Package: a4 Version: 1.54.0 Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats, hgu95av2.db License: GPL-3 MD5sum: 1687fc472eef4eef417be4ef3a3439da Package: a4Base Version: 1.54.0 Depends: a4Preproc, a4Core Imports: methods, graphics, grid, Biobase, annaffy, mpm, genefilter, limma, multtest, glmnet, gplots Suggests: Cairo, ALL, hgu95av2.db, nlcv Enhances: gridSVG, JavaGD License: GPL-3 MD5sum: 1c1ace8622a1d9e6536a7633f05eec04 Package: a4Classif Version: 1.54.0 Depends: a4Core, a4Preproc Imports: methods, Biobase, ROCR, pamr, glmnet, varSelRF, utils, graphics, stats Suggests: ALL, hgu95av2.db, knitr, rmarkdown License: GPL-3 MD5sum: b5896b39f8db719dd3340268f04da492 Package: a4Core Version: 1.54.0 Imports: Biobase, glmnet, methods, stats Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 34d45cfcbfd73ee78adaeb797ed31348 Package: a4Preproc Version: 1.54.0 Imports: BiocGenerics, Biobase Suggests: ALL, hgu95av2.db, knitr, rmarkdown License: GPL-3 MD5sum: 50f8a8b2d4d7b9284e44fbd2ebd7ba40 Package: a4Reporting Version: 1.54.0 Imports: methods, xtable Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 0dad01a442296979f31191198eb98ab3 Package: ABarray Version: 1.74.0 Imports: Biobase, graphics, grDevices, methods, multtest, stats, tcltk, utils Suggests: limma, LPE License: GPL MD5sum: 168eb0d68bca1ae918468a4038d7f862 Package: abseqR Version: 1.24.0 Depends: R (>= 3.5.0) Imports: ggplot2, RColorBrewer, circlize, reshape2, VennDiagram, plyr, flexdashboard, BiocParallel (>= 1.1.25), png, grid, gridExtra, rmarkdown, knitr, vegan, ggcorrplot, ggdendro, plotly, BiocStyle, stringr, utils, methods, grDevices, stats, tools, graphics Suggests: testthat License: GPL-3 | file LICENSE MD5sum: 139bfba5dbfdd03e215fe103623f1f89 Package: ABSSeq Version: 1.60.0 Depends: R (>= 2.10), methods Imports: locfit, limma Suggests: edgeR License: GPL (>= 3) MD5sum: e0fa67df09047a3b7d3a5159e451dfbc Package: acde Version: 1.36.0 Depends: R(>= 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RColorBrewer, rlang, lpSolve, grid, grDevices, graphics, utils, pbapply Suggests: knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0), gplots, tidyr License: GPL-2 MD5sum: 8e2c0fceb574ef4ccd400d1c3c1ebaa5 Package: alabaster Version: 1.6.0 Depends: alabaster.base Imports: alabaster.matrix, alabaster.ranges, alabaster.se, alabaster.sce, alabaster.spatial, alabaster.string, alabaster.vcf, alabaster.bumpy, alabaster.mae Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 58fe4af14180355ecd78aaeace6cf75a Package: alabaster.base Version: 1.6.1 Imports: alabaster.schemas, methods, utils, S4Vectors, rhdf5 (>= 2.47.6), jsonlite, jsonvalidate, Rcpp LinkingTo: Rcpp, Rhdf5lib Suggests: BiocStyle, rmarkdown, knitr, testthat, digest, Matrix, alabaster.matrix License: MIT + file LICENSE MD5sum: a21bfaa8992a9f451a055e60f68b9a99 Package: alabaster.bumpy Version: 1.6.0 Depends: BumpyMatrix, alabaster.base Imports: methods, rhdf5, Matrix, BiocGenerics, S4Vectors, IRanges Suggests: BiocStyle, rmarkdown, knitr, testthat, jsonlite License: MIT + file LICENSE MD5sum: a2727d3174a9ede62a8eafead09d744d Package: alabaster.files Version: 1.4.0 Depends: alabaster.base, Imports: methods, S4Vectors, BiocGenerics, Rsamtools Suggests: BiocStyle, rmarkdown, knitr, testthat, VariantAnnotation, rtracklayer, Biostrings License: MIT + file LICENSE MD5sum: a156ed893bdd00365285c9999f76394a Package: alabaster.mae Version: 1.6.0 Depends: MultiAssayExperiment, alabaster.base Imports: methods, alabaster.se, S4Vectors, jsonlite, rhdf5 Suggests: testthat, knitr, SummarizedExperiment, BiocParallel, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: 707a86f35d0123b5a5ab712a9d83156f Package: alabaster.matrix Version: 1.6.1 Depends: alabaster.base Imports: methods, BiocGenerics, S4Vectors, DelayedArray (>= 0.31.8), S4Arrays, SparseArray (>= 1.5.22), rhdf5 (>= 2.47.1), HDF5Array, Matrix, Rcpp LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, chihaya, BiocSingular, ResidualMatrix License: MIT + file LICENSE MD5sum: 3f64afe4a720488735f3a881805a9abb Package: alabaster.ranges Version: 1.6.0 Depends: GenomicRanges, alabaster.base Imports: methods, S4Vectors, BiocGenerics, IRanges, GenomeInfoDb, rhdf5 Suggests: testthat, knitr, BiocStyle, jsonlite License: MIT + file LICENSE MD5sum: 0bd43807ea56dd2b91d3c1a6e9671cf3 Package: alabaster.sce Version: 1.6.0 Depends: SingleCellExperiment, alabaster.base Imports: methods, alabaster.se, jsonlite Suggests: knitr, testthat, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: 5bfad41425a94d3337121a24f5a3f6bc Package: alabaster.schemas Version: 1.6.0 Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: df5b1a01752a280122fd06565ad5509a Package: alabaster.se Version: 1.6.0 Depends: SummarizedExperiment, alabaster.base Imports: methods, alabaster.ranges, alabaster.matrix, BiocGenerics, S4Vectors, IRanges, GenomicRanges, jsonlite Suggests: rmarkdown, knitr, testthat, BiocStyle License: MIT + 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GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, multtest, directlabels Suggests: testthat, BiocStyle, knitr, rmarkdown, purrr, ggpattern, ggplot2, cowplot, tidyverse, magick License: GPL (>= 3) MD5sum: d94a6843f709fa40a320ba4777fa7600 Package: alevinQC Version: 1.22.0 Depends: R (>= 4.0) Imports: rmarkdown (>= 2.5), tools, methods, ggplot2 (>= 3.4.0), GGally, dplyr, rjson, shiny, shinydashboard, DT, stats, utils, tximport (>= 1.17.4), cowplot, rlang, Rcpp LinkingTo: Rcpp Suggests: knitr, BiocStyle, testthat (>= 3.0.0), BiocManager License: MIT + file LICENSE MD5sum: 5cee504c2a6020f886bbbc7779a3dddb Package: AllelicImbalance Version: 1.44.0 Depends: R (>= 4.0.0), grid, GenomicRanges (>= 1.31.8), SummarizedExperiment (>= 0.2.0), GenomicAlignments (>= 1.15.6) Imports: methods, BiocGenerics, AnnotationDbi, BSgenome (>= 1.47.3), VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Rsamtools (>= 1.99.3), GenomicFeatures (>= 1.31.3), Gviz, lattice, latticeExtra, gridExtra, seqinr, GenomeInfoDb, nlme Suggests: testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 8a74b930679d1f0c1c1f40009f0b5bbf Package: AlphaBeta Version: 1.20.0 Depends: R (>= 3.6.0) Imports: dplyr (>= 0.7), data.table (>= 1.10), stringr (>= 1.3), utils (>= 3.6.0), gtools (>= 3.8.0), optimx (>= 2018-7.10), expm (>= 0.999-4), stats (>= 3.6), BiocParallel (>= 1.18), igraph (>= 1.2.4), graphics (>= 3.6), ggplot2 (>= 3.2), grDevices (>= 3.6), plotly (>= 4.9) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 827d2dbabdd8277c11b58ec7e77ae5ea Package: AlphaMissenseR Version: 1.2.0 Depends: R (>= 4.3.0), dplyr Imports: rjsoncons (>= 1.0.1), DBI, duckdb (>= 0.9.1), rlang, curl, BiocFileCache, spdl, memoise, BiocBaseUtils, utils, stats, tools, methods, whisker, ggplot2 Suggests: BiocManager, BiocGenerics, GenomicRanges, GenomeInfoDb, AnnotationHub, ExperimentHub, ensembldb, httr, tidyr, r3dmol, bio3d, shiny, shiny.gosling, ggdist, gghalves, colorspace, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: d5d3bcb16ab8bfa4878af276d8838922 Package: AlpsNMR Version: 4.8.0 Depends: R (>= 4.2) Imports: utils, generics, graphics, stats, grDevices, cli, magrittr (>= 1.5), dplyr (>= 1.1.0), signal (>= 0.7-6), rlang (>= 0.3.0.1), scales (>= 1.2.0), stringr (>= 1.3.1), tibble(>= 1.3.4), tidyr (>= 1.0.0), tidyselect, readxl (>= 1.1.0), purrr (>= 0.2.5), glue (>= 1.2.0), reshape2 (>= 1.4.3), mixOmics (>= 6.22.0), matrixStats (>= 0.54.0), fs (>= 1.2.6), rmarkdown (>= 1.10), speaq (>= 2.4.0), htmltools (>= 0.3.6), pcaPP (>= 1.9-73), ggplot2 (>= 3.1.0), baseline (>= 1.2-1), vctrs (>= 0.3.0), BiocParallel (>= 1.34.0) Suggests: ASICS, BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5), GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr, NMRphasing, plotly (>= 4.7.1), progressr, SummarizedExperiment, S4Vectors, testthat (>= 2.0.0), writexl (>= 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Depends: R (>= 3.3.0) Imports: stats Suggests: BiocStyle, qgraph, knitr, rmarkdown License: GPL (>= 2) MD5sum: 7618131f723abcb454890837c2944875 Package: amplican Version: 1.28.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.22.0), Biostrings (>= 2.44.2), pwalign, data.table (>= 1.10.4-3) Imports: Rcpp, utils (>= 3.4.1), S4Vectors (>= 0.14.3), ShortRead (>= 1.34.0), IRanges (>= 2.10.2), GenomicRanges (>= 1.28.4), GenomeInfoDb (>= 1.12.2), BiocParallel (>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 3.3.4), ggthemes (>= 3.4.0), waffle (>= 0.7.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), dplyr (>= 0.7.2), rmarkdown (>= 1.6), knitr (>= 1.16), cluster (>= 2.1.4) LinkingTo: Rcpp Suggests: testthat, BiocStyle, GenomicAlignments License: GPL-3 MD5sum: 0bd4c517e41946ce8adf9432ee9fd5f2 Package: Anaquin Version: 2.30.0 Depends: R (>= 3.3), ggplot2 (>= 2.2.0) Imports: ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils, plyr, DESeq2 Suggests: RUnit, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: dcb8077e5b876cdcbeafaa01cd0c2a53 Package: ANCOMBC Version: 2.8.0 Depends: R (>= 4.3.0) Imports: stats, CVXR, DescTools, Hmisc, MASS, Matrix, Rdpack, doParallel, doRNG, energy, foreach, gtools, lme4, lmerTest, multcomp, nloptr, parallel, utils Suggests: mia (>= 1.6.0), DT, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, dplyr, knitr, magrittr, microbiome, phyloseq, rmarkdown, testthat, tidyr, tidyverse License: Artistic-2.0 MD5sum: a4093fd7bd411cbdb76404c078d94970 Package: AneuFinder Version: 1.34.0 Depends: R (>= 3.5), GenomicRanges, ggplot2, cowplot, AneuFinderData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, Rsamtools, bamsignals, DNAcopy, ecp, Biostrings, GenomicAlignments, reshape2, ggdendro, ggrepel, mclust Suggests: knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: 20f9d9c3bdc258c6c8c272836587d282 Package: ANF Version: 1.28.0 Imports: igraph, Biobase, survival, MASS, stats, RColorBrewer Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 6bb771e91c6fa933bf1872e02525bab3 Package: animalcules Version: 1.22.0 Depends: R (>= 4.3.0) Imports: ape, assertthat, caret, covr, DESeq2, dplyr, DT, forcats, ggforce, ggplot2, GUniFrac, lattice, limma, magrittr, Matrix, methods, MultiAssayExperiment, plotly, rentrez, reshape2, ROCit, S4Vectors (>= 0.23.19), scales, shiny, shinyjs, stats, SummarizedExperiment, tibble, tidyr, tsne, umap, utils, vegan, XML Suggests: BiocStyle, biomformat, devtools, glmnet, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: da642ded0c6c3229b74308c81a73f13e Package: annaffy Version: 1.78.0 Depends: R (>= 2.5.0), methods, Biobase, BiocManager, GO.db Imports: AnnotationDbi (>= 0.1.15), DBI Suggests: hgu95av2.db, multtest, tcltk License: LGPL MD5sum: 1785df96734e61c6ebd7924c86a72ade Package: annmap Version: 1.48.0 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: 5502c1ef2a2f53c00a3131d66575d3de Package: annotate Version: 1.84.0 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: d08f97426ce2624e65f4ce46c48c1050 Package: AnnotationDbi Version: 1.68.0 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: 7fc78e993b5d59410dd3b51ff732838c Package: AnnotationFilter Version: 1.30.0 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: 51ee3973ae9e207bb7b4add48b75b484 Package: AnnotationForge Version: 1.48.0 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: 445171ea6b660052995e41094a4fb4b8 Package: AnnotationHub Version: 3.14.0 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr, yaml, dplyr Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR, Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 5a10c32007c4e1bfecad71b4667a649e Package: AnnotationHubData Version: 1.36.0 Depends: R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges (>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15) Imports: GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocManager, biocViews, BiocCheck, graph, AnnotationDbi, Biobase, Biostrings, DBI, GenomeInfoDb (>= 1.15.4), OrganismDbi, RSQLite, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData, rmarkdown, HubPub License: Artistic-2.0 MD5sum: 37421edc2c3a1fdbed4d3def2c106700 Package: annotationTools Version: 1.80.0 Imports: Biobase, stats Suggests: BiocStyle License: GPL MD5sum: 188c5785d356349d0a4a43748e758d60 Package: annotatr Version: 1.32.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures, GenomicRanges, GenomeInfoDb (>= 1.10.3), ggplot2, IRanges, methods, readr, regioneR, reshape2, rtracklayer, S4Vectors (>= 0.23.10), stats, utils Suggests: BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene License: GPL-3 MD5sum: a18f2b7475cb3e3bdd4989d63e2d2791 Package: anota Version: 1.54.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: 9de9ef966d2efd35a9450b03d985de6d Package: anota2seq Version: 1.28.0 Depends: R (>= 3.4.0), methods Imports: multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices, graphics, stats, utils, SummarizedExperiment Suggests: BiocStyle,knitr License: GPL-3 MD5sum: d0eed90da4c3aff17420f72009003431 Package: antiProfiles Version: 1.46.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: a38f173fa2e2b963e525491b5f11f07a Package: AnVIL Version: 1.18.2 Depends: R (>= 3.6), dplyr, AnVILBase Imports: stats, utils, methods, futile.logger, jsonlite, httr, rapiclient (>= 0.1.3), yaml, tibble, tidyselect, tidyr, rlang, shiny, DT, miniUI, htmltools, BiocManager, BiocBaseUtils Suggests: parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools, AnVILAz, AnVILGCP, lifecycle License: Artistic-2.0 MD5sum: 3ef4447a1466bfd2804ef59719566f01 Package: AnVILAz Version: 1.0.0 Imports: AnVILBase, BiocBaseUtils, curl, httr2, jsonlite, methods, rjsoncons, tibble, utils Suggests: BiocStyle, dplyr, knitr, readr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: b78b2a943dfe15616067bdd60307f714 Package: AnVILBase Version: 1.0.0 Imports: httr, httr2, dplyr, jsonlite, methods, tibble Suggests: AnVIL, AnVILAz, AnVILGCP, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), tinytest License: Artistic-2.0 MD5sum: 8971e6861f2b9f0912564145b4805ce0 Package: AnVILBilling Version: 1.16.0 Depends: R (>= 4.1) Imports: methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr, dplyr, lubridate, plotly, ggplot2 Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: ba3ec82d4c17bdb9a57716457af3dd00 Package: AnVILGCP Version: 1.0.0 Imports: AnVILBase, BiocBaseUtils, dplyr, httr, jsonlite, parallel, methods, rlang, stats, tibble, tidyr, utils Suggests: AnVIL, BiocStyle, httr2, knitr, rmarkdown, testthat, withr License: Artistic-2.0 MD5sum: 6fc033d543cc3f4bf1afca33a089199f Package: AnVILPublish Version: 1.16.0 Imports: AnVIL, AnVILGCP, BiocBaseUtils, BiocManager, httr, jsonlite, rmarkdown, yaml, readr, whisker, tools, utils, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 98decd92c053a386ce9595c6adca96d2 Package: AnVILWorkflow Version: 1.6.0 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: 0f44f70f00899a79db9bae72c6c95e03 Package: APAlyzer Version: 1.20.0 Depends: R (>= 3.5.0) Imports: GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq2, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, VariantAnnotation, dplyr, tidyr, repmis, Rsamtools, HybridMTest Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, testthat, pasillaBamSubset License: LGPL-3 MD5sum: be3199fa11358b80e91baedf30c029ba Package: apComplex Version: 2.72.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: 4969a860a574a3984597fe5c55da4c68 Package: apeglm Version: 1.28.0 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 9ce1046134cf938d29f74f6b4de4090b Package: APL Version: 1.10.2 Depends: R (>= 4.4.0) Imports: Matrix, RSpectra, ggrepel, ggplot2, viridisLite, plotly, SeuratObject, SingleCellExperiment, magrittr, SummarizedExperiment, topGO, methods, stats, utils, org.Hs.eg.db, org.Mm.eg.db, rlang Suggests: BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran, sparseMatrixStats, testthat License: GPL (>= 3) MD5sum: f4e6895bb4b7ee4e14a11b1193d40fa4 Package: appreci8R Version: 1.24.0 Imports: shiny, shinyjs, DT, VariantAnnotation, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, Biostrings, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.gnomADex.r2.1.hs37d5, COSMIC.67, rentrez, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137, seqinr, openxlsx, Rsamtools, stringr, stats, GenomicRanges, S4Vectors, GenomicFeatures, IRanges, GenomicScores, SummarizedExperiment Suggests: GO.db, org.Hs.eg.db, utils License: LGPL-3 MD5sum: 8b39c5a342c254288874d827ef46df56 Package: aroma.light Version: 3.36.0 Depends: R (>= 2.15.2) Imports: stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.23.0), R.utils (>= 2.9.0), matrixStats (>= 0.55.0) Suggests: princurve (>= 2.1.4) License: GPL (>= 2) MD5sum: 7522e0280e57088fc78c41fc66a70931 Package: ArrayExpress Version: 1.66.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: oligo, limma, httr, utils, jsonlite, rlang, tools, methods Suggests: affy License: Artistic-2.0 MD5sum: 0fafd20549ac0eb2e06d4f3b9d4239e2 Package: arrayMvout Version: 1.64.0 Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy Imports: mdqc, affyContam, lumi Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf License: Artistic-2.0 MD5sum: 1d1021aba856ae51c4d30111ed70354d Package: arrayQuality Version: 1.84.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL MD5sum: a7d7e3a84493d13f52733a84413076eb Package: arrayQualityMetrics Version: 3.62.0 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, genefilter, graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter, lattice, latticeExtra, limma, methods, RColorBrewer, setRNG, stats, utils, vsn (>= 3.23.3), XML, svglite Suggests: ALLMLL, CCl4, BiocStyle, knitr License: LGPL (>= 2) MD5sum: db1ce369ca76689557977e4446e08212 Package: ARRmNormalization Version: 1.46.0 Depends: R (>= 2.15.1), ARRmData License: Artistic-2.0 MD5sum: e0b00360565890cac6ec2a7b3e4c1ed7 Package: artMS Version: 1.24.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, bit64, circlize, cluster, corrplot, data.table, dplyr, getopt, ggdendro, ggplot2, gplots, ggrepel, graphics, grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db, pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr, tidyr, UpSetR, utils, VennDiagram, yaml Suggests: BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR, knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat License: GPL (>= 3) + file LICENSE MD5sum: f5a5522c90b876276a10abd618c7d1fb Package: ASAFE Version: 1.32.0 Depends: R (>= 3.2) Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 3e04825efaea57800c74263bd55ee130 Package: ASEB Version: 1.50.0 Depends: R (>= 2.8.0), methods Imports: graphics, methods, utils License: GPL (>= 3) MD5sum: 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graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown, RSQLite (>= 1.1) License: GPL-3 MD5sum: ee9be4367723d81357a2f29fb7d9515b Package: ASSET Version: 2.24.0 Depends: R (>= 3.5.0), stats, graphics Imports: MASS, msm, rmeta Suggests: RUnit, BiocGenerics, knitr License: GPL-2 + file LICENSE MD5sum: 4fc48c6f6a7c0eb7384c5a9fb782fa0b Package: ASSIGN Version: 1.42.0 Depends: R (>= 3.4) Imports: gplots, graphics, grDevices, msm, Rlab, stats, sva, utils, ggplot2, yaml Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown License: MIT + file LICENSE MD5sum: cdc5a68baaf52a7fdfac3e6473147032 Package: assorthead Version: 1.0.1 Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 99b7daa8ac4ce5bf26716041df9cf853 Package: ASURAT Version: 1.10.0 Depends: R (>= 4.0.0) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp (>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize, grid, grDevices, graphics LinkingTo: Rcpp Suggests: ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: fce9f72a78bb346a9245d9a5ccda3827 Package: ATACseqQC Version: 1.30.0 Depends: R (>= 3.5.0), BiocGenerics, S4Vectors Imports: BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges, GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid, limma, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats, motifStack, preseqR, utils, KernSmooth, edgeR, BiocParallel Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat, rmarkdown License: GPL (>= 2) MD5sum: 214c7e879f1f3f85d3f1125110ead589 Package: atena Version: 1.12.