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Imports: callr (>= 3.0.0.9001), Matrix, Rcpp, BiocFileCache, DT, MultiAssayExperiment, circlize, curatedTCGAData, foreach, glmnet, httr, limma, matrixStats, readr, reshape2, tibble, rmarkdown, graphics, grid, parallel, stats, knitr, ggplot2, gridExtra, utils LinkingTo: Rcpp Suggests: testthat, MASS, knitr, BiocStyle License: Apache License (== 2.0) + file LICENSE MD5sum: b2c91dac95c2f5c4e36745ed1ed217bc NeedsCompilation: no Package: AMOUNTAIN Version: 1.38.0 Depends: R (>= 3.3.0) Imports: stats Suggests: BiocStyle, qgraph, knitr, rmarkdown License: GPL (>= 2) MD5sum: b92e9f22a39dba23d742dbd49337da67 NeedsCompilation: yes Package: amplican Version: 1.34.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.22.0), Biostrings (>= 2.44.2), pwalign Imports: Rcpp, utils (>= 3.4.1), S4Vectors (>= 0.14.3), ShortRead (>= 1.34.0), IRanges (>= 2.10.2), GenomicRanges (>= 1.61.1), Seqinfo, BiocParallel (>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 3.3.4), ggthemes (>= 3.4.0), 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31cb59e934dcb6ed4ed879eb3feb27bf NeedsCompilation: no Package: ANCOMBC Version: 2.14.0 Depends: R (>= 4.5.0) Imports: stats, DescTools, Hmisc, MASS, Matrix, Rdpack, doParallel, doRNG, energy, foreach, gtools, lme4, lmerTest, multcomp, nloptr, parallel, utils, quadprog Suggests: mia (>= 1.18.0), DT, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, dplyr, knitr, magrittr, microbiome, phyloseq, rmarkdown, testthat, tidyr, tidyverse License: Artistic-2.0 MD5sum: 53eb2ddca4dff9679ddd52ed31ae1f4d NeedsCompilation: no Package: ANF Version: 1.34.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 MD5sum: f8d2329ab1f851f704f97fec459842ba NeedsCompilation: no Package: anglemania Version: 1.1.0 Depends: R (>= 4.5.0) Imports: bigparallelr, bigstatsr, checkmate, digest, dplyr, Matrix, pbapply, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tidyr, withr LinkingTo: 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LGPL MD5sum: 2976853a0bb6611cef81ca4a27bc47b1 NeedsCompilation: no Package: anndataR Version: 1.1.3 Depends: R (>= 4.5.0) Imports: cli, lifecycle, Matrix, methods, purrr, R6 (>= 2.4.0), reticulate (>= 1.41.1), rlang, stats Suggests: BiocFileCache, BiocStyle, knitr, processx, rhdf5 (>= 2.52.1), Rarr (>= 1.11.12), rmarkdown, S4Vectors, Seurat, SeuratObject, SingleCellExperiment, spelling, SummarizedExperiment, testthat (>= 3.0.0), vctrs, withr, yaml License: MIT + file LICENSE MD5sum: f71e996722d4a6e32e13813a941b2c85 NeedsCompilation: no Package: annmap Version: 1.54.0 Depends: R (>= 2.15.0), methods, GenomicRanges Imports: DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice, Rsamtools, genefilter, IRanges, BiocGenerics Suggests: RUnit, rjson, Gviz License: GPL-2 MD5sum: 8ff7d7b63d6a484790d74776d34cbd88 NeedsCompilation: no Package: annoLinker Version: 1.0.0 Depends: R (>= 4.5.0) Imports: AnnotationDbi, BiocGenerics, future.apply, GenomicRanges, GenomeInfoDb, igraph, IRanges, InteractionSet, methods, progressr, S4Vectors, Seqinfo, trackViewer, visNetwork Suggests: BiocStyle, knitr, rtracklayer, rmarkdown, testthat, TxDb.Drerio.UCSC.danRer10.refGene, org.Dr.eg.db, future License: GPL-3 MD5sum: 15dc665443e7c6c2c0c601d130dbe2a7 NeedsCompilation: no Package: annotate Version: 1.90.0 Depends: R (>= 2.10), AnnotationDbi (>= 1.27.5), XML Imports: Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), httr Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 005b6691c7fbc0a173d704dc644fc37a NeedsCompilation: no Package: AnnotationDbi Version: 1.74.0 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: 65b70a0537974d127d44e98225de05ef NeedsCompilation: no Package: AnnotationFilter Version: 1.36.0 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: a797386b47578a7965e6f16910975ba9 NeedsCompilation: no Package: AnnotationForge Version: 1.54.0 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: d45f6cb6e84412a3626e8b0bd7a64ca7 NeedsCompilation: no Package: AnnotationHub Version: 4.2.0 Depends: 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AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub License: Artistic-2.0 MD5sum: db4d57bf1d851c6653b10033a7fcd7f4 NeedsCompilation: no Package: annotationTools Version: 1.86.0 Imports: Biobase, stats Suggests: BiocStyle License: GPL MD5sum: a8f58d245afeee5bed906ac932e21cba NeedsCompilation: no Package: annotatr Version: 1.38.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures (>= 1.61.4), GenomicRanges (>= 1.61.1), Seqinfo, ggplot2 (>= 3.5.0), IRanges, methods, readr, regioneR, reshape2, rlang, rtracklayer (>= 1.69.1), S4Vectors (>= 0.23.10), stats, utils Suggests: GenomeInfoDb, BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Drerio.UCSC.danRer11.refGene, 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59953c8a7b8a033df5a1b0f363dc1422 NeedsCompilation: no Package: AnVILWorkflow Version: 1.11.0 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: 32e14e0a2f94d5d206045069920df74a NeedsCompilation: no Package: APAlyzer Version: 1.26.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq2, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, VariantAnnotation, dplyr, tidyr, repmis, Rsamtools, rlang, txdbmaker, S4Vectors Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset, HybridMTest License: LGPL-3 + file LICENSE MD5sum: 42d4c7da8f427dc03a1961688e4d3798 NeedsCompilation: no Package: apComplex Version: 2.78.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: 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utils, grDevices, rlang, RColorBrewer, gtools, gridExtra, coda (>= 0.19-4) LinkingTo: Rcpp, RcppArmadillo, BH Suggests: testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling License: Artistic-2.0 MD5sum: 83e32dd638793d955befe4c65d17fc11 NeedsCompilation: yes Package: Banksy Version: 1.7.0 Depends: R (>= 4.4.0) Imports: aricode, BiocParallel, data.table, dbscan, SpatialExperiment, SingleCellExperiment, SummarizedExperiment, S4Vectors, stats, Matrix, MatrixGenerics, mclust, igraph, irlba, leidenAlg (>= 1.1.0), utils, uwot, RcppHungarian, GenomeInfoDb Suggests: knitr, rmarkdown, pals, scuttle, scater, scran, cowplot, ggplot2, testthat (>= 3.0.0), harmony, Seurat, ExperimentHub, spatialLIBD, BiocStyle License: file LICENSE MD5sum: cb523670f24301a4521995945b52fca2 NeedsCompilation: no Package: banocc Version: 1.35.0 Depends: R (>= 3.5.1), rstan (>= 2.17.4) Imports: coda (>= 0.18.1), mvtnorm, stringr Suggests: knitr, rmarkdown, methods, testthat, BiocStyle License: MIT + file 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(>= 3.5.0) Imports: devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges Suggests: testthat, knitr, BiocStyle License: GPL-3 MD5sum: b81a7b093459dcc728c53939718b56d4 NeedsCompilation: no Package: bumphunter Version: 1.54.0 Depends: R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), Seqinfo, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats Suggests: testthat, RUnit, doParallel, GenomeInfoDb, txdbmaker, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: c8c9cd005e18fd75986328d55d71f0ec NeedsCompilation: no Package: BumpyMatrix Version: 1.20.0 Imports: utils, methods, Matrix, S4Vectors, IRanges Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 4791be8317522bee8ecaf90263e76543 NeedsCompilation: no Package: BUS Version: 1.68.0 Depends: R (>= 2.3.0), minet Imports: stats, infotheo License: 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Version: 1.18.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots, grDevices, methods, stats, utils Suggests: BiocStyle, knitr, BiocGenerics License: Artistic-2.0 MD5sum: 811957f8e114df5b06ca287afd6c2863 NeedsCompilation: yes Package: CaDrA Version: 1.10.0 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: 5fcb4317557b640cb3a7dfea55f271da NeedsCompilation: yes Package: CAEN Version: 1.20.0 Depends: R (>= 4.1) Imports: stats,PoiClaClu,SummarizedExperiment,methods Suggests: knitr,rmarkdown,BiocManager,SummarizedExperiment,BiocStyle License: GPL-2 MD5sum: ac8d2e5f1a9f30481349b6f34703e00a NeedsCompilation: no Package: CAFE Version: 1.48.0 Depends: R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio Imports: 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clusterProfiler, stringr, DT, MesKit, maftools, data.table, utils, stats, methods, tidyr Suggests: knitr, rmarkdown, BiocStyle, shiny License: GPL-3 MD5sum: f25753752b7e884ae90c31de81ce8719 NeedsCompilation: no Package: canceR Version: 1.46.0 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: 2f78acd44874408961a3b6d3191ab00e NeedsCompilation: no Package: cancerclass Version: 1.56.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 MD5sum: 2dc94449f8388c32d3817d2272edd534 NeedsCompilation: yes Package: cardelino Version: 1.14.0 Depends: R (>= 4.2), stats Imports: combinat, GenomeInfoDb, GenomicRanges, ggplot2, ggtree, Matrix, matrixStats, methods, pheatmap, snpStats, S4Vectors, utils, 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SummarizedExperiment, methods, MCMCpack, fields, wrMisc, concaveman, sp, dplyr, sf, Matrix, RANN, ggplot2, reshape2, RColorBrewer, S4Vectors, scatterpie, grDevices,ggcorrplot, stats, nnls, BiocParallel, NMF, spatstat.random, gtools, SingleCellExperiment, SpatialExperiment LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, RcppML, BiocStyle License: GPL-3 + file LICENSE MD5sum: 005e309cf81deb637287681730660a92 NeedsCompilation: yes Package: carnation Version: 1.0.0 Depends: R (>= 4.6.0) Imports: BiocParallel, colorspace, ComplexUpset, dendextend, DESeq2, dplyr, DT, enrichplot, GeneTonic, ggplot2, ggrepel, heatmaply, htmltools, igraph, methods, MatrixGenerics, plotly, reticulate, RColorBrewer, rintrojs, scales, shiny, shinyBS, shinycssloaders, shinymanager, shinythemes, shinyWidgets, sortable, SummarizedExperiment, tools, utils, viridisLite, visNetwork, yaml Suggests: airway, BiocStyle, DEGreport, GenomicFeatures, goseq, knitr, org.Hs.eg.db, rmarkdown, testthat License: 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matrixStats, methods, nnls, RColorBrewer, reshape2, Rtsne, SummarizedExperiment, S4Vectors, scales, scater, stats Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot License: GPL (>= 2) MD5sum: 7f61b0ace69f80141047c8b1e700c0ba NeedsCompilation: no Package: Category Version: 2.78.0 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: 68959cbcacb1f5c2f5df478fc2e644da NeedsCompilation: no Package: categoryCompare Version: 1.56.0 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: be90547ba151dac3e9e9aec68befff63 NeedsCompilation: no Package: CatsCradle Version: 1.6.0 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: 01dc9c4cbd42b7170341ad5496bbc01a NeedsCompilation: no Package: CausalR Version: 1.44.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 3b603e848e6738b404c08d79ed6dd004 NeedsCompilation: no Package: cbaf Version: 1.34.0 Depends: R (>= 4.1) Imports: BiocFileCache, RColorBrewer, cBioPortalData, genefilter, gplots, grDevices, stats, utils, openxlsx, zip Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 5000d76da5c00c8b7a10d27e341927f3 NeedsCompilation: no Package: cBioPortalData Version: 2.24.0 Depends: R (>= 4.5.0), AnVIL (>= 1.19.5), MultiAssayExperiment Imports: BiocBaseUtils, BiocFileCache (>= 1.5.3), digest, dplyr, Seqinfo, GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment, RTCGAToolbox (>= 2.19.7), S4Vectors, SummarizedExperiment, stats, tibble, tidyr, TCGAutils (>= 1.9.4), utils Suggests: BiocStyle, jsonlite, knitr, survival, survminer, rmarkdown, testthat License: AGPL-3 MD5sum: c158693ea2edf642e3ea59392dd80b0e NeedsCompilation: no Package: CBN2Path Version: 1.2.0 Depends: R (>= 4.1.0) Imports: R6, ggraph, tidygraph, ggplot2, patchwork, cowplot, magrittr, igraph, rlang, grDevices, coda, graphics, stats, TCGAbiolinks, BiocParallel Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE OS_type: unix MD5sum: ce8be58b9fb0ffa6ced9d2c0f90d5313 NeedsCompilation: yes Package: CBNplot Version: 1.12.0 Depends: R (>= 4.3.0) Imports: ggplot2, magrittr, graphite, ggraph, igraph, bnlearn (>= 4.7), patchwork, org.Hs.eg.db, clusterProfiler, utils, enrichplot, reshape2, ggforce, dplyr, tidyr, stringr, depmap, ExperimentHub, Rmpfr, graphlayouts, BiocFileCache, ggdist, purrr, pvclust, stats, rlang Suggests: knitr, arules, concaveman, ReactomePA, bnviewer, rmarkdown, withr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 17b35f7e5e733b86be80ab5568ec9de6 NeedsCompilation: no Package: cbpManager Version: 1.20.0 Depends: shiny, shinydashboard Imports: utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite, rapportools, basilisk, reticulate, shinyBS, shinycssloaders, rintrojs, rlang, markdown Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 5f72a66e32862d35e78c480ace90d5e8 NeedsCompilation: no Package: CCAFE Version: 1.4.0 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: 3728d00c1b2dc9dddb78d76514336873 NeedsCompilation: no Package: ccfindR Version: 1.32.0 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: bc5fbbdaac66b4ad820cd0a15c22dffd NeedsCompilation: yes Package: ccImpute Version: 1.14.0 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: f88ac67b403661032fc9659f5063a315 NeedsCompilation: yes Package: CCPlotR Version: 1.10.0 Imports: plyr, tidyr, dplyr, ggplot2, forcats, ggraph, igraph, scatterpie, circlize, ComplexHeatmap, tibble, grid, stringr, ggtext, ggh4x, patchwork, RColorBrewer, scales, viridis, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: ab48914aae7e41ed79fafe93a5ae9e0c NeedsCompilation: no Package: CCPROMISE Version: 1.38.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: 3015709e90e50bf221171c05da7ef8b7 NeedsCompilation: no Package: ccrepe Version: 1.47.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat, RUnit License: MIT + file LICENSE MD5sum: b924d3088d6e4410545499bf955f45d3 NeedsCompilation: no Package: CDI Version: 1.10.0 Depends: R(>= 3.6) Imports: matrixStats, SeuratObject, Seurat, stats, BiocParallel, ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment, SummarizedExperiment, methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle 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BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData License: MIT + file LICENSE MD5sum: 20e52c2f50ed5cbc19654fb3bde7d4ee NeedsCompilation: yes Package: CellBarcode Version: 1.18.0 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: 6533955a08693eb935a8ba518bf9570f NeedsCompilation: yes Package: cellbaseR Version: 1.36.0 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: 4df0eb7df31dbbb41d0f53bef4fe097e NeedsCompilation: no Package: CellBench Version: 1.28.0 Depends: R (>= 3.6), SingleCellExperiment, 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RefManageR, rmarkdown, testthat (>= 3.0.0), EnsDb.Mmusculus.v79, EnsDb.Hsapiens.v86 License: MIT + file LICENSE MD5sum: ccdf19e25212140e12a0bb65778bc556 NeedsCompilation: no Package: Chicago Version: 1.40.0 Depends: R (>= 3.3.1), data.table Imports: matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, GenomeInfoDb, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub License: Artistic-2.0 MD5sum: 601a40c2c93baf0e7b22a8e4347ffa28 NeedsCompilation: no Package: chihaya Version: 1.12.0 Depends: DelayedArray Imports: methods, Matrix, rhdf5, Rcpp, HDF5Array LinkingTo: Rcpp, Rhdf5lib Suggests: BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix, BiocStyle, testthat, rmarkdown, knitr License: GPL-3 MD5sum: f560aac2fcbfbf634e46d0e30d02b3f8 NeedsCompilation: yes Package: chimeraviz Version: 1.38.0 Depends: Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, 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rmarkdown Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat License: GPL (>= 2) MD5sum: ee33ee008865d63977c770a49d06a2fe NeedsCompilation: no Package: ChIPpeakAnno Version: 3.46.0 Depends: R (>= 3.5), methods, IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), S4Vectors (>= 0.17.25) Imports: AnnotationDbi, BiocGenerics (>= 0.1.0), Biostrings (>= 2.47.6), pwalign, DBI, dplyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics, grid, InteractionSet, KEGGREST, matrixStats, multtest, regioneR, rtracklayer, stats, utils, universalmotif, stringr, tibble, tidyr, data.table, scales, ensembldb Suggests: AnnotationHub, BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, 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scater, ExPosition, BiocStyle, pkgdown License: GPL-3 MD5sum: 34f7fbd1dbb7895901093879da54382a NeedsCompilation: yes Package: ClassifyR Version: 3.16.0 Depends: R (>= 4.1.0), generics, methods, S4Vectors, MultiAssayExperiment, BiocParallel, survival Imports: grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2 (>= 3.5.0), ggpubr, reshape2, ggupset, broom, dcanr Suggests: limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, robustbase, glmnet, class, randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale, TOP, BiocNeighbors License: GPL-3 MD5sum: 2dede77486477b120db6441bed6dc338 NeedsCompilation: yes Package: cleanUpdTSeq Version: 1.50.0 Depends: R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods Imports: BSgenome, GenomicRanges, seqinr, e1071, Biostrings, Seqinfo, IRanges, utils, stringr, stats, S4Vectors Suggests: BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0) License: GPL-2 MD5sum: 26734a3b08b5f20a37e92442cc6d72aa NeedsCompilation: no Package: CleanUpRNAseq Version: 1.6.0 Depends: R (>= 4.4.0) Imports: AnnotationFilter, BiocGenerics, Biostrings, BSgenome, DESeq2, edgeR, ensembldb, Seqinfo, GenomicRanges, ggplot2, ggrepel, graphics, grDevices, KernSmooth, limma, methods, pheatmap, qsmooth, R6, RColorBrewer, Rsamtools, Rsubread, reshape2, SummarizedExperiment, stats, tximport, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86, ggplotify, knitr, patchwork, R.utils, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 4a46ba4c4867ec11ce914414b5a1a2f8 NeedsCompilation: no Package: cleaver Version: 1.50.0 Depends: R (>= 3.0.0), methods, Biostrings (>= 1.29.8) Imports: S4Vectors, IRanges Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.36.5) License: GPL (>= 3) MD5sum: 8b9c43d2258771d60fb8d56d76fcf59e NeedsCompilation: no Package: clevRvis Version: 1.12.0 Imports: shiny, 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fpc, mice, modeest, flock, networkD3, methods, ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices, ggplot2, grid, stats, utils, pbapply Suggests: RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2 License: GPL-2 MD5sum: fd937d5784977f999c5181ca99d2de28 NeedsCompilation: no Package: clustComp Version: 1.40.0 Depends: R (>= 3.3) Imports: sm, stats, graphics, grDevices Suggests: Biobase, colonCA, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 535e89cf7455e8bea39239642dd30002 NeedsCompilation: no Package: clusterExperiment Version: 2.32.0 Depends: R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>= 1.15.4), BiocGenerics Imports: methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, locfdr, matrixStats, graphics, parallel, BiocSingular, kernlab, stringr, S4Vectors, grDevices, DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma, mbkmeans LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, MAST, 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LICENSE MD5sum: 5d04e7c57e758350875b084e055cc98a NeedsCompilation: no Package: ClustIRR Version: 1.10.0 Depends: R (>= 4.3.0) Imports: 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, msa, Biostrings, RADanalysis, ggseqlogo, rBLAST 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, ggrepel, patchwork, htmlwidgets License: GPL-3 + file LICENSE MD5sum: a8b799201fe447d398efe00947ddd111 NeedsCompilation: yes Package: clustSIGNAL Version: 1.4.0 Depends: R (>= 4.4.0), SpatialExperiment Imports: BiocParallel, BiocNeighbors, bluster (>= 1.16.0), scater, harmony, SingleCellExperiment, SummarizedExperiment, methods, Matrix, reshape2 Suggests: knitr, BiocStyle, testthat (>= 3.0.0), aricode, ggplot2, patchwork, 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BSgenome.Hsapiens.UCSC.hg38, TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3 License: GPL-2 | file LICENSE License_restricts_use: yes MD5sum: 2d1b5e22415790430a213ccaea172277 NeedsCompilation: yes Package: CNORdt Version: 1.54.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 MD5sum: 394e85e71f5d1766da81f1b66ae163aa NeedsCompilation: yes Package: CNORfeeder Version: 1.52.0 Depends: R (>= 4.0.0), graph Imports: CellNOptR (>= 1.4.0) Suggests: minet, Rgraphviz, RUnit, BiocGenerics, igraph Enhances: MEIGOR License: GPL-3 MD5sum: 1330e046346fab227eb8ed6b6305f5d1 NeedsCompilation: no Package: CNORfuzzy Version: 1.54.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 MD5sum: 9755a5f676e3067276bb54969ae8766a NeedsCompilation: yes Package: CNORode Version: 1.54.0 Depends: CellNOptR, genalg Suggests: knitr, rmarkdown Enhances: doParallel, foreach License: 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grDevices, plotly, karyoploteR, CopyNumberPlots, GenomicRanges, magrittr, DT, scales, graphics Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: c7263be48dae79a75979f897579a1b59 NeedsCompilation: no Package: CNVMetrics Version: 1.16.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, S4Vectors, BiocParallel, methods, magrittr, stats, pheatmap, gridExtra, grDevices, rBeta2009 Suggests: BiocStyle, knitr, rmarkdown, testthat, XVector License: Artistic-2.0 MD5sum: 10d776dc513e718fdac2f63da9e70a2a NeedsCompilation: no Package: CNVPanelizer Version: 1.44.0 Depends: R (>= 3.2.0), GenomicRanges Imports: BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq, IRanges, Rsamtools, foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx Suggests: knitr, RUnit License: GPL-3 MD5sum: 044f1ae66e02de0fad9a85f7925f2ab9 NeedsCompilation: no Package: CNVRanger Version: 1.28.0 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: 328416afab563c4cc12ba15fda548f78 NeedsCompilation: no Package: CNVrd2 Version: 1.50.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 MD5sum: d45546a39917339bbca9515612fcc818 NeedsCompilation: no Package: CoCiteStats Version: 1.84.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL MD5sum: f0fb86d45e0484e7622e1c920e0487c2 NeedsCompilation: no Package: 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RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5, dplyr, fgsea, forcats, ggplot2 LinkingTo: Rcpp, BH, testthat Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject, BiocFileCache, xml2 License: BSD_3_clause + file LICENSE MD5sum: 81193ab59a3e9833a9f54fdb5c0277f7 NeedsCompilation: yes Package: cogena Version: 1.46.0 Depends: R (>= 3.6), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools Suggests: knitr, rmarkdown (>= 2.1) License: LGPL-3 MD5sum: cbdaa6f3f3b850a7b5658373dc6d2ed6 NeedsCompilation: no Package: cogeqc Version: 1.16.0 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 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impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr, foreach, doParallel, doRNG, irlba LinkingTo: Rcpp Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 License: MIT + file LICENSE MD5sum: 3921c984815e0c640e017281d680ad28 NeedsCompilation: yes Package: comapr Version: 1.16.0 Depends: R (>= 4.1.0) Imports: methods, ggplot2, reshape2, dplyr, gridExtra, plotly, circlize, rlang, GenomicRanges, IRanges, foreach, BiocParallel, GenomeInfoDb, scales, RColorBrewer, tidyr, S4Vectors, utils, Matrix, grid, stats, SummarizedExperiment, plyr, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod License: MIT + file LICENSE MD5sum: b0e0d8b751b205d74cdb60d4ff9104f5 NeedsCompilation: no Package: combi Version: 1.24.0 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: 41252ddd70b5d7105150c9db19374579 NeedsCompilation: no Package: coMethDMR Version: 1.16.0 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: 82148930122164508a0e205c21fd5f0a NeedsCompilation: no Package: COMPASS Version: 1.49.0 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach, coda LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.33.1), 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testthat (>= 3.0.0), BiocStyle License: GPL (>= 3) MD5sum: 7606274292a111fe95c6203b4bbf288b NeedsCompilation: no Package: compEpiTools Version: 1.46.0 Depends: R (>= 3.5.0), methods, topGO, GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, Seqinfo Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer License: GPL MD5sum: 305b0077fd0c4f70a06232de62551f95 NeedsCompilation: no Package: ComplexHeatmap Version: 2.28.0 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, 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BiocParallel, graph, ggplot2, methods, Rfast, pheatmap, survival, topGO, graphics, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat, Seurat License: MIT + file LICENSE MD5sum: b3f790619bd3d2557236aa1bc3fbcae5 NeedsCompilation: no Package: CONSTANd Version: 1.20.0 Depends: R (>= 4.1) Suggests: BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma License: file LICENSE MD5sum: de9be2d5d6cffaaf11f1873a646426a6 NeedsCompilation: no Package: conumee Version: 1.46.0 Depends: R (>= 3.5.0), minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest Imports: methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges, Seqinfo Suggests: BiocStyle, knitr, rmarkdown, minfiData, RCurl License: GPL (>= 2) MD5sum: 871bfbf4e1bc66558cfd796f6ae134a2 NeedsCompilation: no Package: convert Version: 1.88.