinyjs (>= 1.1.0), shinythemes (>= 1.1.0), statmod (>= 1.4.0), tidyr (>= 1.2.0), zip (>= 2.1.0) Suggests: knitr (>= 1.30.0), mCSEA (>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData, BiocStyle License: AGPL-3 + file LICENSE MD5sum: 2dbf770ba566615f0beecbbe88d284ef NeedsCompilation: no Package: shinyMethyl Version: 1.45.0 Imports: Biobase, BiocGenerics, graphics, grDevices, htmltools, MatrixGenerics, methods, minfi, RColorBrewer, shiny, stats, utils Suggests: shinyMethylData, minfiData, BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 3250fb25331b2b00ae732600edcf88bb NeedsCompilation: no Package: ShortRead Version: 1.67.0 Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), pwalign, hwriter, methods, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi, knitr License: Artistic-2.0 MD5sum: ba5e884e04b0b079e683ca2f3cb15e20 NeedsCompilation: yes Package: SIAMCAT Version: 2.13.0 Depends: R (>= 4.2.0), mlr3, phyloseq Imports: beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot, lmerTest, mlr3learners, mlr3tuning, paradox, lgr Suggests: BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr License: GPL-3 MD5sum: 011c9fdcb909b562d1398e896e1b5f2d NeedsCompilation: no Package: SICtools Version: 1.39.0 Depends: R (>= 3.0.0), methods, Rsamtools (>= 1.18.1), doParallel (>= 1.0.8), Biostrings (>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges (>= 1.22.4), IRanges (>= 2.4.8) Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 19299136ce7df8feb855d412f9d88a89 NeedsCompilation: yes Package: SigCheck Version: 2.41.0 Depends: R (>= 4.0.0), MLInterfaces, Biobase, e1071, BiocParallel, survival Imports: graphics, stats, utils, methods Suggests: BiocStyle, breastCancerNKI, qusage License: Artistic-2.0 MD5sum: 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Depends: R(>= 3.3) Imports: MASS(>= 7.3), qvalue(>= 2.2), ggplot2(>= 2.0), reshape2(>= 1.4), lattice(>= 0.2), stats(>= 3.3) Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx License: GPL-3 | file LICENSE MD5sum: 8be4456559fc780c12e420a105bd200e NeedsCompilation: no Package: signatureSearch Version: 1.23.0 Depends: R(>= 4.2.0), Rcpp, SummarizedExperiment, org.Hs.eg.db Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, utils, reshape2, visNetwork, BiocParallel, fastmatch, reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray, BiocGenerics, tibble LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT License: Artistic-2.0 MD5sum: 832a79e9dcf84bdfc059ca63442c9b9e NeedsCompilation: yes Package: signeR Version: 2.11.0 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: a600801b5b96516be40235876ebe6747 NeedsCompilation: yes Package: signifinder Version: 1.11.0 Depends: R (>= 4.4.0) Imports: AnnotationDbi, BiocGenerics, ComplexHeatmap, consensusOV, cowplot, DGEobj.utils, dplyr, ensembldb, ggplot2, ggridges, GSVA, IRanges, magrittr, matrixStats, maxstat, methods, openair, org.Hs.eg.db, patchwork, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, SpatialExperiment, stats, scales, SummarizedExperiment, survival, survminer, viridis Suggests: BiocStyle, edgeR, grid, kableExtra, knitr, limma, testthat (>= 3.0.0) License: AGPL-3 MD5sum: cd9e2195613b34f4df8ca43b83ed4938 NeedsCompilation: no Package: SigsPack Version: 1.23.0 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: 2cc272513ab044d71d715b4f8d5eee65 NeedsCompilation: no Package: sigsquared Version: 1.41.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 11357392d60c2d269d9416cbc5d73f10 NeedsCompilation: no Package: SIM Version: 1.79.0 Depends: R (>= 3.5), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) MD5sum: 40a7d4ae0347b4884212cdd1a44e736c NeedsCompilation: yes Package: SIMAT Version: 1.41.0 Depends: R (>= 3.5.0), Rcpp (>= 0.11.3) Imports: mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 70565bf73ea4eea1ad0948ee40f9d5fa NeedsCompilation: no Package: SimBu Version: 1.11.0 Imports: basilisk, BiocParallel, data.table, dplyr, ggplot2, tools, Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer, RCurl, reticulate, sparseMatrixStats, SummarizedExperiment, tidyr Suggests: curl, knitr, matrixStats, rmarkdown, Seurat (>= 5.0.0), SeuratObject (>= 