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, MatrixGenerics, BiocParallel, S4Vectors, IRanges, GenomicFeatures, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats, cli Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer License: Artistic-2.0 MD5sum: e5e5448fa3126ff11cea5fdd43a0d6b3 Package: atSNP Version: 1.22.0 Depends: R (>= 3.6) Imports: BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testthat, utils, lifecycle LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: f03007aa7f116c428b16a43d9add8855 Package: attract Version: 1.58.0 Depends: R (>= 3.4.0), AnnotationDbi Imports: Biobase, limma, cluster, GOstats, graphics, stats, reactome.db, KEGGREST, org.Hs.eg.db, utils, methods Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) MD5sum: a1a9934de162ad8427b96df1bbd72999 Package: AUCell Version: 1.28.0 Imports: DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats, SummarizedExperiment, BiocGenerics, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: c79343b5cbcfe7d57cb9a41a401d037b Package: autonomics Version: 1.14.7 Depends: R (>= 4.0) Imports: abind, BiocFileCache, BiocGenerics, bit64, cluster, codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma, magrittr, matrixStats, methods, MultiAssayExperiment, parallel, RColorBrewer, rlang, R.utils, readxl, S4Vectors, scales, stats, stringi, SummarizedExperiment, tidyr, tidyselect, tools, utils, vsn Suggests: affy, AnnotationDbi, AnnotationHub, apcluster, Biobase, BiocManager, BiocStyle, Biostrings, diagram, DBI, e1071, ensembldb, GenomicDataCommons, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, jsonlite, knitr, lme4, lmerTest, MASS, patchwork, mixOmics, mpm, nlme, OlinkAnalyze, org.Hs.eg.db, org.Mm.eg.db, pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite, remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer, statmod, survival, survminer, testthat, UniProt.ws, writexl, XML License: GPL-3 MD5sum: 7e49e9054fc00c63eddcf9421bae0a7a Package: AWFisher Version: 1.20.0 Depends: R (>= 3.6) Imports: edgeR, limma, stats Suggests: knitr, tightClust License: GPL-3 MD5sum: 231933fff50187ce7b2abe582980516e Package: awst Version: 1.14.0 Imports: stats, methods, SummarizedExperiment Suggests: airway, ggplot2, testthat, EDASeq, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown License: MIT + file LICENSE MD5sum: f6ff9e0e89a084290d45cbc8386847f1 Package: BaalChIP Version: 1.32.0 Depends: R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools, Imports: GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy, reshape2, scales, coda, foreach, ggplot2, methods, utils, graphics, stats Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 07e1b160e1f5db458d0177bdbcd7ff76 Package: bacon Version: 1.34.0 Depends: R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel, ellipse Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 License: GPL (>= 2) MD5sum: f359138520ca3051056e89f863831bd8 Package: BADER Version: 1.44.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 MD5sum: 87cd82da0dbabcfaf62b041ebd2c5a8a Package: BadRegionFinder Version: 1.34.0 Imports: VariantAnnotation, Rsamtools, biomaRt, GenomicRanges, S4Vectors, utils, stats, grDevices, graphics Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: ad5b8e178c3b22be4191b2bfd16f10d9 Package: BAGS Version: 2.46.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 MD5sum: 2ba856d220edf540e47c997ff415de2b Package: ballgown Version: 2.38.0 Depends: R (>= 3.5.0), methods Imports: GenomicRanges (>= 1.17.25), IRanges (>= 1.99.22), S4Vectors (>= 0.9.39), RColorBrewer, splines, sva, limma, rtracklayer (>= 1.29.25), Biobase (>= 2.25.0), GenomeInfoDb Suggests: testthat, knitr, markdown License: Artistic-2.0 MD5sum: 8792012e3f140d0fcd71a63450bcb502 Package: bambu Version: 3.8.0 Depends: R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>= 0.22.1), BSgenome, IRanges Imports: BiocGenerics, BiocParallel, data.table, dplyr, tidyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost LinkingTo: Rcpp, RcppArmadillo Suggests: AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2, ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq Enhances: parallel License: GPL-3 + file LICENSE MD5sum: 20213e01adb564778375b6375275ac90 Package: bamsignals Version: 1.38.0 Depends: R (>= 3.5.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 26594f5b74de7465a8817d3a0a0addff Package: BANDITS Version: 1.22.0 Depends: R (>= 4.3.0) Imports: Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings License: GPL (>= 3) MD5sum: 612bc42134405c2ea85fb1cd2efa6800 Package: bandle Version: 1.10.0 Depends: R (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc Imports: Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr, knitr, methods, BiocParallel, robustbase, BiocStyle, ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils, grDevices, rlang LinkingTo: Rcpp, RcppArmadillo, BH Suggests: coda (>= 0.19-4), testthat, interp, fields, pheatmap, viridis, rmarkdown, spelling License: Artistic-2.0 MD5sum: f93fcc3db21702d8f96fbb635c4cacc7 Package: Banksy Version: 1.2.0 Depends: R (>= 4.4.0) Imports: aricode, data.table, dbscan, SpatialExperiment, SingleCellExperiment, SummarizedExperiment, S4Vectors, stats, matrixStats, mclust, igraph, irlba, leidenAlg (>= 1.1.0), utils, uwot, RcppHungarian Suggests: knitr, rmarkdown, pals, scuttle, scater, scran, cowplot, ggplot2, testthat (>= 3.0.0), harmony, Seurat, ExperimentHub, spatialLIBD, BiocStyle License: file LICENSE MD5sum: 17c6e59d4f198cc71a8ea85392cb777e Package: banocc Version: 1.30.0 Depends: R (>= 3.5.1), rstan (>= 2.17.4) Imports: coda (>= 0.18.1), mvtnorm, stringr Suggests: knitr, rmarkdown, methods, testthat, BiocStyle License: MIT + file LICENSE MD5sum: aceeee1025530b234ecdcc0558bace32 Package: barcodetrackR Version: 1.14.0 Depends: R (>= 4.1) Imports: cowplot, circlize, dplyr, ggplot2, ggdendro, ggridges, graphics, grDevices, magrittr, plyr, proxy, RColorBrewer, rlang, scales, shiny, stats, SummarizedExperiment, S4Vectors, tibble, tidyr, vegan, viridis, utils Suggests: BiocStyle, knitr, magick, rmarkdown, testthat License: file LICENSE MD5sum: 91656887b7f22060faea2a0fac95df20 Package: basecallQC Version: 1.30.0 Depends: R (>= 3.4), stats, utils, methods, rmarkdown, knitr, prettydoc, yaml Imports: ggplot2, stringr, XML, raster, dplyr, data.table, tidyr, magrittr, DT, lazyeval, ShortRead Suggests: testthat, BiocStyle License: GPL (>= 3) MD5sum: 28e4d29b9f1e101be8b7e238f60da2c8 Package: BaseSpaceR Version: 1.50.0 Depends: R (>= 2.15.0), RCurl, RJSONIO Imports: methods Suggests: RUnit, IRanges, Rsamtools License: Apache License 2.0 MD5sum: f7ce931d093c49c9b42dcfcb3ba8f5d1 Package: Basic4Cseq Version: 1.42.0 Depends: R (>= 3.4), Biostrings, GenomicAlignments, caTools, GenomicRanges, grDevices, graphics, stats, utils Imports: methods, RCircos, BSgenome.Ecoli.NCBI.20080805 Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 58215cdd1677addd89634eb2396f2c62 Package: BASiCS Version: 2.18.0 Depends: R (>= 4.2), SingleCellExperiment Imports: Biobase, BiocGenerics, coda, cowplot, ggExtra, ggplot2, graphics, grDevices, MASS, methods, Rcpp (>= 0.11.3), S4Vectors, scran, scuttle, stats, stats4, SummarizedExperiment, viridis, utils, Matrix (>= 1.5.0), matrixStats, assertthat, reshape2, BiocParallel, posterior, hexbin LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, magick License: GPL-3 MD5sum: a4ee417393317e232d75a7d4ebe294fd Package: BASiCStan Version: 1.8.0 Depends: R (>= 4.2), BASiCS, rstan (>= 2.18.1) Imports: methods, glmGamPoi, scran, scuttle, stats, utils, SingleCellExperiment, SummarizedExperiment, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstantools (>= 2.1.1) LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 MD5sum: f9fbc660a6f29ce741270887530d3e7d Package: BasicSTARRseq Version: 1.34.0 Depends: GenomicRanges,GenomicAlignments Imports: S4Vectors,methods,IRanges,GenomeInfoDb,stats Suggests: knitr License: LGPL-3 MD5sum: a3a331a60c0dcab0dc3b78a5041e2d15 Package: basilisk Version: 1.18.0 Depends: reticulate Imports: utils, methods, parallel, dir.expiry, basilisk.utils (>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, testthat, callr License: GPL-3 MD5sum: 843cfddb7f6fcaf3eb6bb48aab95ab76 Package: basilisk.utils Version: 1.18.0 Imports: utils, methods, tools, dir.expiry Suggests: reticulate, knitr, rmarkdown, BiocStyle, testthat, basilisk License: GPL-3 MD5sum: 69c25f8ddf3b93752b79126d536da668 Package: batchelor Version: 1.22.0 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix, SparseArray, DelayedArray (>= 0.31.5), DelayedMatrixStats, BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq License: GPL-3 MD5sum: b5a05ec9664bf6b1c8f72c2f0a7b15ab Package: BatchQC Version: 2.2.0 Depends: R (>= 4.4.0) Imports: data.table, DESeq2, dplyr, EBSeq, ggdendro, ggnewscale, ggplot2, limma, matrixStats, pheatmap, RColorBrewer, reader, reshape2, scran, shiny, shinyjs, shinythemes, stats, SummarizedExperiment, sva, S4Vectors, tibble, tidyr, tidyverse, utils Suggests: BiocManager, BiocStyle, bladderbatch, devtools, knitr, lintr, plotly, rmarkdown, spelling, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: c90c835f289334034c163120c3852134 Package: BayesKnockdown Version: 1.32.0 Depends: R (>= 3.3) Imports: stats, Biobase License: GPL-3 MD5sum: ada8a6c5d6512893194d451902a1500c Package: BayesSpace Version: 1.16.0 Depends: R (>= 4.0.0), SingleCellExperiment Imports: Rcpp (>= 1.0.4.6), stats, methods, purrr, scater, scran, SummarizedExperiment, coda, rhdf5, S4Vectors, Matrix, magrittr, assertthat, arrow, mclust, RCurl, DirichletReg, xgboost, utils, dplyr, rlang, ggplot2, tibble, rjson, tidyr, scales, microbenchmark, BiocFileCache, BiocSingular, BiocParallel LinkingTo: Rcpp, RcppArmadillo, RcppDist, RcppProgress Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, viridis, patchwork, RColorBrewer, Seurat License: MIT + file LICENSE MD5sum: 362b7a7a46cd921f9804c0af6ab1ac33 Package: bayNorm Version: 1.24.0 Depends: R (>= 3.5), Imports: Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix, parallel, MASS, locfit, fitdistrplus, stats, methods, graphics, grDevices, SingleCellExperiment, SummarizedExperiment, BiocParallel, utils LinkingTo: Rcpp, RcppArmadillo,RcppProgress Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat License: GPL (>= 2) MD5sum: 6a3a2853f2688d388a611803d7bf0d69 Package: baySeq Version: 2.40.0 Depends: R (>= 2.3.0), methods Imports: edgeR, GenomicRanges, abind, parallel, graphics, stats, utils Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: 1863ab26899bcce814e9a830393bb9a4 Package: BBCAnalyzer Version: 1.36.0 Imports: SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices, GenomicRanges, IRanges, Biostrings Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 6cf967c0188f7747ed32a9bbd1d52d2b Package: BCRANK Version: 1.68.0 Depends: methods Imports: Biostrings Suggests: seqLogo License: GPL-2 MD5sum: 2cb6eee60ef842f7598f9fd70057977d Package: bcSeq Version: 1.28.0 Depends: R (>= 3.4.0) Imports: Rcpp (>= 0.12.12), Matrix, Biostrings LinkingTo: Rcpp, Matrix Suggests: knitr License: GPL (>= 2) MD5sum: 188d96cc62c2640fbb30883dfc38a20d Package: beachmat Version: 2.22.0 Imports: methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics, Matrix, Rcpp LinkingTo: Rcpp, assorthead Suggests: testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array, beachmat.hdf5 License: GPL-3 MD5sum: 8d16cbf48fff7fd49a49b23409c4e35b Package: beachmat.hdf5 Version: 1.4.0 Imports: methods, beachmat, HDF5Array, DelayedArray, Rcpp LinkingTo: Rcpp, assorthead, beachmat, Rhdf5lib Suggests: testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix License: GPL-3 MD5sum: ffd99c245773f440d4654ae3bec7d6dc Package: beadarray Version: 2.56.0 Depends: R (>= 2.13.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), hexbin Imports: BeadDataPackR, limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, illuminaio, methods, ggplot2 Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr License: MIT + file LICENSE MD5sum: 820883b1377d0a9a33efea5025817d10 Package: BeadDataPackR Version: 1.58.0 Imports: stats, utils Suggests: BiocStyle, knitr License: GPL-2 MD5sum: 2d3a1c1a5908dc306c50c23736d86f28 Package: BEARscc Version: 1.25.0 Depends: R (>= 3.5.0) Imports: ggplot2, SingleCellExperiment, data.table, stats, utils, graphics, compiler Suggests: testthat, cowplot, knitr, rmarkdown, BiocStyle, NMF License: GPL-3 MD5sum: 7c983852fb180c31a1eabc7dd57aa8fc Package: BEAT Version: 1.44.0 Depends: R (>= 2.13.0) Imports: GenomicRanges, ShortRead, Biostrings, BSgenome License: LGPL (>= 3.0) MD5sum: 465b4b4f7f7cca1cac1001deb0d1d744 Package: BEclear Version: 2.22.0 Depends: BiocParallel (>= 1.14.2) Imports: futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp, abind, stats, graphics, utils, methods, dixonTest, ids LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, pander, seewave License: GPL-3 MD5sum: cc68d126f839f1b0d382e35d2ecfce22 Package: beer Version: 1.10.0 Depends: R (>= 4.2.0), PhIPData (>= 1.1.1), rjags Imports: cli, edgeR, BiocParallel, methods, progressr, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr, rmarkdown, dplyr, ggplot2, spelling License: MIT + file LICENSE MD5sum: 43549a869c9ec62e09d4dfce4ed6622b Package: benchdamic Version: 1.12.2 Depends: R (>= 4.3.0) Imports: stats, stats4, utils, methods, phyloseq, TreeSummarizedExperiment, BiocParallel, zinbwave, edgeR, DESeq2, limma, ALDEx2, corncob, SummarizedExperiment, MAST, Seurat, ANCOMBC, microbiome, mixOmics, lme4, NOISeq, dearseq, MicrobiomeStat, Maaslin2, GUniFrac, metagenomeSeq, MGLM, ggplot2, RColorBrewer, plyr, reshape2, ggdendro, ggridges, graphics, cowplot, grDevices, tidytext Suggests: knitr, rmarkdown, kableExtra, BiocStyle, magick, SPsimSeq, testthat License: Artistic-2.0 MD5sum: 8c952b14e0b9fe25bbdbdb179e059938 Package: BERT Version: 1.2.0 Depends: R (>= 4.3.0) Imports: cluster, comprehenr, foreach (>= 1.5.2), invgamma, iterators (>= 1.0.14), janitor (>= 2.2.0), limma (>= 3.46.0), logging (>= 0.10-108), sva (>= 3.38.0), SummarizedExperiment, methods, BiocParallel Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 0f11e2cfefd31a156c3a8fc385de48a3 Package: betaHMM Version: 1.2.1 Depends: R (>= 4.3.0), SummarizedExperiment, S4Vectors, GenomicRanges Imports: stats, ggplot2, scales, methods, pROC, foreach, doParallel, parallel, cowplot, dplyr, tidyr, tidyselect, stringr, utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: 496c168c0f0ee31b47341e43d5f36bee Package: bettr Version: 1.2.0 Depends: R (>= 4.4.0) Imports: dplyr (>= 1.0), tidyr, ggplot2 (>= 3.4.1), shiny (>= 1.6), tibble, ComplexHeatmap, bslib, rlang, circlize, stats, grid, methods, cowplot, Hmisc, sortable, shinyjqui, grDevices, scales, DT, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: MIT + file LICENSE MD5sum: 14bf948ed20f95f66672e87504d826e7 Package: BG2 Version: 1.6.0 Depends: R (>= 4.2.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), MASS (>= 7.3-58.1), stats (>= 4.2.2) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 139820b4fc9342f474a61b0f5d9b7aa1 Package: BgeeCall Version: 1.22.0 Depends: R (>= 3.6) Imports: GenomicFeatures, tximport, Biostrings, rtracklayer, biomaRt, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5, txdbmaker Suggests: knitr, testthat, rmarkdown, AnnotationHub, httr License: GPL-3 + file LICENSE MD5sum: cb95cad150b21e2ec32c3683b8587d61 Package: BgeeDB Version: 2.32.0 Depends: R (>= 3.6.0), topGO, tidyr Imports: R.utils, data.table, curl, RCurl, digest, methods, stats, utils, dplyr, RSQLite, graph, Biobase, zellkonverter, anndata, HDF5Array, bread Suggests: knitr, BiocStyle, testthat, rmarkdown, markdown License: GPL-3 + file LICENSE MD5sum: a08d43468e98c4ec71f49d6d00348501 Package: bgx Version: 1.72.0 Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), gcrma (>= 2.4.1) Imports: Rcpp (>= 0.11.0) LinkingTo: Rcpp Suggests: affydata, hgu95av2cdf License: GPL-2 MD5sum: 7157c451b6c5e7ee6f2a7632d0193785 Package: BicARE Version: 1.64.0 Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase, GO.db Imports: methods Suggests: hgu95av2 License: GPL-2 MD5sum: 61e8e9b2bfe771f52db5e713857cd8d4 Package: BiFET Version: 1.26.0 Depends: R (>= 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ggplotify, SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr License: Artistic-2.0 MD5sum: 40537043a38da32072942dd0de171f83 Package: Biobase Version: 2.66.0 Depends: R (>= 2.10), BiocGenerics (>= 0.27.1), utils Imports: methods Suggests: tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr, limma License: Artistic-2.0 MD5sum: 389ff1953ae859d270c7e5e5bd61bd4b Package: biobroom Version: 1.38.0 Depends: R (>= 3.0.0), broom Imports: dplyr, tidyr, Biobase Suggests: limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, rmarkdown, SummarizedExperiment License: LGPL MD5sum: 5ee3aa2247cf0cc0ccf0f634e4b40ac7 Package: bioCancer Version: 1.34.0 Depends: R (>= 3.6.0), radiant.data (>= 0.9.1), cBioPortalData, XML(>= 3.98) Imports: R.oo, R.methodsS3, DT (>= 0.3), dplyr (>= 0.7.2), tidyr, shiny (>= 1.0.5), AlgDesign (>= 1.1.7.3), import (>= 1.1.0), methods, AnnotationDbi, shinythemes, Biobase, geNetClassifier, org.Hs.eg.db, 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branchpointer Version: 1.32.0 Depends: caret, R(>= 3.4) Imports: plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt, Biostrings, parallel, utils, stats, BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges, GenomeInfoDb, IRanges, S4Vectors, data.table Suggests: knitr, BiocStyle License: BSD_3_clause + file LICENSE MD5sum: 305947fb4cd73d59a8f63b7bcd5e8653 Package: breakpointR Version: 1.24.0 Depends: R (>= 3.5), GenomicRanges, cowplot, breakpointRdata Imports: methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>= 1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2, BiocGenerics, gtools, doParallel, foreach Suggests: knitr, BiocStyle, testthat License: file LICENSE MD5sum: f4b0b97e317264b1ca678ff9815803c4 Package: brendaDb Version: 1.20.0 Imports: dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel, crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, devtools License: MIT + file 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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: a45c6c23c2d079776fe6170327aec778 Package: ccmap Version: 1.32.0 Imports: AnnotationDbi (>= 1.36.2), BiocManager (>= 1.30.4), ccdata (>= 1.1.2), doParallel (>= 1.0.10), data.table (>= 1.10.4), foreach (>= 1.4.3), parallel (>= 3.3.3), xgboost (>= 0.6.4), lsa (>= 0.73.1) Suggests: crossmeta, knitr, rmarkdown, testthat, lydata License: MIT + file LICENSE MD5sum: c11d779ff3b3eff0cfd27aa0d6d08838 Package: CCPlotR Version: 1.4.0 Imports: plyr, tidyr, dplyr, ggplot2, forcats, ggraph, igraph, scatterpie, circlize, ComplexHeatmap, tibble, grid, ggbump, stringr, ggtext, ggh4x, patchwork, RColorBrewer, scales, viridis, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 60c4d088258ca77a905c6a055c5dd924 Package: CCPROMISE Version: 1.32.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: c15feb82aa6182649ff0dc82faabfead Package: ccrepe Version: 1.42.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat, RUnit License: MIT + file LICENSE MD5sum: 63a2498e5bbbfac21e90fd524d7d73b6 Package: CDI Version: 1.4.0 Depends: R(>= 3.6) Imports: matrixStats, Seurat, SeuratObject, stats, BiocParallel, ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment, SummarizedExperiment, methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle License: GPL-3 + file LICENSE MD5sum: 135f5a07890ed7135817cf1947300754 Package: celaref Version: 1.24.