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 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openxlsx, rio, rlang, stringr Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice, MASS, tensorflow, BSgenome.Hsapiens.UCSC.hg38, BiocFileCache, TxDb.Hsapiens.UCSC.hg38.knownGene, testthat, knitr License: file LICENSE MD5sum: bc3c4a886e57b46d29ff8059109845bd NeedsCompilation: no Package: crisprShiny Version: 1.8.0 Depends: R (>= 4.4.0), shiny Imports: BiocGenerics, Biostrings, BSgenome, crisprBase, crisprDesign, crisprScore, crisprViz, DT, Seqinfo, htmlwidgets, methods, pwalign, S4Vectors, shinyBS, shinyjs, utils, waiter Suggests: BiocStyle, knitr, rmarkdown, shinyFeedback, testthat (>= 3.0.0), BSgenome.Hsapiens.UCSC.hg38 License: MIT + file LICENSE MD5sum: 9e52cc1009d1055637eba2e0d41153c1 NeedsCompilation: no Package: CrispRVariants Version: 1.40.0 Depends: R (>= 4.3.0), ggplot2 (>= 2.2.0) Imports: AnnotationDbi, BiocParallel, Biostrings, 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remotes License: MIT + file LICENSE MD5sum: 112a20b1da421a5aec3300556aaa4802 NeedsCompilation: no Package: ctsGE Version: 1.38.0 Depends: R (>= 3.2) Imports: ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat License: GPL-2 MD5sum: b5dc8bd7d0a0fbaa2dbc549660a3fee9 NeedsCompilation: no Package: CTSV Version: 1.14.0 Depends: R (>= 4.2), Imports: stats, pscl, qvalue, BiocParallel, methods, knitr, SpatialExperiment, SummarizedExperiment Suggests: testthat, BiocStyle License: GPL-3 MD5sum: 12cf4affb91c6e098bede47f87b38cf6 NeedsCompilation: yes Package: CuratedAtlasQueryR Version: 1.10.0 Depends: R (>= 4.2.0) Imports: dplyr, SummarizedExperiment, SingleCellExperiment, purrr (>= 1.0.0), BiocGenerics, glue, HDF5Array, DBI, tools, httr, cli, assertthat, SeuratObject, Seurat, methods, rlang, stats, S4Vectors, tibble, utils, dbplyr (>= 2.3.0), duckdb, stringr Suggests: zellkonverter, rmarkdown, knitr, 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tibble, parallel, preprocessCore, SummarizedExperiment, TCA, PROPER, methods,dplyr, utils, RColorBrewer, graphics, edgeR, BiocParallel, checkmate, mvtnorm, DESeq2, rlang, e1071 Suggests: knitr, rmarkdown, MatrixGenerics, htmltools, RUnit, BiocGenerics, BiocManager, BiocStyle, Biobase License: GPL-2 | GPL-3 MD5sum: 257bae4ebfa23bf1cd80d2e194d8bae3 NeedsCompilation: no Package: CytoDx Version: 1.32.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 0b2884104632d6a36d0b9b3d863e13aa NeedsCompilation: no Package: CyTOFpower Version: 1.17.0 Depends: R (>= 4.1) Imports: CytoGLMM, diffcyt, DT, dplyr, ggplot2, magrittr, methods, rlang, stats, shiny, shinyFeedback, shinyjs, shinyMatrix, SummarizedExperiment, tibble, tidyr Suggests: testthat (>= 3.0.0), BiocStyle, knitr License: LGPL-3 MD5sum: 8c50d4cb3b2d4526273de6a95a91e736 NeedsCompilation: no Package: cytofQC Version: 2.0.0 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License: GPL-3 MD5sum: 0d49296af4acbb83b792f7158b7cc1c8 NeedsCompilation: yes Package: cytolib Version: 2.24.0 Depends: R (>= 3.4) Imports: RProtoBufLib LinkingTo: BH(>= 1.84.0.0), RProtoBufLib(>= 2.13.1),Rhdf5lib Suggests: knitr, rmarkdown License_restricts_use: no MD5sum: 9d09a83be03419372003aaaf007318c7 NeedsCompilation: yes Package: cytomapper Version: 1.24.0 Depends: R (>= 4.0), EBImage, SingleCellExperiment, methods Imports: SpatialExperiment, S4Vectors, BiocParallel, HDF5Array, DelayedArray, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5, nnls Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest License: GPL (>= 2) MD5sum: 931b06258061e0afbc7562877f0a36b4 NeedsCompilation: no Package: CytoMDS Version: 1.8.0 Depends: R (>= 4.4), Biobase Imports: methods, stats, rlang, pracma, withr, flowCore, reshape2, ggplot2, ggrepel, ggforce, patchwork, transport, smacof, BiocParallel, CytoPipeline Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, HDCytoData License: GPL-3 MD5sum: 953400fd4280e589de9c624d1a79f2d3 NeedsCompilation: no Package: cytoMEM Version: 1.16.0 Depends: R (>= 4.2.0) Imports: gplots, tools, flowCore, grDevices, stats, utils, matrixStats, methods Suggests: knitr, rmarkdown License: GPL-3 MD5sum: bdf7086b65890966bed7359aea6e302e NeedsCompilation: no Package: CytoML Version: 2.24.0 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: 255f7d4f54386a9a995dd707794b1eb5 NeedsCompilation: yes Package: CytoPipeline Version: 1.12.0 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: 6f5314aa4c6b137afec77bdcb9caf13b NeedsCompilation: no Package: CytoPipelineGUI Version: 1.10.0 Depends: R (>= 4.4), CytoPipeline (>= 1.9.3) Imports: shiny, plotly, ggplot2, flowCore Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, patchwork License: GPL-3 MD5sum: ee4cc68dd42a02fb98c84f1128394e6b NeedsCompilation: no Package: cytoviewer Version: 1.12.0 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: d6f011976b7ca0e3ba938f8cad838f57 NeedsCompilation: no Package: dada2 Version: 1.40.0 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: 7b804276d0f5e33f11d07da065b5a716 NeedsCompilation: yes Package: dagLogo Version: 1.50.0 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: a0c0c1972cb71562ac2bc712690b9c88 NeedsCompilation: no Package: daMA Version: 1.84.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: 507bb284ad6a03a04dc64adae0b2812f NeedsCompilation: no Package: DAMEfinder Version: 1.24.0 Depends: R (>= 4.0) Imports: stats, Seqinfo, GenomicRanges, IRanges, S4Vectors, readr, SummarizedExperiment, GenomicAlignments, stringr, plyr, VariantAnnotation, parallel, ggplot2, Rsamtools, BiocGenerics, methods, limma, bumphunter, Biostrings, reshape2, cowplot, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 1faf0822ea1f53dba654b7c4d9f09fe6 NeedsCompilation: no Package: damidBind Version: 1.0.0 Depends: R (>= 4.4.0) Imports: ggplot2, ggrepel, dplyr, tibble, stringr, tools, fs, rlang, BiocParallel, AnnotationHub, DBI, ensembldb, GenomeInfoDb, IRanges, GenomicRanges, S4Vectors, rtracklayer, limma, NOISeq, BioVenn, clusterProfiler, enrichplot, forcats, scales, colorspace, ggnewscale, methods, stats, igvShiny, shiny, DT, dbscan, circlize, ComplexHeatmap, patchwork, splines Suggests: testthat, curl, knitr, htmltools, rmarkdown, BiocStyle, bookdown, org.Dm.eg.db License: GPL-3 MD5sum: ecf1e4977db4dd1b375e37dc32aefa7a NeedsCompilation: no Package: DaMiRseq Version: 2.24.0 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, Seqinfo Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 7e7b0f543c2cc32087df78d446768e48 NeedsCompilation: no Package: Damsel Version: 1.8.0 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: f5d8a5163ab5175ecab227862b4794d9 NeedsCompilation: no Package: dandelionR Version: 1.4.0 Depends: R (>= 4.4.0) Imports: BiocGenerics, bluster, destiny, igraph, MASS, Matrix, methods, miloR, purrr, rlang, S4Vectors, SingleCellExperiment, spam, stats, SummarizedExperiment, uwot, RANN Suggests: BiocStyle, fields, knitr, rmarkdown, RColorBrewer, scater, scRepertoire, DelayedMatrixStats, slingshot, testthat License: MIT + file LICENSE MD5sum: 843f67deba87b47d57b396565c6e2c3a NeedsCompilation: no Package: DAPAR Version: 1.44.0 Depends: R (>= 4.5.0) Imports: Biobase, MSnbase, DAPARdata (>= 1.30.0), utils, plotly, 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: d3b8d1a3142534f962242b2d31cbab6b NeedsCompilation: no Package: dar Version: 1.8.0 Depends: R (>= 4.5.0) Imports: checkmate, cli, ComplexHeatmap, crayon, dplyr, generics, ggplot2, glue, gplots, heatmaply, magrittr, methods, mia, phyloseq, purrr, readr, rlang (>= 0.4.11), scales, stringr, tibble, tidyr, UpSetR Suggests: ALDEx2, ANCOMBC, apeglm, ashr, Biobase, corncob, covr, DESeq2, devtools, furrr, future, knitr, lefser, limma, maaslin3, microbiome, rmarkdown, roxygen2, roxyglobals, roxytest, rstatix, SummarizedExperiment, TreeSummarizedExperiment, testthat (>= 3.0.0), GenomeInfoDb, withr License: MIT + file LICENSE MD5sum: c5aabd8bb011b717990b2af26666f585 NeedsCompilation: no Package: DART Version: 1.60.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: be33557b33dd85832f8a757c253a778f NeedsCompilation: no Package: dcanr Version: 1.28.0 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: d414aa625910047d9655306c6141f02b NeedsCompilation: no Package: DCATS Version: 1.10.0 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: d1f81ca2ae40bf674d4f88824fe9646f NeedsCompilation: no Package: dcGSA Version: 1.40.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: 15c61af7c12412b20a7a93005d76c217 NeedsCompilation: no Package: ddCt Version: 1.68.0 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: b9c4d5535908511e0dcd167072ec573d NeedsCompilation: no Package: ddPCRclust Version: 1.32.0 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: 2f94e317632f625fa1e8169dd7ce45ff NeedsCompilation: no Package: dearseq Version: 1.24.0 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: 99e6c77c5eff3ac656e7b587cf6d0609 NeedsCompilation: no Package: debrowser Version: 1.40.0 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: b2f5c5dfbf4529f338c8aa01ede41a0b NeedsCompilation: no Package: decemedip Version: 1.0.0 Depends: R (>= 4.5.0) Imports: bayesplot, cowplot, dplyr, GenomicRanges, ggplot2, IRanges, magrittr, Matrix, matrixStats, MEDIPS, methods, purrr, R.utils, Rcpp, RcppParallel, rlang, rstan, rstantools, S4Vectors, SummarizedExperiment 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: knitr, rmarkdown, BiocStyle, devtools, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 65f8ba45592881abd0092db841c8a722 NeedsCompilation: yes Package: DECIPHER Version: 3.8.0 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: 40aaeca3798283036f7f12cf590e49aa NeedsCompilation: yes Package: decompTumor2Sig Version: 2.28.0 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, Seqinfo, readxl Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: f5568150b8b9ca02368683bb01fffb64 NeedsCompilation: no Package: decontam Version: 1.32.0 Depends: R (>= 3.4.1), methods (>= 3.4.1) Imports: ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats Suggests: BiocStyle, knitr, rmarkdown, phyloseq License: Artistic-2.0 MD5sum: 9f22c39f6511d259ebd714d0b60f5c8e NeedsCompilation: no Package: decontX Version: 1.10.0 Depends: R (>= 4.3.0) Imports: celda, dbscan, DelayedArray, ggplot2, Matrix (>= 1.5.3), MCMCprecision, methods, patchwork, plyr, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.2.0), S4Vectors, scater, Seurat, SingleCellExperiment, SummarizedExperiment, withr LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, dplyr, knitr, rmarkdown, scran, SingleCellMultiModal, TENxPBMCData, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 704fff1e76c120855b90f91f0dba58d6 NeedsCompilation: yes Package: DeconvoBuddies Version: 1.4.0 Depends: R (>= 4.4.0) Imports: AnnotationHub, BiocFileCache, BiocParallel, DelayedMatrixStats, dplyr, ExperimentHub, ggplot2, ggrepel, graphics, grDevices, MatrixGenerics, methods, purrr, rafalib, reshape2, S4Vectors, scran, SingleCellExperiment, spatialLIBD, stats, stringr, SummarizedExperiment, tibble, utils Suggests: Biobase, BiocStyle, covr, HDF5Array, knitr, RColorBrewer, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyr, tidyverse License: Artistic-2.0 MD5sum: 679fb630f6004d398be96ef9925d2713 NeedsCompilation: no Package: deconvR Version: 1.18.0 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 (>= 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apeglm, mosdef, org.Hs.eg.db, topGO, clusterProfiler, DEFormats, ExperimentHub, scater, muscat, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 36b44b1fc067c415a1d5d630e048124c NeedsCompilation: no Package: DeepPINCS Version: 1.20.0 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: 34996bde47e0ed2ebdd0cf79429eabd0 NeedsCompilation: no Package: deepSNV Version: 1.58.0 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: 4007812c210451e645b5b9c7894c7b95 NeedsCompilation: yes Package: DeepTarget Version: 1.6.0 Depends: R (>= 4.2.0) Imports: fgsea, ggplot2, stringr, ggpubr, BiocParallel, pROC, stats, grDevices, 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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: eef998e06eb573e4cf202ed3d43164f3 NeedsCompilation: yes Package: DEGraph Version: 1.64.0 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: ce6c6daa192747790edc100f66454164 NeedsCompilation: no Package: DEGreport Version: 1.48.0 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: 07223a5066fad78f6763e98fc42a7ca1 NeedsCompilation: no Package: DEGseq Version: 1.66.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: 1e2176eb8d8960bb55b96adf5eadc04d NeedsCompilation: yes Package: DelayedArray Version: 0.38.0 Depends: R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>= 0.53.3), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.47.6), IRanges (>= 2.17.3), S4Arrays (>= 1.9.3), SparseArray (>= 1.7.5) Imports: stats Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit License: Artistic-2.0 MD5sum: 675c200193e3822f04b50da20b008051 NeedsCompilation: no Package: DelayedDataFrame 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RcppArmadillo Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply, airway, glmGamPoi, BiocManager License: LGPL (>= 3) MD5sum: 26b00545424cfbe4102f3a6593173427 NeedsCompilation: yes Package: DEsingle Version: 1.32.0 Depends: R (>= 3.4.0) Imports: stats, Matrix (>= 1.2-14), MASS (>= 7.3-45), VGAM (>= 1.0-2), bbmle (>= 1.0.18), gamlss (>= 4.4-0), maxLik (>= 1.3-4), pscl (>= 1.4.9), BiocParallel (>= 1.12.0), Suggests: knitr, rmarkdown, SingleCellExperiment License: GPL-2 MD5sum: 90479ff176c3f5e237f820018d08082a NeedsCompilation: no Package: DESpace Version: 2.4.0 Depends: R (>= 4.5.0) Imports: edgeR, limma, dplyr, stats, Matrix, SpatialExperiment, ggplot2, SummarizedExperiment, S4Vectors, BiocGenerics, data.table, assertthat, terra, sf, spatstat.explore, spatstat.geom, ggforce, ggnewscale, patchwork, BiocParallel, methods, scales, scuttle Suggests: knitr, rmarkdown, testthat, BiocStyle, muSpaData, ExperimentHub, 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scran, grDevices, stats, methods Suggests: testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools, ggplot2, gridExtra, ggpubr, grid, magick, hexbin License: GPL-3 MD5sum: dfeeee6f78a4987e2834f21ddda27233 NeedsCompilation: no Package: dinoR Version: 1.8.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, edgeR, GenomicRanges, ggplot2, Matrix, methods, rlang, stats, stringr, tibble, tidyr, tidyselect Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a7cf1504cc377a7df7d2e169d8b4d661 NeedsCompilation: no Package: dir.expiry Version: 1.20.0 Imports: utils, filelock Suggests: rmarkdown, knitr, testthat, BiocStyle License: GPL-3 MD5sum: d3eabae4bbbf1a529cb640f8899d7682 NeedsCompilation: no Package: DirichletMultinomial Version: 1.54.0 Depends: S4Vectors, IRanges Imports: stats4, methods, BiocGenerics Suggests: lattice, parallel, MASS, RColorBrewer, DT, knitr, rmarkdown, BiocStyle License: LGPL-3 MD5sum: 8fea79ff4405924f38d2e4ea446df3e5 NeedsCompilation: yes Package: discordant Version: 1.36.0 Depends: R (>= 4.1.0) Imports: Rcpp, Biobase, stats, biwt, gtools, MASS, tools, dplyr, methods, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 2781c254be0983475916ca32b5c8c9ac NeedsCompilation: yes Package: DiscoRhythm Version: 1.28.0 Depends: R (>= 3.6.0) Imports: matrixTests, matrixStats, MetaCycle (>= 1.2.0), data.table, ggplot2, ggExtra, dplyr, broom, shiny, shinyBS, shinycssloaders, shinydashboard, shinyjs, BiocStyle, rmarkdown, knitr, kableExtra, magick, VennDiagram, UpSetR, heatmaply, viridis, plotly, DT, gridExtra, methods, stats, SummarizedExperiment, BiocGenerics, S4Vectors, zip, reshape2 Suggests: testthat License: GPL-3 MD5sum: fcc16a0f4c283a5be7c0fb8e32be2b14 NeedsCompilation: no Package: distinct Version: 1.24.0 Depends: R (>= 4.3) Imports: Rcpp, stats, SummarizedExperiment, SingleCellExperiment, methods, Matrix, foreach, parallel, doParallel, doRNG, ggplot2, limma, scater LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, UpSetR, BiocStyle License: GPL (>= 3) MD5sum: 5179229b4ad5553dd14fcb9678d8ac17 NeedsCompilation: yes Package: dittoSeq Version: 1.24.0 Depends: ggplot2 Imports: methods, colorspace (>= 1.4), gridExtra, cowplot, reshape2, pheatmap, grDevices, ggrepel, ggridges, stats, utils, SummarizedExperiment, SingleCellExperiment, S4Vectors Suggests: plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR, ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran, MASS License: MIT + file LICENSE MD5sum: a7fe796362f414d36df945ae6e01226e NeedsCompilation: no Package: divergence Version: 1.28.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown License: GPL-2 MD5sum: bb9dc39fa10534f0ae3484d88f66418e NeedsCompilation: no Package: dks Version: 1.58.0 Depends: R (>= 2.8) Imports: cubature License: GPL MD5sum: 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knitr, rmarkdown, GO.db, KEGGREST, testthat, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, BiocStyle, RUnit License: Artistic-2.0 MD5sum: 1d77fa01395087370b654523c595b28a NeedsCompilation: no Package: DMRcaller Version: 1.44.0 Depends: R (>= 3.5), GenomicRanges, IRanges, S4Vectors Imports: parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils, Rsamtools, GenomicRanges, GenomicAlignments, Biostrings, BSgenome, BiocManager, S4Vectors, IRanges, InteractionSet, stringr, inflection, BiocParallel, Seqinfo, GenomeInfoDb Suggests: knitr, RUnit, BiocGenerics, rmarkdown, bookdown, BiocStyle, betareg, rtracklayer, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 MD5sum: 8bccb96316585f7f67ad62e67ccec0cc NeedsCompilation: no Package: DMRcate Version: 3.7.0 Depends: R (>= 4.3.0) Imports: AnnotationHub, ExperimentHub, bsseq, Seqinfo, limma, edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment, biomaRt, grDevices Suggests: knitr, RUnit, BiocGenerics, GenomeInfoDb, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest License: file LICENSE MD5sum: 9ab603c5063e77d175fc42b1bdaf4d2f NeedsCompilation: no Package: DMRScan Version: 1.34.0 Depends: R (>= 3.6.0) Imports: Matrix, MASS, RcppRoll,GenomicRanges, IRanges, Seqinfo, methods, mvtnorm, stats, parallel Suggests: knitr, rmarkdown, BiocStyle, BiocManager License: GPL-3 MD5sum: ed201b14a89018c8bcb15939d772e20c NeedsCompilation: no Package: dmrseq Version: 1.32.0 Depends: R (>= 3.5), bsseq Imports: GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer, bumphunter, DelayedMatrixStats (>= 1.1.13), matrixStats, BiocParallel, outliers, methods, locfit, IRanges, grDevices, graphics, stats, utils, annotatr, AnnotationHub, rtracklayer, Seqinfo, splines Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 6565f8811b5d093f7a958f7b19489f1b NeedsCompilation: no Package: DNABarcodeCompatibility Version: 1.28.0 Depends: R (>= 3.6.0) Imports: dplyr, tidyr, numbers, purrr, stringr, stats, utils, methods, Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: file LICENSE MD5sum: 178448e411dc400a7868c4f487d19af2 NeedsCompilation: yes Package: DNABarcodes Version: 1.42.0 Depends: Matrix, parallel Imports: Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, BiocStyle, rmarkdown License: GPL-2 MD5sum: cf888f8302ca3506c5c791dbbdd875d1 NeedsCompilation: yes Package: DNAcopy Version: 1.86.0 License: GPL (>= 2) MD5sum: e4ca419dc4356852a35d8a590d6a2ab3 NeedsCompilation: yes Package: DNAcycP2 Version: 1.3.0 Depends: R (>= 4.4.0) Imports: basilisk, reticulate Suggests: knitr, rmarkdown, BiocGenerics, RUnit, tinytest, BiocStyle, Biostrings License: Artistic-2.0 MD5sum: 27e50d877bcfcefc56a533f9e332e42d NeedsCompilation: no Package: DNAfusion Version: 1.14.0 Depends: R (>= 4.4.0) Imports: GenomicRanges, IRanges, Rsamtools, GenomicAlignments, BiocBaseUtils, S4Vectors, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocGenerics Suggests: knitr, rmarkdown, testthat, sessioninfo, BiocStyle License: GPL-3 MD5sum: 6bb3ae0859f679e4e20ba2b7fbed3784 NeedsCompilation: no Package: DNAshapeR Version: 1.40.0 Depends: R (>= 3.4), GenomicRanges Imports: Rcpp (>= 0.12.1), Biostrings, fields LinkingTo: Rcpp Suggests: AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret License: GPL-2 MD5sum: fbbeff6f9781f5e9bd44a06463589616 NeedsCompilation: yes Package: DNEA Version: 1.2.0 Depends: R (>= 4.2) Imports: BiocParallel, dplyr, gdata, glasso, igraph (>= 2.0.3), janitor, Matrix, methods, netgsa, stats, stringr, utils, SummarizedExperiment Suggests: BiocStyle, ggplot2, Hmisc, kableExtra, knitr, pheatmap, rmarkdown, testthat (>= 3.0.0), withr, airway Enhances: massdataset License: MIT + file LICENSE MD5sum: bb3f8a96b9da2e9396788796cac22fcb NeedsCompilation: no Package: dominatR Version: 1.0.0 Depends: R (>= 4.5.0) Imports: scales, ggnewscale, SummarizedExperiment, dplyr, rlang, ggforce, geomtextpath, ggplot2 Suggests: BiocStyle, airway, tidyverse, knitr, rmarkdown, testthat (>= 3.0.0), dominatRData License: MIT + file LICENSE MD5sum: e348cb53e00db1731415c8ff63157be2 NeedsCompilation: no Package: DominoEffect Version: 1.32.0 Depends: R(>= 3.5) Imports: biomaRt, data.table, utils, stats, Biostrings, pwalign, SummarizedExperiment, VariantAnnotation, AnnotationDbi, Seqinfo, IRanges, GenomicRanges, methods Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: 9f4b3c25191566334e4f08d4d6f9edc2 NeedsCompilation: no Package: dominoSignal Version: 1.6.0 Depends: R(>= 4.2.0), Imports: biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid, igraph, Matrix, methods, plyr, stats, utils, magrittr, purrr, dplyr Suggests: knitr, patchwork, rmarkdown, Seurat, testthat, formatR, BiocFileCache, SingleCellExperiment License: GPL-3 | file LICENSE MD5sum: 0f1c9603d929de910cc7de1e73de9cb8 NeedsCompilation: no Package: doppelgangR Version: 1.40.0 Depends: R (>= 3.5.0), Biobase, BiocParallel Imports: sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat License: GPL (>= 2.0) MD5sum: d75594dc78db88ef15e5bb604e364598 NeedsCompilation: no Package: Doscheda Version: 1.34.0 Depends: R (>= 3.4) Imports: methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy, limma, stringr, ggplot2, graphics, grDevices, calibrate, corrgram, gridExtra, DT, shiny, shinydashboard, readxl, prodlim, matrixStats Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 8e79d3f9cd03a0cb9bf92f239c06ac81 NeedsCompilation: no Package: DOSE Version: 4.6.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, enrichit (>= 0.0.4), ggplot2, GOSemSim (>= 2.37.1), methods, reshape2, utils, yulab.utils (> 0.2.2) Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, memoise, org.Hs.eg.db, rmarkdown, testthat License: Artistic-2.0 MD5sum: 43e362425afb697b04fef6e58d59608e NeedsCompilation: no Package: doseR Version: 1.28.0 Depends: R (>= 3.6) Imports: edgeR, methods, stats, graphics, matrixStats, mclust, lme4, RUnit, SummarizedExperiment, digest, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: GPL MD5sum: 0db6535b4d9d2ff6da71a403c7537e04 NeedsCompilation: no Package: DOtools Version: 1.2.0 Depends: R (>= 4.5.0) Imports: Seurat (>= 5.2.0), SeuratObject (>= 5.1.0), ggplot2 (>= 3.5.0), ggpubr (>= 0.6.0), ggtext (>= 0.1.2), ggalluvial (>= 0.12.5), ggrastr (>= 1.0.2), tidyverse (>= 2.0.0), reshape2 (>= 1.4.4), dplyr (>= 1.1.4), tidyr (>= 1.3.1), rstatix (>= 0.7.2), cowplot (>= 1.1.3), reticulate (>= 1.41.0.1), zellkonverter (>= 1.16.0), 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BiocGenerics, BiocParallel, Biostrings, BSgenome, txdbmaker, DESeq2, GenomicAlignments, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicRanges, IRanges, rtracklayer, Rsamtools, S4Vectors, SummarizedExperiment LinkingTo: Rcpp Suggests: BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, org.Hs.eg.db, curl, pasillaBamSubset, BiocStyle, biomaRt, DHARMa, eulerr, ggplot2, ggsignif, knitr, rmarkdown, testthat, withr, magick License: MIT + file LICENSE MD5sum: 4f0cb85f1c5972184ae8e9f04c5b5fe1 NeedsCompilation: yes Package: doubletrouble Version: 1.12.0 Depends: R (>= 4.2.0) Imports: syntenet, GenomicRanges, Biostrings, mclust, MSA2dist (>= 1.1.5), ggplot2, rlang, stats, utils, AnnotationDbi, GenomicFeatures Suggests: txdbmaker, testthat (>= 3.0.0), knitr, feature, patchwork, BiocStyle, rmarkdown, covr, sessioninfo License: GPL-3 MD5sum: f2ada0824b8efff20dba0ef7bc4a765f NeedsCompilation: no Package: drawProteins Version: 1.32.0 Depends: R (>= 4.0) Imports: ggplot2, httr, dplyr, readr, tidyr Suggests: covr, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 802a866a03ea99e5c6d42dc8c565a48e NeedsCompilation: no Package: dreamlet Version: 1.10.0 Depends: R (>= 4.3.0), variancePartition (>= 1.36.1), SingleCellExperiment, ggplot2 Imports: edgeR, SummarizedExperiment, DelayedMatrixStats, sparseMatrixStats, MatrixGenerics, Matrix, methods, purrr, GSEABase, data.table, zenith (>= 1.1.2), mashr (>= 0.2.52), ashr, dplyr, reformulas, BiocParallel, ggbeeswarm, S4Vectors, IRanges, irlba, limma, metafor, remaCor, broom, tidyr, rlang, BiocGenerics, S4Arrays, SparseArray, DelayedArray, gtools, reshape2, ggrepel, scattermore, Rcpp, MASS, Rdpack, utils, stats LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub, RUnit, muscData, scater, scuttle License: Artistic-2.0 MD5sum: d5fa7050630da9d8bd93d6a2c71d7ad3 NeedsCompilation: yes Package: DRIMSeq Version: 1.40.0 Depends: R (>= 3.4.0) Imports: utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2 Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: 32823a796ab253b860abb5446971e3cd NeedsCompilation: no Package: DriverNet Version: 1.52.0 Depends: R (>= 2.10), methods License: GPL-3 MD5sum: 8b42e31704b98e51495c93eab3b140db NeedsCompilation: no Package: DropletUtils Version: 1.32.0 Depends: SingleCellExperiment Imports: utils, stats, methods, Matrix, Rcpp, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiocParallel, SparseArray (>= 1.5.18), DelayedArray (>= 0.31.9), DelayedMatrixStats, HDF5Array, rhdf5, edgeR, R.utils, dqrng, beachmat, scuttle (>= 1.21.4) LinkingTo: Rcpp, beachmat, assorthead, Rhdf5lib, BH, dqrng, scuttle Suggests: testthat, knitr, BiocStyle, rmarkdown, jsonlite, DropletTestFiles License: GPL-3 MD5sum: 2266316518ea1ffd5fba046c18ace1a0 NeedsCompilation: yes Package: drugfindR Version: 1.0.0 Depends: R (>= 4.5.0) Imports: tibble, rlang, dplyr, purrr, readr, stringr, stats, lifecycle, S4Vectors, httr2, curl, DFplyr Suggests: AnnotationDbi, BiocStyle, biocthis, codemetar, devtools, here, httptest2, jsonlite, knitr, rmarkdown, testthat (>= 3.0.0), tidyverse, usethis License: GPL-3 + file LICENSE MD5sum: a74a0f49bb661bea119d51745d0f2453 NeedsCompilation: no Package: drugTargetInteractions Version: 1.20.0 Depends: methods, R (>= 4.1) Imports: utils, RSQLite, UniProt.ws, biomaRt,ensembldb, BiocFileCache,dplyr,rappdirs, AnnotationFilter, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT, EnsDb.Hsapiens.v86 License: Artistic-2.0 MD5sum: 6141c58a1d25164f6ed56b91371b3251 NeedsCompilation: no Package: DrugVsDisease Version: 2.54.0 Depends: R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery, DrugVsDiseasedata, cMap2data, qvalue Imports: annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit, 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parallel, patchwork, scales, segclust2d, stats, stringr, txdbmaker, utils, uuid, zoo Suggests: Rsamtools, BiocManager, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 143dda723e4fb45a55d3225b3d148fa8 NeedsCompilation: no Package: EMDomics Version: 2.42.0 Depends: R (>= 3.2.1) Imports: emdist, BiocParallel, matrixStats, ggplot2, CDFt, preprocessCore Suggests: knitr License: MIT + file LICENSE MD5sum: bca7ab5f10856b2b85ee33c53bcd6c02 NeedsCompilation: no Package: EmpiricalBrownsMethod Version: 1.40.