5.0.0), testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 4914e67ab6fe8a11d9696bb7054f41e4 NeedsCompilation: no Package: SIMD Version: 1.27.0 Depends: R (>= 3.5.0) Imports: edgeR, statmod, methylMnM, stats, utils Suggests: BiocStyle, knitr,rmarkdown License: GPL-3 MD5sum: adddbdbddf05ac7482d652376fdea330 NeedsCompilation: yes Package: SimFFPE Version: 1.21.0 Depends: Biostrings Imports: dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods Suggests: BiocStyle License: LGPL-3 MD5sum: c1abb86e755499f705db3a4137f6a749 NeedsCompilation: no Package: similaRpeak Version: 1.41.0 Depends: R6 (>= 2.0) Imports: stats Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: d0bed20cd37d1b7e98803a0173e4bd46 NeedsCompilation: no Package: SIMLR Version: 1.35.0 Depends: R (>= 4.1.0), Imports: parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra LinkingTo: Rcpp Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph License: file LICENSE MD5sum: f39a50253bc501d7bfc2571064197750 NeedsCompilation: yes Package: simona Version: 1.7.0 Depends: R (>= 4.1.0) Imports: methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions, igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize, ComplexHeatmap, grDevices, stats, utils, shiny LinkingTo: Rcpp Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png, InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment, AnnotationHub, jsonlite License: MIT + file LICENSE MD5sum: b417b88e5db3c7dd397225b7bc978ba1 NeedsCompilation: yes Package: simPIC Version: 1.5.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, Matrix, stats, SummarizedExperiment, actuar, rlang, S4Vectors, methods, scales, scuttle Suggests: ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 0b3e2ab2642afadc8c847ca2c64e2feb NeedsCompilation: no Package: simpleSeg Version: 1.11.0 Depends: R (>= 3.5.0) Imports: BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors, grDevices, SummarizedExperiment, methods, cytomapper Suggests: BiocStyle, testthat (>= 3.0.0), knitr, ggplot2 License: GPL-3 MD5sum: 92c9e65f415b77470eaf729ed50b0646 NeedsCompilation: no Package: simplifyEnrichment Version: 2.3.0 Depends: R (>= 4.1.0) Imports: simona, ComplexHeatmap (>= 2.7.4), grid, circlize, GetoptLong, digest, tm, GO.db, AnnotationDbi, slam, methods, clue, grDevices, stats, utils, cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0) Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc License: MIT + file LICENSE MD5sum: d257883ed57902662418688c425c3909 NeedsCompilation: no Package: sincell Version: 1.41.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: GPL (>= 2) MD5sum: 11feaf347ea9f634257da04ab1981b8d NeedsCompilation: yes Package: SingleCellAlleleExperiment Version: 1.5.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: SummarizedExperiment, BiocParallel, DelayedArray, methods, utils, Matrix, S4Vectors, stats Suggests: scaeData, knitr, rmarkdown, BiocStyle, scran, scater, scuttle, ggplot2, patchwork, org.Hs.eg.db, AnnotationDbi, DropletUtils, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 891b55f0a5cc736f48e60f29cf12fac9 NeedsCompilation: no Package: SingleCellExperiment Version: 1.31.0 Depends: SummarizedExperiment Imports: methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne License: GPL-3 MD5sum: 2268b4960ae5ae6df5a13f5ac510f3c8 NeedsCompilation: no Package: SingleCellSignalR Version: 1.21.0 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: 2c20cbb535bf6f6821c024f4db20905e NeedsCompilation: no Package: SingleMoleculeFootprinting Version: 2.3.0 Depends: R (>= 4.4.0) Imports: BiocGenerics, Biostrings, BSgenome, cluster, dplyr, GenomeInfoDb, GenomicRanges, ggpointdensity, ggplot2, ggrepel, grDevices, IRanges, magrittr, Matrix, methods, miscTools, parallel, parallelDist, patchwork, plyranges, QuasR, RColorBrewer, rlang, S4Vectors, stats, stringr, tibble, tidyr, utils, viridis Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, qs, rmarkdown, readr, rrapply, SingleMoleculeFootprintingData, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: c12542d6af9a65bfc22e9099507c9fa3 NeedsCompilation: no Package: SingleR Version: 2.11.0 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocNeighbors, stats, utils, Rcpp, beachmat (>= 2.23.5) LinkingTo: 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NeedsCompilation: no Package: SpatialExperiment Version: 1.19.0 Depends: R (>= 4.1.0), methods, SingleCellExperiment Imports: rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils License: GPL-3 MD5sum: 2b2017c11d96572ab80afc689846ad01 NeedsCompilation: no Package: spatialFDA Version: 1.1.0 Depends: R (>= 4.3.0) Imports: dplyr, ggplot2, parallel, patchwork, purrr, refund, SpatialExperiment, spatstat.explore, spatstat.geom, SummarizedExperiment, tidyr, methods, stats, fda, graphics, magrittr, ExperimentHub Suggests: stringr, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), mgcv License: GPL (>= 3) + file LICENSE MD5sum: b3f32f07970736e7c031d32a3f8ea959 NeedsCompilation: no Package: spatialHeatmap Version: 2.15.0 Depends: R (>= 3.5.0) Imports: data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid, gridExtra, igraph, methods, Matrix, rsvg, shiny, grDevices, graphics, 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plyranges, TxDb.Hsapiens.UCSC.hg19.knownGene, AnnotationHub, GenomicFeatures, BiocStyle, hues, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 9421d5e51baeb9aa6524af313ffb1a78 NeedsCompilation: no Package: tidyFlowCore Version: 1.3.0 Depends: R (>= 4.3) Imports: Biobase, dplyr, flowCore, ggplot2, methods, purrr, rlang, stats, stringr, tibble, tidyr Suggests: BiocStyle, HDCytoData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 4cf7b3e7fd4482fc73a72e0d7136caa2 NeedsCompilation: no Package: tidyomics Version: 1.5.0 Depends: R (>= 4.2) Imports: tidySummarizedExperiment, tidySingleCellExperiment, tidyseurat, tidybulk, plyranges, nullranges, purrr, rlang, stringr, cli, utils Suggests: tidyr, dplyr, tibble, ggplot2, mockr (>= 0.2.0), knitr (>= 1.41), rmarkdown (>= 2.20), testthat (>= 3.1.6) License: MIT + file LICENSE MD5sum: 83476310d25f9f257afb99c7cca08da2 NeedsCompilation: no Package: tidysbml 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graphics, animation, tibble, dplyr, stringr, purrr, methods, shiny, BiocFileCache, readr, tools, plotly, ggplot2 Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: dc6c57805ef13a65e71b6598fec79c57 NeedsCompilation: no Package: TOP Version: 1.9.0 Depends: R (>= 4.1.0) Imports: assertthat, caret, ClassifyR, directPA, doParallel, dplyr, ggnewscale, ggplot2, ggraph, ggrepel, ggthemes, glmnet, Hmisc, igraph, latex2exp, limma, magrittr, methods, plotly, pROC, purrr, reshape2, stats, stringr, survival, tibble, tidygraph, tidyr, statmod Suggests: knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse License: GPL-3 MD5sum: 2678ef253c4f987eb158db0c44c7b217 NeedsCompilation: no Package: topconfects Version: 1.25.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, assertthat, ggplot2, scales, grid, grDevices Suggests: limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, 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TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack License: GPL (>= 2) MD5sum: f1d118a0a03ba9f7626de772cebad00b NeedsCompilation: no Package: tradeSeq Version: 1.23.0 Depends: R (>= 3.6) Imports: mgcv, edgeR, SingleCellExperiment, SummarizedExperiment, slingshot, magrittr, RColorBrewer, BiocParallel, Biobase, pbapply, igraph, ggplot2, princurve, methods, S4Vectors, tibble, Matrix, TrajectoryUtils, viridis, matrixStats, MASS Suggests: knitr, rmarkdown, testthat, covr, clusterExperiment, DelayedMatrixStats License: MIT + file LICENSE MD5sum: 46ab38635a586db4082fdb20d777d834 NeedsCompilation: no Package: TrajectoryGeometry Version: 1.17.0 Depends: R (>= 4.1) Imports: pracma, rgl, ggplot2, stats, methods Suggests: dplyr, knitr, RColorBrewer, rmarkdown License: MIT + file LICENSE MD5sum: d8c436f587e862e4f2be6cb0642cfd4c NeedsCompilation: no Package: TrajectoryUtils Version: 1.17.0 Depends: SingleCellExperiment 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R (>= 4.1.0), shiny (>= 1.6.0), shinyBS Imports: shinyjs, shinyFiles, plyr, data.table, DT, stringr, stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices, graphics, stats, utils, vegan Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr Enhances: parallel License: MIT + file LICENSE MD5sum: cbefda22136a0e3a96695eab69c5dafa NeedsCompilation: no Package: tRNA Version: 1.27.0 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE MD5sum: d19f3584ef51ec6ec0110fd438976f53 NeedsCompilation: no Package: tRNAdbImport Version: 1.27.0 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: c241337bb2be62279ab0b4898dced1a2 NeedsCompilation: no Package: tRNAscanImport Version: 1.29.0 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: 36d39d59d9a441cbc64a3e841258f5f9 NeedsCompilation: no Package: TRONCO Version: 2.41.0 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 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1.33.0 Depends: R (>= 3.4) Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: c02719570270d7c1415d247ac0847072 NeedsCompilation: no Package: txcutr Version: 1.15.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, GenomicFeatures, txdbmaker, IRanges, GenomicRanges, BiocGenerics, Biostrings, S4Vectors, rtracklayer, BiocParallel, stats, methods, utils Suggests: RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 MD5sum: b3f38b530102c1289ea09e50b4188bab NeedsCompilation: no Package: txdbmaker Version: 1.5.0 Depends: BiocGenerics, S4Vectors, GenomeInfoDb (>= 1.39.9), GenomicRanges, GenomicFeatures Imports: methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>= 2.0), IRanges, UCSC.utils, AnnotationDbi, Biobase, BiocIO, rtracklayer, biomaRt (>= 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Depends: R(>= 4.3.0) Imports: methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel, BiocNeighbors, SingleCellExperiment, SummarizedExperiment Suggests: scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 4422045060fc3a23e6fdb6377998a9eb NeedsCompilation: no Package: UCSC.utils Version: 1.3.1 Imports: methods, stats, httr, jsonlite, S4Vectors Suggests: DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 8de96fb05dacf7820698798998b1d2c5 NeedsCompilation: no Package: Ularcirc Version: 1.27.0 Depends: R (>= 3.4.0) Imports: AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments, Organism.dplyr, plotgardener, R.utils, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, yaml Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: f3124e50842f5c518f7102fc1581f1bb NeedsCompilation: no Package: uncoverappLib Version: 1.19.0 Imports: markdown, shiny, shinyjs, shinyBS, shinyWidgets,shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx, condformat, stringr, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache,rappdirs, TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils,S4Vectors, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, processx, Rsamtools, GenomicRanges Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: f96a156b46121963feb77f2d76545c17 NeedsCompilation: no Package: UNDO Version: 1.51.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 2ea3782924efae9202bdc2c596a5444b NeedsCompilation: no Package: unifiedWMWqPCR Version: 1.45.0 Depends: 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BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, human610quadv1bCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 MD5sum: 39bebe3828472e77cb0f220fee21f655 NeedsCompilation: yes Package: VarCon Version: 1.17.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 8431b9ef89959b451122d54b00479a30 NeedsCompilation: no Package: variancePartition Version: 1.39.0 Depends: R (>= 4.3.0), ggplot2, limma (>= 3.62.1), 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, 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knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: cd4a94ca4040b840ddd509a61fd4c94e NeedsCompilation: yes Package: VegaMC Version: 3.47.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods License: GPL-2 MD5sum: daf44854c67710fc59d207a893b371c5 NeedsCompilation: yes Package: velociraptor Version: 1.19.0 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: ae027d678aa886f54532178e8eebe5d5 NeedsCompilation: no Package: veloviz Version: 1.15.0 Depends: R (>= 4.1) Imports: Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 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