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang, BiocGenerics, S4Vectors, readr, tibble, DelayedArray Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat License: GPL-3 MD5sum: 281e226717af12bb585d8d365ee4a911 Package: celda Version: 1.21.0 Depends: R (>= 4.0), SingleCellExperiment, Matrix Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, reshape2, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, scater (>= 1.14.4), scran, dbscan, DelayedArray, stringr, ComplexHeatmap, gridExtra, circlize LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData License: MIT + file LICENSE MD5sum: 20c5424a53688032f2de52642cb14e8b Package: CellBarcode Version: 1.12.0 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, zlibbioc, Rsamtools LinkingTo: Rcpp, BH Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: Artistic-2.0 MD5sum: 8c62df91da33cdebe252c9353ddcd064 Package: cellbaseR Version: 1.30.0 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: ef98f930daa2f43cfea61136a8a5cf1f Package: CellBench Version: 1.22.0 Depends: R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils Imports: assertthat, BiocGenerics, BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr, tidyselect, lubridate Suggests: BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2 License: GPL-3 MD5sum: fce2e914f50d04127add653603018fad Package: CelliD Version: 1.14.0 Depends: R (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment Imports: Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater, stringr, irlba, data.table, glue, pbapply, umap, Rtsne, reticulate, fastmatch, matrixStats, ggplot2, BiocParallel, SummarizedExperiment, fgsea LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr, destiny, ggrepel License: GPL-3 + file LICENSE MD5sum: 956716f272cea1d73d865a3650d897e5 Package: cellity Version: 1.34.0 Depends: R (>= 3.3) Imports: AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid, mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats, topGO, utils Suggests: BiocStyle, caret, knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: ba1119b6fd6322d7254681815936bf74 Package: CellMapper Version: 1.32.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 MD5sum: 5c9306939106266cc1b3de4f6c974711 Package: cellmigRation Version: 1.14.0 Depends: R (>= 4.1), methods, foreach Imports: tiff, graphics, stats, utils, reshape2, parallel, doParallel, grDevices, matrixStats, FME, SpatialTools, sp, vioplot, FactoMineR, Hmisc Suggests: knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl License: GPL-2 MD5sum: 809aaff135aaa42b36b0fee8f09bc00d Package: CellMixS Version: 1.22.0 Depends: kSamples, R (>= 4.0) Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne License: GPL (>= 2) MD5sum: 1ee59becc58e943c628379ebc0c1be11 Package: CellNOptR Version: 1.52.0 Depends: R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML, ggplot2, rmarkdown Imports: igraph, stringi, stringr Suggests: data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics, Enhances: doParallel, foreach License: GPL-3 MD5sum: 4ca0b6a8b7edaa958a3e9d45f24c8861 Package: cellscape Version: 1.30.0 Depends: R (>= 3.3) Imports: dplyr (>= 0.4.3), gtools (>= 3.5.0), htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 999ca01cb3d4767558b85304d9ef9688 Package: CellScore Version: 1.26.0 Depends: R (>= 4.3.0) Imports: Biobase (>= 2.39.1), graphics (>= 3.5.0), grDevices (>= 3.5.0), gplots (>= 3.0.1), lsa (>= 0.73.1), methods (>= 3.5.0), RColorBrewer(>= 1.1-2), squash (>= 1.0.8), stats (>= 3.5.0), utils(>= 3.5.0), SummarizedExperiment Suggests: hgu133plus2CellScore, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: f0b32b9cc39f0c436578511dee7b795d Package: CellTrails Version: 1.24.0 Depends: R (>= 3.5), SingleCellExperiment Imports: BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats, ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv, reshape2, Rtsne, stats, splines, SummarizedExperiment, utils Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown License: Artistic-2.0 MD5sum: ed24ae6b09786d37a17e213722369fa2 Package: cellxgenedp Version: 1.10.0 Depends: dplyr Imports: httr, curl, utils, tools, cli, shiny, DT, rjsoncons Suggests: zellkonverter, SingleCellExperiment, HDF5Array, tidyr, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery License: Artistic-2.0 MD5sum: 1f82bb797cdc722bcf02cad3208dfb30 Package: CEMiTool Version: 1.30.0 Depends: R (>= 4.0) Imports: methods, scales, dplyr, data.table (>= 1.9.4), WGCNA, grid, ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler, fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools, pracma, intergraph, grDevices, utils, network, matrixStats, ggdendro, gridExtra, gtable, fastcluster Suggests: testthat, BiocManager License: GPL-3 MD5sum: 810f92a9677ffdbc4d581af382847aa1 Package: censcyt Version: 1.14.0 Depends: R (>= 4.0), diffcyt Imports: BiocParallel, broom.mixed, dirmult, dplyr, edgeR, fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp, purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment, survival, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 License: MIT + file LICENSE MD5sum: 010b284a64f92acdbcf6d0ba6ce75b0f Package: Cepo Version: 1.12.0 Depends: GSEABase, R (>= 4.1) Imports: DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors, methods, SingleCellExperiment, SummarizedExperiment, ggplot2, rlang, grDevices, patchwork, reshape2, BiocParallel, stats, dplyr, purrr Suggests: knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater, scMerge, fgsea, escape, pheatmap License: MIT + file LICENSE MD5sum: 7cf04c40f9cdbe1828be780f4b0bb1b5 Package: ceRNAnetsim Version: 1.18.0 Depends: R (>= 4.0.0), dplyr, tidygraph Imports: furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, stats Suggests: knitr, png, rmarkdown, testthat, covr License: GPL (>= 3.0) MD5sum: 279c57cb7e1179ed33093d25cdd9c911 Package: CeTF Version: 1.18.0 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, clusterProfiler, DESeq2, dplyr, GenomicTools.fileHandler, GGally, ggnetwork, ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3, stats, SummarizedExperiment, S4Vectors, utils, methods LinkingTo: Rcpp, RcppArmadillo Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat License: GPL-3 MD5sum: d0a9b8a7bd4296387d5c752b2f8fd339 Package: CexoR Version: 1.44.0 Depends: R (>= 4.2.0), S4Vectors, IRanges Imports: Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | GPL-2 + file LICENSE MD5sum: a64a92702f3ebf5ae4d39438a3a60ef1 Package: CFAssay Version: 1.40.0 Depends: R (>= 2.10.0) License: LGPL MD5sum: aea49092242836e40ab0676cca7d6f93 Package: cfdnakit Version: 1.4.0 Depends: R (>= 4.3) Imports: Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges, magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats, rlang Suggests: rmarkdown, knitr, roxygen2, BiocStyle License: GPL-3 MD5sum: 51a34181a19255092710da5662f49841 Package: cfDNAPro Version: 1.12.0 Depends: R (>= 4.1.0), magrittr (>= 1.5.0) Imports: tibble, GenomicAlignments, IRanges, plyranges, GenomeInfoDb, GenomicRanges, BiocGenerics, stats, utils, dplyr (>= 0.8.3), stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1), Rsamtools (>= 2.4.0), rlang (>= 0.4.0), BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.NCBI.GRCh38 Suggests: scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat License: GPL-3 MD5sum: db4c573858ab892a80ff220f7a7e7ed7 Package: cfTools Version: 1.6.0 Imports: Rcpp, utils, GenomicRanges, basilisk, R.utils, stats, cfToolsData LinkingTo: Rcpp, BH Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: file LICENSE MD5sum: 3c63fcdcd91732593a5a4a54d7e70a08 Package: CGEN Version: 3.42.0 Depends: R (>= 4.0), survival, mvtnorm Imports: stats, graphics, utils, grDevices Suggests: cluster License: GPL-2 + file LICENSE MD5sum: 86bba2dc34d4e36c4ac3bc6386241f71 Package: CGHbase Version: 1.66.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL MD5sum: d245fad90208d324e593b3f0a9960f49 Package: CGHcall Version: 2.68.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall MD5sum: 18711617da0f76580285da084bbac2dd Package: cghMCR Version: 1.64.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL MD5sum: 9d4f39e8f3b1f16de26a17e6641f40a5 Package: CGHnormaliter Version: 1.60.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) MD5sum: e0b67be35633f1abc6bb117f76e2f592 Package: CGHregions Version: 1.64.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase MD5sum: 0682ef75f3f2e677351e46d0c90b7a30 Package: ChAMP Version: 2.36.0 Depends: R (>= 3.3), minfi, ChAMPdata (>= 2.6.0),DMRcate, Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest, DT, RPMM Imports: prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b4.hg19, limma, DNAcopy, preprocessCore,impute, marray, wateRmelon, plyr,goseq,missMethyl,kpmt,ggplot2, GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly (>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat Suggests: knitr,rmarkdown License: GPL-3 MD5sum: cb827643842200996281ffcbe81fb370 Package: ChemmineR Version: 3.58.0 Depends: R (>= 2.10.0), methods Imports: rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp (>= 0.11.0), ggplot2,grid,gridExtra, png,base64enc,DT,rsvg,jsonlite,stringi LinkingTo: Rcpp, BH Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png,rmarkdown, BiocManager,bibtex,codetools Enhances: ChemmineOB License: Artistic-2.0 MD5sum: cfe2301d54450d69a9612be80910d2f4 Package: CHETAH Version: 1.22.0 Depends: R (>= 4.2), ggplot2, SingleCellExperiment Imports: shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr License: file LICENSE MD5sum: 424eaaac6f8b1612ac1f22e77fc3ac8a Package: Chicago Version: 1.34.0 Depends: R (>= 3.3.1), data.table Imports: matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub License: Artistic-2.0 MD5sum: 02c34013e76ca017ed5fdaff94a6f9a1 Package: chihaya Version: 1.6.0 Depends: DelayedArray Imports: methods, Matrix, rhdf5, Rcpp, HDF5Array LinkingTo: Rcpp, Rhdf5lib Suggests: BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix, BiocStyle, testthat, rmarkdown, knitr License: GPL-3 MD5sum: 564be964ddf09c6e1138320e673b3a24 Package: chimeraviz Version: 1.32.0 Depends: Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, AnnotationFilter, data.table Imports: methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, checkmate, gtools, magick Suggests: testthat, roxygen2, devtools, knitr, lintr License: Artistic-2.0 MD5sum: 1e036364022fdd612194c31d7bdcc34f Package: ChIPanalyser Version: 1.28.0 Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb,RColorBrewer Suggests: BSgenome.Dmelanogaster.UCSC.dm6,knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 7e3fd7c22f6a6b5d880a729999ce6bbd Package: ChIPComp Version: 1.36.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,rtracklayer,GenomeInfoDb,S4Vectors Imports: Rsamtools,limma,BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,BiocGenerics Suggests: BiocStyle,RUnit License: GPL MD5sum: d9488fda9dfa7b366ab9dc381fa5b1b2 Package: chipenrich Version: 2.30.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, chipenrich.data, GenomeInfoDb, GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra, MASS, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer, S4Vectors (>= 0.23.10), stats, stringr, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat License: GPL-3 MD5sum: 7158bac8c0ad7f9cc7b4dfc39ac5e06f Package: ChIPexoQual Version: 1.30.0 Depends: R (>= 3.5.0), GenomicAlignments (>= 1.0.1) Imports: methods, utils, GenomeInfoDb, stats, BiocParallel, GenomicRanges (>= 1.14.4), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools (>= 1.16.1), IRanges (>= 1.6), S4Vectors (>= 0.8), biovizBase (>= 1.18), broom (>= 0.4), RColorBrewer (>= 1.1), dplyr (>= 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BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, reshape2, testthat, trackViewer, motifStack, OrganismDbi, BiocFileCache License: GPL (>= 2) MD5sum: b11e27044ec46460be6735ed4e405390 Package: ChIPQC Version: 1.42.0 Depends: R (>= 3.5.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19), BiocParallel Imports: BiocGenerics (>= 0.11.3), S4Vectors (>= 0.1.0), IRanges (>= 1.99.17), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), chipseq (>= 1.12.0), gtools, methods, reshape2, Nozzle.R1, Biobase, grDevices, stats, utils, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene Suggests: BiocStyle License: GPL (>= 3) MD5sum: 8410866a54f51548bd1a263ea673f6fa Package: ChIPseeker Version: 1.42.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, aplot, BiocGenerics, boot, dplyr, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, graphics, grDevices, gtools, magrittr, methods, plotrix, parallel, RColorBrewer, rlang, rtracklayer, S4Vectors, scales, stats, tibble, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, yulab.utils (>= 0.1.5) Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, knitr, org.Hs.eg.db, prettydoc, ReactomePA, rmarkdown, testthat License: Artistic-2.0 MD5sum: c4ac9a2249589836fcb537309da26444 Package: chipseq Version: 1.56.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), ShortRead Imports: methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges, ShortRead Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr License: Artistic-2.0 MD5sum: 2d4752fc764b0720c75e7ddae2160fb8 Package: ChIPseqR Version: 1.60.0 Depends: R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25) Imports: Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14), graphics, grDevices, HilbertVis, ShortRead, stats, timsac, utils License: GPL (>= 2) MD5sum: 6c6427bf07fae841e7d668831d78b378 Package: ChIPsim Version: 1.60.0 Depends: Biostrings (>= 2.29.2) Imports: IRanges, XVector, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) MD5sum: f61248720563e1a03368c96def32d7b1 Package: ChIPXpress Version: 1.50.0 Depends: R (>= 2.10), ChIPXpressData Imports: Biobase, GEOquery, frma, affy, bigmemory, biganalytics Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: c67bc9f1cdfe79a56348f0b12e00087f Package: chopsticks Version: 1.72.0 Imports: graphics, stats, utils, methods, survival Suggests: hexbin License: GPL-3 MD5sum: f2df36a59372b39aa9d42d7c2e47732b Package: chromDraw Version: 2.36.0 Depends: R (>= 3.0.0) Imports: Rcpp (>= 0.11.1), GenomicRanges (>= 1.17.46) LinkingTo: Rcpp License: GPL-3 MD5sum: 2e190aee633c985aeac7e47c893ac6e3 Package: ChromHeatMap Version: 1.60.0 Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0) Imports: Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer, GenomicRanges Suggests: ALL, hgu95av2.db License: Artistic-2.0 MD5sum: 717f6985183d8fe95403f3ff64d0b971 Package: chromPlot Version: 1.34.0 Depends: stats, utils, graphics, grDevices, datasets, base, biomaRt, GenomicRanges, R (>= 3.1.0) Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 3048cd024b35988f45e593172a0d137b Package: ChromSCape Version: 1.16.0 Depends: R (>= 4.1) Imports: shiny, colourpicker, shinyjs, rtracklayer, shinyFiles, shinyhelper, shinyWidgets, shinydashboardPlus, shinycssloaders, Matrix, plotly, shinydashboard, colorRamps, kableExtra, viridis, batchelor, BiocParallel, parallel, Rsamtools, ggplot2, ggrepel, gggenes, gridExtra, qualV, stringdist, stringr, fs, qs, DT, scran, scater, ConsensusClusterPlus, Rtsne, dplyr, tidyr, GenomicRanges, IRanges, irlba, rlist, umap, tibble, methods, jsonlite, edgeR, stats, graphics, grDevices, utils, S4Vectors, SingleCellExperiment, SummarizedExperiment, msigdbr, forcats, Rcpp, coop, matrixTests, DelayedArray LinkingTo: Rcpp Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future, igraph, bluster, httr License: GPL-3 MD5sum: e4f800bfc2c7e1f01ffe61caa82570c0 Package: chromstaR Version: 1.32.0 Depends: R (>= 3.5.0), GenomicRanges, ggplot2, chromstaRData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, reshape2, Rsamtools, GenomicAlignments, bamsignals, mvtnorm Suggests: knitr, BiocStyle, testthat, biomaRt License: Artistic-2.0 MD5sum: 07eb53dba79ebda522beaf593c2d4086 Package: cicero Version: 1.24.0 Depends: R (>= 3.5.0), monocle, Gviz (>= 1.22.3) Imports: assertthat (>= 0.2.0), Biobase (>= 2.37.2), BiocGenerics (>= 0.23.0), data.table (>= 1.10.4), dplyr (>= 0.7.4), FNN (>= 1.1), GenomicRanges (>= 1.30.3), ggplot2 (>= 2.2.1), glasso (>= 1.8), grDevices, igraph (>= 1.1.0), IRanges (>= 2.10.5), Matrix (>= 1.2-12), methods, parallel, plyr (>= 1.8.4), reshape2 (>= 1.4.3), S4Vectors (>= 0.14.7), stats, stringi, stringr (>= 1.2.0), tibble (>= 1.4.2), tidyr, VGAM (>= 1.0-5), utils Suggests: AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr License: MIT + file LICENSE MD5sum: 945da303284c8d859f8b62b518365a51 Package: CIMICE Version: 1.14.0 Imports: dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork, ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat, tidygraph, expm, Matrix Suggests: BiocStyle, knitr, rmarkdown, testthat, webshot License: Artistic-2.0 MD5sum: da5153fdcfc8270bfdb9dd2f12e74298 Package: CINdex Version: 1.34.0 Depends: R (>= 3.3), GenomicRanges Imports: bitops,gplots,grDevices,som, dplyr,gridExtra,png,stringr,S4Vectors, IRanges, GenomeInfoDb,graphics, stats, utils Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens, R.utils License: GPL (>= 2) MD5sum: 47661c4bfd0f6b766951b27a0d754bf1 Package: circRNAprofiler Version: 1.20.0 Depends: R(>= 4.3.0) Imports: dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2, edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb, universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, Biostrings, gwascat, BSgenome, Suggests: testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager, License: GPL-3 MD5sum: d814d1c46539e74e69db25817cd7a9f9 Package: CircSeqAlignTk Version: 1.8.0 Depends: R (>= 4.2) Imports: stats, tools, utils, R.utils, methods, S4Vectors, rlang, magrittr, dplyr, tidyr, ggplot2, BiocGenerics, Biostrings, IRanges, ShortRead, Rsamtools, Rbowtie2, Rhisat2, shiny, shinyFiles, shinyjs, plotly, parallel, htmltools Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 61349dec011c2d29155f273572f7efc5 Package: cisPath Version: 1.46.0 Depends: R (>= 2.10.0) Imports: methods, utils License: GPL (>= 3) MD5sum: 14bf0b89735bd32a79bcb0e59f705c5c Package: CiteFuse Version: 1.18.0 Depends: R (>= 4.0) Imports: SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>= 1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid, dbscan, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph, scales, scran (>= 1.14.6), graphics, methods, stats, utils, reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5, rlang, Rcpp, compositions LinkingTo: Rcpp Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown License: GPL-3 MD5sum: af493ce4ed245d319e8840176a689a33 Package: ClassifyR Version: 3.10.5 Depends: R (>= 4.1.0), generics, methods, S4Vectors, MultiAssayExperiment, BiocParallel, survival Imports: grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2 (>= 3.0.0), 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 License: GPL-3 MD5sum: d30ae2691ca75d2700bddc554d01114a Package: cleanUpdTSeq Version: 1.44.0 Depends: R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods Imports: BSgenome, GenomicRanges, seqinr, e1071, Biostrings, GenomeInfoDb, IRanges, utils, stringr, stats, S4Vectors Suggests: BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0) License: GPL-2 MD5sum: f01ac68d66ade326e2e2e2000617edb1 Package: CleanUpRNAseq Version: 1.0.0 Depends: R (>= 4.4.0) Imports: AnnotationFilter, BiocGenerics, Biostrings, BSgenome, DESeq2, edgeR, ensembldb, GenomeInfoDb, 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: 59c01cbe4bfbcb000a91f0c465815fc5 Package: cleaver Version: 1.44.0 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: 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1.12.0 Depends: S4Vectors, methods, R (>= 4.1) Imports: dplyr, rtracklayer, GenomicRanges, ggplot2, BSgenome, Biostrings, utils Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: a660dd5670500dd529306c9c7f55c6f7 Package: cliqueMS Version: 1.20.