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 8e91cbc6ba5ffa443341db0bee25bd38 NeedsCompilation: no Package: EnhancedVolcano Version: 1.30.0 Depends: ggplot2, ggrepel Imports: methods, scales, grid, grDevices Suggests: RUnit, ggrastr, BiocGenerics, knitr, DESeq2, pasilla, airway, org.Hs.eg.db, gridExtra, magrittr, rmarkdown License: GPL-3 MD5sum: 72465f61b39151c7a65f312b27c8eafe NeedsCompilation: no Package: 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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: e73454fc84d57226fdb7771f1156a717 NeedsCompilation: no Package: epidecodeR Version: 1.20.0 Depends: R (>= 3.1.0) Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 92e464ff81af883d9179d4ac1f41b782 NeedsCompilation: no Package: EpiDISH Version: 2.28.0 Depends: R (>= 4.1) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix, genefilter Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat License: GPL-2 MD5sum: 7c83ae95cc73e9acce0203d34d436b88 NeedsCompilation: no Package: epigenomix Version: 1.52.0 Depends: R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment Imports: BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray License: LGPL-3 MD5sum: cc2a4c371475f9cc9eca0bce2df976ad NeedsCompilation: no Package: epigraHMM Version: 1.20.0 Depends: R (>= 3.5.0) Imports: Rcpp, magrittr, data.table, SummarizedExperiment, methods, Seqinfo, GenomicRanges, rtracklayer, IRanges, Rsamtools, bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5, Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap, grDevices LinkingTo: Rcpp, RcppArmadillo, Rhdf5lib Suggests: GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, gcapc, genomationData License: MIT + file LICENSE MD5sum: d1e0750241ae012db048d8886ed7ab40 NeedsCompilation: yes Package: EpiMix Version: 1.14.0 Depends: R (>= 4.2.0), EpiMix.data (>= 1.2.2) Imports: AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table, doParallel, doSNOW, downloader, dplyr, ELMER.data, ExperimentHub, foreach, Seqinfo, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, impute, IRanges, limma, methods, parallel, plyr, progress, R.matlab, RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, utils Suggests: BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter License: GPL-3 MD5sum: 9cfc3c222802f2bc91b77f7514793d17 NeedsCompilation: no Package: epimutacions Version: 1.15.0 Depends: R (>= 4.3.0), epimutacionsData Imports: minfi, bumphunter, isotree, robustbase, ggplot2, GenomicRanges, GenomicFeatures, IRanges, 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4.5.0), GenomicRanges Imports: magrittr, dplyr, ggplot2, tibble, org.Hs.eg.db, org.Mm.eg.db, reshape2, tidyr, methods, jsonlite, karyoploteR, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, bamsignals, DESeq2, GenomeInfoDb, graphics, stringr, yaml Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: LGPL-3 MD5sum: 34ce6c65d2532c5cef43a5a2cd28dd0e NeedsCompilation: no Package: fRagmentomics Version: 1.0.0 Depends: R (>= 4.1.0) Imports: Biostrings, data.table, dplyr, future, future.apply, GenomeInfoDb, GenomicRanges, ggh4x, ggplot2, ggseqlogo, IRanges, purrr, RColorBrewer, readr, rlang, Rsamtools (>= 2.4.0), S4Vectors, VariantAnnotation, scales, stringr, tibble, tidyr Suggests: ragg, covr, testthat (>= 3.0.0), knitr, rmarkdown (>= 1.14), BiocStyle License: GPL (>= 3) MD5sum: 973020b18ec0178dedbab6e08791b8fa NeedsCompilation: no Package: fraq Version: 1.0.0 Depends: R (>= 4.5.0) Imports: Rcpp, ShortRead, Biostrings, RcppParallel, edlibR, stringfish LinkingTo: Rcpp, RcppParallel, edlibR Suggests: knitr, rmarkdown, BiocStyle, processx License: GPL-3 MD5sum: 431880acc8814bfeb04ab25b63d9af6c NeedsCompilation: yes Package: FRASER Version: 2.8.0 Depends: BiocParallel, Rsamtools, SummarizedExperiment Imports: AnnotationDbi, BBmisc, Biobase, BiocGenerics, biomaRt, BSgenome, cowplot, data.table, DelayedArray (>= 0.5.11), DelayedMatrixStats, extraDistr, generics, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges, grDevices, ggplot2, ggrepel, HDF5Array, matrixStats, methods, OUTRIDER, pcaMethods, pheatmap, plotly, PRROC, RColorBrewer, rhdf5, Rsubread, R.utils, S4Vectors, stats, tibble, tools, txdbmaker, utils, VGAM, RMTstat, pracma LinkingTo: RcppArmadillo, Rcpp Suggests: magick, BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, rtracklayer, SGSeq, ggbio, biovizBase, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.UCSC.hg19 License: file LICENSE MD5sum: a78189f958f643914d9de3ea4861e4e3 NeedsCompilation: yes Package: frenchFISH Version: 1.24.0 Imports: utils, MCMCpack, NHPoisson Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 501c9056283312a1eb4dc40c636e90fe NeedsCompilation: no Package: FRGEpistasis Version: 1.48.0 Depends: R (>= 2.15), MASS, fda, methods, stats Imports: utils License: GPL-2 MD5sum: 032a57241c889e238f7c52b2ad721caf NeedsCompilation: no Package: frma Version: 1.64.0 Depends: R (>= 2.10.0), Biobase (>= 2.6.0) Imports: Biobase, MASS, DBI, affy, methods, oligo, oligoClasses, preprocessCore, utils, BiocGenerics Suggests: hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: a9431ae031197d9000b837e0cd2a4ffb NeedsCompilation: no Package: frmaTools Version: 1.64.0 Depends: R (>= 2.10.0), affy Imports: Biobase, DBI, methods, preprocessCore, stats, utils Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: 499a83203db685e8b5848d79ea814fbd NeedsCompilation: no Package: funOmics Version: 1.6.0 Depends: R (>= 4.4.0), NMF Imports: NMF, pathifier, stats, KEGGREST, AnnotationDbi, org.Hs.eg.db, dplyr, stringr Suggests: knitr, rmarkdown, testthat (>= 3.0.0), MultiAssayExperiment, SummarizedExperiment, airway License: MIT + file LICENSE MD5sum: 8e3fa525c2ce1a546384dacde8149bad NeedsCompilation: no Package: funtooNorm Version: 1.36.0 Depends: R(>= 3.4) Imports: pls, matrixStats, minfi, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb, grDevices, graphics, stats Suggests: prettydoc, minfiData, knitr, rmarkdown License: GPL-3 MD5sum: 6c105f610c2c0b81598f9b7980fc2340 NeedsCompilation: no Package: FuseSOM Version: 1.14.0 Depends: R (>= 4.2.0) Imports: psych, FCPS, analogue, coop, pheatmap, ggplotify, fastcluster, fpc, ggplot2, stringr, ggpubr, proxy, cluster, diptest, methods, SummarizedExperiment, stats, S4Vectors LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown, SingleCellExperiment License: GPL-2 MD5sum: 113fef0579fe37a493526b9f34b7564e NeedsCompilation: yes Package: G4SNVHunter Version: 1.4.0 Depends: R (>= 4.3.0) Imports: Biostrings, stats, GenomicRanges, IRanges, Rcpp, RcppRoll, data.table, Seqinfo, S4Vectors, ggplot2, cowplot, progress, ggseqlogo, viridis, ggpointdensity, tools, SummarizedExperiment, VariantAnnotation, dplyr, openxlsx, tidyr, magrittr, ggdensity LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown, BiocManager, BSgenome.Hsapiens.UCSC.hg19, DT, rtracklayer, testthat (>= 3.0.0), RBGL License: MIT + file LICENSE MD5sum: bd171a94d29c96e8e1a9605e52fb6d4a NeedsCompilation: yes Package: GA4GHclient Version: 1.36.0 Depends: R (>= 3.5.0), S4Vectors Imports: BiocGenerics, Biostrings, dplyr, Seqinfo, GenomicRanges, httr, IRanges, jsonlite, methods, VariantAnnotation Suggests: GenomeInfoDb, AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 9ccc29252b78293e83383d77d4f722f7 NeedsCompilation: no Package: GA4GHshiny Version: 1.34.0 Depends: GA4GHclient Imports: AnnotationDbi, BiocGenerics, dplyr, DT, Seqinfo, 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: 0244d4a588c8671d9ffe3a8e987464e1 NeedsCompilation: no Package: gaga Version: 2.58.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: parallel License: GPL (>= 2) MD5sum: aa0d071b4aa451660d18a20352832a46 NeedsCompilation: yes Package: gage Version: 2.62.0 Depends: R (>= 3.5.0) Imports: graph, KEGGREST, AnnotationDbi, GO.db Suggests: pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma License: GPL (>= 2.0) MD5sum: 298d7dbebe2c13bac69da57628f9a90c NeedsCompilation: no Package: GAprediction Version: 1.38.0 Depends: R (>= 3.3) Imports: glmnet, stats, utils, Matrix Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 995bb53c57ec5eac477d9e92d56de2f5 NeedsCompilation: no Package: garfield Version: 1.40.0 Suggests: knitr License: GPL-3 MD5sum: df304cc8993496f4b44d05020afa4fea NeedsCompilation: yes Package: GARS Version: 1.32.0 Depends: R (>= 3.5), ggplot2, cluster Imports: DaMiRseq, MLSeq, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 2dc862ef544692ab913aab68a97674c3 NeedsCompilation: no Package: GateFinder Version: 1.32.0 Imports: splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: fa8a7f0ee2ba27d964dc578e6bb9f5d9 NeedsCompilation: no Package: gatom Version: 1.10.0 Depends: R (>= 4.3.0) Imports: data.table, igraph, BioNet, plyr, methods, XML, sna, intergraph, network, ggnetwork, scales, grid, ggplot2, mwcsr, htmlwidgets, htmltools, shinyCyJS (>= 1.0.0) Suggests: testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi, org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils License: MIT + file LICENCE MD5sum: 396a5774050447c9c59283dfd12df49b NeedsCompilation: no Package: GBScleanR Version: 2.6.0 Depends: SeqArray Imports: stats, utils, methods, ggplot2, tidyr, expm, Rcpp, RcppParallel, gdsfmt LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 15f9188bc27c140af5b1293f4327ccbf NeedsCompilation: yes Package: gcapc Version: 1.36.0 Depends: R (>= 3.4) Imports: BiocGenerics, Seqinfo, S4Vectors, IRanges, Biostrings, BSgenome, GenomicRanges, Rsamtools, GenomicAlignments, matrixStats, MASS, splines, grDevices, graphics, stats, methods Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: GPL-3 MD5sum: ac9f5d6690f1c514604583c3d1c8bf5a NeedsCompilation: no Package: gcatest Version: 2.12.0 Depends: R (>= 4.0) Imports: methods, lfa Suggests: knitr, rmarkdown, ggplot2, testthat, BEDMatrix, genio License: GPL (>= 3) MD5sum: 89e6693ed49a01355a12cdf2225599dc NeedsCompilation: no Package: GCPtools Version: 1.2.0 Depends: R (>= 4.5.0) Imports: AnVILBase, BiocBaseUtils, dplyr, httr, rlang, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 905a652e611e7b2a0468c64c9f1fc69d NeedsCompilation: no Package: gCrisprTools Version: 2.18.0 Depends: R (>= 4.1) Imports: Biobase, limma, ggplot2, SummarizedExperiment, grid, rmarkdown, grDevices, graphics, methods, ComplexHeatmap, stats, utils, parallel, MatrixGenerics, methods Suggests: edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea License: Artistic-2.0 MD5sum: e2fb6ad83a58d49c53a7981c9bad511d NeedsCompilation: no Package: gcrma Version: 2.84.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector, Biostrings (>= 2.11.32), splines, BiocManager Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL MD5sum: 1a59ee8280329c2a91b541cba8260049 NeedsCompilation: yes Package: GDCRNATools Version: 1.32.0 Depends: R (>= 3.5.0) Imports: shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel Suggests: knitr, testthat, prettydoc, rmarkdown License: Artistic-2.0 MD5sum: 69f2aaae2720ea28327c0df71c03caaa NeedsCompilation: no Package: gDNAx Version: 1.10.0 Depends: R (>= 4.3) Imports: methods, BiocGenerics, BiocParallel, matrixStats, Biostrings, S4Vectors, IRanges, Seqinfo, GenomeInfoDb, GenomicRanges, GenomicFiles, GenomicAlignments, GenomicFeatures, Rsamtools, AnnotationHub, RColorBrewer, AnnotationDbi, bitops, plotrix, SummarizedExperiment, grDevices, graphics, stats, utils, cli Suggests: BiocStyle, knitr, rmarkdown, RUnit, TxDb.Hsapiens.UCSC.hg38.knownGene, gDNAinRNAseqData License: Artistic-2.0 MD5sum: f389988024826ab6c3b1268f634b5e39 NeedsCompilation: no Package: gDR Version: 1.10.0 Depends: R (>= 4.2), gDRcore (>= 1.7.1), gDRimport (>= 1.7.1), gDRutils (>= 1.7.1) Suggests: BiocStyle, BumpyMatrix, futile.logger, gDRstyle (>= 1.7.1), gDRtestData (>= 1.7.1), kableExtra, knitr, markdown, purrr, rmarkdown, SummarizedExperiment, testthat, yaml License: Artistic-2.0 MD5sum: d3dcce83808f36f138e3632c90c43b89 NeedsCompilation: no Package: gDRcore Version: 1.10.0 Depends: R (>= 4.2) Imports: BumpyMatrix, BiocParallel, checkmate, futile.logger, gDRutils (>= 1.7.1), MultiAssayExperiment, purrr, stringr, S4Vectors, SummarizedExperiment, data.table Suggests: BiocStyle, gDRstyle (>= 1.7.1), gDRimport (>= 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NeedsCompilation: no Package: gemini Version: 1.26.0 Depends: R (>= 4.1.0) Imports: dplyr, grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: c752df06e2269b4a359a069dd3ec6804 NeedsCompilation: no Package: gemma.R Version: 3.8.0 Imports: magrittr, glue, memoise, jsonlite, data.table, rlang, lubridate, utils, stringr, SummarizedExperiment, Biobase, tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat, digest, R.utils, kableExtra, base64enc Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, listviewer, shiny License: Apache License (>= 2) MD5sum: 1ae5adc85ab9c37327d175a730f8dd17 NeedsCompilation: no Package: genArise Version: 1.88.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: 5253d9749b7f17e69ae0e71e7f1c22bc NeedsCompilation: no Package: geneAttribution Version: 1.38.0 Imports: utils, GenomicRanges, org.Hs.eg.db, BiocGenerics, Seqinfo, GenomicFeatures, IRanges, rtracklayer Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: eec9891a3c9dce9504d95083d1863f09 NeedsCompilation: no Package: GeneBreak Version: 1.42.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: e0f3bc1939b88d993e096c889051ead5 NeedsCompilation: no Package: geneClassifiers Version: 1.36.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: 3ca4f403c73abefd8fe7e26514f1c4b3 NeedsCompilation: no Package: GeneExpressionSignature Version: 1.58.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: a61f4816e1d78307c4431a79ee8ad5bc NeedsCompilation: no Package: genefilter Version: 1.94.0 Imports: MatrixGenerics (>= 1.11.1), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 MD5sum: 1cdcf9a109b9d4987433d424ac1dac91 NeedsCompilation: yes Package: genefu Version: 2.44.0 Depends: R (>= 4.1), survcomp, biomaRt, iC10, AIMS Imports: amap, impute, mclust, limma, graphics, stats, utils, iC10TrainingData Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown License: Artistic-2.0 MD5sum: 14febc206786579d80368d80bf60b71e NeedsCompilation: no Package: GeneGA Version: 1.62.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: 071e581b603081b21b6a5f28854359dd NeedsCompilation: no Package: 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BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: 4c41eab53ba9af78c678b1ec7fb47810 NeedsCompilation: no Package: geneplotter Version: 1.90.0 Depends: R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate Imports: AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db, BiocStyle, knitr License: Artistic-2.0 MD5sum: 45339619dad75ed1706406ed542c6811 NeedsCompilation: no Package: geneRecommender Version: 1.84.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: 642d0318b2d5e5d5b70c79def27228e7 NeedsCompilation: no Package: GeneRegionScan Version: 1.68.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) MD5sum: 7a3d049433cd1ef5b1fce35a4ad4c3fe NeedsCompilation: no Package: geneRxCluster Version: 1.48.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 48b653f86a6ce01c6ae8cc522e8e5f67 NeedsCompilation: yes Package: GeneSelectMMD Version: 2.56.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: d15b7b8c7609205de9227083cd9e2382 NeedsCompilation: yes Package: GENESIS Version: 2.42.0 Imports: Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, GenomeInfoDb License: GPL-3 MD5sum: 42efc64adce290400bb1899890edd68b NeedsCompilation: yes Package: GeneStructureTools Version: 1.32.0 Imports: Biostrings,GenomicRanges,IRanges,data.table,plyr,stringdist,stringr,S4Vectors,BSgenome.Mmusculus.UCSC.mm10,stats,utils,Gviz,rtracklayer,methods Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: ebf308cd1150ff044b8ece1fe5e8137a NeedsCompilation: no Package: geNetClassifier Version: 1.52.0 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: d33369bdaa1b7ec0d54d2670357f59f5 NeedsCompilation: no Package: GeneticsPed Version: 1.74.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: f4a31e93c12f51ec7e1c3792fe86d6b9 NeedsCompilation: yes Package: GeneTonic Version: 3.6.0 Depends: R (>= 4.0.0) Imports: AnnotationDbi, backbone, bs4Dash (>= 2.0.0), circlize, colorspace, colourpicker, ComplexHeatmap, ComplexUpset, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce, ggplot2 (>= 3.5.0), ggrepel, ggridges, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, mosdef (>= 1.1.0), plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinyAce, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tippy, tools, utils, viridis, visNetwork Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 57cc054485193348256c59acfe55ab48 NeedsCompilation: no Package: geneXtendeR Version: 1.37.0 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: d22dbceda39fecb2a662556414f89abc NeedsCompilation: yes Package: GENIE3 Version: 1.34.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle License: GPL (>= 2) MD5sum: df9dfbdf635c6f13b0fb5ba43271e43c NeedsCompilation: yes Package: genomation Version: 1.44.0 Depends: R (>= 3.5.0), grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, Seqinfo, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 6b74657b214f3f6778fb73b1b53bf705 NeedsCompilation: yes Package: GenomAutomorphism Version: 1.14.0 Depends: R (>= 4.4.0), Imports: Biostrings, BiocGenerics, BiocParallel, Seqinfo, GenomicRanges, IRanges, matrixStats, XVector, dplyr, data.table, parallel, doParallel, foreach, methods, S4Vectors, stats, numbers, utils Suggests: spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr License: Artistic-2.0 MD5sum: 3e98576d4b0226d3d737483fe840254f NeedsCompilation: no Package: GenomeInfoDb Version: 1.48.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.47.6), IRanges (>= 2.41.1), Seqinfo (>= 0.99.2) Imports: stats, utils, UCSC.utils Suggests: GenomeInfoDbData, R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: a2a1c79535a195453468244d738b17da NeedsCompilation: no Package: genomeIntervals Version: 1.68.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: Seqinfo, GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: 6a9938fed0984cf7bc899b6b8d95cfde NeedsCompilation: no Package: genomes Version: 3.42.0 Depends: readr, curl License: GPL-3 MD5sum: 91fd237cd40901e828d3768cfb820ab8 NeedsCompilation: no Package: GenomicAlignments Version: 1.48.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.47.6), IRanges (>= 2.23.9), Seqinfo, GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel, cigarillo (>= 0.99.2) LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, knitr, BiocStyle License: Artistic-2.0 MD5sum: 37dc95156b10e04873ca4d08f13802ce NeedsCompilation: yes Package: GenomicCoordinates Version: 1.0.0 Depends: R (>= 4.5), GenomicRanges, IRanges Imports: S4Vectors, Seqinfo, InteractionSet, methods, plyranges, plyinteractions Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 561554911cb723d8a0941ad585f5f04d NeedsCompilation: no Package: GenomicDataCommons Version: 1.36.0 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: e3e31cca4bcc20811e9068d3fd5e83e2 NeedsCompilation: no Package: GenomicDistributions Version: 1.20.0 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: d71982156610ad09208f5cc62566ef9b NeedsCompilation: no Package: GenomicFeatures Version: 1.64.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.51.2), S4Vectors (>= 0.47.6), IRanges (>= 2.37.1), Seqinfo (>= 0.99.2), GenomicRanges (>= 1.61.1), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, DBI, XVector, Biostrings (>= 2.77.2), rtracklayer (>= 1.69.1) LinkingTo: S4Vectors, IRanges Suggests: GenomeInfoDb, txdbmaker, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown License: Artistic-2.0 MD5sum: 4e4c38905ba534adbb5ee3e55fdd1e19 NeedsCompilation: yes Package: GenomicFiles Version: 1.48.0 Depends: BiocGenerics, BiocParallel, GenomicRanges, MatrixGenerics, methods, Rsamtools (>= 2.25.1), rtracklayer (>= 1.69.1), SummarizedExperiment (>= 1.39.1) Imports: BiocBaseUtils, GenomeInfoDb (>= 1.45.7), GenomicAlignments (>= 1.45.1), IRanges, S4Vectors, Seqinfo, VariantAnnotation (>= 1.55.1) Suggests: BiocStyle, Biostrings, deepSNV, genefilter, Homo.sapiens, knitr, RNAseqData.HNRNPC.bam.chr14, RUnit, snpStats License: Artistic-2.0 MD5sum: ddd5c8b57e0e858a864e2053375fb008 NeedsCompilation: no Package: genomicInstability Version: 1.18.0 Depends: R (>= 4.1.0), checkmate Imports: mixtools, SummarizedExperiment Suggests: SingleCellExperiment, ExperimentHub, pROC License: file LICENSE MD5sum: fe32fd0045c1e4fc77bed353687dc69b NeedsCompilation: no Package: GenomicInteractionNodes Version: 1.16.0 Depends: R (>= 4.2.0), stats Imports: AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, Seqinfo, methods, IRanges, RBGL, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: file LICENSE MD5sum: 4dbe58cd747b660c511a7ba244401f5a NeedsCompilation: no Package: GenomicInteractions Version: 1.46.0 Depends: R (>= 3.5), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, Seqinfo, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: ce156a817a7c8b47d92b7bd1ead99232 NeedsCompilation: no Package: GenomicOZone Version: 1.26.0 Depends: R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2 Imports: grDevices, stats, utils, plyr, gridExtra, lsr, parallel, ggbio, S4Vectors, IRanges, Seqinfo, Rdpack Suggests: readxl, GEOquery, knitr, rmarkdown License: LGPL (>= 3) MD5sum: 0a9ab9405490baac38722aca6e89c327 NeedsCompilation: no Package: GenomicPlot Version: 1.10.0 Depends: R (>= 4.4.0), GenomicRanges (>= 1.46.1) Imports: methods, Rsamtools, parallel, tidyr, rtracklayer (>= 1.54.0), plyranges (>= 1.14.0), cowplot (>= 1.1.1), VennDiagram, ggplotify, Seqinfo, IRanges, ComplexHeatmap, RCAS (>= 1.20.0), scales (>= 1.2.0), GenomicAlignments (>= 1.30.0), edgeR, circlize, viridis, ggsignif (>= 0.6.3), ggsci (>= 2.9), ggpubr, grDevices, graphics, stats, utils, GenomicFeatures, genomation (>= 1.36.0), txdbmaker, ggplot2 (>= 3.3.5), BiocGenerics, dplyr, grid, GenomeInfoDb Suggests: knitr, rmarkdown, R.utils, Biobase, BiocStyle, testthat, AnnotationDbi License: GPL-2 MD5sum: b32c9204d8f95090c9004a223c6c0056 NeedsCompilation: no Package: GenomicRanges Version: 1.64.0 Depends: R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.45.2), IRanges (>= 2.43.6), Seqinfo (>= 0.99.3) Imports: utils, stats Suggests: GenomeInfoDb, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.77.2), SummarizedExperiment (>= 1.39.1), Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, UCSC.utils, txdbmaker, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart51, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 16b687fa031d965176f4e50532fef0a1 NeedsCompilation: no Package: GenomicScores Version: 2.24.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache, IRanges (>= 2.3.23), Biostrings, Seqinfo, GenomeInfoDb (>= 1.45.5), AnnotationHub, rhdf5, DelayedArray, HDF5Array Suggests: RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard, BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38, MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v4.0.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: a7907b25565bea5eac9c85b33a342e88 NeedsCompilation: no Package: GenomicSuperSignature Version: 1.20.0 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: a710c6656fb87162560d6ef2caf3b7db NeedsCompilation: no Package: GenomicTuples Version: 1.46.0 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), Seqinfo, S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, covr, GenomicAlignments, Biostrings, GenomeInfoDb License: Artistic-2.0 MD5sum: bc0d1977bf1677b720b625b4b2a082c2 NeedsCompilation: yes Package: GenProSeq Version: 1.16.0 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: 9f9fdb72c8b8127b6959f6465f59e74a NeedsCompilation: no Package: GenVisR Version: 1.44.0 Depends: R (>= 3.3.0), methods Imports: AnnotationDbi, biomaRt (>= 2.45.8), BiocGenerics, Biostrings, DBI, GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, viridis, data.table, BSgenome, Seqinfo, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 + file LICENSE MD5sum: e34b943be7e8a0c29768bc69fdd47ae2 NeedsCompilation: no Package: GeoDiff Version: 1.18.0 Depends: R (>= 4.1.0), Biobase Imports: Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods, graphics, stats, testthat, GeomxTools, NanoStringNCTools LinkingTo: Rcpp, RcppArmadillo, roptim Suggests: knitr, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: 5236bfd9a01318aad6381ba26a11d4e0 NeedsCompilation: yes Package: GEOfastq Version: 1.20.0 Imports: xml2, rvest, stringr, RCurl, doParallel, foreach, plyr Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 8e3944dc802b3f3ba582c4068b87dd67 NeedsCompilation: no Package: GEOmetadb Version: 1.74.0 Depends: R.utils,RSQLite Suggests: knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud License: Artistic-2.0 MD5sum: 6874df852cf7c7fd16e98f0ca697c6ca NeedsCompilation: no Package: geomeTriD Version: 1.6.0 Depends: R (>= 4.4.0) Imports: aricode, BiocGenerics, Biostrings, clue, cluster, dbscan, future.apply, Seqinfo, GenomicRanges, graphics, grDevices, grid, htmlwidgets, igraph, InteractionSet, IRanges, MASS, Matrix, methods, plotrix, progressr, RANN, rgl, rjson, S4Vectors, scales, stats, trackViewer Suggests: RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, manipulateWidget, shiny, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 52768ef2fb4cbd4d455a11b4fce57ec8 NeedsCompilation: no Package: GeomxTools Version: 3.16.0 Depends: R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors Imports: BiocGenerics, rjson, readxl, EnvStats, reshape2, methods, utils, stats, data.table, lmerTest, dplyr, stringr, grDevices, graphics, GGally, rlang, ggplot2, SeuratObject Suggests: rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork License: MIT MD5sum: c9aa1ef52b288bbcbfbb1ced34f4fa29 NeedsCompilation: no Package: GEOquery Version: 2.80.0 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, 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tibble, tidyselect, tidyr, yaml Suggests: airway, knitr, DESeq2, rmarkdown, stringr, testthat (>= 3.0.0) License: CC0 MD5sum: 9fb0e322053c2be0b841ce9e0e07dfda NeedsCompilation: no Package: gg4way Version: 1.10.0 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: 11ba137da14e60d8d1ecea73f20e2fd5 NeedsCompilation: no Package: ggbio Version: 1.60.0 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), Seqinfo, GenomeInfoDb (>= 1.45.5), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1), GenomicAlignments (>= 1.45.1), BSgenome (>= 1.77.1), VariantAnnotation (>= 1.55.1), rtracklayer (>= 1.69.1), GenomicFeatures (>= 1.61.4), OrganismDbi, ensembldb (>= 2.33.1), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: f94990df68acf0f1435f71ba03176975 NeedsCompilation: no Package: ggcyto Version: 1.40.0 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: 32ac87dd51d76a7c19f6ab5050c2cc8f NeedsCompilation: no Package: ggkegg Version: 1.10.0 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: a6ed0fcd05bbfa97720a6b8ac55cc184 NeedsCompilation: no Package: ggmanh Version: 1.16.0 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: 5b5da1cde85353e5ef8d1357c4eb33cc NeedsCompilation: no Package: ggmsa Version: 1.18.0 Depends: R (>= 4.1.0) Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot, RColorBrewer, ggfun (>= 0.2.0), ggforce, dplyr, R4RNA, grDevices, seqmagick, grid, methods, ggtree (>= 1.17.1) Suggests: ggtreeExtra, ape, cowplot, knitr, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, statebins, prettydoc, testthat (>= 3.0.0), yulab.utils License: 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NeedsCompilation: yes Package: ggseqalign Version: 1.6.0 Depends: R (>= 4.4.0) Imports: pwalign, dplyr, ggplot2 Suggests: Biostrings, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 57e573d5165eb0cd9eb962e03f90de71 NeedsCompilation: no Package: ggspavis Version: 1.18.0 Depends: ggplot2 Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, ggrepel, RColorBrewer, scales, grDevices, methods, stats Suggests: BiocStyle, rmarkdown, knitr, OSTA.data, VisiumIO, arrow, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork License: MIT + file LICENSE MD5sum: de685f82354cfc459a20157e37f81a32 NeedsCompilation: no Package: ggtree Version: 4.2.0 Depends: R (>= 4.2.0) Imports: ape, aplot, cli, dplyr, ggfun (>= 0.1.7), ggiraph (>= 0.9.1), ggplot2 (>= 4.0.0), grid, magrittr, methods, purrr, rlang, scales, stats, tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0), utils, yulab.utils (>= 0.2.3) Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, igraph, testthat, tibble, glue, Biostrings License: Artistic-2.0 MD5sum: caa3e4092ae8102e642df8d3fef6282a NeedsCompilation: no Package: ggtreeDendro Version: 1.14.0 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: 6e5a32ac07ad654b99d3885e31b21520 NeedsCompilation: no Package: ggtreeExtra Version: 1.22.0 Imports: ggplot2 (>= 4.0.0), utils, rlang, ggnewscale, stats, ggtree, tidytree (>= 0.3.9), cli, magrittr, yulab.utils Suggests: treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown, testthat (>= 3.0.0), pillar License: GPL (>= 3) MD5sum: 833d79a29dfed3696c95721510ba7952 NeedsCompilation: no Package: ggtreeSpace Version: 1.8.0 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: a3a698e7d56ac1bbfd374cb39bc6dff4 NeedsCompilation: no Package: GIGSEA Version: 1.30.0 Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils Suggests: knitr, rmarkdown License: LGPL-3 MD5sum: fa7951aed448d48237ea08a6f8921139 NeedsCompilation: no Package: ginmappeR Version: 1.8.0 Imports: KEGGREST, UniProt.ws, XML, rentrez, httr, utils, memoise, cachem, jsonlite, rvest Suggests: RUnit, BiocGenerics, markdown, knitr License: GPL-3 + file LICENSE MD5sum: cae958e85ac325fffac0c75fe10dbacf NeedsCompilation: no Package: gINTomics Version: 1.8.0 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: 98c654f74d30644cd48e9fc2cff15b73 NeedsCompilation: no Package: GLAD Version: 2.76.0 Depends: R (>= 2.10) Imports: aws License: GPL-2 MD5sum: 8830caa320ffb3665e824a2f8c1ad9ca NeedsCompilation: yes Package: GladiaTOX Version: 1.28.0 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: 905791afdad9468187eec34daa296ed2 NeedsCompilation: no Package: Glimma Version: 2.21.0 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: a8e42c888602e732c127a20b46ff2184 NeedsCompilation: no Package: glmGamPoi Version: 1.24.0 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: 8734a0f6d8e3e0393e253ce866324561 NeedsCompilation: yes Package: glmSparseNet Version: 1.30.0 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: 97fe2b842dfb9e322df6161017b4f13f NeedsCompilation: no Package: GlobalAncova Version: 4.30.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: 37e825e3623ee89a579cd93497bba1ce NeedsCompilation: yes Package: globalSeq Version: 1.40.0 Depends: R (>= 3.0.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 MD5sum: 6770d3c78577731e5a62b4cf40fd36eb NeedsCompilation: no Package: globaltest Version: 5.66.0 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: d27ea2e53c307d32b6104cedd5cd1426 NeedsCompilation: no Package: GloScope Version: 2.2.0 Depends: R (>= 4.4.0) Imports: utils, stats, MASS, mclust, ggplot2, RANN, FNN, BiocParallel, mvnfast, SingleCellExperiment, rlang, RColorBrewer, pheatmap, vegan, cluster, boot, permute Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown, zellkonverter License: Artistic-2.0 MD5sum: fe8a054c4a9ae6e32c58e02b0a4fee95 NeedsCompilation: no Package: glycoTraitR Version: 1.0.0 Depends: R (>= 4.5.0) Imports: igraph, SummarizedExperiment, pbapply, car, ggplot2, rlang Suggests: knitr, BiocStyle, rmarkdown, markdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: c3561b7ca0fe6afdfee103f278602705 NeedsCompilation: no Package: gmapR Version: 1.54.0 Depends: R (>= 2.15.0), methods, Seqinfo, GenomicRanges (>= 1.61.1), 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: GenomeInfoDb, 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: f9f78f90d80ae7ac7720982cdfce8bff NeedsCompilation: yes Package: GmicR Version: 1.26.0 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: 13cd3cf043dfc9226e72d2c505827988 NeedsCompilation: no Package: gmoviz Version: 1.24.0 Depends: circlize, GenomicRanges, graphics, R (>= 4.0) Imports: grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics, Biostrings, Seqinfo, methods, GenomicAlignments, GenomicFeatures, IRanges, rtracklayer, pracma, colorspace, S4Vectors Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager, GenomeInfoDb License: GPL-3 MD5sum: efaa2ecb5b759e4c983ae6bdc929f0ec NeedsCompilation: no Package: GMRP Version: 1.40.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: 9089b074760fd36be70b343fde8b90d3 NeedsCompilation: no Package: GNET2 Version: 1.27.0 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: 8c6a4f7a88c7d56a2a9b97d69431668c NeedsCompilation: yes Package: GNOSIS Version: 1.10.0 Depends: R (>= 4.3.0), shiny, 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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: c71766b029ea50d401e3dad5dea262e3 NeedsCompilation: no Package: GOfan Version: 1.0.0 Depends: R (>= 4.5.0), ggplot2 Imports: AnnotationDbi, grid, grDevices, GO.db, igraph, methods, plotly, rlang, stats, scales, vctrs Suggests: BiocStyle, knitr, rmarkdown, testthat, org.Dr.eg.db License: GPL-3 MD5sum: eb994ff3496d5ba6c0b5e1e912d72dfa NeedsCompilation: no Package: GOfuncR Version: 1.31.0 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: ccf0d9e507d98865c59ea05aaf35b485 NeedsCompilation: yes Package: GOpro Version: 1.38.0 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: 5165aaff07ba07682409cef2d9dea23f NeedsCompilation: yes Package: goProfiles Version: 1.74.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: e8c28eb5ecd8a296ecbe9d0a8455d9bc NeedsCompilation: no Package: GOSemSim Version: 2.38.0 Depends: R (>= 4.2.0) Imports: AnnotationDbi, DBI, digest, GO.db, methods, rlang, stats, utils, yulab.utils (>= 0.2.3) LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, readr, rmarkdown, testthat, tidyr, tidyselect, ROCR License: Artistic-2.0 MD5sum: 0b3bfb14dacebec94ce07d0b06ec03f3 NeedsCompilation: yes Package: goseq Version: 1.64.0 Depends: R (>= 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License: Artistic-2.0 MD5sum: 78faa68dbf62b36e2c453f5767be03f3 NeedsCompilation: yes Package: GraphAlignment Version: 1.76.0 License: file LICENSE License_restricts_use: yes MD5sum: 1ffa4518263c81771456bf0af694e9ed NeedsCompilation: yes Package: GraphAT Version: 1.84.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL MD5sum: b517b66c34c07c6b32f4ce489f73ef4c NeedsCompilation: no Package: GraphExperiment Version: 1.0.0 Depends: SingleCellExperiment, igraph Imports: methods, SummarizedExperiment, BiocBaseUtils, S4Vectors Suggests: knitr, BiocStyle, testthat, rmarkdown, covr, sessioninfo License: GPL-3 MD5sum: 256b3e37e8fdb92d5f27ccdae009afab NeedsCompilation: no Package: graphite Version: 1.58.0 Depends: R (>= 4.2), methods Imports: AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats, utils, graphics, rlang, lifecycle, purrr, dir.expiry Suggests: checkmate, a4Preproc, ALL, BiocStyle, clipper, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) License: AGPL-3 MD5sum: 62fe4ba1dafebe6d92b89f8da116e581 NeedsCompilation: no Package: GRENITS Version: 1.64.0 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: b750290df4d5338b8b57b238f3b20f21 NeedsCompilation: yes Package: GreyListChIP Version: 1.44.0 Depends: R (>= 4.0), methods, GenomicRanges Imports: GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, Seqinfo, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, RUnit, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 3c0b9201ffc0de73e0a8c242421b1b2a NeedsCompilation: no Package: GRmetrics Version: 1.38.0 Depends: R (>= 4.0), SummarizedExperiment Imports: drc, plotly, ggplot2, S4Vectors, stats Suggests: knitr, rmarkdown, 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GOstats, RColorBrewer License: Artistic-2.0 MD5sum: 359e2387520ee44cb45f80a96186043a NeedsCompilation: no Package: GSEAmining Version: 1.22.0 Depends: R (>= 4.0) Imports: dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud, stringr, gridExtra, rlang, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat, tm License: GPL-3 | file LICENSE MD5sum: bb7c4cf44b2020e5c851b0e5bab513ac NeedsCompilation: no Package: gsean Version: 1.32.0 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi, knitr, plotly, WGCNA, rmarkdown License: Artistic-2.0 MD5sum: bc3a9e52d59d7f70f596408f2e3efe53 NeedsCompilation: yes Package: GSgalgoR Version: 1.22.0 Imports: cluster, doParallel, foreach, matchingR, nsga2R, survival, proxy, stats, methods, Suggests: knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp, Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP, iC10TrainingData, pamr, testthat License: 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knitr, rmarkdown, limma, RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, sva, TENxPBMCData, TENxVisiumData, scrapper, bluster, igraph, shiny, shinydashboard, ggplot2, data.table, plotly, future, promises, shinybusy, shinyjs License: Artistic-2.0 MD5sum: 07f5b609203fe20a84ccb96dee9180d6 NeedsCompilation: yes Package: gtrellis Version: 1.44.0 Depends: R (>= 4.0.0), 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: 5a139e7dc0af9920dc4dbbf815d25423 NeedsCompilation: no Package: GUIDEseq Version: 1.42.0 Depends: R (>= 3.5.0), GenomicRanges, BiocGenerics Imports: Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma,dplyr, 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ggplot2 (>= 3.5.0), reshape2 (>= 1.4.4), testthat (>= 3.0.0), BiocManager, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome License: GPL-3 | file LICENSE MD5sum: e1c9a225979955b51fe352bedee05d54 NeedsCompilation: yes Package: hicVennDiagram Version: 1.10.0 Depends: R (>= 4.3.0) Imports: Seqinfo, GenomicRanges, IRanges, InteractionSet, rtracklayer, ggplot2, ComplexUpset, reshape2, eulerr, S4Vectors, methods, utils, htmlwidgets, svglite Suggests: BiocStyle, knitr, rmarkdown, testthat, ChIPpeakAnno, grid, TxDb.Hsapiens.UCSC.hg38.knownGene License: GPL-3 MD5sum: 5851b009d40b1c1dc2c70107e482366e NeedsCompilation: no Package: hierGWAS Version: 1.42.0 Depends: R (>= 3.2.0) Imports: fastcluster,glmnet, fmsb Suggests: BiocGenerics, RUnit, MASS License: GPL-3 MD5sum: 20edcf2ab3ad9113f6152f5935970a60 NeedsCompilation: no Package: hierinf Version: 1.30.0 Depends: R (>= 3.6.0) Imports: fmsb, glmnet, methods, parallel, stats Suggests: knitr, MASS, testthat License: GPL-3 | file LICENSE MD5sum: 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BiocStyle, markdown, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, htmltools, edgeR License: MIT + file LICENSE MD5sum: c18fffb538b140d382d45c0ffd33eda0 NeedsCompilation: no Package: IdeoViz Version: 1.48.0 Depends: R (>= 3.5.0), Biobase, IRanges, GenomicRanges, RColorBrewer, rtracklayer, graphics, GenomeInfoDb License: GPL-2 MD5sum: c70708ba4e93d81bac7b665a4930bac5 NeedsCompilation: no Package: idiogram Version: 1.88.0 Depends: R (>= 2.10), methods, Biobase, annotate, plotrix Suggests: hu6800.db, hgu95av2.db, golubEsets License: GPL-2 MD5sum: 02237a71da3be80a34ff5e5d9817db33 NeedsCompilation: no Package: idpr Version: 1.22.0 Depends: R (>= 4.1.0) Imports: ggplot2 (>= 3.3.0), magrittr (>= 1.5), dplyr (>= 0.8.5), plyr (>= 1.8.6), jsonlite (>= 1.6.1), rlang (>= 0.4.6), Biostrings (>= 2.56.0), methods (>= 4.0.0) Suggests: knitr, rmarkdown, pwalign, msa, ape, testthat, seqinr License: LGPL (>= 3) MD5sum: 014496425562bbf2fe63946550780747 NeedsCompilation: no Package: 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Package: infercnv Version: 1.28.0 Depends: R(>= 4.0) Imports: graphics, grDevices, RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, phyclust, Matrix, fastcluster, parallelDist, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, digest, RANN, igraph, reshape2, rjags, fitdistrplus, future, foreach, doParallel, Seurat, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse Suggests: BiocStyle, knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 2a581b7d1b4b0f3fa043878b1e935a7e NeedsCompilation: no Package: infinityFlow Version: 1.22.0 Depends: R (>= 4.0.0), flowCore Imports: stats, grDevices, utils, graphics, pbapply, matlab, png, raster, grid, uwot, gtools, Biobase, generics, parallel, methods, xgboost (>= 3.0.0) Suggests: knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071 License: GPL-3 MD5sum: faa8e766fbeaf81a3fbb5e319a06ddc6 NeedsCompilation: no Package: Informeasure Version: 1.22.0 Depends: R (>= 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RcppEigen Suggests: BiocStyle, dplyr, DT, ExperimentHub, htmlTable, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 4bef4ebfb40fe430cac240cb12cbb4f8 NeedsCompilation: yes Package: metabomxtr Version: 1.46.0 Depends: methods,Biobase Imports: optimx, Formula, plyr, multtest, BiocParallel, ggplot2 Suggests: xtable, reshape2 License: GPL-2 MD5sum: 45f5cb5efc4f1237eef61617c00be075 NeedsCompilation: no Package: MetaboSignal Version: 1.42.0 Depends: R(>= 3.3) Imports: KEGGgraph, hpar, igraph, RCurl, 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: 2eac2d8d1cbe077089e7d232087b783b NeedsCompilation: no Package: metaCCA Version: 1.40.0 Suggests: knitr License: MIT + file LICENSE MD5sum: 5de7d87ac8bbbccafe06b3bc4dc4883d NeedsCompilation: no Package: MetaCyto Version: 1.34.0 Depends: R (>= 3.4) Imports: flowCore (>= 1.4),tidyr (>= 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ggupset, ggVennDiagram, kableExtra, knitr, pkgdown, svglite, testthat (>= 3.1.4) License: BSD_3_clause + file LICENSE MD5sum: a90bc6fbac81dcbab5db401ea3c652a2 NeedsCompilation: no Package: metaSeq Version: 1.52.0 Depends: R (>= 2.13.0), NOISeq, snow, Rcpp License: Artistic-2.0 MD5sum: 4cc390b6c390be4ec2b958086e9aca02 NeedsCompilation: no Package: metaseqR2 Version: 1.24.0 Depends: R (>= 4.0.0), DESeq2, limma, locfit, splines Imports: ABSSeq, Biobase, BiocGenerics, BiocParallel, biomaRt, Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter, Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, gplots, graphics, grDevices, harmonicmeanp, heatmaply, htmltools, httr, IRanges, jsonlite, lattice, log4r, magrittr, MASS, Matrix, methods, NBPSeq, pander, parallel, qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite, rtracklayer, S4Vectors, stats, stringr, SummarizedExperiment, survcomp, txdbmaker, utils, VennDiagram, vsn, yaml, zoo Suggests: BiocStyle, BiocManager, BSgenome, knitr, RMySQL, RUnit Enhances: TCC License: GPL (>= 3) MD5sum: 6e903be117a284b322ab266da86efcf7 NeedsCompilation: yes Package: MetCirc Version: 1.42.0 Depends: R (>= 4.4), amap (>= 0.8), circlize (>= 0.4.16), scales (>= 1.3.0), shiny (>= 1.8.1.1), Spectra (>= 1.15.3) Imports: ggplot2 (>= 3.5.1), MsCoreUtils (>= 1.17.0), S4Vectors (>= 0.43.1) Suggests: BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr (>= 1.48), testthat (>= 3.2.1.1) License: GPL (>= 3) MD5sum: 4be53ef2fac6ef589067cc021e881675 NeedsCompilation: no Package: methimpute Version: 1.34.0 Depends: R (>= 3.5.0), GenomicRanges, ggplot2 Imports: Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats, GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm, data.table LinkingTo: Rcpp Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: 9bbacd096a5bd272d0d8f9b7ab83becb NeedsCompilation: yes Package: methInheritSim Version: 1.34.0 Depends: R (>= 3.5.0) Imports: methylKit, GenomicRanges, Seqinfo, parallel, 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knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 8821ba3ed66a79ac61a4a4999708500a NeedsCompilation: no Package: MethTargetedNGS Version: 1.44.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign Imports: utils, graphics, stats License: Artistic-2.0 MD5sum: ab4a2ded31cb1ffe7c6914a28f0b962a NeedsCompilation: no Package: MethylAid Version: 1.46.0 Depends: R (>= 3.4) Imports: Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: b7c8d7565a174163ae1fee5c34d8ae0c NeedsCompilation: no Package: methylCC Version: 1.26.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: GPL-3 MD5sum: 0df9929c8ba336b7eb0e7c01fe9689dd NeedsCompilation: no Package: methylclock Version: 1.18.0 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: ea22f30f3b5464afd15139ed0b113649 NeedsCompilation: yes Package: methylGSA Version: 1.30.0 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: 63b3ba8fd39847e2e592bebe9dd612f5 NeedsCompilation: no Package: methyLImp2 Version: 1.8.0 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: 8d522f559937b960958ebed455271edb NeedsCompilation: no Package: methylInheritance Version: 1.36.0 Depends: R (>= 3.5) Imports: methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors, methods, parallel, ggplot2, gridExtra, rebus Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 4c22162897e37f655a03511b2e1244e1 NeedsCompilation: no Package: methylKit 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methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, Seqinfo, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) MD5sum: a60dcad30f872dd8545d3af561cf0afd NeedsCompilation: yes Package: methylscaper Version: 1.19.0 Depends: R (>= 4.4.0) Imports: shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings, pwalign, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, devtools, R.utils License: GPL-2 MD5sum: 88163af39a32e226d6a9d46baece9ad8 NeedsCompilation: no Package: MethylSeekR Version: 1.52.0 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), 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parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 MD5sum: a66c70db19a02af80935e261b01af202 NeedsCompilation: no Package: MetID Version: 1.30.0 Depends: R (>= 3.5) Imports: utils (>= 3.3.1), stats (>= 3.4.2), devtools (>= 1.13.0), stringr (>= 1.3.0), Matrix (>= 1.2-12), igraph (>= 1.2.1), ChemmineR (>= 2.30.2) Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) License: Artistic-2.0 MD5sum: 4c3c0a24e48eaf015d1ba215aec043b9 NeedsCompilation: no Package: MetMashR Version: 1.6.0 Depends: R (>= 4.3.0), struct Imports: dplyr, methods, httr, scales, ggthemes, utils, rlang, stats, ggplot2 Suggests: covr, httptest, knitr, rmarkdown, testthat (>= 3.0.0), rgoslin, DT, RSQLite, CompoundDb, BiocStyle, BiocFileCache, msPurity, rsvg, metabolomicsWorkbenchR, KEGGREST, plyr, magick, structToolbox, ggVennDiagram, patchwork, XML, GO.db, tidytext, tidyr, tidyselect, ComplexUpset, 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TreeSummarizedExperiment, utils, vegan Suggests: BiocStyle, knitr, philr, remotes, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: f4570766a390cae04d694762954859b4 NeedsCompilation: no Package: miaSim Version: 1.18.0 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: 17591eaf63ec92e62981891604a5c21e NeedsCompilation: no Package: miaTime Version: 1.2.0 Depends: R (>= 4.5.0), mia Imports: dplyr, methods, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tidyr, TreeSummarizedExperiment Suggests: BiocStyle, devtools, ggplot2, knitr, lubridate, miaViz, rmarkdown, scater, testthat, vegan License: Artistic-2.0 | file LICENSE MD5sum: 0aa362b11845f31f39548abdc8ee7c22 NeedsCompilation: no Package: miaViz Version: 1.20.0 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, patchwork, rlang, S4Vectors, scales, scater, SingleCellExperiment, stats, tibble, tidygraph, tidyr, tidytext, tidytree, viridis Suggests: beeswarm, BiocStyle, bluster, circlize, ComplexHeatmap, ggh4x, ggpubr, knitr, maaslin3, mediation, miaTime, patchwork, rmarkdown, rstatix, shadowtext, testthat, vegan, vipor License: Artistic-2.0 | file LICENSE MD5sum: 7563ccfaa6a40bd1bf8dee47fa04d663 NeedsCompilation: no Package: MiChip Version: 1.66.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: 563be243df5fa3f189aac94962c55707 NeedsCompilation: no Package: microbiome Version: 1.34.0 Depends: R (>= 3.6.0), phyloseq, ggplot2 Imports: Biostrings, compositions, dplyr, reshape2, Rtsne, 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withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager, rhdf5 License: GPL (>= 3.0) MD5sum: b444f9e50739bd1efb696686fb8b8028 NeedsCompilation: no Package: microRNA Version: 1.70.