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, coop, slam, matrixStats, methods LinkingTo: Rcpp, BH, RcppArmadillo Suggests: BiocParallel, knitr, rmarkdown, testthat, CAMERA License: GPL (>= 2) MD5sum: 455e06f4e04101715d7f0e2523795831 Package: Clomial Version: 1.42.0 Depends: R (>= 2.10), matrixStats Imports: methods, permute License: GPL (>= 2) MD5sum: fc19d75a8eab1a6f440ff709f3cd1823 Package: clst Version: 1.54.0 Depends: R (>= 2.10) Imports: ROC, lattice Suggests: RUnit License: GPL-3 MD5sum: 7039fe394b5ec6ee589ff027e34ed535 Package: clstutils Version: 1.54.0 Depends: R (>= 2.10), clst, rjson, ape Imports: lattice, RSQLite Suggests: RUnit License: GPL-3 MD5sum: 2506fbb908530f65a096aed87989c707 Package: ClustAll Version: 1.2.0 Depends: R (>= 4.2.0) Imports: FactoMineR, bigstatsr, clValid, doSNOW, parallel, foreach, dplyr, fpc, mice, modeest, flock, networkD3, methods, ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices, ggplot2, grid, stats, utils, pbapply Suggests: RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2 License: GPL-2 MD5sum: 411b9bc4fb0273bd5fe47e318ea0478e Package: clustComp Version: 1.34.0 Depends: R (>= 3.3) Imports: sm, stats, graphics, grDevices Suggests: Biobase, colonCA, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 02ef109152c1172780df125811f1a1a4 Package: clusterExperiment Version: 2.26.0 Depends: R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>= 1.15.4), BiocGenerics Imports: methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, locfdr, matrixStats, graphics, parallel, BiocSingular, kernlab, stringr, S4Vectors, grDevices, DelayedArray (>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma, mbkmeans LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown License: Artistic-2.0 MD5sum: d7e81931ae5dbc8e0f0736913d67f290 Package: ClusterFoldSimilarity Version: 1.2.0 Imports: methods, igraph, ggplot2, scales, BiocParallel, graphics, stats, utils, Matrix, cowplot, dplyr, reshape2, Seurat, SeuratObject, SingleCellExperiment, ggdendro Suggests: knitr, rmarkdown, kableExtra, scRNAseq, BiocStyle License: Artistic-2.0 MD5sum: 91aae62cbc17cf4ddcbb24e20b9ff03d Package: ClusterJudge Version: 1.28.0 Depends: R (>= 3.6), stats, utils, graphics, infotheo, lattice, latticeExtra, httr, jsonlite Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt License: Artistic-2.0 MD5sum: 50cd608914404caac4e1667dc08c37b3 Package: clusterProfiler Version: 4.14.4 Depends: R (>= 3.5.0) Imports: AnnotationDbi, DOSE (>= 3.23.2), dplyr, enrichplot (>= 1.9.3), GO.db, GOSemSim (>= 2.27.2), gson (>= 0.0.7), httr, igraph, magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils (>= 0.1.6) Suggests: AnnotationHub, knitr, jsonlite, readr, rmarkdown, org.Hs.eg.db, prettydoc, BiocManager, testthat License: Artistic-2.0 MD5sum: cd616b06aab819ef57a61b274a3962b2 Package: clusterSeq Version: 1.30.0 Depends: R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats, utils Imports: BiocGenerics Suggests: BiocStyle License: GPL-3 MD5sum: 0773088331fba1bde078628969f01213 Package: ClusterSignificance Version: 1.34.0 Depends: R (>= 3.3.0) Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr License: GPL-3 MD5sum: d936ab96b8767864519bf0c89e7ec939 Package: clusterStab Version: 1.78.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 MD5sum: 60c07d05070335e47dbd36d57fcebf7d Package: clustifyr Version: 1.18.0 Depends: R (>= 2.10) Imports: cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang, scales, stringr, tibble, tidyr, stats, methods, SingleCellExperiment, SummarizedExperiment, SeuratObject, matrixStats, S4Vectors, proxy, httr, utils Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr, data.table, R.utils License: MIT + file LICENSE MD5sum: c51a0bc6477ea6562232173cb79d01e5 Package: ClustIRR Version: 1.4.0 Depends: R (>= 4.4.0) Imports: blaster, future, future.apply, grDevices, igraph, methods, pwalign, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils, visNetwork LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork License: GPL-3 + file LICENSE MD5sum: c0b178ef262934b8ad8c37041539a237 Package: CMA Version: 1.64.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm License: GPL (>= 2) MD5sum: f2a8fd1b18b2456997cd06b3f187344b Package: cmapR Version: 1.18.0 Depends: R (>= 4.0) Imports: methods, rhdf5, data.table, flowCore, SummarizedExperiment, matrixStats Suggests: knitr, testthat, BiocStyle, rmarkdown License: file LICENSE MD5sum: f1490e60c8f26f1a1097b154cbc2e658 Package: CNAnorm Version: 1.52.0 Depends: R (>= 2.10.1), methods Imports: DNAcopy License: GPL-2 MD5sum: aaa5985a4a9bf9065e44965d265c5af9 Package: cn.farms Version: 1.54.0 Depends: R (>= 3.0), Biobase, methods, ff, oligoClasses, snow Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 License: LGPL (>= 2.0) MD5sum: c9dd7c5a94fd77f566ce5e5b1cea6c5e Package: cn.mops Version: 1.52.0 Depends: R (>= 3.5.0), methods, utils, stats, graphics, parallel, GenomicRanges Imports: BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb, S4Vectors Suggests: DNAcopy License: LGPL (>= 2.0) MD5sum: 2ab1ac8459efe4c881dbec32b6d8c1ed Package: CNORdt Version: 1.48.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 MD5sum: 79d93cadf1f84c3ac158c0408d91ddf3 Package: CNORfeeder Version: 1.46.0 Depends: R (>= 3.6.0), CellNOptR (>= 1.4.0), graph Suggests: minet, Rgraphviz, RUnit, BiocGenerics, igraph Enhances: MEIGOR License: GPL-3 MD5sum: 55e2ee64a27b2179ccc48b31b12f673a Package: CNORfuzzy Version: 1.48.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 MD5sum: e66650d0e424a498bb8eb47e02dc9d87 Package: CNORode Version: 1.48.0 Depends: CellNOptR, genalg Suggests: knitr, rmarkdown Enhances: doParallel, foreach License: GPL-2 MD5sum: f4fe1c6823a5a4c87e9650d42f3b0069 Package: CNTools Version: 1.62.0 Depends: R (>= 2.10), methods, tools, stats, genefilter License: LGPL MD5sum: 6ea0855d7358943f8befe4ff76ec561a Package: CNVfilteR Version: 1.20.0 Depends: R (>= 4.3) Imports: IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods Suggests: knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown License: Artistic-2.0 MD5sum: 67efb75451fe3f59c87ad067b986debb Package: cnvGSA Version: 1.50.0 Depends: brglm, doParallel, foreach, GenomicRanges, methods, splitstackshape Suggests: cnvGSAdata, org.Hs.eg.db License: LGPL MD5sum: 71657fbcd7b55485b93a42445e99fa9b Package: CNViz Version: 1.14.0 Depends: R (>= 4.0), shiny (>= 1.5.0) Imports: dplyr, stats, utils, grDevices, plotly, karyoploteR, CopyNumberPlots, GenomicRanges, magrittr, DT, scales, graphics Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: 6816104c50ec5274e918d307e7ece368 Package: CNVMetrics Version: 1.10.0 Depends: R (>= 4.0) Imports: GenomicRanges, IRanges, S4Vectors, BiocParallel, methods, magrittr, stats, pheatmap, gridExtra, grDevices, rBeta2009 Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: ab3bc096c8fceecb442aef76a59adcc0 Package: CNVPanelizer Version: 1.38.0 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: f47ce4bac47a6836cd6f8bf14b4951ed Package: CNVRanger Version: 1.22.0 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: 1e5886e2e321c48374da5c8dfc5ff89e Package: CNVrd2 Version: 1.44.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 MD5sum: b7d6fe71c248807fa644d8d48eb4b6c4 Package: CoCiteStats Version: 1.78.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL MD5sum: 636225495d01202b79997d72675bc184 Package: COCOA Version: 2.20.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices, simpleCache, fitdistrplus Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 0916f17926eadcf65f015f55253f6da3 Package: codelink Version: 1.74.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 MD5sum: e9738874e2c46d65a2d04a7143ee49db Package: CODEX Version: 1.38.0 Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors Suggests: WES.1KG.WUGSC License: GPL-2 MD5sum: 2e650aa106ca53fc696c05e26bfbbd0c Package: CoGAPS Version: 3.26.0 Depends: R (>= 3.5.0) Imports: BiocParallel, cluster, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5, dplyr, fgsea, forcats, ggplot2 LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject, BiocFileCache License: BSD_3_clause + file LICENSE MD5sum: 4372c0502a1059bcf7caa7b84802f2cf Package: cogena Version: 1.40.0 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: 844c147b0df533c226aee6c8473c4b33 Package: cogeqc Version: 1.10.0 Depends: R (>= 4.2.0) Imports: utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr License: GPL-3 MD5sum: 083bbda7dcd2c25306cd3c0fc193691e Package: Cogito Version: 1.12.0 Depends: R (>= 4.1), GenomicRanges, jsonlite, GenomicFeatures, entropy Imports: BiocManager, rmarkdown, GenomeInfoDb, S4Vectors, AnnotationDbi, graphics, stats, utils, methods, magrittr, ggplot2, TxDb.Mmusculus.UCSC.mm9.knownGene Suggests: BiocStyle, knitr, markdown, testthat (>= 3.0.0) License: LGPL-3 MD5sum: ef99d5b7bb976fd30705b35719d98a70 Package: coGPS Version: 1.50.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 MD5sum: 4d58ab17151a0f5040d2fb82c77f7a88 Package: cola Version: 2.12.0 Depends: R (>= 4.0.0) Imports: grDevices, graphics, grid, stats, utils, ComplexHeatmap (>= 2.5.4), matrixStats, GetoptLong, circlize (>= 0.4.7), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer, cluster, skmeans, png, mclust, crayon, methods, xml2, microbenchmark, httr, knitr (>= 1.4.0), markdown (>= 1.6), digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr, foreach, doParallel, doRNG, irlba LinkingTo: Rcpp Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 License: MIT + file LICENSE MD5sum: 86666651f4be94119fb04e37ff839b4d Package: comapr Version: 1.10.0 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: 05ef5657ca4ef5ec2959a5f1351c99bd Package: combi Version: 1.18.0 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: 5755ffd4d6e738b751752ed0cbeaa936 Package: coMET Version: 1.38.0 Depends: R (>= 4.1.0), grid, utils, biomaRt, Gviz, psych Imports: hash,grDevices, gridExtra, rtracklayer, IRanges, S4Vectors, GenomicRanges, stats, corrplot Suggests: BiocStyle, knitr, RUnit, BiocGenerics, showtext License: GPL (>= 2) MD5sum: 33dfc23886c9b34a96f9ea975b6c1d12 Package: coMethDMR Version: 1.10.0 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: d8ac75a7f04fe3e5ddc7ce8171e228c1 Package: COMPASS Version: 1.44.0 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach, coda LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2, progress License: Artistic-2.0 MD5sum: 52a09dc724e00c0f19e119e631f55ed6 Package: compcodeR Version: 1.42.0 Depends: R (>= 4.0), sm Imports: knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods, stats, utils, ape, phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny, shinydashboard Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk Enhances: rpanel, DSS License: GPL (>= 2) MD5sum: 6b165abf7957cc1349e692c9efbf978a Package: compEpiTools Version: 1.40.0 Depends: R (>= 3.5.0), methods, topGO, GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, GenomeInfoDb Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer License: GPL MD5sum: acde8cfe319bfd90bd57a0a51cca1e31 Package: ComplexHeatmap Version: 2.22.0 Depends: R (>= 3.5.0), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.14), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges, matrixStats, foreach, doParallel, codetools Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff, fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12), gridGraphics, gplots, rmarkdown, Cairo, magick License: MIT + file LICENSE MD5sum: 9e6e671a29161af55bab3bf972c571cf Package: CompoundDb Version: 1.10.0 Depends: R (>= 4.1), methods, AnnotationFilter, S4Vectors Imports: BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges, Spectra (>= 1.15.10), MsCoreUtils, MetaboCoreUtils, BiocParallel Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf License: Artistic-2.0 MD5sum: 9e5caac5ca7fed6a3625afafd2208e38 Package: ComPrAn Version: 1.14.0 Imports: data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr, rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio, scales, shinydashboard, shinyjs, stats, tibble, grid Suggests: testthat (>= 2.1.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 31d3076daeb0a04a11291e5a235fd5a4 Package: compSPOT Version: 1.4.0 Depends: R (>= 4.3.0) Imports: stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra, utils, data.table Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: fe2fae890e8881e193d06a89ef5072b2 Package: concordexR Version: 1.6.0 Depends: R (>= 4.4.0) Imports: BiocGenerics, BiocNeighbors, BiocParallel, bluster, cli, DelayedArray, Matrix, methods, purrr, rlang, SingleCellExperiment, sparseMatrixStats, SpatialExperiment, SummarizedExperiment Suggests: BiocManager, BiocStyle, ggplot2, glue, knitr, mbkmeans, patchwork, rmarkdown, scater, SFEData, SpatialFeatureExperiment, TENxPBMCData, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 39078d0119f05f796d4ec39c9ee78152 Package: condiments Version: 1.14.0 Depends: R (>= 4.0) Imports: slingshot (>= 1.9), mgcv, RANN, stats, SingleCellExperiment, SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume (>= 0.9.1), methods, pbapply, matrixStats, BiocParallel, TrajectoryUtils, igraph, distinct Suggests: knitr, testthat, rmarkdown, covr, viridis, ggplot2, RColorBrewer, randomForest, tidyr, TSCAN, DelayedMatrixStats License: MIT + file LICENSE MD5sum: 38108044a4e19b42fd5947c4fb4f93b3 Package: CONFESS Version: 1.34.0 Depends: R (>= 3.3),grDevices,utils,stats,graphics Imports: methods,changepoint,cluster,contrast,data.table(>= 1.9.7),ecp,EBImage,flexmix,flowCore,flowClust,flowMeans,flowMerge,flowPeaks,foreach,ggplot2,grid,limma,MASS,moments,outliers,parallel,plotrix,raster,readbitmap,reshape2,SamSPECTRAL,waveslim,wavethresh,zoo Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata License: GPL-2 MD5sum: fb562eccd3eaf302cdacb8307ba12b28 Package: consensus Version: 1.24.0 Depends: R (>= 3.5), RColorBrewer Imports: matrixStats, gplots, grDevices, methods, graphics, stats, utils Suggests: knitr, RUnit, rmarkdown, BiocGenerics License: BSD_3_clause + file LICENSE MD5sum: 2d0e6d978c6060115a26c29b4ebfdf57 Package: ConsensusClusterPlus Version: 1.70.0 Imports: Biobase, ALL, graphics, stats, utils, cluster License: GPL-2 MD5sum: 7f2e9e1d90bb4a8831dcde0d8fffc850 Package: consensusDE Version: 1.24.0 Depends: R (>= 3.5), BiocGenerics Imports: airway, AnnotationDbi, BiocParallel, Biobase, Biostrings, data.table, dendextend, DESeq2 (>= 1.20.0), EDASeq, ensembldb, edgeR, EnsDb.Hsapiens.v86, GenomicAlignments, GenomicFeatures, limma, org.Hs.eg.db, pcaMethods, RColorBrewer, Rsamtools, RUVSeq, S4Vectors, stats, SummarizedExperiment, TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 963819fed3715ee5465f024f9974403a Package: consensusOV Version: 1.28.0 Depends: R (>= 3.6) Imports: Biobase, GSVA (>= 1.50.0), gdata, genefu, limma, matrixStats, randomForest, stats, utils, methods, BiocParallel Suggests: BiocStyle, ggplot2, knitr, rmarkdown, magick License: Artistic-2.0 MD5sum: 3dbcc6c053367e46048eb0e6a7d4b774 Package: consensusSeekeR Version: 1.34.0 Depends: R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, BiocParallel Imports: GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 1ec116d7f0591cde587013b7a04c262d Package: consICA Version: 2.4.0 Depends: R (>= 4.2.0) Imports: fastICA (>= 1.2.1), sm, org.Hs.eg.db, GO.db, stats, SummarizedExperiment, BiocParallel, graph, ggplot2, methods, Rfast, pheatmap, survival, topGO, graphics, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat, Seurat License: MIT + file LICENSE MD5sum: c75edbac8cb87dbc9aa44591b4c3448f Package: CONSTANd Version: 1.14.0 Depends: R (>= 4.1) Suggests: BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra, magick, Cairo, limma License: file LICENSE MD5sum: d0a549a666b950895533ea856498759a Package: conumee Version: 1.40.0 Depends: R (>= 3.5.0), minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest Imports: methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges, GenomeInfoDb Suggests: BiocStyle, knitr, rmarkdown, minfiData, RCurl License: GPL (>= 2) MD5sum: 011339eaae01a0106b12b97d06c53377 Package: convert Version: 1.82.0 Depends: R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray, utils, methods License: LGPL MD5sum: d208e104565b5673363b68038dbd1f99 Package: copa Version: 1.74.0 Depends: Biobase, methods Suggests: colonCA License: Artistic-2.0 MD5sum: 6501bbc89a6b45f8c7a568e3b406e4e5 Package: CopyNumberPlots Version: 1.22.0 Depends: R (>= 3.6), karyoploteR Imports: regioneR, IRanges, Rsamtools, SummarizedExperiment, VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges, cn.mops, rhdf5, utils Suggests: BiocStyle, knitr, rmarkdown, panelcn.mops, BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat License: Artistic-2.0 MD5sum: 9441bdc8dbfc54125b2126f262f1f76a Package: coRdon Version: 1.24.0 Depends: R (>= 3.5) Imports: methods, stats, utils, Biostrings, Biobase, dplyr, stringr, purrr, ggplot2, data.table Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: cdce7cfe16f568bed7039d6a75ff2206 Package: CoreGx Version: 2.10.0 Depends: R (>= 4.1), BiocGenerics, SummarizedExperiment Imports: Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics, piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods, stats, utils, graphics, grDevices, lsa, data.table, crayon, glue, rlang, bench Suggests: pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat License: GPL (>= 3) MD5sum: d48db52dcd55ad7f70542e6cfddd8517 Package: Cormotif Version: 1.52.0 Depends: R (>= 2.12.0), affy, limma Imports: affy, graphics, grDevices License: GPL-2 MD5sum: f2f83fb69c27e264b43be2620b435f11 Package: corral Version: 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bionetdata, PerfMeas, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 7ef591bfb0a3521ce5b177b29d9702af Package: COTAN Version: 2.6.1 Depends: R (>= 4.3) Imports: stats, plyr, dplyr, methods, grDevices, Matrix, ggplot2, ggrepel, ggthemes, graphics, parallel, parallelly, tibble, tidyr, BiocSingular, PCAtools, parallelDist, ComplexHeatmap, circlize, grid, scales, RColorBrewer, utils, rlang, Rfast, stringr, Seurat, umap, dendextend, zeallot, assertthat, withr, SingleCellExperiment, SummarizedExperiment, S4Vectors Suggests: testthat (>= 3.2.0), proto, spelling, knitr, data.table, gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery, sf, torch License: GPL-3 MD5sum: 633e6f1ff292fe48dbc2d656f290c343 Package: countsimQC Version: 1.24.0 Depends: R (>= 3.5) Imports: rmarkdown (>= 2.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr, ggplot2, grDevices, tools, SummarizedExperiment, genefilter, DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods, ragg Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 8f822dce6751a78f5a3bf2314c74ead0 Package: covEB Version: 1.32.0 Depends: R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats, LaplacesDemon, Matrix Suggests: curatedBladderData License: GPL-3 MD5sum: a6e628a4a0b07d6eeba54622c1ea227c Package: CoverageView Version: 1.44.0 Depends: R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer Imports: S4Vectors (>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges, GenomicAlignments, parallel, tools License: Artistic-2.0 MD5sum: 39531fc9726a72176708510eed3a6276 Package: covRNA Version: 1.32.0 Depends: ade4, Biobase Imports: parallel, genefilter, grDevices, stats, graphics Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 32b4f1971d616310ae56bf519e57de4d Package: cpvSNP Version: 1.38.0 Depends: R (>= 3.5.0), GenomicFeatures, GSEABase (>= 1.24.0) Imports: methods, corpcor, BiocParallel, ggplot2, plyr Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: 18937c9509235ba8bedf7dcfac1cdc7a Package: cqn Version: 1.52.0 Depends: R (>= 2.10.0), mclust Imports: splines, graphics, nor1mix, stats, quantreg Suggests: scales, edgeR License: Artistic-2.0 MD5sum: 021fd74e41e46f5234e06a908cde3f9d Package: CRImage Version: 1.54.0 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach, sgeostat License: Artistic-2.0 MD5sum: 00619cf85e803eb2cba660c2a66f5cc7 Package: CRISPRball Version: 1.2.0 Depends: R (>= 4.4.0), shinyBS Imports: DT, shiny, grid, ComplexHeatmap, InteractiveComplexHeatmap, graphics, stats, ggplot2, plotly, shinyWidgets, shinycssloaders, shinyjqui, dittoSeq, matrixStats, colourpicker, shinyjs, MAGeCKFlute, circlize, PCAtools, utils, grDevices, htmlwidgets, methods Suggests: BiocStyle, msigdbr, depmap, pool, RSQLite, mygene, testthat (>= 3.0.