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: ccac39bcd10acf3c4094334b917fbb4a NeedsCompilation: yes Package: MICSQTL Version: 1.10.0 Depends: R (>= 4.3.0), SummarizedExperiment, stats Imports: TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2, ggpubr, ggridges, glue, S4Vectors, dirmult Suggests: testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle License: GPL-3 MD5sum: f8f414de62cb99cdf470414a3a45c8ae NeedsCompilation: no Package: midasHLA Version: 1.20.0 Depends: R (>= 4.1), MultiAssayExperiment (>= 1.8.3) Imports: assertthat (>= 0.2.0), broom (>= 0.5.1), dplyr (>= 0.8.0.1), formattable (>= 0.2.0.1), 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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: fda001fc0155c650c2985ab5062fa37e NeedsCompilation: yes Package: mimager Version: 1.36.0 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: ac52c5edfb83f36e2587c504439e84eb NeedsCompilation: no Package: mina Version: 1.20.0 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 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ggridges, Gviz, gwasrapidd, knitr, MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 79e824da9bfdca3cb19dff9f3a5e2345 NeedsCompilation: yes Package: miRLAB Version: 1.42.0 Imports: methods, stats, utils, RCurl, httr, stringr, Hmisc, energy, entropy, gplots, glmnet, impute, limma, pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc, InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit,rmarkdown License: GPL (>= 2) MD5sum: 901848ec63032f4f6116e4f05b894e07 NeedsCompilation: no Package: miRNAmeConverter Version: 1.40.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 55406ddc82d2692e0b5aece0d99527a1 NeedsCompilation: no Package: miRNApath Version: 1.72.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: 99993a16e0778bcab2587daba351adf8 NeedsCompilation: no Package: miRNAtap Version: 1.46.0 Depends: R (>= 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9ea37fcb7164793bc925ec8f63427219 NeedsCompilation: yes Package: mirTarRnaSeq Version: 1.20.0 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: b13385d3600399c0b2d5e3c6c2419fb3 NeedsCompilation: no Package: missMethyl Version: 1.45.0 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomeInfoDb, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICv2manifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, 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MD5sum: f958317591ce28095623fb16a7446558 NeedsCompilation: no Package: mogsa Version: 1.46.0 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: c80fbc167ff68ffb8835eee23ee74dde NeedsCompilation: no Package: MoleculeExperiment Version: 1.12.0 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: 1b9f8b848ae27247eeca88d61a41c916 NeedsCompilation: no Package: MOMA Version: 1.23.0 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: 07cf68913e5578426c213263f2a1a374 NeedsCompilation: no Package: monaLisa Version: 1.18.0 Depends: R (>= 4.1) Imports: BiocGenerics, BiocParallel, Biostrings, BSgenome, circlize, ComplexHeatmap (>= 2.11.1), Seqinfo, GenomicRanges, cli, ggplot2 (>= 4.0.0), glmnet, grDevices, grid, IRanges, methods, rlang, RSQLite, stabs, stats, SummarizedExperiment, S4Vectors, TFBSTools, tidyr, tools, utils, XVector Suggests: BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, ggrepel, gridExtra, JASPAR2020, JASPAR2024, knitr, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL (>= 3) MD5sum: 635c2542ac6af92af88fa3494a4f91fe NeedsCompilation: no Package: monocle Version: 2.40.0 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: ed0dcfe116008d5edcfe457d1f5365b9 NeedsCompilation: yes Package: Moonlight2R Version: 1.10.0 Depends: R (>= 4.5), doParallel, foreach Imports: parmigene, randomForest, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, grDevices, graphics, GEOquery, stats, purrr, RISmed, grid, utils, ComplexHeatmap, GenomicRanges, dplyr, fuzzyjoin, rtracklayer, magrittr, qpdf, readr, seqminer, stringr, tibble, tidyHeatmap, tidyr, AnnotationHub, easyPubMed, org.Hs.eg.db, EpiMix, BiocGenerics, ggplot2, ExperimentHub, rlang, withr, data.table, fgsea Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), devtools, roxygen2, png License: GPL-3 MD5sum: cf496f59486944cb5626a0d4a1724098 NeedsCompilation: no Package: MoonlightR Version: 1.38.0 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: 4d445202ef34cecd97df7ce8f5c5f7e9 NeedsCompilation: no Package: mosaics Version: 2.50.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, Seqinfo, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: dbadab5e37eb60796da706f46bf8c806 NeedsCompilation: yes Package: mosbi Version: 1.17.0 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: a6bf1df7bcda5638fda67de833c62e24 NeedsCompilation: yes Package: MOSClip Version: 1.6.0 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: cb92f9eb0c9a632164d37cb2d329e664 NeedsCompilation: no Package: mosdef Version: 1.8.0 Depends: R (>= 4.4.0) Imports: DT, ggplot2, ggforce, ggrepel, graphics, grDevices, htmltools, methods, AnnotationDbi, topGO, GO.db, clusterProfiler, goseq, utils, RColorBrewer, rlang, DESeq2, scales, SummarizedExperiment, S4Vectors, stats Suggests: knitr, rmarkdown, macrophage, org.Hs.eg.db, GeneTonic, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene, BiocStyle License: MIT + file LICENSE MD5sum: 52379b66b0fbf27d9f5228c0ecadd8c8 NeedsCompilation: no Package: MOSim Version: 2.8.0 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: 27cd525f0a3e44cb392da4d3c61e1457 NeedsCompilation: yes Package: Motif2Site Version: 1.16.0 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: a8e9dd25e270c7e940092767e36c668e NeedsCompilation: no Package: motifcounter Version: 1.35.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: d9625af8429bd6166a51c882fbe0ace0 NeedsCompilation: yes Package: MotifDb Version: 1.54.0 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: ec12e429794141f16e3b025e92091226 NeedsCompilation: no Package: motifmatchr Version: 1.34.0 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, Seqinfo LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 + file LICENSE MD5sum: 42e200649693ab40511fc643e9dd4f9f NeedsCompilation: yes Package: MotifPeeker Version: 1.4.0 Depends: R (>= 4.6.0) Imports: BiocFileCache, BiocParallel, DT, ggplot2, plotly, universalmotif, GenomicRanges, IRanges, rtracklayer, tools, htmltools, rmarkdown, viridis, SummarizedExperiment, htmlwidgets, Rsamtools, GenomicAlignments, Seqinfo, Biostrings, BSgenome, memes, S4Vectors, dplyr, purrr, tidyr, heatmaply, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, downloadthis, knitr, markdown, methods, remotes, rworkflows, testthat (>= 3.0.0), withr, emoji, curl, jsonlite License: GPL (>= 3) MD5sum: 9d4708948c140bfd8d110430c0ebd299 NeedsCompilation: no Package: motifStack Version: 1.56.0 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: a9eabb46c820b508af5d11636d142294 NeedsCompilation: no Package: motifTestR Version: 1.8.0 Depends: Biostrings, GenomicRanges, ggplot2 (>= 4.0.0), R (>= 4.5.0), Imports: Seqinfo, graphics, harmonicmeanp, IRanges, matrixStats, methods, parallel, patchwork, rlang, S4Vectors, stats, universalmotif, Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, extraChIPs (>= 1.13.3), ggdendro, knitr, MASS, MotifDb, rmarkdown, rtracklayer, SimpleUpset, testthat (>= 3.0.0), VGAM License: GPL-3 MD5sum: 25e2d01a32f1ab35ee82d61aed212ed5 NeedsCompilation: no Package: MouseFM Version: 1.22.0 Depends: R (>= 4.0.0) Imports: httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales, gtools, tidyr, 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stringi, stringr, tibble, tidyr, utils LinkingTo: Rcpp, RcppThread Suggests: rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle License: GPL-3 + file LICENSE MD5sum: 310921e3474f7eb69d6ffefe38650eef NeedsCompilation: yes Package: MsBackendMassbank Version: 1.20.0 Depends: R (>= 4.0), Spectra (>= 1.21.5) Imports: BiocParallel, S4Vectors, IRanges, methods, ProtGenerics (>= 1.35.3), MsCoreUtils, DBI, utils Suggests: testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), RSQLite, rmarkdown License: Artistic-2.0 MD5sum: 915d454b5b207c724a5b8b01fc8bba8a NeedsCompilation: no Package: MsBackendMetaboLights Version: 1.6.0 Depends: R (>= 4.2.0), Spectra (>= 1.15.12) Imports: curl, ProtGenerics, BiocFileCache, S4Vectors, methods, progress, utils, MsCoreUtils (>= 1.23.8) Suggests: testthat, rmarkdown, mzR, knitr, BiocStyle License: Artistic-2.0 MD5sum: 7ed461d2254e80b5b4f35b5de6758203 NeedsCompilation: no Package: MsBackendMgf Version: 1.20.0 Depends: R (>= 4.0), Spectra (>= 1.5.14) 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ggbio, ggplot2, IRanges, parallel, plyr, Rsamtools, R.utils, stats, SummarizedExperiment, S4Vectors, utils Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-2 MD5sum: b204335238b021248bdb5e42bd55abae NeedsCompilation: no Package: msImpute Version: 1.22.0 Depends: R (>= 3.5.0) Imports: softImpute, methods, stats, graphics, pdist, reticulate, scran, data.table, FNN, matrixStats, limma, mvtnorm, tidyr, dplyr Suggests: BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD License: GPL (>= 2) MD5sum: 47b18d3bdf3fa325a52bb7657761626a NeedsCompilation: no Package: mslp Version: 1.14.0 Depends: R (>= 4.2.0) Imports: data.table (>= 1.13.0), doRNG, fmsb, foreach, magrittr, org.Hs.eg.db, pROC, randomForest, RankProd, stats, utils Suggests: BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2, tinytest License: GPL-3 MD5sum: 05ab28b74c7896de1a4a4184b021ccee NeedsCompilation: no Package: msmsEDA Version: 1.50.0 Depends: R (>= 3.0.1), MSnbase Imports: MASS, gplots, RColorBrewer 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30b639f6fef1a59081db11c65d77fcf5 NeedsCompilation: no Package: nempi Version: 1.20.0 Depends: R (>= 4.1), mnem Imports: e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats, epiNEM Suggests: knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle License: GPL-3 MD5sum: 792522e41eb09a9df492bfc6558f8bfa NeedsCompilation: no Package: NetActivity Version: 1.14.0 Depends: R (>= 4.1.0) Imports: airway, DelayedArray, DelayedMatrixStats, DESeq2, methods, methods, NetActivityData, SummarizedExperiment, utils Suggests: AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse License: MIT + file LICENSE MD5sum: 79dfa0f7962d71735e9bea2fe45e169c NeedsCompilation: no Package: netboost Version: 2.20.0 Depends: R (>= 4.0.0) Imports: Rcpp, RcppParallel, parallel, grDevices, graphics, stats, utils, dynamicTreeCut, WGCNA, impute, colorspace, methods, R.utils LinkingTo: Rcpp, RcppParallel Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 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rmarkdown, methods, minet, mclust, reshape2 Imports: ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer Suggests: knitr License: GPL (>= 2) MD5sum: ee0aea5d6356c21ee21be5b50135c3e9 NeedsCompilation: yes Package: NetSAM Version: 1.52.0 Depends: R (>= 3.0.0), seriation (>= 1.0-6), igraph (>= 2.0.0), tools (>= 3.0.0), WGCNA (>= 1.34.0), biomaRt (>= 2.18.0) Imports: methods, AnnotationDbi (>= 1.28.0), doParallel (>= 1.0.10), foreach (>= 1.4.0), survival (>= 2.37-7), GO.db (>= 2.10.0), R2HTML (>= 2.2.0), DBI (>= 0.5-1) Suggests: RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr, markdown License: LGPL MD5sum: 037c8e58d04786f5b94d995bbf2b87cd NeedsCompilation: no Package: netSmooth Version: 1.32.0 Depends: R (>= 3.5), scater (>= 1.15.11), clusterExperiment (>= 2.1.6) Imports: entropy, SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods, DelayedArray, HDF5Array (>= 1.15.13) Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot License: GPL-3 MD5sum: 3b1c571b2922de55cbef1c95d4c47b02 NeedsCompilation: no Package: NewWave Version: 1.21.0 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: fe25d4f4663de6b173bf0dcb77c9b003 NeedsCompilation: no Package: ngsReports Version: 2.14.0 Depends: R (>= 4.2.0), BiocGenerics, ggplot2 (>= 4.0.0), patchwork (>= 1.1.1), tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro, grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate, methods, plotly (>= 4.9.4), rlang, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo Suggests: BiocStyle, 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methods Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat License: MIT + file LICENSE MD5sum: 6d5cb0c0fb5295948d9c0427feb69602 NeedsCompilation: no Package: NOISeq Version: 2.56.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 MD5sum: ce024ddd917e125dca553569add28855 NeedsCompilation: no Package: nondetects Version: 2.42.0 Depends: R (>= 3.2), Biobase (>= 2.22.0) Imports: limma, mvtnorm, utils, methods, arm, HTqPCR (>= 1.16.0) Suggests: knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics (>= 0.8.0) License: GPL-3 MD5sum: 2edd952fd327ef643ca827ac249bc19e NeedsCompilation: no Package: NoRCE Version: 1.24.0 Depends: R (>= 4.4.0) Imports: KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,stringr,Seqinfo, S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl, dbplyr,utils,ggplot2,igraph,stats,reshape2,readr, GO.db, biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi,methods Suggests: knitr, TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene, testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown, TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene, org.Mm.eg.db, org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics, org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, markdown License: MIT + file LICENSE MD5sum: e3f48118416a91f74cda4469e364fdec NeedsCompilation: no Package: normalize450K Version: 1.40.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 24d141eebc50bd9968d5773f723a4c19 NeedsCompilation: no Package: NormalyzerDE Version: 1.30.0 Depends: R (>= 4.1.0) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, 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testthat License: MIT + file LICENSE MD5sum: 20977072563c87b46f7c34bfef64f65f NeedsCompilation: no Package: notameStats Version: 1.2.0 Depends: R (>= 4.5.0), SummarizedExperiment, Imports: BiocGenerics, BiocParallel, broom, dplyr, methods, notame, stats, tibble, tidyr, utils Suggests: BiocStyle, car, knitr, lmerTest, missForest, mixOmics, MuMIn, MUVR2, notameViz, PERMANOVA, PK, randomForest, rmcorr, testthat License: MIT + file LICENSE MD5sum: 10946d61fd83c2f14fc8381ae3cdd32c NeedsCompilation: no Package: notameViz Version: 1.2.0 Depends: R (>= 4.5.0), ggplot2, SummarizedExperiment Imports: BiocGenerics, cowplot, devEMF, dplyr, ggbeeswarm, ggdendro, ggrepel, grDevices, limma, methods, notame, pcaMethods, qpdf, Rtsne, scales, stringr, stats, tibble, tidyr, utils Suggests: batchCorr, BiocStyle, igraph, knitr, notameStats, testthat License: MIT + file LICENSE MD5sum: ab6179372497e4401e53a8ede6d39ccf NeedsCompilation: no Package: NPARC Version: 1.24.0 Depends: R (>= 4.0.0) Imports: dplyr, 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rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, GenomeInfoDbData License: MIT + file LICENSE MD5sum: 0041f5dff4429c64f68039c8920032e1 NeedsCompilation: yes Package: OrganismDbi Version: 1.54.0 Depends: R (>= 2.14.0), BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), Seqinfo, GenomicFeatures (>= 1.61.4) Imports: methods, utils, stats, DBI, BiocManager, Biobase, graph, RBGL, S4Vectors, IRanges, GenomicRanges (>= 1.61.1) Suggests: txdbmaker, GenomeInfoDbData, Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr License: Artistic-2.0 MD5sum: 12819856cfba802a85768635f4d51346 NeedsCompilation: no Package: orthogene Version: 1.18.0 Depends: R (>= 4.5.0) Imports: dplyr, methods, stats, utils, Matrix, jsonlite, homologene, gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr, patchwork, DelayedArray, repmis, ggtree, tools, magrittr Suggests: remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB License: GPL-3 MD5sum: fc1318a3e9302c8ac8b0852ff8f0b424 NeedsCompilation: no Package: orthos Version: 1.10.0 Depends: R (>= 4.3), SummarizedExperiment Imports: AnnotationHub, basilisk, BiocParallel, colorspace, cowplot, DelayedArray, dplyr, ExperimentHub, ggplot2 (>= 3.4.0), ggpubr, ggrepel, ggsci, grDevices, grid, HDF5Array, keras (>= 2.16.0), methods, orthosData, parallel, plyr, reticulate, rlang, S4Vectors, stats, tensorflow, tidyr Suggests: BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 5b833e1d0d846a15ec85f27fb3c38d02 NeedsCompilation: no Package: OSAT Version: 1.60.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 MD5sum: 5d7e6c7e4d9bdc4ffdee23afb98ad50f NeedsCompilation: no Package: Oscope Version: 1.42.0 Depends: EBSeq, cluster, testthat, BiocParallel Suggests: 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RcppArmadillo Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr, GenomeInfoDb, ggbio, biovizBase License: file LICENSE MD5sum: 3ac1d0583adda8b47d26b32a6c3248c1 NeedsCompilation: yes Package: OutSplice Version: 1.12.0 Depends: R(>= 4.3) Imports: AnnotationDbi (>= 1.60.0), GenomicRanges (>= 1.49.0), GenomicFeatures (>= 1.50.2), IRanges (>= 2.32.0), org.Hs.eg.db (>= 3.16.0), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.16.0), S4Vectors (>= 0.36.0) Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 25a265fed80e9ef4bd46806c59575df8 NeedsCompilation: no Package: OVESEG Version: 1.28.0 Depends: R (>= 3.6) Imports: stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales License: GPL-2 MD5sum: 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NeedsCompilation: no Package: PADOG Version: 1.54.0 Depends: R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase Imports: limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db, hgu133a.db, KEGGREST, nlme Suggests: doParallel, parallel License: GPL (>= 2) MD5sum: 45060f4dc5f7c35f5d33413e31b92ae5 NeedsCompilation: no Package: pageRank Version: 1.22.0 Depends: R (>= 4.0) Imports: GenomicRanges, igraph, motifmatchr, stats, utils, grDevices, graphics Suggests: bcellViper, BSgenome.Hsapiens.UCSC.hg19, JASPAR2018, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, TFBSTools, GenomicFeatures, annotate License: GPL-2 MD5sum: 90560baec0c9cd4b2db0797593b063f3 NeedsCompilation: no Package: PAIRADISE Version: 1.28.0 Depends: R (>= 3.6), nloptr Imports: SummarizedExperiment, S4Vectors, stats, methods, abind, BiocParallel Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 6932e8c59f7cb43192a50eae93e71114 NeedsCompilation: no Package: paircompviz Version: 1.50.0 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utils, xgboost License: GPL-2 MD5sum: 124ac5f0d408d96fa9a3113e541f779b NeedsCompilation: no Package: PathNet Version: 1.52.0 Suggests: PathNetData, RUnit, BiocGenerics License: GPL-3 MD5sum: b02488a354a81ad33c20c1f9fa0f4bce NeedsCompilation: no Package: PathoStat Version: 1.38.0 Depends: R (>= 3.5) Imports: limma, corpcor,matrixStats, reshape2, scales, ggplot2, rentrez, DT, tidyr, plyr, dplyr, phyloseq, shiny, stats, methods, XML, graphics, utils, BiocStyle, edgeR, DESeq2, ComplexHeatmap, plotly, webshot, vegan, shinyjs, glmnet, gmodels, ROCR, RColorBrewer, knitr, devtools, ape Suggests: rmarkdown, testthat License: GPL (>= 2) MD5sum: b8958799c50285e8cf47d78121716a21 NeedsCompilation: no Package: pathRender Version: 1.80.0 Depends: graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods, stats4 Suggests: ALL, hgu95av2.db License: LGPL MD5sum: 862dd8db50b2448e96c331cdda65ca3d NeedsCompilation: no Package: pathview Version: 1.52.0 Depends: R (>= 3.5.0) Imports: KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) MD5sum: 015d82d87e1d6f7a870e8d54b583f609 NeedsCompilation: no Package: pathwayPCA Version: 1.28.0 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: 4893327d174e201838b1949108af4649 NeedsCompilation: no Package: pcaExplorer Version: 3.6.0 Imports: DESeq2, SummarizedExperiment, mosdef (>= 1.1.0), GenomicRanges, IRanges, S4Vectors, genefilter, ggplot2 (>= 2.0.0), heatmaply, plotly, scales, NMF, plyr, topGO, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, ggrepel, DT, shinyAce, threejs, biomaRt, pheatmap, knitr, rmarkdown, base64enc, tidyr, grDevices, methods Suggests: testthat, BiocStyle, markdown, airway, org.Hs.eg.db, htmltools License: MIT + file LICENSE MD5sum: 7c525950bdd927d6f40d4a804ac1e2ad NeedsCompilation: no Package: pcaMethods Version: 2.4.0 Depends: Biobase, methods Imports: BiocGenerics, Rcpp (>= 0.11.3), MASS LinkingTo: Rcpp Suggests: matrixStats, lattice, ggplot2 License: GPL (>= 3) MD5sum: 987803852b4e8eb7d6fbc854d502ac65 NeedsCompilation: yes Package: PCAN Version: 1.40.0 Depends: R (>= 3.3), BiocParallel Imports: grDevices, stats Suggests: BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb License: CC BY-NC-ND 4.0 MD5sum: 9999097341ac9afdf213e005ba1a6a51 NeedsCompilation: no Package: PCAtools Version: 2.24.0 Depends: ggplot2, ggrepel Imports: lattice, grDevices, cowplot, methods, reshape2, stats, Matrix, DelayedMatrixStats, DelayedArray, beachmat (>= 2.21.1), BiocSingular, BiocParallel, Rcpp, dqrng LinkingTo: Rcpp, beachmat, assorthead, BH, dqrng Suggests: testthat, scran, BiocGenerics, knitr, Biobase, GEOquery, hgu133a.db, ggplotify, RMTstat, ggforce, concaveman, DESeq2, airway, org.Hs.eg.db, magrittr, rmarkdown, airway License: GPL-3 MD5sum: be5ba9c7fc5c111436e7c1a2a6c802b0 NeedsCompilation: yes Package: PDATK Version: 1.20.0 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: 62dedecb10fce21620c88c5cdaf2e81b NeedsCompilation: no Package: pdInfoBuilder Version: 1.76.0 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: 531cad737672b9edc469c3ff16a7929e NeedsCompilation: yes Package: PeacoQC Version: 1.22.0 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: 2b10a5dc2e383344303ca907d240afd4 NeedsCompilation: no Package: peakCombiner Version: 1.2.0 Depends: R (>= 4.5.0) Imports: tidyr, dplyr (>= 1.1.2), IRanges, GenomicRanges, tidyselect, purrr, readr (>= 2.1.2), tibble (>= 3.2.1), rlang, stringr, here, stats, Seqinfo Suggests: testthat (>= 3.0.0), tidyverse, rmarkdown, styler, cli, lintr, rtracklayer, knitr, devtools, ggplot2, BiocStyle, BiocManager, usethis, utils, AnnotationHub, GenomeInfoDb License: MIT + file LICENSE MD5sum: 2a60f02d6f67aa5fbb7f82fd376ae9e0 NeedsCompilation: no Package: peakPantheR Version: 1.26.0 Depends: R (>= 4.5) Imports: foreach (>= 1.4.4), doParallel (>= 1.0.11), ggplot2 (>= 3.5.0), gridExtra (>= 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Package: Pedixplorer Version: 1.8.0 Depends: R (>= 4.4.0) Imports: graphics, stats, methods, ggplot2, utils, grDevices, stringr, plyr, dplyr, tidyr, quadprog, Matrix, S4Vectors, shiny, readxl, DT, igraph, shinycssloaders, shinyhelper, shinyjs, shinyjqui, shinyWidgets, htmlwidgets, plotly, colourpicker, shinytoastr Suggests: diffviewer, gridExtra, testthat (>= 3.0.0), vdiffr, rmarkdown, BiocStyle, knitr, withr, qpdf, shinytest2, devtools, R.devices, usethis, rlang, magick, cowplot License: Artistic-2.0 MD5sum: 646418bd546a9d701830d720759ab104 NeedsCompilation: no Package: pengls Version: 1.18.0 Depends: R (>= 4.5.0) Imports: glmnet, nlme, stats, BiocParallel Suggests: knitr,rmarkdown,testthat License: GPL-2 MD5sum: 8b2e2c7ca09ee06e9d80b263bad8f585 NeedsCompilation: no Package: PepSetTest Version: 1.6.0 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: 66edd670866fc03ee8981e1525f29ae3 NeedsCompilation: no Package: PepsNMR Version: 1.30.0 Depends: R (>= 3.6) Imports: Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2, methods, graphics, stats Suggests: knitr, markdown, rmarkdown, BiocStyle, PepsNMRData License: GPL-2 | file LICENSE MD5sum: d532d5319c944afd8d2a656cd990f3ff NeedsCompilation: no Package: pepStat Version: 1.46.0 Depends: R (>= 3.0.0), Biobase, IRanges Imports: limma, fields, GenomicRanges, ggplot2, plyr, tools, methods, data.table Suggests: pepDat, Pviz, knitr, shiny License: Artistic-2.0 MD5sum: 179fa4a3d64f194aa077c92b243e4b39 NeedsCompilation: no Package: pepXMLTab Version: 1.46.0 Depends: R (>= 3.0.1) Imports: XML(>= 3.98-1.1) Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 815440489861e7c0994c41a05e269887 NeedsCompilation: no Package: periodicDNA Version: 1.22.0 Depends: R (>= 4.0), Biostrings, GenomicRanges, IRanges, BSgenome, BiocParallel Imports: S4Vectors, rtracklayer, stats, Seqinfo, magrittr, zoo, ggplot2, methods, parallel, cowplot Suggests: BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr, knitr, rmarkdown, pkgdown License: GPL-3 + file LICENSE MD5sum: 0804e9fc9255b751796f1fc35e2c2bf4 NeedsCompilation: no Package: pfamAnalyzeR Version: 1.12.0 Depends: R (>= 4.3.0), readr, stringr, dplyr Imports: utils, tibble, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 406e7aa876a846f8e8b010ee06c493c6 NeedsCompilation: no Package: pgca Version: 1.36.0 Imports: utils, stats Suggests: knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: 42b2eb9e3e3e80c0f00db3c03a198214 NeedsCompilation: no Package: pgxRpi Version: 1.7.0 Depends: R (>= 4.2) Imports: utils, methods, grDevices, graphics, circlize, httr, dplyr, attempt, lubridate, survival, survminer, ggplot2, GenomicRanges, SummarizedExperiment, S4Vectors, yaml, parallel, future, future.apply Suggests: BiocStyle, rmarkdown, knitr, testthat License: Artistic-2.0 MD5sum: fb0c3265efdb271ec6b3d9f8a0862158 NeedsCompilation: no Package: phantasus Version: 1.32.0 Depends: R (>= 4.3) Imports: ggplot2, protolite, Biobase, GEOquery, htmltools, httpuv, jsonlite, limma, edgeR, opencpu, assertthat, methods, httr, rhdf5, utils, parallel, stringr, fgsea (>= 1.9.4), svglite, gtable, stats, Matrix, pheatmap, scales, ccaPP, grid, grDevices, AnnotationDbi, DESeq2, data.table, curl, apeglm, config (>= 0.3.2), rhdf5client (>= 1.25.1), yaml, fs, phantasusLite, XML Suggests: testthat, BiocStyle, knitr, rmarkdown, org.Hs.eg.db, org.Mm.eg.db License: MIT + file LICENSE MD5sum: 58fab5a3c5c66eebcbfc771417cc687a NeedsCompilation: no Package: phantasusLite Version: 1.10.0 Depends: R (>= 4.2) Imports: data.table, rhdf5client(>= 1.25.1), httr, stringr, stats, utils, Biobase, methods Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5, GEOquery License: MIT + file LICENSE MD5sum: b3a578c9da8f8f9944a3a0ee100c371d NeedsCompilation: no Package: PharmacoGx Version: 3.16.0 Depends: R (>= 4.1.0), CoreGx Imports: BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, RColorBrewer, magicaxis, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, checkmate, boot, coop LinkingTo: Rcpp Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils License: GPL (>= 3) MD5sum: fb8c81677fb3a6e0684af2202b232869 NeedsCompilation: yes Package: PhenoGeneRanker Version: 1.20.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 International License MD5sum: 27ff337a2c6363e5d6922911b12a579b NeedsCompilation: no Package: phenopath Version: 1.36.0 Imports: Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr, tibble, ggplot2, tidyr LinkingTo: Rcpp Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment License: Apache License (== 2.0) MD5sum: 22fda78f8f5b8298442af8c5b550a030 NeedsCompilation: yes Package: phenoTest Version: 1.60.0 Depends: R (>= 3.6.0), Biobase, methods, annotate, Heatplus, BMA, ggplot2, Hmisc Imports: survival, limma, gplots, Category, AnnotationDbi, hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv, hgu133a.db, ellipse Suggests: GSEABase, GO.db Enhances: parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, org.Dm.eg.db License: GPL (>= 2) MD5sum: 9f3c5abfbcea543ea1f627fa76b356f2 NeedsCompilation: no Package: philr Version: 1.38.0 Imports: ape, phangorn, tidyr, ggplot2, ggtree, methods Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia License: GPL-3 MD5sum: 2d94187fb3506b0f4fcd773763eb5f08 NeedsCompilation: no Package: PhIPData Version: 1.20.0 Depends: R (>= 4.1.0), SummarizedExperiment (>= 1.3.81) Imports: BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors, edgeR, cli, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr, withr License: MIT + file LICENSE MD5sum: 55b79f6c4a6c8b6958b5937c2ba3d831 NeedsCompilation: no Package: phosphonormalizer Version: 1.36.0 Depends: R (>= 4.0) Imports: plyr, stats, graphics, matrixStats, methods Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) MD5sum: 4d4e15166705b66e64fab5be53c92671 NeedsCompilation: no Package: PhosR Version: 1.22.0 Depends: R (>= 4.2.0) Imports: ruv, e1071, dendextend, limma, pcaMethods, stats, RColorBrewer, circlize, dplyr, igraph, pheatmap, preprocessCore, tidyr, rlang, graphics, grDevices, utils, SummarizedExperiment, methods, S4Vectors, BiocGenerics, ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext, stringi Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate License: GPL-3 + file LICENSE MD5sum: 563edb2aad2635b79f3b4b89df57572f NeedsCompilation: no Package: PhyloProfile Version: 2.4.0 Depends: R (>= 4.5.0) Imports: ape, bioDist, BiocStyle, Biostrings, bsplus, colourpicker, data.table, dplyr, DT, energy, fastcluster, ggplot2, gridExtra, htmlwidgets, pbapply, plotly, RColorBrewer, RCurl, Rfast, scattermore, shiny, shinycssloaders, shinyFiles, shinyjs, stringr, tsne, svglite, umap, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat, OmaDB License: MIT + file LICENSE MD5sum: 37eb7fa8e74288ea48407f77839b9f4e NeedsCompilation: no Package: phyloseq Version: 1.56.0 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 (>= 1.4.3), ggplot2 (>= 2.1.0), igraph (>= 1.0.1), methods 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openxlsx, dplyr, S4Vectors, methods Suggests: GenomeInfoDb, knitr, rtracklayer, testthat, BiocStyle, prettydoc, BSgenome, BSgenome.Dmelanogaster.UCSC.dm6, BiocManager, rmarkdown, ggplot2 License: CC0 MD5sum: f4d07d54c9f9c92c8b9a7fe884468e36 NeedsCompilation: no Package: pickgene Version: 1.84.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: cf5cce301a080ade6bfb299332e0f2c8 NeedsCompilation: no Package: Pigengene Version: 1.38.0 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: 17a48c5aa6c01f689a81e7027aff65fd NeedsCompilation: no Package: pipeComp Version: 1.22.0 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GenomicFeatures, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene License: MIT + file LICENSE MD5sum: 82aa7d9a851c9189ad354eb7882bbf67 NeedsCompilation: yes Package: plotGrouper Version: 1.30.0 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: 1c6584ca77c765f05630e7095551c832 NeedsCompilation: no Package: PLPE Version: 1.72.0 Depends: R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods License: GPL (>= 2) MD5sum: 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knitr, rmarkdown, tibble, tidyr, BiocStyle, RefManageR, sessioninfo, DBI, chunked, RSQLite, dbplyr License: AGPL (>= 3) MD5sum: 80cacc1f66e3cc15968cfb8a1e950833 NeedsCompilation: yes Package: postNet Version: 1.0.0 Depends: R (>= 4.5.0), Imports: dplyr, plyr, Biostrings, data.table, gridExtra, seqinr, R.utils, reshape2, vioplot, stringr, plotrix, gplots, ggplot2, ggrepel, anota2seq, memes, GenomicRanges, IRanges, WriteXLS, randomForest, igraph, Boruta, ROCR, caret, msigdb, ExperimentHub, AnnotationHub, GSEABase, fgsea, org.Hs.eg.db, org.Mm.eg.db, RColorBrewer, httr2, rvest, umap, clusterProfiler (>= 4.18.4), gage, withr, grDevices, graphics, methods, stats, utils, tools, BiocFileCache, curl LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, BiocStyle, pdftools, magick, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: e65bcf016235c7226ee04a987a7657d3 NeedsCompilation: yes Package: powerTCR Version: 1.32.0 Imports: cubature, doParallel, evmix, foreach, magrittr, methods, parallel, 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SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl, pheatmap, tibble, rmarkdown, testthat (>= 2.1.0) License: Apache License (== 2.0) | file LICENSE MD5sum: aaf6279bbb920c78e3b8315a5046f235 NeedsCompilation: no Package: projectR Version: 1.28.0 Depends: R (>= 4.0.0) Imports: SingleCellExperiment, methods, cluster, stats, limma, NMF, ROCR, ggalluvial, RColorBrewer, dplyr, fgsea, reshape2, viridis, scales, Matrix, MatrixModels, msigdbr, ggplot2, cowplot, ggrepel, umap, tsne Suggests: BiocStyle, CoGAPS, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap, gplots, SeuratObject License: GPL (== 2) MD5sum: 5e8dfce5b61b5388d1d4a98d4a0bf7e6 NeedsCompilation: no Package: pRoloc Version: 1.52.0 Depends: R (>= 3.5), MSnbase (>= 1.19.20), MLInterfaces (>= 1.67.10), methods, Rcpp (>= 0.10.3), BiocParallel Imports: stats4, Biobase, mclust (>= 4.3), caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin, BiocGenerics, stats, dendextend, 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testthat (>= 3.0.0), plyranges, plotgardener, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, tibble License: MIT + file LICENSE MD5sum: 570a6be1d4cd41fe541c4e7fbae6a9a4 NeedsCompilation: no Package: RImmPort Version: 1.40.0 Imports: plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools, utils, RSQLite Suggests: knitr License: GPL-3 MD5sum: bd1438bc9da737cc59dab55db8e8a9b0 NeedsCompilation: no Package: RITAN Version: 1.36.0 Depends: R (>= 4.0), Imports: graphics, methods, stats, utils, grid, gridExtra, reshape2, gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL, dynamicTreeCut, gsubfn, hash, png, sqldf, igraph, BgeeDB, knitr, RITANdata, GenomicFeatures, ensembldb, AnnotationFilter, EnsDb.Hsapiens.v86 Suggests: rmarkdown, BgeeDB License: file LICENSE MD5sum: 41f46d762d15d583cfbd0157f2f914cf NeedsCompilation: no Package: RIVER Version: 1.36.0 Depends: R (>= 3.3.2) Imports: glmnet, pROC, ggplot2, graphics, stats, Biobase, methods, utils Suggests: BiocStyle, knitr, rmarkdown, 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Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, RnBeads.hg38, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame, dplyr License: GPL-3 MD5sum: 0861c0fb964f074148242f6a8dd78933 NeedsCompilation: no Package: Rnits Version: 1.46.0 Depends: R (>= 3.6.0), Biobase, ggplot2, limma, methods Imports: affy, boot, impute, splines, graphics, qvalue, reshape2 Suggests: BiocStyle, knitr, GEOquery, stringr License: GPL-3 MD5sum: e41fafdf03a5511e36f706a6c5031c4a NeedsCompilation: no Package: roar Version: 1.48.0 Depends: R (>= 3.0.1) Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, GenomicAlignments (>= 0.99.4), rtracklayer, GenomeInfoDb 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testthat License: CeCILL MD5sum: fd09c01c4662e77354bab0d49668f5c6 NeedsCompilation: no Package: ROSeq Version: 1.24.0 Depends: R (>= 4.0) Imports: pbmcapply, edgeR, limma Suggests: knitr, rmarkdown, testthat, RUnit, BiocGenerics License: GPL-3 MD5sum: 84288fa81b5062b0136b5205bb9d318b NeedsCompilation: no Package: ROTS Version: 2.4.0 Depends: R (>= 3.6) Imports: Rcpp, stats, Biobase, methods, BiocParallel, lme4, survival LinkingTo: Rcpp Suggests: testthat License: GPL (>= 2) MD5sum: c7f5d5db96671ea255afdd828d6c1360 NeedsCompilation: yes Package: RPA Version: 1.68.0 Depends: R (>= 3.1.1), affy, BiocGenerics, BiocStyle, methods, rmarkdown Imports: phyloseq Suggests: knitr, parallel License: BSD_2_clause + file LICENSE MD5sum: 69e49fba7cf3d1d95e555f4ed025ced0 NeedsCompilation: no Package: rprimer Version: 1.16.0 Depends: R (>= 4.1) Imports: Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods, patchwork, reshape2, S4Vectors, shiny, shinycssloaders, shinyFeedback Suggests: BiocStyle, 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org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db License: GPL-3 MD5sum: dc0fec429933a82798ba03c2df9daf71 NeedsCompilation: no Package: Rsamtools Version: 2.28.0 Depends: R (>= 3.5.0), methods, Seqinfo, GenomicRanges (>= 1.61.1), Biostrings (>= 2.77.2) Imports: utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), bitops, BiocParallel, stats LinkingTo: Rhtslib (>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, VariantAnnotation, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr License: Artistic-2.0 | file LICENSE MD5sum: 25f396ca7d0e44d30f6e46d70c7c1fc6 NeedsCompilation: yes Package: rsbml Version: 2.70.0 Depends: R (>= 2.6.0), BiocGenerics 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RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 461587535a9748deb0a9e0c0ba4049dd NeedsCompilation: no Package: RTNduals Version: 1.36.0 Depends: R(>= 4.4.0), RTN(>= 2.32), methods Imports: graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: a972c504aa43fb283403010c8b68f82a NeedsCompilation: no Package: RTNsurvival Version: 1.36.0 Depends: R(>= 4.4.0), RTN(>= 2.32), RTNduals(>= 1.32), methods Imports: survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 7e015ad5d5836fedee73f54c0f9ab688 NeedsCompilation: no Package: RTopper Version: 1.58.0 Depends: R (>= 2.12.0), Biobase Imports: limma, multtest Suggests: org.Hs.eg.db, KEGGREST, GO.db License: GPL (>= 3) + file LICENSE MD5sum: 7a9fa8cbd817396986ec5a4da6dc6334 NeedsCompilation: no Package: 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1.50.0 Depends: R (>= 2.10), igraph (>= 1.0) Imports: methods, AnnotationDbi, DBI, RSQLite Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: f21caf78b6384b1197fb27ff60492070 NeedsCompilation: no Package: rTRMui Version: 1.50.0 Imports: shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 52b5d3485caa32bb38caf81e9efab39d NeedsCompilation: no Package: RUCova Version: 1.4.0 Depends: R (>= 4.4.0) Imports: dplyr, fastDummies, ggplot2, stringr, tibble, Matrix, ComplexHeatmap, grid, circlize, SingleCellExperiment, SummarizedExperiment, tidyverse, tidyr, magrittr, S4Vectors Suggests: knitr, rmarkdown, BiocManager, BiocStyle, remotes, ggpubr, ggcorrplot, ggh4x, testthat (>= 3.0.0) License: GPL-3 MD5sum: b4a84a7d6e1eec5faea5409619856167 NeedsCompilation: no Package: runibic Version: 1.33.0 Depends: R (>= 3.4.0), 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rmarkdown, mclust, scater, BiocStyle License: GPL-3 MD5sum: f4089e1dadec2cca0927773aecc430c5 NeedsCompilation: yes Package: scafari Version: 1.2.0 Depends: R (>= 4.5.0) Imports: magrittr, shiny, shinycssloaders, DT, dplyr, waiter, ggplot2, tibble, stringr, reshape2, shinyjs, shinyBS, shinycustomloader, factoextra, markdown, plotly, ggbio, GenomicRanges, rhdf5, ComplexHeatmap, biomaRt, org.Hs.eg.db, SummarizedExperiment, SingleCellExperiment, S4Vectors, parallel, httr, jsonlite, scales, tidyr, txdbmaker, circlize, R.utils, dbscan, igraph, RANN Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: LGPL-3 MD5sum: 1279180443f62051756cde4989be26c8 NeedsCompilation: no Package: Scale4C Version: 1.34.0 Depends: R (>= 3.5.0), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: 5b845032763c1d0d6fae1c2d9c38592e NeedsCompilation: no Package: ScaledMatrix Version: 1.20.0 Imports: methods, Matrix, S4Vectors, 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GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs, rtracklayer, S4Vectors, scanMiRData, shiny, shinycssloaders, shinydashboard, shinyjqui, stats, utils, txdbmaker, waiter Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-3 MD5sum: 05b89007ec150a9b37043f8ccf045408 NeedsCompilation: no Package: scAnnotatR Version: 1.18.0 Depends: R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment Imports: dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, AnnotationHub, utils Suggests: knitr, rmarkdown, scRNAseq, testthat License: MIT + file LICENSE MD5sum: a7fa9ef5a52c80694fe1886cede61502 NeedsCompilation: no Package: SCANVIS Version: 1.26.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file 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methods, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, MatrixGenerics, SparseArray, DelayedArray, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer, RcppML, uwot, pheatmap, ggrepel, ggrastr Suggests: BiocStyle, DelayedMatrixStats, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore License: GPL-3 MD5sum: f576257c4592de4c0167ded4e1949836 NeedsCompilation: no Package: scatterHatch Version: 1.18.0 Depends: R (>= 4.1) Imports: grid, ggplot2, plyr, spatstat.geom, stats, grDevices Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 4897a41f14bdfff63b68d8ea33671937 NeedsCompilation: no Package: scBFA Version: 1.26.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods, Matrix Suggests: knitr, rmarkdown, testthat, Rtsne License: GPL-3 + file LICENSE MD5sum: 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Depends: R (>= 4.0) Imports: S4Vectors, limma, ggraph, igraph, methods, cluster, minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix, ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo Suggests: knitr, rmarkdown, BiocStyle, pkgdown License: GPL-3 MD5sum: db33f02bc913b9e5238799f3c735d947 NeedsCompilation: no Package: sccomp Version: 2.4.0 Depends: R (>= 4.3.0), instantiate (>= 0.2.3) Imports: stats, boot, utils, scales, lifecycle, rlang, tidyselect, magrittr, crayon, cli, fansi, dplyr, tidyr, purrr, tibble, ggplot2, ggrepel, patchwork, forcats, readr, stringr, glue, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), markdown, loo, prettydoc, SeuratObject, tidyseurat, tidySingleCellExperiment, bayesplot, posterior License: GPL-3 MD5sum: b855d2424c6b17fd6433c3e4757f93f9 NeedsCompilation: no Package: scConform Version: 1.0.0 Depends: R (>= 4.6.0) Imports: igraph, stats, SummarizedExperiment, BiocParallel, Rgraphviz Suggests: knitr, Matrix, rmarkdown, BiocStyle, VGAM, ontoProc, MerfishData, doParallel, scuttle, SingleCellExperiment, scran, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: da3c11bc318821f525d157393b9be8d6 NeedsCompilation: no Package: scDataviz Version: 1.22.0 Depends: R (>= 4.0), S4Vectors, SingleCellExperiment, Imports: ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales, RColorBrewer, corrplot, stats, grDevices, graphics, utils, MASS, matrixStats, methods Suggests: PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: cadbf9b76356b68891d8fbdcd53c33e5 NeedsCompilation: no Package: scDblFinder Version: 1.26.0 Depends: R (>= 4.0), SingleCellExperiment Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost (>= 3.1), stats, utils, MASS, IRanges, GenomicRanges, GenomeInfoDb, Rsamtools, rtracklayer Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans License: GPL-3 + file LICENSE MD5sum: 205a6fbe8bcd48908e77a342f3aab9c9 NeedsCompilation: no Package: scDD Version: 1.36.0 Depends: R (>= 3.5.0) Imports: fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm, SingleCellExperiment, SummarizedExperiment, grDevices, graphics, stats, S4Vectors, scran Suggests: BiocStyle, knitr, gridExtra License: GPL-2 MD5sum: 407d68b9ebcfbf1aa4b7ace1a2eafa8d NeedsCompilation: yes Package: scDDboost Version: 1.14.0 Depends: R (>= 4.2), ggplot2 Imports: Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0),EBSeq, BiocParallel, mclust, SingleCellExperiment, cluster, Oscope, SummarizedExperiment, stats, methods LinkingTo: Rcpp, RcppEigen, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: cc882f2ac84ac1d18ffe47d8e1844fe9 NeedsCompilation: yes Package: scde Version: 2.40.0 Depends: R (>= 3.0.0), flexmix Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 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transport, cramer, rlang, bluster, scales, MASS, stringr, Matrix, grDevices Suggests: AUCell, BiocStyle, knitr, rmarkdown, scran, scRNAseq, SingleR, celldex, scuttle, scater, dplyr, ComplexHeatmap, grid, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 7648317b71f419ef864dddeea9ea73a2 NeedsCompilation: no Package: scDotPlot Version: 1.6.0 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: 107328376c343557e15f9d7b819747a4 NeedsCompilation: no Package: scds Version: 2.0.0 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: 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stats, methods Suggests: testthat, knitr, rmarkdown, BiocStyle, MASS, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE MD5sum: 11c8f687ab7d8ee66f78981828fdf311 NeedsCompilation: no Package: scFeatures Version: 1.12.0 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, MatrixGenerics, Seurat, DT Suggests: knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler, pheatmap, limma, ggplot2, plotly, igraph, data.table, enrichplot, DOSE, rmarkdown License: GPL-3 MD5sum: 95d415fc95a7d35870ba957b0c49656c NeedsCompilation: no Package: scGPS Version: 1.26.0 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: 5e22275120f0e47d9993d9df4848aba9 NeedsCompilation: yes Package: scGraphVerse Version: 1.2.0 Depends: R (>= 4.5.0) Imports: BiocBaseUtils, BiocParallel (>= 1.30.0), doParallel, doRNG, GENIE3, Matrix, MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, distributions3, dplyr, grDevices, graphics, httr, igraph, jsonlite, methods, parallel, reticulate, tidyr, glmnet, MASS, utils, stats, S4Vectors, graph, mpath Suggests: AnnotationDbi, BiocStyle, clusterProfiler, DOSE, enrichplot, fmsb, ggplot2, ggraph, gridExtra, INetTool, org.Hs.eg.db, org.Mm.eg.db, patchwork, pROC, RColorBrewer, ReactomePA, rentrez, robin, scales, Seurat, STRINGdb, testthat (>= 3.0.0), knitr, rmarkdown, tidyverse, magick, celldex, SingleR, TENxPBMCData, scater, GenomeInfoDb, GenomicRanges, License: GPL-3 + file LICENSE MD5sum: 545db35762866db28742dc72f0676966 NeedsCompilation: yes Package: schex Version: 1.26.0 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: 429cce0faca7b51dfd9a0a4a8b1245cf NeedsCompilation: no Package: scHiCcompare Version: 1.4.0 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: e9efbcac1c1144d4e9a671c515552e61 NeedsCompilation: no Package: scHOT Version: 1.24.0 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: ed7fb61a7c7bcb79a44d9db7feca4cbf NeedsCompilation: no Package: scider Version: 1.10.0 Depends: R (>= 4.3) Imports: SpatialExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, sf, lwgeom, SpatialPack, ggplot2, stats, pheatmap, plotly, shiny, igraph, janitor, knitr, methods, utils, isoband, S4Vectors, grDevices, dbscan, hexDensity, hexbin, uwot, SingleCellExperiment, BiocNeighbors, irlba, DropletUtils, arrow, RBioFormats, Matrix Suggests: edgeR, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 1344a174d2a3edeb5a2d2d509dc0a44b NeedsCompilation: yes Package: scifer Version: 1.14.0 Imports: dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra, tibble, scales, rlang, flowCore, methods, basilisk, basilisk.utils, reticulate, here, pwalign, utils Suggests: BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0) Enhances: parallel License: MIT + file LICENSE MD5sum: 99f3f41086611ad5fc58815385d661dc NeedsCompilation: no Package: scLANE Version: 1.2.0 Depends: glm2, magrittr, R (>= 4.5.0) Imports: geeM, MASS, mpath, dplyr, stats, utils, withr, purrr, tidyr, furrr, doSNOW, gamlss, scales, future, Matrix, ggplot2, splines, foreach, glmmTMB, parallel, RcppEigen, bigstatsr, tidyselect, broom.mixed, Rcpp LinkingTo: Rcpp, RcppEigen Suggests: covr, grid, coop, uwot, scran, ggh4x, knitr, UCell, irlba, rlang, magick, igraph, scater, gtable, ggpubr, viridis, bluster, cluster, circlize, speedglm, rmarkdown, gridExtra, BiocStyle, slingshot, gprofiler2, GenomeInfoDb, BiocParallel, BiocGenerics, BiocNeighbors, ComplexHeatmap, Seurat (>= 5.0.0), testthat (>= 3.0.0), SingleCellExperiment, SummarizedExperiment License: MIT + file LICENSE MD5sum: f50f99e43562134a1dd34221458c997e NeedsCompilation: yes Package: scLang Version: 1.0.0 Imports: dplyr, ggplot2, henna, methods, paletteer, rlang, S4Vectors, SeuratObject, SingleCellExperiment, stats, SummarizedExperiment Suggests: BiocStyle, knitr, qs2, rmarkdown, scater, scRNAseq, Seurat, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 5f0030c3cf2562978fc81996d2321ec8 NeedsCompilation: no Package: scmap Version: 1.34.0 Depends: R(>= 3.4) Imports: Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 6fd59e785d0517d72085738f14290447 NeedsCompilation: yes Package: scMerge Version: 1.28.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, BiocNeighbors, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), proxyC, ruv, cvTools, scater, batchelor, scran, methods, S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3), SummarizedExperiment Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger License: GPL-3 MD5sum: 081f9bc1df602d89e163f8db4eb157d1 NeedsCompilation: no Package: scMET Version: 1.14.0 Depends: R (>= 4.2.0) Imports: methods, Rcpp (>= 1.0.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), rstantools (>= 2.1.0), VGAM, data.table, MASS, logitnorm, ggplot2, matrixStats, assertthat, viridis, coda, BiocStyle, cowplot, stats, SummarizedExperiment, SingleCellExperiment, Matrix, dplyr, S4Vectors LinkingTo: BH (>= 1.66.0), Rcpp (>= 1.0.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), StanHeaders (>= 2.21.0.7) Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: c0cba7ed78dfcdf19f01e977014dba61 NeedsCompilation: yes Package: scmeth Version: 1.32.0 Depends: R (>= 3.5.0) Imports: BiocGenerics, bsseq, AnnotationHub, Seqinfo, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: knitr, rmarkdown, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, ggplot2, ggthemes License: GPL-2 MD5sum: 2da5bed83d30109610a0db68e839a4c0 NeedsCompilation: no Package: scMitoMut Version: 1.7.0 Depends: R (>= 4.3.0) Imports: data.table, Rcpp, magrittr, plyr, stringr, utils, stats, methods, ggplot2, pheatmap, RColorBrewer, rhdf5, readr, parallel, grDevices LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils License: Artistic-2.0 MD5sum: 29fb65b01ced2cd60592d2acfe2d7fae NeedsCompilation: yes Package: scMultiSim Version: 1.8.0 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: 6b0330934194dc09cabbc4a547929767 NeedsCompilation: no Package: SCnorm Version: 1.34.0 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: 0fa25093eb11a25a4fbf5959d20b169b NeedsCompilation: no Package: scone Version: 1.36.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment, DelayedMatrixStats, sparseMatrixStats, SparseArray (>= 1.7.6) Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, DelayedArray, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData License: Artistic-2.0 MD5sum: 136bd4579837aed0a9568ae0e83062ae NeedsCompilation: no Package: Sconify Version: 1.32.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 972fc4535dec2d32dea4b43555ce3cc4 NeedsCompilation: no Package: SCOPE Version: 1.24.0 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: 0b6cacecb5ca3d371507680fc66b4bbd NeedsCompilation: no Package: scoreInvHap Version: 1.34.