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 0630c8a61cb28bc78658901f09a8ef8a Package: crisprBase Version: 1.10.0 Depends: utils, methods, R (>= 4.1) Imports: BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges, S4Vectors, stringr Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: b6196a9bff3605b942a2bc2fd72eb9c5 Package: crisprBowtie Version: 1.10.0 Depends: methods Imports: BiocGenerics, Biostrings, BSgenome, crisprBase (>= 0.99.15), GenomeInfoDb, GenomicRanges, IRanges, Rbowtie, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 89d025ef61c464a18b48831e2cd5aaf8 Package: crisprBwa Version: 1.10.0 Depends: methods Imports: BiocGenerics, BSgenome, crisprBase (>= 0.99.15), GenomeInfoDb, Rbwa, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE OS_type: unix MD5sum: 836f92bb271f795abbfd1b8be7ce0eb6 Package: crisprDesign Version: 1.8.0 Depends: R (>= 4.2.0), crisprBase (>= 1.1.3) Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, crisprBowtie (>= 0.99.8), crisprScore (>= 1.1.6), GenomeInfoDb, GenomicFeatures, GenomicRanges (>= 1.38.0), IRanges, Matrix, MatrixGenerics, methods, rtracklayer, S4Vectors, stats, txdbmaker, utils, VariantAnnotation Suggests: biomaRt, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7), knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat License: MIT + file LICENSE MD5sum: a05afe29cd0896adf9a78a06a2c6c187 Package: crisprScore Version: 1.10.0 Depends: R (>= 4.1), crisprScoreData (>= 1.1.3) Imports: basilisk (>= 1.9.2), basilisk.utils (>= 1.9.1), BiocGenerics, Biostrings, IRanges, methods, randomForest, reticulate, stringr, utils, XVector Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: f6abafae887b99654b72a782d2301fdd Package: CRISPRseek Version: 1.46.0 Depends: R (>= 3.5.0), BiocGenerics, Biostrings Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges, BSgenome, hash, methods,reticulate,rhdf5,XVector, DelayedArray, GenomeInfoDb, GenomicRanges, dplyr, keras, mltools Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice, MASS, tensorflow, testthat License: GPL (>= 2) MD5sum: 46124041646c930ccbabf95246675d78 Package: crisprShiny Version: 1.2.0 Depends: R (>= 4.4.0), shiny Imports: BiocGenerics, Biostrings, BSgenome, crisprBase, crisprDesign, crisprScore, crisprViz, DT, GenomeInfoDb, htmlwidgets, methods, pwalign, S4Vectors, shinyBS, shinyjs, utils, waiter Suggests: BiocStyle, knitr, rmarkdown, shinyFeedback, testthat (>= 3.0.0), BSgenome.Hsapiens.UCSC.hg38 License: MIT + file LICENSE MD5sum: d1368be882a0b538a0dc7b1ad082b3b9 Package: CrispRVariants Version: 1.34.0 Depends: R (>= 4.3.0), ggplot2 (>= 2.2.0) Imports: AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>= 0.9.38), utils Suggests: BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl, rtracklayer, sangerseqR, testthat, VariantAnnotation License: GPL-2 MD5sum: 07258ae54128be9ec33e4ec9d18e215d Package: crisprVerse Version: 1.8.0 Depends: R (>= 4.2.0) Imports: BiocManager, cli, crisprBase, crisprBowtie, crisprScore, crisprScoreData, crisprDesign, crisprViz, rlang, tools, utils Suggests: BiocStyle, knitr, testthat License: MIT + file LICENSE MD5sum: a424dff783e8c3c3a8c1e36f83200dd7 Package: crisprViz Version: 1.8.0 Depends: R (>= 4.2.0), crisprBase (>= 0.99.15), crisprDesign (>= 0.99.77) Imports: BiocGenerics, Biostrings, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, grDevices, Gviz, IRanges, methods, S4Vectors, txdbmaker Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, rtracklayer, testthat, utils License: MIT + file LICENSE MD5sum: 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Depends: R (>= 4.1) Imports: RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils, grid, gridExtra, methods, stats, BiocFileCache Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: acb336d9353b91672c74a3ce8d86e196 Package: CTexploreR Version: 1.2.0 Depends: R (>= 4.3), CTdata (>= 1.5.3) Imports: BiocGenerics, ComplexHeatmap, grid, SummarizedExperiment, GenomicRanges, IRanges, dplyr, tidyr, tibble, ggplot2, rlang, grDevices, stats, circlize, ggrepel, SingleCellExperiment, MatrixGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), InteractiveComplexHeatmap License: Artistic-2.0 MD5sum: ba01256ec1eeb34a11f81d76740a0402 Package: cTRAP Version: 1.24.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, binr, cowplot, data.table, dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics, highcharter, htmltools, httr, limma, methods, parallel, pbapply, purrr, qs, R.utils, readxl, reshape2, rhdf5, rlang, scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble, tools, utils Suggests: testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes License: MIT + file LICENSE MD5sum: efad3bd12b03091ffab66f7f267bad70 Package: ctsGE Version: 1.32.0 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: d969ba91b95a24d07c7aa8694291d2af Package: CTSV Version: 1.8.0 Depends: R (>= 4.2), Imports: stats, pscl, qvalue, BiocParallel, methods, knitr, SpatialExperiment, SummarizedExperiment Suggests: testthat, BiocStyle License: GPL-3 MD5sum: 58771bfbf714b536378cf9611fcbce3a Package: cummeRbund Version: 2.48.0 Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz Imports: methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson License: Artistic-2.0 MD5sum: 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1.10.2), GenomicAlignments, Biostrings (>= 2.26.3), GenomicFeatures (>= 1.32.0), stringr, RCurl, plyr, VariantAnnotation (>= 1.13.44), rtracklayer, RSQLite, txdbmaker, AhoCorasickTrie, methods Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 1872011004e3fb9e37d39d43b0ec5783 Package: cyanoFilter Version: 1.14.0 Depends: R(>= 4.1.0) Imports: Biobase, flowCore, flowDensity, flowClust, cytometree, ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats, utils Suggests: magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr License: MIT + file LICENSE MD5sum: 2d5ac951251c76848385eba9059c18d3 Package: cycle Version: 1.60.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 MD5sum: 1f298761504581d5fa345b10fd46c3fd Package: cydar Version: 1.30.0 Depends: SingleCellExperiment Imports: viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment, flowCore, Biobase, Rcpp, 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shinyFeedback, shinyjs, shinyMatrix, SummarizedExperiment, tibble, tidyr Suggests: testthat (>= 3.0.0), BiocStyle, knitr License: LGPL-3 MD5sum: 8239f0fa593c681360ab4b6c7d4b71e1 Package: cytofQC Version: 1.6.0 Imports: CATALYST, flowCore, e1071, EZtune, gbm, ggplot2, hrbrthemes, matrixStats, randomForest, rmarkdown, SingleCellExperiment, stats, SummarizedExperiment, ssc, S4Vectors, graphics, methods Suggests: gridExtra, knitr, RColorBrewer, testthat, uwot License: Artistic-2.0 MD5sum: 0402268a2194d7304b6113ec94480437 Package: CytoGLMM Version: 1.14.0 Imports: stats, methods, BiocParallel, RColorBrewer, cowplot, doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr, mbest, pheatmap, stringr, strucchange, tibble, ggrepel, MASS, logging, Matrix, tidyr, caret, rlang, grDevices Suggests: knitr, rmarkdown, testthat, BiocStyle License: LGPL-3 MD5sum: 0369d21bc40b2894d76c0025515ba714 Package: cytoKernel Version: 1.12.0 Depends: R (>= 4.1) Imports: Rcpp, SummarizedExperiment, utils, 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License_restricts_use: no MD5sum: 45f5f5b8f1908c87e91d5a91d2996704 Package: CytoPipeline Version: 1.6.0 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: b7cbf7d0dbf6ec111ac200d4cca8d579 Package: CytoPipelineGUI Version: 1.4.0 Depends: R (>= 4.4), CytoPipeline Imports: shiny, plotly, ggplot2, flowCore Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown, BiocStyle, patchwork License: GPL-3 MD5sum: 9b3f88dabb013a7c9a579d88e4fc9c94 Package: cytoviewer Version: 1.6.0 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: 5ac2c059478fd8db18377835476cd034 Package: dada2 Version: 1.34.0 Depends: R (>= 3.4.0), Rcpp (>= 0.12.0), methods (>= 3.4.0) Imports: Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), ShortRead (>= 1.32.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0), IRanges (>= 2.6.0), XVector (>= 0.16.0), BiocGenerics (>= 0.22.0) LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, knitr, rmarkdown License: LGPL-2 MD5sum: 5efe3fa20b4893c16facab8ae7e9f8fd Package: dagLogo Version: 1.44.0 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: f7ecf64a7f8056cfa01a80e264aa3349 Package: daMA Version: 1.78.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: 07c6cb492fbb28cdbe24d295dc72f3ba Package: DAMEfinder Version: 1.18.0 Depends: R (>= 4.0) Imports: stats, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, readr, SummarizedExperiment, GenomicAlignments, stringr, plyr, VariantAnnotation, parallel, ggplot2, Rsamtools, BiocGenerics, methods, limma, bumphunter, Biostrings, reshape2, cowplot, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: c521090e40d65c0417eb748e15f6216d Package: DaMiRseq Version: 2.18.0 Depends: R (>= 3.5.0), SummarizedExperiment, ggplot2 Imports: DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap, FactoMineR, corrplot, randomForest, e1071, caret, MASS, lubridate, plsVarSel, kknn, FSelector, methods, stats, utils, graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR, plyr Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: ff9fe871e093125464d58089186aa343 Package: Damsel Version: 1.2.0 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: 2a4e41433303d9e3dd1718728b9b57d3 Package: DAPAR Version: 1.38.0 Depends: R (>= 4.3.0) Imports: Biobase, MSnbase, DAPARdata (>= 1.30.0), utils, highcharter, foreach Suggests: testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph, diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR, factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster, forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr, norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr, limma, preprocessCore, stringr, tidyr, impute, gplots, grDevices, reshape2, graphics, stats, methods, ggplot2, RColorBrewer, Matrix, org.Sc.sgd.db License: Artistic-2.0 MD5sum: 4a11548e6cc9d5144c5fb665afe66799 Package: dar Version: 1.2.0 Depends: R (>= 4.4.0) Imports: cli, ComplexHeatmap, crayon, dplyr, generics, ggplot2, glue, gplots, heatmaply, magrittr, methods, mia, phyloseq, purrr, readr, rlang (>= 0.4.11), scales, stringr, tibble, tidyr, UpSetR, waldo Suggests: ALDEx2, ANCOMBC, apeglm, ashr, Biobase, corncob, covr, DESeq2, devtools, furrr, future, knitr, lefser, limma, Maaslin2, metagenomeSeq, microbiome, rmarkdown, roxygen2, roxyglobals, roxytest, rstatix, SummarizedExperiment, TreeSummarizedExperiment, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 29c394814b4a37ac7110de89104e07fa Package: DART Version: 1.54.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: ea8225a0a367230201f270b5ec92e401 Package: dcanr Version: 1.22.0 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: 138cc57c68c740b6ba21da8a8c6ed53c Package: DCATS Version: 1.4.0 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: ba16358dc565459c62c9d82047e4a6ff Package: dce Version: 1.13.0 Depends: R (>= 4.1) Imports: stats, methods, assertthat, graph, pcalg, purrr, tidyverse, Matrix, ggraph, tidygraph, ggplot2, rlang, expm, MASS, edgeR, epiNEM, igraph, metap, mnem, naturalsort, ppcor, glm2, graphite, reshape2, dplyr, magrittr, glue, Rgraphviz, harmonicmeanp, org.Hs.eg.db, logger, shadowtext Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, cowplot, ggplotify, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment, RcppParallel, docopt, CARNIVAL License: GPL-3 MD5sum: 28d3959a64ce14d629e31d9cdd1e212e Package: dcGSA Version: 1.34.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: adf01c0d98029bcf658028fe075ee353 Package: ddCt Version: 1.62.0 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: 18d40038e0318523ab2049cca92dc05d Package: ddPCRclust Version: 1.26.0 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: d2cfdef496b19406168641764a5d3b8c Package: dearseq Version: 1.18.0 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: c43b1d7499a8edc7ca7e2227a97bfbfd Package: debCAM Version: 1.24.0 Depends: R (>= 3.5) Imports: methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR2, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 MD5sum: 69e70f84411522cfa45d3ea00efd54fc Package: debrowser Version: 1.34.0 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: 9078bd87570ac3cbf6df450f28841df0 Package: DECIPHER Version: 3.2.0 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: a4740d65c470f0ee7a1b31f4eac4cd2a Package: DeconRNASeq Version: 1.48.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 MD5sum: 6372d15ea3c1d925c24b0bb23c7257d2 Package: decontam Version: 1.26.0 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: 6426b172f6e247583076bc048ce6141e Package: decontX Version: 1.4.0 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: 4b284e9f6eef989d10b5263f46b72a93 Package: deconvR Version: 1.12.0 Depends: R (>= 4.1), data.table (>= 1.14.0) Imports: S4Vectors (>= 0.30.0), methylKit (>= 1.18.0), IRanges (>= 2.26.0), GenomicRanges (>= 1.44.0), BiocGenerics (>= 0.38.0), stats, methods, foreach (>= 1.5.1), magrittr (>= 2.0.1), matrixStats (>= 0.61.0), e1071 (>= 1.7.9), quadprog (>= 1.5.8), nnls (>= 1.4), rsq (>= 2.2), MASS, utils, dplyr (>= 1.0.7), tidyr (>= 1.1.3), assertthat, minfi Suggests: testthat (>= 3.0.0), roxygen2 (>= 7.1.2), doParallel (>= 1.0.16), parallel, knitr (>= 1.34), BiocStyle (>= 2.20.2), reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), rmarkdown, devtools (>= 2.4.2), sessioninfo (>= 1.1.1), covr, granulator, RefManageR License: Artistic-2.0 MD5sum: f33d419c7ef85378133043184915cbea Package: DeepPINCS Version: 1.14.0 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: 21b0714886b808c640a35108af6c8d6a Package: deepSNV Version: 1.52.0 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: 7957b61abaa077dd0731be272b9d3693 Package: DeepTarget Version: 1.0.0 Depends: R (>= 4.2.0) Imports: fgsea, ggplot2, stringr, ggpubr, BiocParallel, pROC, stats, grDevices, graphics, depmap, readr, dplyr Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 149845880636a1ebe5d12d7239f551ea Package: DEFormats Version: 1.34.0 Imports: checkmate, data.table, DESeq2, edgeR (>= 3.13.4), GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat License: GPL-3 MD5sum: d6d52d594447d401a269df89f3eefc5a Package: DegCre Version: 1.1.0 Depends: R (>= 4.4) Imports: GenomicRanges, InteractionSet, plotgardener, S4Vectors, stats, graphics, grDevices, BiocGenerics, GenomeInfoDb, IRanges, utils Suggests: BSgenome, BSgenome.Hsapiens.UCSC.hg38, org.Hs.eg.db, BiocStyle, magick, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 8fe21ddf11c43a35e58fd0f80d8f4a4e Package: DegNorm Version: 1.16.0 Depends: R (>= 4.0.0), methods Imports: Rcpp (>= 1.0.2),GenomicFeatures, txdbmaker, parallel, foreach, S4Vectors, doParallel, Rsamtools (>= 1.31.2), GenomicAlignments, heatmaply, data.table, stats, ggplot2, GenomicRanges, IRanges, plyr, plotly, utils,viridis LinkingTo: Rcpp, RcppArmadillo,S4Vectors,IRanges Suggests: knitr,rmarkdown,formatR License: LGPL (>= 3) MD5sum: 8f3f8b3e132822b34ad7ab60133c3c84 Package: DEGreport Version: 1.42.0 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: c7ee7715773d241c3a44b541f35fac42 Package: DEGseq Version: 1.60.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: acd86f118a88b7f290d38ad46aedc16e Package: DelayedArray Version: 0.32.0 Depends: R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>= 0.51.3), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2), IRanges (>= 2.17.3), S4Arrays (>= 1.5.4), SparseArray (>= 1.5.42) Imports: stats LinkingTo: S4Vectors Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit License: Artistic-2.0 MD5sum: d6d683b4c75a954b69314dbf5dc8c103 Package: DelayedDataFrame Version: 1.22.0 Depends: R (>= 3.6), S4Vectors (>= 0.23.19), DelayedArray (>= 0.7.5) Imports: methods, stats, BiocGenerics Suggests: testthat, knitr, rmarkdown, BiocStyle, SeqArray, GDSArray License: GPL-3 MD5sum: fd05b98e3519e4ec6bb7c541b623d5d3 Package: DelayedMatrixStats Version: 1.28.0 Depends: MatrixGenerics (>= 1.15.1), DelayedArray (>= 0.31.7) Imports: methods, sparseMatrixStats (>= 1.13.2), Matrix (>= 1.5-0), S4Vectors (>= 0.17.5), IRanges (>= 2.25.10), SparseArray (>= 1.5.19) Suggests: testthat, knitr, rmarkdown, BiocStyle, microbenchmark, profmem, HDF5Array, matrixStats (>= 1.0.0) License: MIT + file LICENSE MD5sum: fef45f69c18c5635bab8d784d4b6d186 Package: DelayedRandomArray Version: 1.14.0 Depends: SparseArray (>= 1.5.15), DelayedArray (>= 0.31.6) Imports: methods, dqrng, Rcpp LinkingTo: dqrng, BH, Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, Matrix License: GPL-3 MD5sum: ed4a60f66b19938e0e0f1e7bf1d219a1 Package: DelayedTensor Version: 1.12.0 Depends: R (>= 4.1.0) Imports: methods, utils, S4Arrays, SparseArray, DelayedArray (>= 0.31.8), HDF5Array, BiocSingular, rTensor, DelayedRandomArray (>= 1.13.1), irlba, Matrix, einsum, Suggests: markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr, dplyr, reticulate License: Artistic-2.0 MD5sum: 228ce527bd2182fba22b9fa76a28d1ee Package: DELocal Version: 1.6.0 Imports: DESeq2, dplyr, reshape2, limma, SummarizedExperiment, ggplot2, matrixStats, stats Suggests: biomaRt, knitr, rmarkdown, stringr, BiocStyle License: MIT + file LICENSE MD5sum: ca4c75a530dd0b4442f1c5ee6d49a759 Package: deltaCaptureC Version: 1.20.0 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2, tictoc Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 0c303dceabb985f1ea008b61f8cf231d Package: deltaGseg Version: 1.46.0 Depends: R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh, tseries, pvclust, fBasics, grid, reshape, scales Suggests: knitr License: GPL-2 MD5sum: 2faced2049a1a18b0331a723159de0d1 Package: DeMAND Version: 1.36.0 Depends: R (>= 2.14.0), KernSmooth, methods License: file LICENSE MD5sum: 10ae469e17c271206985a69d5ee7b5f9 Package: DeMixT Version: 1.22.0 Depends: R (>= 3.6.