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: 7bf55e0a6d4390189fd5034162152603 NeedsCompilation: no Package: scoup Version: 1.6.0 Depends: R (>= 4.4), Matrix Imports: Biostrings, methods Suggests: BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat (>= 3.0.0), yaml License: GPL (>= 2) MD5sum: da8c1cc136a0d3913ae04083453dabcc NeedsCompilation: no Package: scp Version: 1.22.0 Depends: R (>= 4.3.0), QFeatures (>= 1.19.1) 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: 43d20e51ba11af852b9e94cf15d5f7b5 NeedsCompilation: no Package: scPassport Version: 1.0.0 Depends: R (>= 4.3) Imports: shiny, miniUI, Rcpp, S4Vectors LinkingTo: Rcpp Suggests: Seurat, SingleCellExperiment, SummarizedExperiment, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: d98d37e0f85c70d9dde588e19eb72cda NeedsCompilation: yes Package: scPCA Version: 1.26.0 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: 1f4f638445b30be36335084f31cf9535 NeedsCompilation: no Package: scPipe Version: 2.12.0 Depends: R (>= 4.2.0), SingleCellExperiment Imports: AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings, data.table, dplyr, DropletUtils, flexmix, GenomicRanges, GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grDevices, graphics, hash, IRanges, magrittr, MASS, Matrix (>= 1.5.0), mclust, methods, MultiAssayExperiment, org.Hs.eg.db, org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate, Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer, SummarizedExperiment, S4Vectors, scales, stats, stringr, tibble, tidyr, tools, utils, vctrs (>= 0.5.2) LinkingTo: Rcpp, Rhtslib (>= 1.13.1), testthat Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap License: GPL (>= 2) MD5sum: 92a291f69f6db61391cdbc32ae405f5d NeedsCompilation: yes Package: scQTLtools Version: 1.4.0 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), yulab.utils (>= 0.2.3) 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: 7afda95d531bd2f7120e84a9cb844f8e NeedsCompilation: no Package: scran Version: 1.40.0 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, scrapper License: GPL-3 MD5sum: 9819f8ebba78e5cc70eb80dd2e00860e NeedsCompilation: yes Package: scrapper Version: 1.6.0 Imports: methods, Rcpp, beachmat (>= 2.25.1), S4Vectors, SparseArray, DelayedArray, BiocNeighbors (>= 1.99.0), parallel LinkingTo: Rcpp, assorthead (>= 1.5.16), beachmat, BiocNeighbors, Rigraphlib Suggests: testthat, knitr, rmarkdown, BiocStyle, Matrix, IRanges, SummarizedExperiment, SingleCellExperiment, scRNAseq, org.Mm.eg.db, scater, igraph License: MIT + file LICENSE MD5sum: 987e307b4538169e66407539b7e94d06 NeedsCompilation: yes Package: scReClassify Version: 1.18.0 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: 2a6865d7992aa8c6caa8c179474095c6 NeedsCompilation: no Package: scRecover Version: 1.28.0 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL MD5sum: 3a3efed65ef999bb2f756d4a29739588 NeedsCompilation: no Package: screenCounter Version: 1.12.0 Depends: S4Vectors, SummarizedExperiment Imports: Rcpp, BiocParallel LinkingTo: Rcpp Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: b0b4c0eb8ce3144339b358acac31f555 NeedsCompilation: yes Package: ScreenR Version: 1.14.0 Depends: R (>= 4.3) Imports: methods (>= 4.0), rlang (>= 0.4), stringr (>= 1.4), limma (>= 3.46), patchwork (>= 1.1), tibble (>= 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circlize, ComplexHeatmap, colourpicker, data.table, desc, DBI, DT, fs, GenomicRanges, GenomeInfoDb, ggdendro, ggforce, ggnewscale, ggplot2, ggrepel, ggridges, grDevices, grid, gridExtra, htmltools, IRanges, jsonlite, Matrix, magrittr, methods, patchwork, plotly, RColorBrewer, RefManageR, reshape2, rhdf5, Rsamtools, RSQLite, rtracklayer, S4Vectors, scales, scrypt, Seurat, SeuratObject, shiny, shinyhelper, shinymanager, slingshot, SingleCellExperiment, sortable, stats, tools, xfun, xml2, utils Suggests: rmarkdown, knitr, testthat, BiocStyle, shinytest2 Enhances: celldex, future, SingleR, SummarizedExperiment, tricycle, terra License: GPL-3 MD5sum: d6502c92a0fe3ae77aec9e234d11f327 NeedsCompilation: no Package: scruff Version: 1.30.0 Depends: R (>= 4.0) Imports: data.table, GenomicAlignments, GenomicFeatures, txdbmaker, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread, parallelly, patchwork Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: c9ee5cc0c2b2af245a28aefc9af34f6b NeedsCompilation: no Package: scry Version: 1.24.0 Depends: R (>= 4.0), stats, methods Imports: DelayedArray, glmpca (>= 0.2.0), Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array, knitr, markdown, rmarkdown, TENxPBMCData, testthat License: Artistic-2.0 MD5sum: a71847f12282fec658ee9ad3f04520cc NeedsCompilation: no Package: scShapes Version: 1.18.0 Depends: R (>= 4.1) Imports: Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS, emdbook, magrittr, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 10b55cec4529de5d8d05ec78f144bb16 NeedsCompilation: yes Package: scTensor Version: 2.22.0 Depends: R (>= 4.1.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8), abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics, stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2 Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens License: Artistic-2.0 MD5sum: c7f213867cfb914638f4f1b762c623a0 NeedsCompilation: no Package: scTGIF Version: 1.26.0 Depends: R (>= 3.6.0) Imports: GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly, tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr, S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor, methods, scales, msigdbr, schex, tibble, ggplot2, igraph Suggests: testthat License: Artistic-2.0 MD5sum: 6ffcdf2bceb5e335ec1fd625bdcfe6b8 NeedsCompilation: no Package: scTHI Version: 1.24.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 9b17f1ef6e8eaee6ebbb4bb992b357d1 NeedsCompilation: no Package: scToppR Version: 1.0.0 Depends: R (>= 4.5.0) Imports: dplyr, forcats, ggplot2, stringr, openxlsx, viridis, patchwork, utils, httr2 Suggests: airway, BiocStyle, curl, DESeq2, knitr, rmarkdown, S4Vectors, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 839ba2105a338b8da4d74581a0034ddb NeedsCompilation: no Package: scTreeViz Version: 1.18.0 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: 122b4e941d8529e61f11d50de18367de NeedsCompilation: no Package: scTypeEval Version: 1.0.0 Depends: R (>= 4.6.0) Imports: Matrix (>= 1.6-5), BiocParallel (>= 1.34.2), dplyr (>= 1.1.4), tidyr (>= 1.3.1), scran (>= 1.30.2), bluster (>= 1.12.0), ggplot2 (>= 3.5.1), ggrepel (>= 0.9.6), cluster (>= 2.1.4), SingleR (>= 2.4.1), irlba (>= 2.3.5.1), transport (>= 0.15-4), grDevices, methods, stats, utils Suggests: testthat (>= 3.0.0), transformGamPoi (>= 1.8.0), glmGamPoi (>= 1.14.3), anndata (>= 0.8.0), SummarizedExperiment (>= 1.32.0), igraph (>= 2.1.1), Seurat, SingleCellExperiment, knitr, rmarkdown, BiocStyle, BiocManager, SeuratObject, ggpubr, rlang, stringr, tibble License: GPL-3 + file LICENSE MD5sum: a7ccdf6d24b8d2a957f576f331be8527 NeedsCompilation: no Package: scuttle Version: 1.22.0 Depends: SingleCellExperiment Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays, MatrixGenerics, SparseArray, DelayedArray, beachmat LinkingTo: Rcpp, beachmat, assorthead Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, sparseMatrixStats, DelayedMatrixStats, scran License: GPL-3 MD5sum: 0b280ee4d496aeaf91e773e5808b9ad9 NeedsCompilation: yes Package: scviR Version: 1.12.0 Depends: R (>= 4.3), basilisk, shiny, SingleCellExperiment Imports: reticulate, BiocFileCache, utils, pheatmap, SummarizedExperiment, S4Vectors, limma, scater, stats, MatrixGenerics Suggests: knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle License: Artistic-2.0 MD5sum: 46b73492a1e1585649a0f4ac5afdc670 NeedsCompilation: no Package: SDAMS Version: 1.32.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: 3332fdbaa26bfd07b6487c1e0b04cad1 NeedsCompilation: no Package: seahtrue Version: 1.6.0 Depends: R (>= 4.2.0) Imports: dplyr (>= 1.1.2), readxl (>= 1.4.1), logger (>= 0.2.2), tidyxl (>= 1.0.8), purrr (>= 0.3.5), tidyr (>= 1.3.0), lubridate (>= 1.8.0), stringr (>= 1.4.1), tibble (>= 3.1.8), validate (>= 1.1.1), rlang (>= 1.0.0), glue (>= 1.6.2), cli (>= 3.4.1), janitor (>= 2.2.0), ggplot2 (>= 3.5.0), RColorBrewer (>= 1.1.3), colorspace (>= 2.1.0), forcats (>= 1.0.0), ggridges (>= 0.5.6), readr (>= 2.1.5), scales (>= 1.3.0) Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: Artistic-2.0 MD5sum: 751132e4274becf84d106b8ffd8ffa75 NeedsCompilation: no Package: sechm Version: 1.20.0 Depends: R (>= 4.0), SummarizedExperiment, ComplexHeatmap Imports: S4Vectors, seriation, circlize, methods, randomcoloR, stats, grid, grDevices, matrixStats Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 616226c4b2c11a06ae08f613b203eb16 NeedsCompilation: no Package: segmenter Version: 1.18.0 Depends: R (>= 4.1) Imports: ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges, S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils, methods, chromhmmData Suggests: testthat, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz License: GPL-3 MD5sum: 1bfb9a84842bfb270cb77588519c9a8c NeedsCompilation: no Package: segmentSeq Version: 2.46.0 Depends: R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, Seqinfo, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown License: GPL-3 MD5sum: 8d4b97d711d432454aa1c570feeb4b2a NeedsCompilation: no Package: selectKSigs Version: 1.24.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: 588162d8498640a21975214669a354f9 NeedsCompilation: yes Package: SELEX Version: 1.44.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: 49e6ecc8724071c411045da09c4aeed9 NeedsCompilation: no Package: SemDist Version: 1.46.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate 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rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 36e68cf3d360913af1307b35a19a3fac NeedsCompilation: no Package: seq2pathway Version: 1.44.0 Depends: R (>= 3.6.2) Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data License: GPL-2 MD5sum: df45a71ef2de6fd216ec46560f96891d NeedsCompilation: no Package: SeqArray Version: 1.52.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.31.1) Imports: methods, parallel, digest, S4Vectors, IRanges, GenomicRanges, Seqinfo, Biostrings LinkingTo: gdsfmt Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation License: GPL-3 MD5sum: 9cba1176e463c130c6f3f019cc233726 NeedsCompilation: yes Package: seqCAT Version: 1.34.0 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 (>= 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eulerr, Seqinfo, GenomicAlignments, GenomicRanges, ggplotify, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, scales, stats, UpSetR Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, GenomeInfoDb, covr, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 9053fa5dbc7f25521c3bfdd468af4741 NeedsCompilation: no Package: SeqSQC Version: 1.34.0 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: 6e20d3ae8acfad9dcb4a47cd62f6d2c3 NeedsCompilation: no Package: Seqtometry Version: 1.0.0 Depends: R (>= 4.5.0) Imports: BiocSingular, checkmate, data.table, future.apply, Matrix, MatrixGenerics, purrr, Rcpp, RcppHNSW, RSpectra, zeallot LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, box, dplyr, future, ggplot2, harmony, knitr, MASS, patchwork, rmarkdown, scater, scuttle, SingleCellExperiment, sparseMatrixStats, stringr, TENxPBMCData, testthat (>= 3.0.0), tibble License: MIT + file LICENSE MD5sum: 593c7d3a37f145d033b2aeebba694e80 NeedsCompilation: yes Package: SeqVarTools Version: 1.50.0 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: 8fded3ee280037b1467ca29079677a05 NeedsCompilation: no Package: SEraster Version: 1.4.0 Depends: R (>= 4.5.0) Imports: BiocParallel, ggplot2, Matrix, methods, rearrr, sf, SpatialExperiment, SummarizedExperiment Suggests: CooccurrenceAffinity, nnSVG, testthat (>= 3.0.0), knitr, rmarkdown, BiocManager, remotes License: GPL-3 MD5sum: 41d1caa7c6a5d6ffab3456832853a5ab NeedsCompilation: no Package: sesame Version: 1.30.0 Depends: R (>= 4.5.0), sesameData Imports: graphics, BiocParallel, utils, methods, stringr, readr, tibble, MASS, wheatmap (>= 0.2.0), GenomicRanges (>= 1.61.1), IRanges, grid, preprocessCore, S4Vectors, ggplot2, BiocFileCache, Seqinfo, stats, SummarizedExperiment (>= 1.39.1), dplyr, reshape2 Suggests: scales, BiocManager, GenomeInfoDb, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals License: MIT + file LICENSE MD5sum: dd539b2ed9bc4704d8f4cd19f4b4ea56 NeedsCompilation: no Package: SETA Version: 1.2.0 Depends: R (>= 4.5.0) Imports: dplyr, MASS, Matrix, SingleCellExperiment (>= 1.30.1), stats, tidygraph, rlang, utils Suggests: BiocStyle, caret, glmnet, corrplot, ggplot2, ggraph, knitr, methods, patchwork, reshape2, rmarkdown, SeuratObject, Seurat, SummarizedExperiment, TabulaMurisSenisData, tidyr, tidytext, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 4797d07185c37ef1a80642445de21c86 NeedsCompilation: no Package: SEtools Version: 1.26.0 Depends: R (>= 4.0), SummarizedExperiment, sechm Imports: BiocParallel, Matrix, DESeq2, S4Vectors, data.table, edgeR, openxlsx, pheatmap, stats, circlize, methods, sva Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL MD5sum: d978d1616b35f7d4ad8395aa72ec22f7 NeedsCompilation: no Package: sevenbridges Version: 1.42.0 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: 6e52103f12cbe95a6530eb78bcfed9b5 NeedsCompilation: no Package: sevenC Version: 1.32.0 Depends: R (>= 3.5), InteractionSet (>= 1.2.0) Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), Seqinfo, GenomicRanges (>= 1.28.5), IRanges (>= 2.10.3), S4Vectors (>= 0.14.4), readr (>= 1.1.0), purrr (>= 0.2.2), data.table (>= 1.10.4), boot (>= 1.3-20), methods (>= 3.4.1) Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr License: 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GlobalOptions, igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize, ComplexHeatmap, grDevices, stats, utils, shiny, fastmatch LinkingTo: Rcpp Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png, InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment, AnnotationHub, jsonlite License: MIT + file LICENSE MD5sum: d34b866b918e371071da396ab499195e NeedsCompilation: yes Package: simPIC Version: 1.8.0 Depends: R (>= 4.5.0), SingleCellExperiment Imports: BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, actuar, Matrix, stats, SummarizedExperiment, rlang, S4Vectors, methods, scales, scuttle, edgeR, withr Suggests: ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), scater, scran, magick License: GPL-3 MD5sum: 2ae5347ba173915a3bc21cdbe0da4f0f NeedsCompilation: no Package: simpleSeg Version: 1.14.0 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: b09374166775ed69ab7888019ce0f74b NeedsCompilation: no Package: simplifyEnrichment Version: 2.6.0 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: 3d452a9c99b4af996bd11e6c5187767e NeedsCompilation: no Package: sincell Version: 1.43.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, 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scrapper (>= 1.5.16), scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 MD5sum: b55c89ac0cd4e3f872e708f0259c62c7 NeedsCompilation: yes Package: singscore Version: 1.32.0 Depends: R (>= 3.6) Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, reshape2, S4Vectors Suggests: pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: 35529670a8cf97cef113f7718f65b763 NeedsCompilation: no Package: SiPSiC Version: 1.12.0 Depends: Matrix, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle License: file LICENSE MD5sum: 6fcc24b849c28f45eebad9d1d539b2b1 NeedsCompilation: no Package: sitadela Version: 1.20.0 Depends: R (>= 4.1.0) Imports: Biobase, BiocGenerics, biomaRt, Biostrings, Seqinfo, GenomicFeatures, GenomicRanges, IRanges, methods, parallel, Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, txdbmaker, utils Suggests: GenomeInfoDb, BiocStyle, BSgenome, knitr, rmarkdown, RMySQL, RUnit License: Artistic-2.0 MD5sum: 3fa1ef86cdeeabba398725dcf3f8e327 NeedsCompilation: no Package: Site2Target Version: 1.4.0 Depends: R (>= 4.4) Imports: S4Vectors, stats, utils, BiocGenerics, GenomeInfoDb, MASS, IRanges, GenomicRanges Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-2 MD5sum: 583cbdf8e02b48b6bbca88cc62a3e407 NeedsCompilation: no Package: sitePath Version: 1.28.0 Depends: R (>= 4.2) Imports: RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree, graphics, grDevices, gridExtra, methods, parallel, seqinr, stats, tidytree, utils LinkingTo: Rcpp Suggests: BiocStyle, devtools, knitr, magick, rmarkdown, testthat License: MIT + file LICENSE MD5sum: a16ea73250cfe4755fa2533582406221 NeedsCompilation: yes Package: sizepower Version: 1.82.0 Depends: stats License: LGPL MD5sum: 6d27f31ec4cddbbc786c9ef47ef3b62c NeedsCompilation: no Package: sketchR Version: 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Package: smartid Version: 1.8.0 Depends: R (>= 4.4) Imports: dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools, sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater, splatter, testthat (>= 3.0.0), tibble, tidytext, UpSetR License: MIT + file LICENSE MD5sum: a0c234ed7944ba2760b864fd64dbcf41 NeedsCompilation: no Package: SmartPhos Version: 1.2.0 Depends: R (>= 4.4.0) Imports: MultiAssayExperiment, SummarizedExperiment, data.table, shiny, shinythemes, shinyjs, shinyBS, shinyWidgets, parallel, DT, tools, stats, ggplot2, plotly, ggbeeswarm, pheatmap, grid, XML, MsCoreUtils, imputeLCMD, missForest, limma, proDA, decoupleR, piano, BiocParallel, doParallel, doRNG, e1071, magrittr, matrixStats, rlang, stringr, tibble, dplyr, tidyr, Biobase, vsn, factoextra, cowplot Suggests: knitr, BiocStyle, PhosR, testthat License: GPL-3 MD5sum: 5fa9989cf01e9aa699153810a55dbd81 NeedsCompilation: no Package: SMITE Version: 1.40.0 Depends: R (>= 3.5), GenomicRanges Imports: scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2, reactome.db, KEGGREST, BioNet, goseq, methods, IRanges, igraph, Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics, stats, utils Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: c4d5146b2b1b5dd51aab8b29b7713593 NeedsCompilation: no Package: smoothclust Version: 1.8.0 Depends: R (>= 4.4.0) Imports: SpatialExperiment, SummarizedExperiment, BiocNeighbors, Matrix, methods, utils Suggests: BiocStyle, knitr, STexampleData, scuttle, scran, scater, ggspavis, testthat License: MIT + file LICENSE MD5sum: c488e9268603044f87094623c795cc25 NeedsCompilation: no Package: smoppix Version: 1.4.0 Depends: R (>= 4.5.0) Imports: spatstat.geom(>= 3.2.0),spatstat.random,methods,BiocParallel,SummarizedExperiment,SpatialExperiment,Rdpack,stats,utils,lmerTest,lme4,ggplot2,graphics,grDevices,Rcpp (>= 1.0.11),spatstat.model,openxlsx,Rfast,reformulas,mgcv LinkingTo: Rcpp Suggests: 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knitr, rmarkdown, BiocStyle, ExperimentHub, lme4, lmerTest, ggfortify, tidyr, testthat (>= 3.0.0) License: GPL (>= 3) + file LICENSE MD5sum: b19833732558308ae9d606d63620850a NeedsCompilation: no Package: SpaceMarkers Version: 2.2.0 Depends: R (>= 4.4.0) Imports: matrixStats, matrixTests, rstatix, spatstat.explore, spatstat.geom, ape, hdf5r, nanoparquet, jsonlite, Matrix, qvalue, stats, utils, methods, ggplot2, reshape2, RColorBrewer, circlize, mixtools, dplyr, readbitmap, rlang, effsize, viridis Suggests: data.table, devtools, knitr, cowplot, rjson, rmarkdown, BiocStyle, testthat (>= 3.0.0), CoGAPS, ComplexHeatmap Enhances: BiocParallel License: MIT + file LICENSE MD5sum: 38b082f9d4c057fd42f3f6020db461ec NeedsCompilation: no Package: SpaceTrooper Version: 1.2.0 Depends: R (>= 4.4.0), SpatialExperiment Imports: DropletUtils, S4Vectors, SummarizedExperiment, arrow, data.table, dplyr, e1071, ggplot2, ggpubr, robustbase, scater, scuttle, sf, sfheaders, cowplot, glmnet, rhdf5, methods, 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matrixStats, methods, rlang, scran, SeuratObject, SingleCellExperiment, SpatialExperiment, stats, SummarizedExperiment, S4Vectors, utils, BiocParallel, BiocSingular Suggests: testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown, covr, BiocStyle, scater, Seurat (>= 5.0.0), patchwork, ggforce, ggnewscale, tensorflow License: GPL (>= 3) MD5sum: 3f5c8bf2b174c33176318476fe82a0e0 NeedsCompilation: no Package: spARI Version: 1.2.0 Depends: R (>= 4.1.0) Imports: Rcpp, stats, Matrix, SpatialExperiment, SummarizedExperiment, BiocParallel (>= 1.0) LinkingTo: Rcpp Suggests: FNN, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 8e4019069d8502f119ec120b78d9a5aa NeedsCompilation: yes Package: sparrow Version: 1.18.0 Depends: R (>= 4.1.0) Imports: babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet, checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>= 1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>= 2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix, methods, plotly (>= 4.9.0), stats, utils, viridis Suggests: AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, KernSmooth, knitr, magrittr, matrixStats, msigdbr (>= 10.0), orthogene, PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot License: MIT + file LICENSE MD5sum: 58911412f643e5ab067a951e223e1927 NeedsCompilation: no Package: SparseArray Version: 1.12.0 Depends: R (>= 4.3.0), methods, Matrix, BiocGenerics (>= 0.43.1), MatrixGenerics (>= 1.11.1), S4Vectors (>= 0.43.2), S4Arrays (>= 1.11.1) Imports: utils, stats, matrixStats, IRanges, XVector LinkingTo: S4Vectors, IRanges, XVector Suggests: HDF5Array, ExperimentHub, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 52c7e4bf2d628e28639791c80e6676b7 NeedsCompilation: yes Package: sparseMatrixStats Version: 1.24.0 Depends: MatrixGenerics (>= 1.5.3) Imports: Rcpp, Matrix, matrixStats (>= 0.60.0), methods LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: e4fa1a5604d206580a5e7fb7ffa753eb NeedsCompilation: yes Package: sparsenetgls Version: 1.30.0 Depends: R (>= 4.0.0), Matrix, MASS Imports: methods, glmnet, huge, stats, graphics, utils Suggests: testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) License: GPL-3 MD5sum: e91501d6465a14b064bcadc06a865558 NeedsCompilation: no Package: SparseSignatures Version: 2.22.0 Depends: R (>= 4.1.0), NMF Imports: nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2, gridExtra, reshape2, RhpcBLASctl Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr, License: file LICENSE MD5sum: 4e77fc214bc6f849efd13b644822fb96 NeedsCompilation: no Package: spaSim Version: 1.14.0 Depends: R (>= 4.2.0) Imports: ggplot2, methods, stats, dplyr, spatstat.geom, 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ExperimentHub, scales, S4Vectors, mgcv Suggests: stringr, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL (>= 3) + file LICENSE MD5sum: c292c4bfdd8299423b56d3415846ae1c NeedsCompilation: no Package: SpatialFeatureExperiment Version: 1.14.0 Depends: R (>= 4.3.0) Imports: Biobase, BiocGenerics (>= 0.51.2), BiocNeighbors, BiocParallel, data.table, DropletUtils, EBImage, grDevices, lifecycle, Matrix, methods, rjson, rlang, S4Vectors, sf, sfheaders, SingleCellExperiment, SpatialExperiment, spatialreg, spdep (>= 1.1-7), SummarizedExperiment, stats, terra, utils, zeallot Suggests: arrow, BiocStyle, dplyr, gmp, knitr, OSTA.data, RBioFormats, rhdf5, rmarkdown, scater, sfarrow, SFEData (>= 1.5.3), Seurat, SeuratObject, sparseMatrixStats, testthat (>= 3.0.0), tidyr, VisiumIO, Voyager (>= 1.7.2), withr, xml2 License: Artistic-2.0 MD5sum: bdb6aeefcdaa9dae64752c0c8e2dc648 NeedsCompilation: no Package: spatialHeatmap Version: 2.17.3 Depends: R (>= 4.5.0) Imports: data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid, gridExtra, igraph, methods, Matrix, rsvg, shiny, grDevices, graphics, ggplotify, parallel, reshape2, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2 Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend, DT, dynamicTreeCut, flashClust, gplots, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, scater, scuttle, scran, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, xlsx, yaml License: Artistic-2.0 MD5sum: b072bfa53020872b4ee1d7884ea267ca NeedsCompilation: no Package: SpatialOmicsOverlay Version: 1.12.0 Depends: R (>= 4.1.0) Imports: S4Vectors, 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a64bfd51452d04d2e982c70f594de97e NeedsCompilation: no Package: SpectralTAD Version: 1.28.0 Depends: R (>= 3.6) Imports: dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges, utils Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr License: MIT + file LICENSE MD5sum: 81d88a20ba419894748997af8313b73a NeedsCompilation: no Package: SpectraQL Version: 1.5.1 Depends: R (>= 4.4.0), ProtGenerics (>= 1.25.1) Imports: Spectra (>= 1.5.6), MsCoreUtils, methods Suggests: testthat, MsDataHub, roxygen2, rmarkdown, knitr, S4Vectors, BiocStyle, mzR License: Artistic-2.0 MD5sum: a8989867b93eb8ca5bdc89da3f2a9f06 NeedsCompilation: no Package: SpectriPy Version: 1.2.0 Depends: R (>= 4.4.0), reticulate (>= 1.42.0) Imports: Spectra (>= 1.19.9), IRanges, S4Vectors, MsCoreUtils, ProtGenerics, methods, data.table, snakecase Suggests: testthat, quarto, MsBackendMgf, MsDataHub, mzR, knitr, BiocStyle License: Artistic-2.0 MD5sum: 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ComplexHeatmap, elsa License: Artistic-2.0 + file LICENSE MD5sum: ce8ff5d2160971e18ec9cafe36cf5fef NeedsCompilation: no Package: SPICEY Version: 1.2.0 Depends: R (>= 4.5.0), utils, stats, grDevices Imports: GenomicRanges, GenomicFeatures, AnnotationDbi, S4Vectors, ggplot2, dplyr, tidyr, tibble, GenomeInfoDb, scales, cowplot Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 5f27e34a237e7c13fc165025e556c248 NeedsCompilation: no Package: spicyR Version: 1.24.0 Depends: R (>= 4.1) Imports: BiocParallel, ClassifyR, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, cli, concaveman, coxme, data.table, dplyr, ggforce, ggh4x, ggnewscale, ggplot2, ggthemes, grDevices, lifecycle, lmerTest, magrittr, methods, pheatmap, rlang, scales, scam, simpleSeg, spatstat.explore, spatstat.geom, stats, survival, tibble, tidyr Suggests: SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, 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scrapper, scuttle, stats, SummarizedExperiment, utils, withr Suggests: BASiCS (>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), igraph, IRanges, knitr, limSolve, lme4, magick, mfa, phenopath, preprocessCore, progress, pscl, rmarkdown, scales, scater (>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave License: GPL-3 + file LICENSE MD5sum: 4f64a2c9f840fc497c929a5a2439d1d5 NeedsCompilation: no Package: SpliceImpactR Version: 1.0.0 Depends: R (>= 3.5.0) Imports: data.table, BiocFileCache, BiocParallel, Biostrings, GenomicRanges, SummarizedExperiment, biomaRt, IRanges, PFAM.db, dplyr, ggplot2, ggpubr, patchwork, pwalign, rtracklayer, scales, stats, tidyr, tools, utils, magrittr, methods, S4Vectors Suggests: devtools, testthat (>= 3.0.0), knitr, rmarkdown, cowplot, stringr, readr, tibble, BiocStyle, clusterProfiler, AnnotationDbi, msigdbr, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 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rhandsontable, DT, grDevices, heatmaply, matrixStats, RColorBrewer, rvest, httr LinkingTo: ompBAM, Rcpp, RcppProgress Suggests: knitr, rmarkdown, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, AnnotationDbi, fgsea, Rsubread License: MIT + file LICENSE MD5sum: e7701b381610071592c179523423e10c NeedsCompilation: yes Package: SplicingFactory Version: 1.20.