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment, knitr, KernSmooth, matrixcalc, rmarkdown, DSS, dendextend, psych, sva Imports: matrixStats, stats, truncdist, base64enc, ggplot2 LinkingTo: Rcpp License: GPL-3 MD5sum: 6894df86ac885d1f282faa460a367591 Package: demuxmix Version: 1.8.0 Depends: R (>= 4.0.0) Imports: stats, MASS, Matrix, ggplot2, gridExtra, methods Suggests: BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 289ca433a5fcd37e2dd95ead1b17c402 Package: demuxSNP Version: 1.4.0 Depends: R (>= 4.3.0), SingleCellExperiment, VariantAnnotation, ensembldb Imports: MatrixGenerics, BiocGenerics, class, GenomeInfoDb, IRanges, Matrix, SummarizedExperiment, demuxmix, methods, KernelKnn, dplyr Suggests: knitr, rmarkdown, ComplexHeatmap, viridisLite, ggpubr, dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat (>= 3.0.0), Seurat License: GPL-3 MD5sum: 9c58795253007876ca4374af0480b128 Package: densvis Version: 1.16.0 Imports: Rcpp, basilisk, assertthat, reticulate, Rtsne, irlba LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, ggplot2, uwot, testthat License: MIT + file LICENSE MD5sum: 310f14d437f2aa95c12d4c14d72ce441 Package: DEP Version: 1.28.0 Depends: R (>= 3.5) Imports: ggplot2, dplyr, purrr, readr, tibble, tidyr, SummarizedExperiment (>= 1.11.5), MSnbase, limma, vsn, fdrtool, ggrepel, ComplexHeatmap, RColorBrewer, circlize, shiny, shinydashboard, DT, rmarkdown, assertthat, gridExtra, grid, stats, imputeLCMD, cluster Suggests: testthat, enrichR, knitr, BiocStyle License: Artistic-2.0 MD5sum: 9bd6a346f67a0fd3296ebd11746087ea Package: DepecheR Version: 1.22.0 Depends: R (>= 4.0) Imports: ggplot2 (>= 3.1.0), MASS (>= 7.3.51), Rcpp (>= 1.0.0), dplyr (>= 0.7.8), gplots (>= 3.0.1), viridis (>= 0.5.1), foreach (>= 1.4.4), doSNOW (>= 1.0.16), matrixStats (>= 0.54.0), mixOmics (>= 6.6.1), moments (>= 0.14), grDevices (>= 3.5.2), graphics (>= 3.5.2), stats (>= 3.5.2), utils (>= 3.5), methods (>= 3.5), parallel (>= 3.5.2), reshape2 (>= 1.4.3), beanplot (>= 1.2), FNN (>= 1.1.3), robustbase (>= 0.93.5), gmodels (>= 2.18.1), collapse (>= 1.9.2), ClusterR (>= 1.3.2) LinkingTo: Rcpp, RcppEigen Suggests: uwot, testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 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(>= 0.99.0), sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, RefManageR, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, covr License: Artistic-2.0 MD5sum: 9f5bf56cb76b8622f0292a0d58e4d4b4 Package: DEScan2 Version: 1.26.0 Depends: R (>= 3.5), GenomicRanges Imports: BiocParallel, BiocGenerics, ChIPpeakAnno, data.table, DelayedArray, GenomeInfoDb, GenomicAlignments, glue, IRanges, plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors (>= 0.23.19), SummarizedExperiment, tools, utils LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod License: Artistic-2.0 MD5sum: 4c8b4cb334c3dbc8e5d29e28402ec828 Package: DESeq2 Version: 1.46.0 Depends: S4Vectors (>= 0.23.18), IRanges, GenomicRanges, SummarizedExperiment (>= 1.1.6) Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, matrixStats, methods, stats4, locfit, ggplot2 (>= 3.4.0), Rcpp (>= 0.11.0), MatrixGenerics LinkingTo: Rcpp, 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GreyListChIP LinkingTo: Rhtslib (>= 1.99.1), Rcpp Suggests: BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid License: Artistic-2.0 MD5sum: 9d4275eb90795253472d190ce88f47f1 Package: diffcoexp Version: 1.26.0 Depends: R (>= 3.5), WGCNA, SummarizedExperiment Imports: stats, DiffCorr, psych, igraph, BiocGenerics Suggests: GEOquery, RUnit License: GPL (> 2) MD5sum: 9e464b943ea1fca072f56833be100918 Package: diffcyt Version: 1.26.0 Depends: R (>= 3.4.0) Imports: flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma, edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats, methods, utils, grDevices, graphics, ComplexHeatmap, circlize, grid Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST License: MIT + file LICENSE MD5sum: 8b071a2dde5876e64b6702147fc32710 Package: DifferentialRegulation Version: 2.4.0 Depends: R (>= 4.3.0) Imports: methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, 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S4Vectors, zip, reshape2 Suggests: testthat License: GPL-3 MD5sum: 3e811fd52bf1cd171629e0c3c58e3064 Package: distinct Version: 1.18.0 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: 55c8e12340cd05dd47c94ddb8d7cbb87 Package: dittoSeq Version: 1.18.0 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 License: MIT + file LICENSE MD5sum: 63821746aeb15d8f0ef5ce6cf1683711 Package: divergence Version: 1.22.0 Depends: R (>= 3.6), SummarizedExperiment 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parallel, Rcpp, RcppRoll, betareg, grDevices, graphics, methods, stats, utils Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: c6c79d67f471457769d0385f1835601a Package: DMRcate Version: 3.2.1 Depends: R (>= 4.3.0) Imports: AnnotationHub, ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats, utils, S4Vectors, methods, graphics, SummarizedExperiment, biomaRt, grDevices Suggests: knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38, FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest License: file LICENSE MD5sum: 9941b9533cf8e3f7bc6c96ebd8291ed0 Package: dmrseq Version: 1.26.0 Depends: R (>= 3.5), bsseq Imports: GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer, bumphunter, DelayedMatrixStats (>= 1.1.13), matrixStats, BiocParallel, outliers, methods, locfit, IRanges, grDevices, graphics, stats, utils, annotatr, AnnotationHub, rtracklayer, GenomeInfoDb, splines Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: MIT + file LICENSE MD5sum: ae20100479a6dd81fc36fbf5d2987cfc Package: DNABarcodeCompatibility Version: 1.22.0 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: 0d4eaf5ca980958ed6e7adc5cc4efec5 Package: DNABarcodes Version: 1.36.0 Depends: Matrix, parallel Imports: Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, BiocStyle, rmarkdown License: GPL-2 MD5sum: 16794e627f4ad184c1eef3860cebd118 Package: DNAcopy Version: 1.80.0 License: GPL (>= 2) MD5sum: b9f3d62321e137b8a8ae6a565b2ecb50 Package: DNAfusion Version: 1.8.0 Depends: R (>= 4.2.0) Imports: bamsignals, GenomicRanges, IRanges, Rsamtools, GenomicAlignments, BiocBaseUtils, S4Vectors, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocGenerics Suggests: knitr, rmarkdown, testthat, sessioninfo, BiocStyle License: GPL-3 MD5sum: 3199624d2494206275c30947456c16e6 Package: DNAshapeR Version: 1.34.0 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: 671ceb4541ddd1d060679f478274c58f Package: DominoEffect Version: 1.26.0 Depends: R(>= 3.5) Imports: biomaRt, data.table, utils, stats, Biostrings, pwalign, SummarizedExperiment, VariantAnnotation, AnnotationDbi, GenomeInfoDb, IRanges, GenomicRanges, methods Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: 790cc9f50167c1c3c3b9546ad4ba88a4 Package: dominoSignal Version: 1.0.0 Depends: R(>= 4.2.0), Imports: biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid, igraph, Matrix, methods, plyr, stats, utils Suggests: knitr, patchwork, rmarkdown, Seurat, testthat, formatR, BiocFileCache, SingleCellExperiment License: GPL-3 | file LICENSE MD5sum: 0cbcec85e1df3cf9ed231623a090dd3d Package: doppelgangR Version: 1.34.0 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: 9f7a06dcd9604fc492776cb3792f4c70 Package: Doscheda Version: 1.28.0 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: 3ac35336093c98233ef667e85048ae07 Package: DOSE Version: 4.0.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, BiocParallel, fgsea, ggplot2, GOSemSim (>= 2.31.2), methods, qvalue, reshape2, stats, utils, yulab.utils 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BiocStyle, testthat, SummarizedExperiment, viper License: MIT + file LICENSE MD5sum: 0c3c9e933c505959d807dc1d24141c06 Package: EasyCellType Version: 1.8.0 Depends: R (>= 4.2.0) Imports: clusterProfiler, dplyr, forcats, ggplot2, magrittr, rlang, stats, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, vctrs (>= 0.6.4), BiocStyle Suggests: knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager, devtools, BiocStyle License: Artistic-2.0 MD5sum: a94561ea523256f4ede1f6c292e9c761 Package: easylift Version: 1.4.0 Depends: GenomicRanges, BiocFileCache Imports: rtracklayer, GenomeInfoDb, R.utils, tools, methods Suggests: testthat (>= 3.0.0), IRanges, knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: 2fef788d5c0a73bc469b8a24449289f0 Package: easyreporting Version: 1.18.0 Depends: R (>= 3.5.0) Imports: rmarkdown, methods, tools, shiny, rlang Suggests: distill, BiocStyle, knitr, readxl, edgeR, limma, EDASeq, statmod License: Artistic-2.0 MD5sum: 191941f7cad300a2359554e954005a2f Package: 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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: 383bccb28fc5b33e7782983c3159730c Package: epidecodeR Version: 1.14.0 Depends: R (>= 3.1.0) Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 16db01c4acf8356feb0b6d0a0b067847 Package: EpiDISH Version: 2.22.0 Depends: R (>= 4.1) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat License: GPL-2 MD5sum: f2ba6109b957723efb9fd4f3c9543b86 Package: epigenomix Version: 1.46.0 Depends: R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment Imports: BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray License: LGPL-3 MD5sum: e522f1ef0a3bb3b6a8361075d61061ce Package: epigraHMM Version: 1.14.0 Depends: R (>= 3.5.0) Imports: Rcpp, magrittr, data.table, SummarizedExperiment, methods, GenomeInfoDb, GenomicRanges, rtracklayer, IRanges, Rsamtools, bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5, Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap, grDevices LinkingTo: Rcpp, RcppArmadillo, Rhdf5lib Suggests: testthat, knitr, rmarkdown, BiocStyle, BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData License: MIT + file LICENSE MD5sum: 9bc2edc1484941662d857e777622b218 Package: EpiMix Version: 1.8.0 Depends: R (>= 4.2.0), EpiMix.data (>= 1.2.2) Imports: AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table, doParallel, doSNOW, downloader, dplyr, ELMER.data, ExperimentHub, foreach, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, impute, IRanges, limma, methods, parallel, plyr, progress, R.matlab, RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, utils Suggests: BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr, org.Hs.eg.db, regioneR, Seurat, survival, survminer, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, multiMiR, miRBaseConverter License: GPL-3 MD5sum: 791d8c5cd35eaf3c674818e9d95646a1 Package: epimutacions Version: 1.10.0 Depends: R (>= 4.3.0), epimutacionsData Imports: minfi, bumphunter, isotree, robustbase, ggplot2, GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment, stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt, BiocParallel, GenomeInfoDb, Homo.sapiens, purrr, tibble, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, AnnotationDbi, AnnotationHub, ExperimentHub, reshape2, grid, ensembldb, gridExtra, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, ggrepel Suggests: testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra, methods, grDevices License: MIT + file LICENSE MD5sum: 27fd049ef16a256a5ffb1bac99ce5c92 Package: epiNEM Version: 1.30.0 Depends: R (>= 4.1) Imports: BoutrosLab.plotting.general, BoolNet, e1071, gtools, stats, igraph, utils, lattice, latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph, mnem, latex2exp Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle License: GPL-3 MD5sum: e8c97c223617ba6e027fce0b6727919d Package: EpipwR Version: 1.0.0 Depends: R (>= 4.4.0) Imports: EpipwR.data, ExperimentHub (>= 2.10.0), ggplot2 Suggests: knitr, rmarkdown, testthat (>= 3.0.0), sessioninfo License: Artistic-2.0 MD5sum: 69c399ba83d656f8525ae88b74856623 Package: epiregulon.extra Version: 1.2.0 Depends: R (>= 4.4), SingleCellExperiment Imports: scran, ComplexHeatmap, Matrix, SummarizedExperiment, checkmate, circlize, clusterProfiler, ggplot2, ggraph, igraph, lifecycle, patchwork, reshape2, scales, scater, stats Suggests: epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), EnrichmentBrowser, msigdbr, dorothea, scMultiome, S4Vectors, scuttle, vdiffr, ggrastr, ggrepel License: MIT + file LICENSE MD5sum: b991ac6fec281d71d6eaa0480c933ea7 Package: epistack Version: 1.12.0 Depends: R (>= 4.1) Imports: GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, graphics, plotrix, grDevices, stats, methods Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick License: MIT + file LICENSE MD5sum: 1bcd194a0b46b7b77047c41007239783 Package: epistasisGA Version: 1.8.0 Depends: R (>= 4.2) Imports: BiocParallel, data.table, matrixStats, stats, survival, igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid, bigmemory, graphics, utils LinkingTo: Rcpp, RcppArmadillo, BH, bigmemory Suggests: BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0) License: GPL-3 MD5sum: 2bd92d409d340bfe2b2acfc64ce9b15a Package: EpiTxDb Version: 1.18.0 Depends: R (>= 4.0), AnnotationDbi, Modstrings Imports: methods, utils, httr, xml2, curl, rex, GenomicFeatures, txdbmaker, GenomicRanges, GenomeInfoDb, BiocGenerics, BiocFileCache, S4Vectors, IRanges, RSQLite, DBI, Biostrings, tRNAdbImport Suggests: BiocStyle, knitr, rmarkdown, testthat, httptest, AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: bb8cc03379409f4806db240e9943f28a Package: epivizr Version: 2.36.0 Depends: R (>= 3.5.0), methods Imports: epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4), GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown License: Artistic-2.0 MD5sum: a18fa528e3919f81bb9f542c18b16371 Package: epivizrChart Version: 1.28.0 Depends: R (>= 3.5.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub License: Artistic-2.0 MD5sum: 43487128345247a2aff360e0a2ab6626 Package: epivizrData Version: 1.34.0 Depends: R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase Imports: S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0), OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats License: MIT + file LICENSE MD5sum: f8abd4db94bae0dbb2a40454ba3ff18f Package: epivizrServer Version: 1.34.0 Depends: R (>= 3.2.3), methods Imports: httpuv (>= 1.3.0), R6 (>= 2.0.0), rjson, mime (>= 0.2) Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: efa224ff87397d9d8f958295aa848ecc Package: epivizrStandalone Version: 1.34.0 Depends: R (>= 3.2.3), epivizr (>= 2.3.6), methods Imports: git2r, epivizrServer, GenomeInfoDb, BiocGenerics, GenomicFeatures, S4Vectors Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle License: MIT + file LICENSE MD5sum: 60b4c0a47905bb949cd1b4930acca33a Package: erccdashboard Version: 1.40.0 Depends: R (>= 4.0), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0) Imports: edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr, qvalue, reshape2, ROCR, scales, stringr, knitr Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 4a2a25afbc60364c7e5e68fda17ac22c Package: erma Version: 1.22.0 Depends: R (>= 3.1), methods, Homo.sapiens, GenomicFiles (>= 1.5.2) Imports: rtracklayer (>= 1.38.1), S4Vectors (>= 0.23.18), BiocGenerics, GenomicRanges, SummarizedExperiment, ggplot2, GenomeInfoDb, Biobase, shiny, BiocParallel, IRanges, AnnotationDbi Suggests: rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel License: Artistic-2.0 MD5sum: ee247d738f4938f719d53f69d2c0e08e Package: ERSSA Version: 1.24.0 Depends: R (>= 4.0.0) Imports: edgeR (>= 3.23.3), DESeq2 (>= 1.21.16), ggplot2 (>= 3.0.0), RColorBrewer (>= 1.1-2), plyr (>= 1.8.4), BiocParallel (>= 1.15.8), apeglm (>= 1.4.2), grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 43be4c8ec51cb6618bd8c8f623f2435f Package: escape Version: 2.2.2 Depends: R (>= 4.1) Imports: AUCell, BiocParallel, grDevices, dplyr, ggdist, ggplot2, ggpointdensity, GSEABase, GSVA, SingleCellExperiment, ggridges, msigdbr, stats, reshape2, patchwork, MatrixGenerics, utils, SummarizedExperiment, UCell, stringr, methods, SeuratObject, Matrix Suggests: Seurat, hexbin, scran, knitr, rmarkdown, markdown, BiocStyle, RColorBrewer, rlang, spelling, testthat (>= 3.0.0), vdiffr License: MIT + file LICENSE MD5sum: 09fcf9aa91a39b5c8a21fabb1d7e23a6 Package: escheR Version: 1.6.0 Depends: ggplot2, R (>= 4.3) Imports: SpatialExperiment (>= 1.6.1), SingleCellExperiment, rlang, SummarizedExperiment Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat, hexbin License: MIT + file LICENSE MD5sum: 001cf81791ab9aee62cd0a478eaabfaa Package: esetVis Version: 1.32.0 Imports: mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils, grDevices, methods Suggests: ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db License: GPL-3 MD5sum: 13010df39fd5dade181466f5fec20f1d Package: eudysbiome Version: 1.36.0 Depends: R (>= 3.1.0) Imports: plyr, Rsamtools, R.utils, Biostrings License: GPL-2 MD5sum: 5e7234059523551f5cf11d65d58d4cd8 Package: evaluomeR Version: 1.22.0 Depends: R (>= 3.6), SummarizedExperiment, MultiAssayExperiment, cluster (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14), flexmix (>= 2.3.15), RSKC (>= 2.4.2), sparcl (>= 1.0.4) Imports: corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2, ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class, prabclus, mclust, kableExtra, dplyr, dendextend (>= 1.16.0) Suggests: BiocStyle, knitr, rmarkdown, magrittr License: GPL-3 MD5sum: f45a6ccc438105307340f7567a0de21c Package: EventPointer Version: 3.14.0 Depends: R (>= 3.5.0), SGSeq, Matrix, SummarizedExperiment Imports: GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls, limma, matrixStats, RBGL, prodlim, graph, methods, utils, stats, doParallel, foreach, affxparser, GenomicRanges, S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome, Biostrings, glmnet, abind, iterators, lpSolve, poibin, speedglm, tximport, fgsea Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr, kableExtra License: Artistic-2.0 MD5sum: 0a1d204ec9742ba4ceaca994c5bb1fa2 Package: EWCE Version: 1.14.0 Depends: R (>= 4.2), RNOmni (>= 1.0) Imports: stats, utils, methods, ewceData (>= 1.7.1), dplyr, ggplot2, reshape2, limma, stringr, HGNChelper, Matrix, parallel, SingleCellExperiment, SummarizedExperiment, DelayedArray, BiocParallel, orthogene (>= 0.99.8), data.table Suggests: rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2, MAST, DelayedMatrixStats, ggdendro, scales, patchwork License: GPL-3 MD5sum: 1e11b4318b0db67b21b8e4587fce53bb Package: ExCluster Version: 1.24.0 Depends: Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges Imports: stats, methods, grDevices, graphics, utils License: GPL-3 MD5sum: 4f77b5c8d37e4c7035ca9cead5e4263b Package: ExiMiR Version: 2.48.0 Depends: R (>= 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TreeSummarizedExperiment Imports: methods, Matrix, S4Vectors Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran, scater, scds, TENxPBMCData, airway License: MIT + file LICENSE MD5sum: f422d62a3e46c34b9d975428a96ecf55 Package: ExploreModelMatrix Version: 1.18.0 Imports: shiny (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr, magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales, tibble, MASS, limma, S4Vectors, shinyjs Suggests: testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle License: MIT + file LICENSE MD5sum: 3da13f7b72f918619013c19112b4a7c9 Package: ExpressionAtlas Version: 1.34.0 Depends: R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2, RCurl, jsonlite, BiocStyle Imports: utils, XML, httr Suggests: knitr, testthat, rmarkdown License: GPL (>= 3) MD5sum: 05f636e20111d95bacab244ca704faeb Package: extraChIPs Version: 1.10.0 Depends: BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 3.5.0), ggside (>= 0.3.1), SummarizedExperiment, tibble Imports: BiocIO, broom, ComplexUpset, csaw, dplyr (>= 1.1.1), edgeR (>= 4.0), forcats, GenomeInfoDb, GenomicAlignments, GenomicInteractions, ggforce, ggrepel, glue, grDevices, grid, InteractionSet, IRanges, matrixStats, methods, patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales, stats, stringr, tidyr, tidyselect, utils, vctrs, VennDiagram Suggests: apeglm, BiocStyle, covr, DESeq2, EnrichedHeatmap, Gviz, harmonicmeanp, here, knitr, limma, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: 4ce1cfb65e026b4c3fa7959902def8bf Package: fabia Version: 2.52.0 Depends: R (>= 3.6.0), Biobase Imports: methods, graphics, grDevices, stats, utils License: LGPL (>= 2.1) MD5sum: f847326806ebc723c74ed7b996ec17fc Package: factDesign Version: 1.82.0 Depends: Biobase (>= 2.5.5) Imports: stats Suggests: affy, genefilter, multtest License: LGPL MD5sum: c88440ae3d7b5c4d39ffb2441b765360 Package: factR Version: 1.8.0 Depends: R (>= 4.2) Imports: BiocGenerics (>= 0.46), Biostrings (>= 2.68), GenomeInfoDb (>= 1.36), dplyr (>= 1.1), GenomicFeatures (>= 1.52), GenomicRanges (>= 1.52), IRanges (>= 2.34), purrr (>= 1.0), rtracklayer (>= 1.60), tidyr (>= 1.3), methods (>= 4.3), BiocParallel (>= 1.34), S4Vectors (>= 0.38), data.table (>= 1.14), rlang (>= 1.1), tibble (>= 3.2), wiggleplotr (>= 1.24), RCurl (>= 1.98), XML (>= 3.99), drawProteins (>= 1.20), ggplot2 (>= 3.4), stringr (>= 1.5), pbapply (>= 1.7), stats (>= 4.3), utils (>= 4.3), graphics (>= 4.3), crayon (>= 1.5) Suggests: AnnotationHub (>= 2.22), BSgenome (>= 1.58), BSgenome.Mmusculus.UCSC.mm10, testthat, knitr, rmarkdown, markdown, zeallot, rmdformats, bio3d (>= 2.4), signalHsmm (>= 1.5), tidyverse (>= 1.3), covr, patchwork License: file LICENSE MD5sum: 2b5ba7d7c8bc00a57d437f56865f6b59 Package: faers Version: 1.2.0 Depends: R (>= 3.5.0) Imports: BiocParallel, brio, cli, curl (>= 5.0.0), data.table, httr2 (>= 1.0.0), MCMCpack, methods, openEBGM, rlang (>= 1.1.0), rvest, tools, utils, vroom, xml2 Suggests: BiocStyle, countrycode, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 032ff8c5d441aae9f141faed7231e6ea Package: FamAgg Version: 1.34.0 Depends: methods, kinship2, igraph Imports: gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey Suggests: BiocStyle, knitr, RUnit, rmarkdown License: MIT + file LICENSE MD5sum: e1d29da55ecbee8477bf0ca4c1dd5fcf Package: famat Version: 1.16.0 Depends: R (>= 4.0) Imports: KEGGREST, mgcv, stats, BiasedUrn, dplyr, gprofiler2, rWikiPathways, reactome.db, stringr, GO.db, ontologyIndex, tidyr, shiny, shinydashboard, shinyBS, plotly, magrittr, DT, clusterProfiler, org.Hs.eg.db Suggests: BiocStyle, knitr, rmarkdown, testthat, BiocManager License: GPL-3 MD5sum: 5a0cd9f3922d1f3b54de038ecfea0235 Package: fastLiquidAssociation Version: 1.42.0 Depends: methods, LiquidAssociation, parallel, doParallel, stats, Hmisc, utils Imports: WGCNA, impute, preprocessCore Suggests: GOstats, yeastCC, org.Sc.sgd.db License: GPL-2 MD5sum: 0ad195701cc5f45487bd3b6d32e42f8e Package: FastqCleaner Version: 1.24.0 Imports: methods, shiny, stats, IRanges, Biostrings, ShortRead, DT, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12) LinkingTo: Rcpp Suggests: BiocStyle, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: ea2847a308cd097e65d288be04b9b72a Package: fastreeR Version: 1.10.0 Depends: R (>= 4.4) Imports: ape, data.table, dynamicTreeCut, methods, R.utils, rJava, stats, stringr, utils Suggests: BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: 3e7ec922362739ea8821dd6cd2029e40 Package: fastseg Version: 1.52.0 Depends: R (>= 2.13), GenomicRanges, Biobase Imports: methods, graphics, grDevices, stats, BiocGenerics, S4Vectors, IRanges Suggests: DNAcopy, oligo, BiocStyle, knitr License: LGPL (>= 2.0) MD5sum: 020104ffa83d202ca7362b6940b57cb7 Package: fCCAC Version: 1.32.0 Depends: R (>= 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SingleCellExperiment, methods, stats, utils, irlba, TSCAN, SC3, matrixStats Suggests: rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-2 MD5sum: 12bbccff04056e2885f1202606f46185 Package: FeatSeekR Version: 1.6.0 Imports: pheatmap, MASS, pracma, stats, SummarizedExperiment, methods Suggests: rmarkdown, knitr, BiocStyle, DmelSGI, testthat (>= 3.0.0) License: GPL-3 MD5sum: 03b6ae28d3c6bb70205bb951a18bd8f3 Package: fedup Version: 1.14.0 Depends: R (>= 4.1) Imports: openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes, forcats, RColorBrewer, RCy3, utils, stats Suggests: biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr License: MIT + file LICENSE MD5sum: 40f8941e81a14b43dc45cf277d88a7e6 Package: FELLA Version: 1.26.0 Depends: R (>= 3.5.0) Imports: methods, igraph, Matrix, KEGGREST, plyr, stats, graphics, utils Suggests: shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim License: GPL-3 MD5sum: 8a19cccccc1957f21cc2e34b97f35b3c Package: fenr Version: 1.4.0 Depends: R (>= 4.1.0) Imports: tools, methods, assertthat, rlang, dplyr, tidyr, tidyselect, tibble, purrr, readr, stringr, httr2, rvest, progress, BiocFileCache, shiny, ggplot2 Suggests: BiocStyle, testthat, knitr, rmarkdown, topGO License: MIT + file LICENSE MD5sum: 68a12c08961fc55ef63d5ee061c5a0a7 Package: ffpe Version: 1.50.0 Depends: R (>= 2.10.0), TTR, methods Imports: Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc Suggests: genefilter, ffpeExampleData License: GPL (> 2) MD5sum: 6fe44468abf57450c999edb138275b16 Package: fgga Version: 1.14.0 Depends: R (>= 4.3), RBGL Imports: graph, stats, e1071, methods, gRbase, jsonlite, BiocFileCache, curl, igraph Suggests: knitr, rmarkdown, GOstats, GO.db, BiocGenerics, pROC, RUnit, BiocStyle License: GPL-3 MD5sum: 4cf1f4e179cee7dae9bdcee32ae30061 Package: FGNet Version: 3.40.0 Depends: R (>= 4.2.0) Imports: igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2, RColorBrewer, png, methods, stats, utils, graphics, grDevices Suggests: RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, BiocManager License: GPL (>= 2) MD5sum: 01103c61ea58d703e488ba9dde7daecf Package: fgsea Version: 1.32.0 Depends: R (>= 4.1) Imports: Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0), cowplot, grid, fastmatch, Matrix, scales, utils LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation, Seurat License: MIT + file LICENCE MD5sum: 62d2cd88962d3bd3573270e7020f705f Package: FilterFFPE Version: 1.16.0 Imports: foreach, doParallel, GenomicRanges, IRanges, Rsamtools, parallel, S4Vectors Suggests: BiocStyle License: LGPL-3 MD5sum: c7838a42e6bc1fe4113badb516d0c32d Package: findIPs Version: 1.2.0 Depends: graphics, R (>= 4.4.0) Imports: Biobase, BiocParallel, parallel, stats, SummarizedExperiment, 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tidyr, utils, withr, future, methods, tibble, tidyselect, IRanges LinkingTo: Rcpp, Rhtslib, testthat Suggests: BiocStyle, GEOquery, knitr, rmarkdown, BiocFileCache, R.utils, ShortRead, uwot, testthat (>= 3.0.0), xml2 License: GPL (>= 3) MD5sum: 4d5ddd6e7a02727232c66de9ccb3715e Package: flowAI Version: 1.36.0 Depends: R (>= 4.3.0) Imports: ggplot2, flowCore, plyr, changepoint, knitr, reshape2, RColorBrewer, scales, methods, graphics, stats, utils, rmarkdown Suggests: testthat, shiny, BiocStyle License: GPL (>= 2) MD5sum: e35121562b1e9ce6fbd3cacffcfe3d96 Package: flowBeads Version: 1.44.0 Depends: R (>= 2.15.0), methods, Biobase, rrcov, flowCore Imports: flowCore, rrcov, knitr, xtable Suggests: flowViz License: Artistic-2.0 MD5sum: 71e05bfb63e8da5395601a58fcc0320b Package: flowBin Version: 1.42.0 Depends: methods, flowCore, flowFP, R (>= 2.10) Imports: class, limma, snow, BiocGenerics Suggests: parallel License: Artistic-2.0 MD5sum: d64faadf2b42008e350f93317ecdb978 Package: flowcatchR 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rmarkdown, KEGGREST, AnnotationDbi, org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils License: MIT + file LICENCE MD5sum: fd1264880a4cf2e59f494ab8f17b6359 Package: GBScleanR Version: 2.0.2 Depends: SeqArray Imports: stats, utils, methods, ggplot2, tidyr, expm, Rcpp, RcppParallel, gdsfmt LinkingTo: Rcpp, RcppParallel Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: a5b31740ab476cd60b74dbe599ef2a10 Package: gcapc Version: 1.30.0 Depends: R (>= 3.4) Imports: BiocGenerics, GenomeInfoDb, 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: 7194e6d18ecf137a82195f7f42f1b231 Package: gcatest Version: 2.6.0 Depends: R (>= 4.0) Imports: methods, lfa Suggests: knitr, ggplot2, testthat, BEDMatrix, genio License: GPL (>= 3) MD5sum: 4ce940bcdb0e30ed42e949b0d50d5713 Package: gCrisprTools Version: 2.12.0 Depends: R (>= 4.1) Imports: Biobase, limma, RobustRankAggreg, ggplot2, SummarizedExperiment, grid, rmarkdown, grDevices, graphics, methods, ComplexHeatmap, stats, utils, parallel Suggests: edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea License: Artistic-2.0 MD5sum: 6455152f91cdbc372dde0fa9bb0b84f9 Package: gcrma Version: 2.78.0 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: 17686194c6e70c492a3d06a9738c358a Package: GDCRNATools Version: 1.26.0 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: 7786db2654d9d827e2acced4f0f6bdff Package: gDNAx Version: 1.4.0 Depends: R (>= 4.3) Imports: methods, BiocGenerics, BiocParallel, matrixStats, Biostrings, S4Vectors, IRanges, 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: a3cc1411a95731069a2b0451b3a542ce Package: gDR Version: 1.4.0 Depends: R (>= 4.2), gDRcore (>= 1.1.19), gDRimport (>= 1.1.9), gDRutils (>= 1.1.12) Suggests: BiocStyle, BumpyMatrix, futile.logger, gDRstyle (>= 1.1.5), gDRtestData (>= 1.1.10), kableExtra, knitr, markdown, purrr, rmarkdown, SummarizedExperiment, testthat, yaml License: Artistic-2.0 MD5sum: 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BiocManager, checkmate, desc, git2r, lintr (>= 3.0.0), rcmdcheck, remotes, yaml, rjson, pkgbuild, withr Suggests: BiocStyle, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 680d342ec119aa86cc73dcecf7180c6b Package: gDRutils Version: 1.4.0 Depends: R (>= 4.2) Imports: BiocParallel, BumpyMatrix, checkmate, data.table, drc, jsonlite, jsonvalidate, methods, MultiAssayExperiment, S4Vectors, stats, stringr, SummarizedExperiment Suggests: BiocManager, BiocStyle, futile.logger, gDRstyle (>= 1.1.5), gDRtestData (>= 1.1.10), IRanges, knitr, lintr, purrr, qs, rcmdcheck, rmarkdown, scales, testthat, tools, yaml License: Artistic-2.0 MD5sum: 30985f6674bf00d4e1600f0edb5a98e8 Package: GDSArray Version: 1.26.0 Depends: R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>= 0.5.32) Imports: tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager License: GPL-3 MD5sum: 2a2779f4d2389ecf62f1e47fcf506f9c Package: gdsfmt Version: 1.42.1 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, Matrix, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics License: LGPL-3 MD5sum: f2d644c2edfae5d69a958d6b81136ed2 Package: GeDi Version: 1.2.0 Depends: R (>= 4.4.0) Imports: GOSemSim, Matrix, shiny, shinyWidgets, bs4Dash, rintrojs, utils, DT, dplyr, shinyBS, STRINGdb, igraph, visNetwork, shinycssloaders, fontawesome, grDevices, parallel, stats, ggplot2, plotly, GeneTonic, RColorBrewer, scales, readxl, ggdendro, ComplexHeatmap, BiocNeighbors, tm, wordcloud2, tools, BiocParallel, BiocFileCache, cluster, circlize Suggests: knitr, rmarkdown, testthat (>= 3.0.0), DESeq2, htmltools, pcaExplorer, AnnotationDbi, macrophage, topGO, biomaRt, ReactomePA, clusterProfiler, BiocStyle, org.Hs.eg.db License: MIT + file LICENSE MD5sum: fcc8df5a5508503a6e1ed53ea2fd077e Package: GEM Version: 1.32.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown License: Artistic-2.0 MD5sum: d5116b69fb7a58e7c432b07bc4bca5b5 Package: gemini Version: 1.20.0 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: bcad35512e8a0519f3e24eea6a86535d Package: gemma.R Version: 3.2.1 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: b77a64d0f0a39ef7e0c157d9dcbd2fff Package: genArise Version: 1.82.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: d253f2e233df7d9de6d1f0d73fbad1b4 Package: geneAttribution Version: 1.32.0 Imports: utils, GenomicRanges, org.Hs.eg.db, BiocGenerics, GenomeInfoDb, GenomicFeatures, IRanges, rtracklayer Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: d8d1476255f3f5a25b587a0fe00a7594 Package: GeneBreak Version: 1.36.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: e374d81009dc656327b4f1368829ed92 Package: geneClassifiers Version: 1.30.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: 45c2866f297c50e16f92f9d1b0301715 Package: GeneExpressionSignature Version: 1.52.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 9f3b372aa6aa212dfae0ed18de1e4031 Package: genefilter Version: 1.88.0 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: ddfc9b6580c7b36f618a0554064ff09f Package: genefu Version: 2.37.0 Depends: R (>= 4.1), survcomp, biomaRt, iC10, AIMS Imports: amap, impute, mclust, limma, graphics, stats, utils Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown License: Artistic-2.0 MD5sum: 8dc18c9d4743fb780d616d864f18fb88 Package: GeneGA Version: 1.56.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: 800a6601dacae9d324d45581b63d244b Package: GeneGeneInteR Version: 1.32.0 Depends: R (>= 4.0) Imports: snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods License: GPL (>= 2) MD5sum: 9e9479f065a7d7ad2a9ebf717dc35189 Package: GeneMeta Version: 1.78.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: cbf169807c649bd1e0bbbba3e3d009f1 Package: GeneNetworkBuilder Version: 1.48.0 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, RCy3, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db License: GPL (>= 2) MD5sum: 962a4bbfffd838bb8e319d5c89e01632 Package: GeneOverlap Version: 1.42.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 580372a16a0abba6fea55fe08de132c0 Package: geneplast Version: 1.32.0 Depends: R (>= 4.0), methods Imports: igraph, snow, ape, grDevices, graphics, stats, utils, data.table Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: d9598a65606dd851835044a93db66985 Package: geneplotter Version: 1.84.0 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: 5fadbabe63eff3c0329c01922c2f1ce2 Package: geneRecommender Version: 1.78.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: cf1b2e4068c9fa4bcc278bddda117c3d Package: GeneRegionScan Version: 1.62.0 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: e2bbe9fed0b431b37f3a9e48a029a25f Package: geneRxCluster Version: 1.42.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 6a37f6e827ecbc3d0db4c0da8872f5dc Package: GeneSelectMMD Version: 2.50.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: 3d4d2c807702667202c642c4ca601650 Package: GENESIS Version: 2.36.0 Imports: Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: c74368e197411d1b420e4686387c1f81 Package: GeneStructureTools Version: 1.26.0 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: ceb81cfd03cbf89fd92a6dc9fdae0d2c Package: geNetClassifier Version: 1.46.0 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: f520b68dc70f05723d18f5a12452e70d Package: GeneticsPed Version: 1.68.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: 9f074a20fc4d25eb6811c9e42a242c0c Package: GeneTonic Version: 3.0.0 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: 381894a6791877ac63c9aca39e05ab19 Package: geneXtendeR Version: 1.32.0 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: 585c8fae811a70146f5c1c9d9de7e316 Package: GENIE3 Version: 1.28.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle License: GPL (>= 2) MD5sum: 8b8999f934f50f279f8bbf33cd1349f7 Package: genoCN Version: 1.58.0 Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: 06344548618cae8301da51d24d1447e0 Package: genomation Version: 1.38.0 Depends: R (>= 3.5.0), grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 1710d5868431e3b2ddb70cfd73b866c9 Package: GenomAutomorphism Version: 1.8.1 Depends: R (>= 4.4.0), Imports: Biostrings, BiocGenerics, BiocParallel, GenomeInfoDb, GenomicRanges, IRanges, matrixStats, XVector, dplyr, data.table, parallel, doParallel, foreach, methods, S4Vectors, stats, numbers, utils Suggests: spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr License: Artistic-2.0 MD5sum: 209f2d73c41bd26cbbf9d7c590fcda98 Package: GenomeInfoDb Version: 1.42.1 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.25.12), IRanges (>= 2.13.12) Imports: stats, stats4, utils, UCSC.utils, GenomeInfoDbData Suggests: R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: e44d570d8b26939be4603224cb682666 Package: genomeIntervals Version: 1.62.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 1.5.8), GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: dc41e895d2fdabfef86259a5b4a2ed1c Package: genomes Version: 3.36.0 Depends: readr, curl License: GPL-3 MD5sum: 883877fad68be1097419ce01b495496d Package: GenomicAlignments Version: 1.42.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.55.3), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.55.7), Rsamtools (>= 1.31.2) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, knitr, BiocStyle License: Artistic-2.0 MD5sum: 9d3756a0526c48f2fee799447efd67b3 Package: GenomicDataCommons Version: 1.30.0 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: 2e0f730546ca4de982794aaadea7eb44 Package: GenomicDistributions Version: 1.14.0 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: 344313dc0eaf1f234f7f6a79f7098422 Package: GenomicFeatures Version: 1.58.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.51.2), S4Vectors (>= 0.17.29), IRanges (>= 2.37.1), GenomeInfoDb (>= 1.35.8), GenomicRanges (>= 1.55.2), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, DBI, XVector, Biostrings, rtracklayer Suggests: txdbmaker, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown License: Artistic-2.0 MD5sum: a448365e371aef6b2e3c43719cc91b11 Package: GenomicFiles Version: 1.42.0 Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), MatrixGenerics, GenomicRanges (>= 1.31.16), SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3) Imports: GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25), VariantAnnotation (>= 1.27.9), GenomeInfoDb Suggests: BiocStyle, RUnit, genefilter, deepSNV, snpStats, knitr, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens License: Artistic-2.0 MD5sum: fcfb5e6889b8a1b8fbc35b3230d0ef20 Package: genomicInstability Version: 1.12.0 Depends: R (>= 4.1.0), checkmate Imports: mixtools, SummarizedExperiment Suggests: SingleCellExperiment, ExperimentHub, pROC License: file LICENSE MD5sum: a9827320779298ad17de190798f88890 Package: GenomicInteractionNodes Version: 1.10.0 Depends: R (>= 4.2.0), stats Imports: AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, GenomeInfoDb, methods, IRanges, RBGL, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: file LICENSE MD5sum: 6012be2662795df76ef109b89b46b692 Package: GenomicInteractions Version: 1.40.0 Depends: R (>= 3.5), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 9b5e4793f9b439ef410fa50ecd648b3d Package: GenomicOZone Version: 1.20.0 Depends: R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2 Imports: grDevices, stats, utils, plyr, gridExtra, lsr, parallel, ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack Suggests: readxl, GEOquery, knitr, rmarkdown License: LGPL (>= 3) MD5sum: f5695b4240c4c7b6e3d1556fb362cf7f Package: GenomicPlot Version: 1.4.0 Depends: R (>= 4.4.0), GenomicRanges (>= 1.46.1) Imports: methods, Rsamtools, parallel, tidyr, rtracklayer (>= 1.54.0), plyranges 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DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: e69b769039c08cb748c3835723c79575 Package: GenomicScores Version: 2.18.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache, IRanges (>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub, rhdf5, DelayedArray, HDF5Array Suggests: RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard, BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38, MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v4.0.