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, methods, stats Suggests: testthat, knitr, rmarkdown, ggplot2, tidyr License: GPL-3 + file LICENSE MD5sum: 5f63428290677d666532e390d60fa10d NeedsCompilation: no Package: SplicingGraphs Version: 1.52.0 Depends: R (>= 3.5.0), GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22), Rgraphviz (>= 2.3.7) Imports: methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>= 0.17.5), BiocParallel, IRanges (>= 2.21.2), Seqinfo, GenomicRanges (>= 1.23.21), Rsamtools, graph Suggests: igraph, Gviz, txdbmaker, TxDb.Hsapiens.UCSC.hg19.refGene, 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459ca06c359bd6f1f67cde45de38e662 NeedsCompilation: no Package: TFutils Version: 1.32.0 Depends: R (>= 4.1.0) Imports: methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase, rjson, BiocFileCache, DT, httr, readxl, AnnotationDbi, org.Hs.eg.db, utils, GenomicFiles, SummarizedExperiment Suggests: knitr, data.table, testthat, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, Seqinfo, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer, rmarkdown License: Artistic-2.0 MD5sum: 26037d6f34201474721ecd5c6159f064 NeedsCompilation: no Package: tidybulk Version: 2.2.0 Depends: R (>= 4.4.0), ttservice (>= 0.3.6) Imports: tibble, dplyr (>= 1.1.0), magrittr, tidyr, stringr, rlang, purrr, tidyselect, stats, parallel, utils, lifecycle, scales, ggplot2, SummarizedExperiment, GenomicRanges, methods, S4Vectors, crayon, Matrix Suggests: BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva, GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne, widyr, clusterProfiler, msigdbr, DESeq2, broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel, devtools, fastmatch, functional, survminer, tidySummarizedExperiment, markdown, uwot, matrixStats, preprocessCore, igraph, EGSEA, IRanges, here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS, pkgconfig, enrichplot, patchwork, airway License: GPL-3 MD5sum: 02e4b027782a427c26f570d53e0e96fc NeedsCompilation: no Package: tidyCoverage Version: 1.8.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, BiocParallel, BiocIO, rtracklayer, methods, tidyr, tibble, ggplot2, ggrastr, dplyr, fansi, pillar, rlang, scales, cli, purrr, vctrs, stats Suggests: tidySummarizedExperiment, plyranges, TxDb.Mmusculus.UCSC.mm10.knownGene, AnnotationHub, GenomicFeatures, BiocStyle, hues, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + 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ggplot2, methods, purrr, rlang, stats, stringr, tibble, tidyr Suggests: BiocStyle, HDCytoData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: c7f823272e8dbf6ac838587e2979511e NeedsCompilation: no Package: tidyomics Version: 1.8.0 Depends: R (>= 4.2) Imports: tidySummarizedExperiment, tidySingleCellExperiment, tidySpatialExperiment, tidyseurat, plyranges, purrr, rlang, stringr, cli, Suggests: utils, tidyr, dplyr, tibble, ggplot2, mockr (>= 0.2.0), knitr (>= 1.41), rmarkdown (>= 2.20), testthat (>= 3.1.6), nullranges, tidybulk, plyinteractions License: MIT + file LICENSE MD5sum: aba331472f924d3efb836c0fd18d4df6 NeedsCompilation: no Package: tidyprint Version: 1.0.0 Depends: R (>= 4.4.0) Imports: magrittr, tidyr, tibble, dplyr, purrr, pillar, S4Vectors, stringr, cli, vctrs, SummarizedExperiment, methods, rlang, fansi, pkgconfig Suggests: knitr, rmarkdown, BiocStyle, airway, pasilla, testthat (>= 3.0.0) License: GPL-3 MD5sum: 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rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse License: GPL-3 MD5sum: 5fbc705683b64e9efdbe72cf0a791a30 NeedsCompilation: no Package: topconfects Version: 1.28.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, assertthat, ggplot2, scales, grid, grDevices Suggests: limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat, reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr, rmarkdown, BiocStyle License: LGPL-2.1 | file LICENSE MD5sum: b2eb2724ee9073a56030bfab6b229c54 NeedsCompilation: no Package: topdownr Version: 1.34.0 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.20.0), ProtGenerics (>= 1.10.0), Biostrings (>= 2.42.1), S4Vectors (>= 0.12.2) Imports: grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2), MSnbase (>= 2.33.5), PSMatch (>= 1.11.4), ggplot2 (>= 2.2.1), mzR (>= 2.27.5) Suggests: topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2 License: GPL (>= 3) MD5sum: 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tidyr, data.table, assertthat, scales, graphics, grDevices, parallel, stats, utils, limma, jsonlite Suggests: rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools, PharmacoGx, xtable, markdown License: MIT + file LICENSE MD5sum: a7d8f6dc9155569cf56885968bc64340 NeedsCompilation: no Package: TPP Version: 3.40.0 Depends: R (>= 3.4), Biobase, dplyr, magrittr, tidyr Imports: biobroom, data.table, doParallel, foreach, futile.logger, ggplot2, grDevices, gridExtra, grid, knitr, limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr, purrr, RColorBrewer, RCurl, reshape2, rlang, rmarkdown, splines, stats, stringr, tibble, utils, VennDiagram, VGAM Suggests: BiocStyle, testthat License: Artistic-2.0 MD5sum: 46449faeb52b2bda0efcd3ee0bb0a4f6 NeedsCompilation: no Package: TPP2D Version: 1.28.0 Depends: R (>= 3.6.0), stats, utils, dplyr, methods Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl, parallel, MASS, BiocParallel, limma Suggests: knitr, testthat, rmarkdown, 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scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, InteractionSet, utils, rhdf5, strawr, txdbmaker Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack License: GPL (>= 2) MD5sum: 0617a9fc933cd1f220372919ddbd6391 NeedsCompilation: no Package: tradeSeq Version: 1.26.0 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: b43fcba0e5817b4b919cc933f7809bc2 NeedsCompilation: no Package: TrajectoryGeometry Version: 1.20.0 Depends: R (>= 4.1) Imports: pracma, rgl, ggplot2, stats, methods Suggests: dplyr, knitr, RColorBrewer, rmarkdown License: MIT + file LICENSE MD5sum: e87e1350892031119cf06d07badee9df NeedsCompilation: no Package: TrajectoryUtils Version: 1.20.0 Depends: SingleCellExperiment Imports: methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: bae154763cacd47ae89521800a2c5a2f NeedsCompilation: no Package: transcriptogramer Version: 1.34.0 Depends: R (>= 3.4), methods Imports: biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 1088210cd19bbf1f1d32aabb0f845434 NeedsCompilation: no Package: transcriptR Version: 1.40.0 Depends: R (>= 3.5.0), methods Imports: BiocGenerics, caret, chipseq, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2, Rsamtools, rtracklayer, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat, e1071 License: GPL-3 MD5sum: a9dea790ad5b000ea609fc5c104c0988 NeedsCompilation: no Package: transformGamPoi Version: 1.18.0 Imports: glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp LinkingTo: Rcpp Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 8a5927bad96d7544d9f9d09d77f018de NeedsCompilation: yes Package: transite Version: 1.30.0 Depends: R (>= 3.5) Imports: BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), stringr (>= 1.5.1), utils LinkingTo: Rcpp (>= 1.0.4.8) Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 96570aa42477bfac43ba9220479ae2ba NeedsCompilation: yes Package: tRanslatome Version: 1.50.0 Depends: R (>= 2.15.0), methods, limma, anota, DESeq2, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 MD5sum: fb69b77c53fbd7184c6d4e7a5b11720b NeedsCompilation: no Package: transmogR Version: 1.8.0 Depends: R (>= 4.1.0), Biostrings, GenomicRanges Imports: BSgenome, data.table, Seqinfo, GenomicFeatures, ggplot2 (>= 4.0.0), IRanges, jsonlite, matrixStats, methods, parallel, patchwork, scales, stats, S4Vectors, SummarizedExperiment, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, edgeR, extraChIPs, InteractionSet, knitr, readr, rmarkdown, rtracklayer, SimpleUpset, testthat (>= 3.0.0) License: GPL-3 MD5sum: b7c6381aa8f2e09815c42df824fcfde2 NeedsCompilation: yes Package: transomics2cytoscape Version: 1.22.0 Imports: RCy3, KEGGREST, dplyr, purrr, tibble, pbapply Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown 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matrixStats, stats, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi Suggests: knitr, rmarkdown,BiocStyle License: GPL-3 + file LICENSE MD5sum: 05732a70595436031c9c36159470c64b NeedsCompilation: no Package: tricycle Version: 1.20.0 Depends: R (>= 4.0), SingleCellExperiment Imports: methods, circular, ggplot2, ggnewscale, AnnotationDbi, scater, GenomicRanges, IRanges, S4Vectors, scattermore, dplyr, RColorBrewer, grDevices, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 401432ed1c8fa1968c2dd60ca9c95a51 NeedsCompilation: no Package: TrIdent Version: 1.4.0 Depends: R (>= 4.2.0) Imports: graphics, utils, stats, dplyr, ggplot2, patchwork, stringr, tidyr, roll Suggests: BiocStyle, knitr, rmarkdown, kableExtra License: GPL-2 MD5sum: 763f9e2f37a2d3a3643f920af4130675 NeedsCompilation: no Package: trio Version: 3.50.0 Depends: 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shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis Enhances: parallel License: MIT + file LICENSE MD5sum: e5f5b25bf385155a760df7e21e064697 NeedsCompilation: no Package: tRNA Version: 1.30.0 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: c53bf1ad8e5005ae295981836e239204 NeedsCompilation: no Package: tRNAdbImport Version: 1.30.0 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: e5fb868f068e6fdd0b4843dad7148c33 NeedsCompilation: no Package: tRNAscanImport 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Suggests: scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: a5527df722e0d4d7926047764917f99f NeedsCompilation: no Package: UCSC.utils Version: 1.8.0 Imports: methods, stats, httr, jsonlite, S4Vectors (>= 0.47.6) Suggests: DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: dd0c6c3e0db772995886e0cc65debb9f NeedsCompilation: no Package: UMI4Cats Version: 1.22.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats, annotate, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, 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seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio Enhances: PWMEnrich, rGADEM License: GPL-3 MD5sum: 3f1acb3e474242fb82f3f5ecce593d70 NeedsCompilation: yes Package: updateObject Version: 1.16.0 Depends: R (>= 4.2.0), methods, BiocGenerics (>= 0.51.1), S4Vectors Imports: utils, digest Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, SingleCellExperiment, MultiAssayExperiment, BiSeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 2826c0eccbdfa046e15b45518fb3a918 NeedsCompilation: no Package: UPDhmm Version: 1.8.0 Depends: R (>= 4.1.0) Imports: HMM, utils, VariantAnnotation, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, stats, BiocParallel, GenomeInfoDb Suggests: knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown, karyoploteR, regioneR, dplyr, BiocManager License: MIT + file LICENSE MD5sum: ac0b721e63876841bfc5ec9b2a386cdc NeedsCompilation: no Package: uSORT Version: 1.38.0 Depends: R (>= 3.3.0), tcltk Imports: igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 MD5sum: d2ddad3489023074e3885845864febc3 NeedsCompilation: no Package: VAExprs Version: 1.18.0 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: a62db142bd29ac92e10f0525766839ab NeedsCompilation: no Package: VanillaICE Version: 1.74.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, human610quadv1bCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 MD5sum: 75a77aaa0a6b295296333fdd497de109 NeedsCompilation: yes Package: VarCon Version: 1.20.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 9d9737b4a609ccd7a7004241ff616ccf NeedsCompilation: no Package: variancePartition Version: 1.42.0 Depends: R (>= 4.3.0), ggplot2, limma (>= 3.62.2), BiocParallel Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, gplots, corpcor, reformulas, matrixStats, RhpcBLASctl, reformulas, reshape2, gtools, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack, rlang, lme4 (>= 2.0-1), grDevices, graphics, Biobase, methods, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr License: GPL-2 MD5sum: 2864a77efcd8ede6796bfd8199b280e7 NeedsCompilation: no Package: VariantAnnotation Version: 1.58.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, Seqinfo, GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Rsamtools (>= 2.25.1) Imports: utils, DBI, Biobase, S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.77.2), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.69.1), BSgenome (>= 1.77.1), GenomicFeatures (>= 1.61.4), curl LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0) Suggests: GenomeInfoDb, RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr, magick, jsonlite, httr, rjsoncons License: Artistic-2.0 MD5sum: 96879f37b37f8407b57701ae0a125615 NeedsCompilation: yes Package: VariantExperiment Version: 1.26.0 Depends: R (>= 3.6.0), S4Vectors (>= 0.21.24), SummarizedExperiment (>= 1.13.0), GenomicRanges, Imports: GDSArray (>= 1.11.1), DelayedDataFrame (>= 1.6.0), tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray, DelayedArray, Biostrings, IRanges Suggests: testthat, knitr, rmarkdown, markdown, BiocStyle License: GPL-3 MD5sum: 4d7a0efdc9387eeaad1ee863c22e6751 NeedsCompilation: no Package: VariantFiltering Version: 1.48.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.25.1), VariantAnnotation (>= 1.13.29) Imports: utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Seqinfo (>= 0.99.2), GenomeInfoDb (>= 1.45.7), Biostrings (>= 2.77.2), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), GenomicFeatures (>= 1.61.4), Rsamtools (>= 2.25.1), BSgenome (>= 1.77.1), GenomicScores (>= 2.21.4), Gviz (>= 1.53.1), shiny, shinythemes, shinyjs, DT, shinyTree LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 License: Artistic-2.0 MD5sum: 6dde9e280f7994d84e10c37b0b3c7d61 NeedsCompilation: yes Package: VariantTools Version: 1.54.0 Depends: R (>= 3.5.0), S4Vectors (>= 0.17.33), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), VariantAnnotation (>= 1.11.16), methods Imports: Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel, GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7), BiocParallel, GenomeInfoDb, BSgenome, Biobase Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3), TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: Artistic-2.0 MD5sum: ee88d5acbc931d74029f7edd1cea2c01 NeedsCompilation: no Package: VaSP Version: 1.24.0 Depends: R (>= 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stats, SummarizedExperiment, utils LinkingTo: Rcpp Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: 232c43959f88e49848809abef77c6291 NeedsCompilation: yes Package: VegaMC Version: 3.50.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods License: GPL-2 MD5sum: 1f37cc910054752b1bbcde32f60e2fc3 NeedsCompilation: yes Package: velociraptor Version: 1.22.0 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: 77c9866e149023a7b30f96a6c27b04f1 NeedsCompilation: no Package: veloviz Version: 1.18.0 Depends: R (>= 4.1) Imports: Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 034277c82104ff37640fb38ff91538ee NeedsCompilation: yes Package: VennDetail Version: 1.28.0 Depends: R (>= 4.0.0) Imports: dplyr, DT, ggplot2, grid, gridExtra, magrittr, methods, patchwork, plotly, purrr, rlang, shiny, stats, tibble, tidyr, htmlwidgets, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0), markdown, RColorBrewer, rstudioapi License: GPL-2 MD5sum: 45b6d596938c329a6b3f519764fa62cf NeedsCompilation: no Package: VERSO Version: 1.22.0 Depends: R (>= 4.1.0) Imports: utils, data.tree, ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 4fd350723f4db117acc4680a73e5e905 NeedsCompilation: no Package: vidger Version: 1.32.0 Depends: R (>= 3.5) Imports: Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr, RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, testthat License: GPL-3 | file LICENSE MD5sum: d3e39ad4424557439180938d10f321ed NeedsCompilation: no Package: viper Version: 1.46.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: 09bcf9a50d62ec5251da3ce732c98c96 NeedsCompilation: no Package: ViSEAGO Version: 1.26.0 Depends: R (>= 3.6) Imports: data.table, AnnotationDbi, dendextend, dynamicTreeCut, GOSemSim, GO.db, heatmaply, topGO, AnnotationForge, DT, DiagrammeR, R.utils, RColorBrewer, UpSetR, biomaRt, fgsea, ggplot2, htmlwidgets, igraph, methods, plotly, scales, ComplexHeatmap, circlize Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager, stats, utils, grDevices, processx MD5sum: 8c7c43c5fbf3d214c017490e18ee4a27 NeedsCompilation: no Package: VisiumIO Version: 1.8.0 Depends: R (>= 4.5.0), TENxIO Imports: BiocBaseUtils, BiocGenerics, BiocIO (>= 1.15.1), jsonlite, methods, S4Vectors, sf, SingleCellExperiment, SpatialExperiment, SummarizedExperiment Suggests: arrow, BiocStyle, data.table, knitr, readr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: b086ac2e008a2bff5bd3037a931296fd NeedsCompilation: no Package: visiumStitched Version: 1.4.0 Depends: R (>= 4.4), SpatialExperiment Imports: BiocBaseUtils, BiocGenerics, clue, dplyr, DropletUtils, grDevices, imager, Matrix, methods, pkgcond, readr, rjson, S4Vectors, SingleCellExperiment, spatialLIBD (>= 1.17.8), stringr, SummarizedExperiment, tibble, tidyr, xml2 Suggests: BiocFileCache, BiocStyle, ggplot2, knitr, RefManageR, rmarkdown, sessioninfo, Seurat, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: f0c8c90ef6910d9a232170163fc7f07a NeedsCompilation: no Package: vissE Version: 1.20.0 Depends: R (>= 4.1) Imports: igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm, ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb, ggrepel, textstem, tidygraph, stats, scales, ggraph Suggests: testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore, knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr License: GPL-3 MD5sum: 4865ba41d11b17a333805478f51493f1 NeedsCompilation: no Package: VISTA Version: 1.0.0 Depends: R (>= 4.3) Imports: AnnotationDbi, cli, clusterProfiler, colorspace, DESeq2, dplyr, edgeR, forcats, ggplot2, ggrepel, GGally, ggpubr, grid, matrixStats, methods, msigdbr, limma, purrr, rlang, S4Vectors, scales, stringr, SummarizedExperiment, tibble, tidyr, tidyselect, viridis Suggests: airway, BiocStyle, circlize, ComplexHeatmap, DT, EnhancedVolcano, ggpointdensity, ggridges, ggalluvial, ggcorrplot, ggrain, ggvenn, enrichplot, knitr, magrittr, patchwork, org.Hs.eg.db, org.Mm.eg.db, quarto, rmarkdown, yaml, writexl, testthat (>= 3.0.0), uwot, xCell2 License: GPL-3 MD5sum: b8d29082b4f071cdf712c643e6724a7c NeedsCompilation: no Package: vmrseq Version: 1.4.0 Depends: R (>= 4.5.0) Imports: bumphunter, dplyr, BiocParallel, DelayedArray, GenomicRanges, ggplot2, methods, tidyr, locfit, gamlss.dist, recommenderlab, HDF5Array, data.table, SummarizedExperiment, IRanges, S4Vectors, devtools Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 7758df65218f744fcba3a245b0555977 NeedsCompilation: no Package: Voyager Version: 1.14.0 Depends: R (>= 4.2.0), SpatialFeatureExperiment (>= 1.7.3) Imports: BiocParallel, bluster, DelayedArray, ggnewscale, ggplot2 (>= 3.4.0), grDevices, grid, lifecycle, Matrix, MatrixGenerics, memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, spdep, stats, SummarizedExperiment, terra, utils, zeallot Suggests: arrow, automap, BiocSingular, BiocStyle, biscale, cowplot, data.table, DelayedMatrixStats, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, matrixStats, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, xml2 License: Artistic-2.0 MD5sum: 276ce21bbfc64b17bd0a707681b6751f NeedsCompilation: no Package: VplotR Version: 1.22.0 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, Seqinfo, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown License: GPL (>= 3) MD5sum: 30980b756f16efc4781f1004a881cabe NeedsCompilation: no Package: vsclust Version: 1.14.0 Depends: R (>= 4.2.0) Imports: matrixStats, limma, parallel, shiny, qvalue, grDevices, stats, MultiAssayExperiment, clusterProfiler, DOSE, httr, graphics LinkingTo: Rcpp Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, httr, magick License: GPL-2 MD5sum: 7ec83c3777459f80e8649ed7ba6a305b NeedsCompilation: yes Package: vsn Version: 3.80.0 Depends: R (>= 4.0.0), methods, Biobase Imports: affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat, hexbin License: Artistic-2.0 MD5sum: 6d661979c99a5d680faf23f7dc668117 NeedsCompilation: yes Package: vtpnet Version: 0.52.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: 6b87d722e152be7bc415e3a059899c57 NeedsCompilation: no Package: waddR Version: 1.26.0 Depends: R (>= 3.6.0) Imports: Rcpp (>= 1.0.1), arm (>= 1.10-1), eva, BiocFileCache (>= 2.6.0), BiocParallel, SingleCellExperiment, parallel, methods, stats LinkingTo: Rcpp, RcppArmadillo, Suggests: knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown, scater License: MIT + file LICENSE MD5sum: 3af356d154f7d640f77810e816fbab0b NeedsCompilation: yes Package: wateRmelon Version: 2.18.0 Depends: R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi, lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19, illuminaio Imports: Biobase Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BiocStyle, knitr, rmarkdown, IlluminaHumanMethylationEPICmanifest, irlba, FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore Enhances: minfi License: GPL-3 MD5sum: bff08da7caef0fb96ec16cf3412c1e5e NeedsCompilation: no Package: wavClusteR Version: 2.46.0 Depends: R (>= 3.2), GenomicRanges (>= 1.31.8), Rsamtools Imports: methods, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Biostrings (>= 2.47.6), foreach, GenomicFeatures (>= 1.31.3), ggplot2, Hmisc, mclust, rtracklayer (>= 1.39.7), seqinr, stringr, txdbmaker Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 Enhances: doMC License: GPL-2 MD5sum: c737ba78c0d741aa9e9da615704009e0 NeedsCompilation: no Package: wavFeatExt Version: 1.0.0 Depends: R (>= 4.6) Imports: DNAcopy, wavethresh, MASS, randomForest, glmnet, pROC, neuralnet, e1071, class, caret, ica, stats, graphics, utils, pls, matrixStats Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 91728ab6ab7d7c8b6165a333fa485ae0 NeedsCompilation: no 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Package: widgetTools Version: 1.90.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: 0f42b98de351d3b18a490729ca83bc4d NeedsCompilation: no Package: wiggleplotr Version: 1.36.0 Depends: R (>= 3.6) Imports: dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer, cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter, arrow License: Apache License 2.0 MD5sum: 97ed8136721898ad9cf50b3988b878ff NeedsCompilation: no Package: wpm Version: 1.22.0 Depends: R (>= 4.1.0) Imports: utils, methods, cli, Biobase, SummarizedExperiment, config, golem, shiny, DT, ggplot2, dplyr, rlang, stringr, shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer, logging Suggests: MSnbase, testthat, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: ae27aae92b3e36c7b8415e17185868d0 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