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: a4ee1759e49364858779adaecbe1920c Package: GenomicSuperSignature Version: 1.14.0 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: b1cf95d0ad2a2133951920a7b8a8456a Package: GenomicTuples Version: 1.40.0 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), GenomeInfoDb (>= 1.15.2), S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, covr, GenomicAlignments, Biostrings License: Artistic-2.0 MD5sum: d6d29acb6c88868f470c8733e73e3821 Package: GenProSeq Version: 1.10.0 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: bebfc3bb8246db894ce117d73ca6dff0 Package: GenVisR Version: 1.38.0 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, GenomeInfoDb, 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: 8659108bc10c5039bafea3f78920700b Package: GeoDiff Version: 1.12.0 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: 3b96d450c79d0237a0c83333ebbe5637 Package: GEOexplorer Version: 1.11.0 Depends: shiny, limma, Biobase, plotly, enrichR, R (>= 4.1.0) Imports: DT, XML, httr, sva, xfun, edgeR, htmltools, factoextra, heatmaply, pheatmap, scales, shinyHeatmaply, shinybusy, ggplot2, stringr, umap, GEOquery, impute, grDevices, stats, graphics, markdown, knitr, utils, xml2, R.utils, readxl, shinycssloaders, car Suggests: rmarkdown, usethis, testthat (>= 3.0.0) License: GPL-3 MD5sum: f3eaf6f5f7740715988f63e424899039 Package: GEOfastq Version: 1.14.0 Imports: xml2, rvest, stringr, RCurl, doParallel, foreach, plyr Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: bc1c598a5cfbaa96f308950052c498c6 Package: GEOmetadb Version: 1.68.1 Depends: R.utils,RSQLite Suggests: knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud License: Artistic-2.0 MD5sum: 891e0702431202e73e39d5aa5a14c32c Package: geomeTriD Version: 1.0.0 Depends: R (>= 4.4.0) Imports: BiocGenerics, GenomeInfoDb, GenomicRanges, graphics, grDevices, grid, htmlwidgets, igraph, InteractionSet, IRanges, MASS, Matrix, methods, plotrix, rgl, rjson, S4Vectors, scales, stats, trackViewer Suggests: RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, manipulateWidget, shiny, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 1e727008da38c9a71a2f1db4946dacfb Package: GeomxTools Version: 3.9.1 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: 67c1ce8473c560f8d28a8e6fc0881f46 Package: GEOquery Version: 2.74.0 Depends: methods, Biobase Imports: readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr, limma, curl, rentrez, R.utils, stringr, SummarizedExperiment, S4Vectors, rvest, httr2 Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr, markdown License: MIT + file LICENSE MD5sum: a29dab8a97a166a814433048d536d2d4 Package: GEOsubmission Version: 1.58.0 Imports: affy, Biobase, utils License: GPL (>= 2) MD5sum: f9644ff5f35eb2fcc2612590ad6517c1 Package: GeoTcgaData Version: 2.6.0 Depends: R (>= 4.2.0) Imports: utils, data.table, plyr, cqn, topconfects, stats, SummarizedExperiment, methods Suggests: knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr, clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq, testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery, BiocGenerics License: Artistic-2.0 MD5sum: 762aaba465ee22ba671627106e496755 Package: gep2pep Version: 1.26.0 Imports: repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods, Biobase, XML, rhdf5, digest, iterators Suggests: WriteXLS, testthat, knitr, rmarkdown License: GPL-3 MD5sum: e0fd4c8bb86e12b66fc7cba94e885403 Package: getDEE2 Version: 1.16.0 Depends: R (>= 4.0) Imports: stats, utils, SummarizedExperiment, htm2txt Suggests: knitr, testthat, rmarkdown License: GPL-3 MD5sum: 301d27fa73a16175f4a1a638d5878d28 Package: geva Version: 1.14.0 Depends: R (>= 4.1) Imports: grDevices, graphics, methods, stats, utils, dbscan, fastcluster, matrixStats Suggests: devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat (>= 3.0.0) License: LGPL-3 MD5sum: 9723248cefba75a5e00a19c2375c2d75 Package: GEWIST Version: 1.50.0 Depends: R (>= 2.10), car License: GPL-2 MD5sum: ee2b0ef39c4718f18249b7190726a413 Package: gg4way Version: 1.4.0 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: 415fd1a5c1a828c8d763356aae294e80 Package: ggbio Version: 1.54.0 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.29.14), SummarizedExperiment, Biostrings, Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer (>= 1.25.16), GenomicFeatures (>= 1.29.11), OrganismDbi, GGally, ensembldb (>= 1.99.13), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: 94f2839215543867d978e2347506deac Package: ggcyto Version: 1.34.0 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: de96c6c57dec24875052dfb3273ee52e Package: ggkegg Version: 1.4.0 Depends: R (>= 4.3.0), ggplot2, ggraph, XML, igraph, tidygraph Imports: BiocFileCache, GetoptLong, 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: 76e6af3c25c5922875addc9ea9efea0b Package: ggmanh Version: 1.10.0 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: 53d49ee08ddcc464578cd33830bfb101 Package: ggmsa Version: 1.12.0 Depends: R (>= 4.1.0) Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot, RColorBrewer, ggalt, ggforce, dplyr, R4RNA, grDevices, seqmagick, grid, methods, statebins, ggtree (>= 1.17.1) Suggests: ggtreeExtra, ape, cowplot, knitr, BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 3d1cdfb157e733b9cf2302335290872e Package: GGPA Version: 1.18.0 Depends: R (>= 4.0.0), stats, methods, graphics, GGally, network, sna, scales, matrixStats Imports: Rcpp (>= 0.11.3) LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle License: GPL (>= 2) MD5sum: 3e2664b419ed2fd933d1f9fa046eadd0 Package: ggsc Version: 1.4.0 Imports: Rcpp, RcppParallel, cli, dplyr, ggfun (>= 0.1.5), ggplot2, grDevices, grid, methods, rlang, scattermore, stats, Seurat, SingleCellExperiment, SummarizedExperiment, tidydr, tidyr, tibble, utils, RColorBrewer, yulab.utils, scales LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph, knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater, scatterpie (>= 0.2.4), scuttle, shadowtext, sf, SeuratObject, SpatialExperiment, STexampleData, testthat (>= 3.0.0), MASS License: Artistic-2.0 MD5sum: 4842d94eb26266232e81c9c319b0b57f Package: ggseqalign Version: 1.0.0 Depends: R (>= 4.4.0) Imports: pwalign, dplyr, ggplot2 Suggests: Biostrings, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 7a6d8de935831d6d0608d4a647df23de Package: ggspavis Version: 1.12.0 Depends: ggplot2 Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, ggside, grid, ggrepel, RColorBrewer, scales, grDevices, methods, stats Suggests: BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix, scater, scran, uwot, testthat, patchwork License: MIT + file LICENSE MD5sum: 107dfdd67bcbbcb39d93f0fc25bcdb72 Package: ggtree Version: 3.14.0 Depends: R (>= 3.5.0) Imports: ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.1.7), yulab.utils (>= 0.1.6), tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0), utils, scales, stats, cli Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue License: Artistic-2.0 MD5sum: 5c657ebae3d491957539c2a50553c9f3 Package: ggtreeDendro Version: 1.8.0 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: fe011f5d6390eab500f43e0a6d4e5569 Package: ggtreeExtra Version: 1.16.0 Imports: ggplot2, utils, rlang, ggnewscale, stats, ggtree, tidytree (>= 0.3.9), cli, magrittr Suggests: treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown, testthat (>= 3.0.0), pillar License: GPL (>= 3) MD5sum: 600cfe3cb36c951f94535ec16a54a6c2 Package: ggtreeSpace Version: 1.2.0 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: d112fd1b9c2b4ecdce6bd02f4cc7b996 Package: GIGSEA Version: 1.24.0 Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils Suggests: knitr, rmarkdown License: LGPL-3 MD5sum: 080321c2bdd2f3123c7a90bb0174cddb Package: ginmappeR Version: 1.2.3 Imports: KEGGREST, UniProt.ws, XML, rentrez, httr, utils, memoise, cachem, jsonlite, rvest Suggests: RUnit, BiocGenerics, markdown, knitr License: GPL-3 + file LICENSE MD5sum: 27d2cce42bacb3c2a1ad8dd7e7f22c18 Package: gINTomics Version: 1.2.0 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 Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 MD5sum: bab22e5673031c31c2a83b40d706b814 Package: girafe Version: 1.58.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), Rsamtools (>= 1.31.2), intervals (>= 0.13.1), ShortRead (>= 1.37.1), genomeIntervals (>= 1.25.1), grid Imports: methods, Biobase, Biostrings (>= 2.47.6), pwalign, graphics, grDevices, stats, utils, IRanges (>= 2.13.12) Suggests: MASS, org.Mm.eg.db, RColorBrewer Enhances: genomeIntervals License: Artistic-2.0 MD5sum: 3a1450aa3af6a4dd0ac52fcfa4cd5c24 Package: GLAD Version: 2.70.0 Depends: R (>= 2.10) Imports: aws License: GPL-2 MD5sum: fe84eee7d41b531fd30ec476f7baaa91 Package: GladiaTOX Version: 1.22.0 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: ba283220f89855caa47178093ee5f8e8 Package: Glimma Version: 2.16.0 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 License: GPL-3 MD5sum: 427dc09fe296e6de93b2d9dbc9df1877 Package: glmGamPoi Version: 1.18.0 Imports: Rcpp, DelayedMatrixStats, matrixStats, MatrixGenerics, SparseArray (>= 1.5.21), DelayedArray, HDF5Array, SummarizedExperiment, SingleCellExperiment, BiocGenerics, methods, stats, utils, splines, rlang, vctrs LinkingTo: Rcpp, RcppArmadillo, beachmat Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, muscData, scran, Matrix, dplyr License: GPL-3 MD5sum: 2cc7b79f8bafd61a930e0f70caada4d9 Package: glmSparseNet Version: 1.24.0 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: b3cc1c0d48cabac82369b88e1c9d768b Package: GlobalAncova Version: 4.24.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: f2db718268fd43fb7b195702bec8a2bf Package: globalSeq Version: 1.34.0 Depends: R (>= 3.0.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 MD5sum: af3e0a89fd752903f99fda9b0d9a4dc3 Package: GloScope Version: 1.4.0 Depends: R (>= 4.4.0) Imports: utils, stats, MASS, mclust, ggplot2, RANN, FNN, BiocParallel, mvnfast, SingleCellExperiment, rlang Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown, zellkonverter License: Artistic-2.0 MD5sum: a236352a86173bee4795dd28d20f3242 Package: gmapR Version: 1.48.0 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2) Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome, GenomicAlignments (>= 1.15.6), BiocParallel Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines License: Artistic-2.0 MD5sum: 4c8354c7c67cff913b654869a73633a2 Package: GmicR Version: 1.20.0 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: 82020b996e467a6a88fd28c7863e29f0 Package: gmoviz Version: 1.18.0 Depends: circlize, GenomicRanges, graphics, R (>= 4.0) Imports: grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics, Biostrings, GenomeInfoDb, methods, GenomicAlignments, GenomicFeatures, IRanges, rtracklayer, pracma, colorspace, S4Vectors Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager License: GPL-3 MD5sum: 7ba666cdbdaa5b303bce0ea6fe31326c Package: GMRP Version: 1.34.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: 2819bc42938c092d7ea60d299e883703 Package: GNET2 Version: 1.22.0 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: d73c618e8d4f98e69a3b500df57f3165 Package: GNOSIS Version: 1.4.0 Depends: R (>= 4.3.0), shiny, shinydashboard, shinydashboardPlus, dashboardthemes, shinyWidgets, shinymeta, tidyverse, operator.tools, maftools Imports: DT, fontawesome, shinycssloaders, cBioPortalData, shinyjs, reshape2, RColorBrewer, survival, survminer, stats, compareGroups, rpart, partykit, DescTools, car, rstatix, fabricatr, shinylogs, magrittr Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 8a69a7a05b64ee25900288ff59bb6f1d Package: GOexpress Version: 1.40.0 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), randomForest (>= 4.6), RCurl (>= 1.95) Suggests: BiocStyle License: GPL (>= 3) MD5sum: a2512037d1d99fad6eb6dd724341ddcd Package: GOfuncR Version: 1.26.0 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: 4b2699b6471d9e866e4f7efc91d12778 Package: GOpro Version: 1.32.0 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: 5195249ddaaaaa2a22e1035d43a25735 Package: goProfiles Version: 1.68.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: fe6c4be2b9fb67ebda4c490c99671f66 Package: GOSemSim Version: 2.32.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, DBI, digest, GO.db, methods, rlang, R.utils, stats, utils, yulab.utils (>= 0.1.6) LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, rappdirs, readr, rmarkdown, testthat, tidyr, tidyselect, ROCR License: Artistic-2.0 MD5sum: 0c30da50f9d4ea8042a7ed8f9afbba10 Package: goseq Version: 1.58.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2) Imports: mgcv, graphics, stats, utils, AnnotationDbi, GO.db, BiocGenerics, methods, rtracklayer, GenomicFeatures, GenomeInfoDb Suggests: edgeR, org.Hs.eg.db License: LGPL (>= 2) MD5sum: 4009eea42d5e701e4c3c277c654bf389 Package: goSorensen Version: 1.8.0 Depends: R (>= 4.3) Imports: clusterProfiler, goProfiles, org.Hs.eg.db, parallel, stats, stringr Suggests: BiocManager, BiocStyle, knitr, rmarkdown, org.At.tair.db, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcSakai.eg.db, org.EcK12.eg.db, org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Pt.eg.db, org.Xl.eg.db License: GPL-3 MD5sum: 63c2c9d82206b0be1c7c8cd4ba866306 Package: goSTAG Version: 1.30.0 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: e952ac6bcb9c6a3339c3755ae64fc4e0 Package: GOstats Version: 2.72.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.43.2), graph Imports: methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr License: Artistic-2.0 MD5sum: a35cdda62d988560b428dd9cc594a543 Package: GOTHiC Version: 1.42.0 Depends: R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome, data.table Imports: BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils, stats, GenomeInfoDb Suggests: HiCDataLymphoblast Enhances: parallel License: GPL-3 MD5sum: 9d955b9ea9530c8c178e274bdf117a9d Package: goTools Version: 1.80.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 MD5sum: 95044faa7f2b291df1800c2d35ad45d1 Package: GPA Version: 1.18.0 Depends: R (>= 4.0.0), methods, graphics, Rcpp Imports: parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS, stats, utils, grDevices LinkingTo: Rcpp Suggests: gpaExample License: GPL (>= 2) MD5sum: 837192fc2b948fc080406097baa1b678 Package: gpls Version: 1.78.0 Imports: stats Suggests: MASS License: Artistic-2.0 MD5sum: 85388c97cb51d1cc860f6face7ed25a7 Package: GrafGen Version: 1.2.0 Depends: R (>= 4.3.0) Imports: stats, utils, graphics, ggplot2, plotly, zlibbioc, scales, RColorBrewer, dplyr, grDevices, GenomicRanges, shiny, cowplot, ggpubr, stringr, rlang Suggests: knitr, rmarkdown, RUnit, BiocManager, BiocGenerics, BiocStyle, devtools License: GPL-2 MD5sum: 1edd020b61986fa0f4f50e46e960aa08 Package: GRaNIE Version: 1.10.0 Depends: R (>= 4.2.0) Imports: futile.logger, checkmate, patchwork (>= 1.2.0), reshape2, data.table, matrixStats, Matrix, GenomicRanges, RColorBrewer, ComplexHeatmap, DESeq2, circlize, progress, utils, methods, stringr, tools, scales, igraph, S4Vectors, ggplot2, rlang, Biostrings, GenomeInfoDb (>= 1.34.8), SummarizedExperiment, forcats, gridExtra, limma, tidyselect, readr, grid, tidyr (>= 1.3.0), dplyr, stats, grDevices, graphics, magrittr, tibble, viridis, colorspace, biomaRt, topGO, AnnotationHub, ensembldb Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7, BSgenome.Dmelanogaster.UCSC.dm6, BSgenome.Mmulatta.UCSC.rheMac10, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm39.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn6.refGene, TxDb.Rnorvegicus.UCSC.rn7.refGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW, clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker, testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA, variancePartition, purrr, EDASeq, JASPAR2022, JASPAR2024, RSQLite, TFBSTools, motifmatchr, rbioapi, LDlinkR License: Artistic-2.0 MD5sum: d5567483b0c1dbd7d1cc62fe22f982c8 Package: granulator Version: 1.14.0 Depends: R (>= 4.1) Imports: cowplot, e1071, epiR, dplyr, dtangle, ggplot2, ggplotify, grDevices, limSolve, magrittr, MASS, nnls, parallel, pheatmap, purrr, rlang, stats, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 2f735d94debff13c6677f0a4e87aa68f Package: graper Version: 1.22.0 Depends: R (>= 3.6) Imports: Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: 5e161e431342b52fb01446bb9d4faf0a Package: graph Version: 1.84.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.11) Imports: stats, stats4, utils Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle, knitr Enhances: Rgraphviz License: Artistic-2.0 MD5sum: c5901eb51bee798b29a97888d44d87f5 Package: GraphAlignment Version: 1.70.0 License: file LICENSE License_restricts_use: yes MD5sum: 7ef71fae46734f3fbfb75af04bc55586 Package: GraphAT Version: 1.78.0 Depends: R (>= 2.10), graph, methods Imports: graph, MCMCpack, methods, stats License: LGPL MD5sum: 69396c3ba40057878bb361b55637a21b Package: graphite Version: 1.52.0 Depends: R (>= 4.2), methods Imports: AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats, utils, graphics, rlang, purrr Suggests: checkmate, a4Preproc, ALL, BiocStyle, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) License: AGPL-3 MD5sum: c041395900e26213f1e624036b2010e8 Package: GraphPAC Version: 1.48.0 Depends: R(>= 2.15),iPAC, igraph, TSP, RMallow Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 7d69614b3c3d891eaec4eee57a39f197 Package: GRENITS Version: 1.58.0 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: 06e41a21eee10ebb984bf50c0e8a6a9d Package: GreyListChIP Version: 1.38.0 Depends: R (>= 4.0), methods, GenomicRanges Imports: GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, RUnit, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: ec4f8d12e88c5d296670bc0039a6691a Package: GRmetrics Version: 1.32.0 Depends: R (>= 4.0), SummarizedExperiment Imports: drc, plotly, ggplot2, S4Vectors, stats Suggests: knitr, rmarkdown, BiocStyle, tinytex License: GPL-3 MD5sum: 6d3af312eccdf22c7b78f5b9d3dc7096 Package: groHMM Version: 1.40.3 Depends: R (>= 3.0.2), MASS, parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), rtracklayer (>= 1.39.7) Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: be39ed04f763446e6d0fe76770ff69f4 Package: GSALightning Version: 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(>= 2.6.0), BiocGenerics (>= 0.13.8), Biobase (>= 2.17.8), annotate (>= 1.45.3), methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr, RUnit License: Artistic-2.0 MD5sum: e4331428a161a8ccbc6a3bb3b76dd449 Package: GSEABenchmarkeR Version: 1.26.0 Depends: R (>= 3.5.0), Biobase, SummarizedExperiment Imports: AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, S4Vectors, stats, utils Suggests: BiocStyle, GSE62944, knitr, rappdirs, rmarkdown License: Artistic-2.0 MD5sum: 1cd6eed4a1d866d33df075ae22ca7764 Package: GSEAlm Version: 1.66.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: 451480bbd00ff6f39606594220ab37d9 Package: GSEAmining Version: 1.16.0 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: 7bd366b0bdbd5ad8e22beaf999865c39 Package: gsean Version: 1.26.0 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi, knitr, plotly, WGCNA, rmarkdown License: Artistic-2.0 MD5sum: 839f48e727b7ef5ec1a478039fe09c7e Package: GSgalgoR Version: 1.16.0 Imports: cluster, doParallel, foreach, matchingR, nsga2R, survival, proxy, stats, methods, Suggests: knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp, Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP, iC10TrainingData, pamr, testthat License: MIT + file LICENSE MD5sum: 8ab4989fccbd1c96d0c0116266bffc76 Package: GSReg Version: 1.40.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi Suggests: GenomicRanges, GSBenchMark License: GPL-2 MD5sum: afd24b8ae81b4f6531465b618c4ab38a Package: GSRI Version: 2.54.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 MD5sum: c443cf30be2b0a36f3ae98a2b6259025 Package: GSVA Version: 2.0.4 Depends: R (>= 3.5.0) Imports: methods, stats, utils, graphics, S4Vectors, IRanges, Biobase, SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel, BiocParallel, SingleCellExperiment, SpatialExperiment, sparseMatrixStats, DelayedArray, DelayedMatrixStats, HDF5Array, BiocSingular, cli LinkingTo: cli Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinydashboard, ggplot2, data.table, plotly, future, promises, shinybusy, shinyjs License: GPL (>= 2) MD5sum: eafd48d60d81a32532cdabc3b74b32f5 Package: gtrellis Version: 1.38.0 Depends: R (>= 3.1.2), grid, IRanges, GenomicRanges Imports: circlize (>= 0.4.8), GetoptLong, grDevices, utils Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff License: MIT + file LICENSE MD5sum: 69d304c9d56b93b54752e0075bb184de Package: GUIDEseq Version: 1.36.0 Depends: R (>= 3.5.0), GenomicRanges, BiocGenerics Imports: Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma,dplyr, GenomicFeatures, rio, tidyr, tools, methods, purrr, ggplot2, openxlsx, patchwork, rlang Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 41de79f3ccd63cef4bf5a8d51514bb70 Package: Guitar Version: 2.22.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, 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Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr License: Artistic-2.0 MD5sum: 7ca8c3eeb58852926419bc478d20ba69 Package: gwasurvivr Version: 1.24.0 Depends: R (>= 3.4.0) Imports: GWASTools, survival, VariantAnnotation, parallel, matrixStats, SummarizedExperiment, stats, utils, SNPRelate Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 1e31529f41c655c10af6c53da47c5308 Package: GWENA Version: 1.16.0 Depends: R (>= 4.1) Imports: WGCNA (>= 1.67), dplyr (>= 0.8.3), dynamicTreeCut (>= 1.63-1), ggplot2 (>= 3.1.1), gprofiler2 (>= 0.1.6), magrittr (>= 1.5), tibble (>= 2.1.1), tidyr (>= 1.0.0), NetRep (>= 1.2.1), igraph (>= 1.2.4.1), RColorBrewer (>= 1.1-2), purrr (>= 0.3.3), rlist (>= 0.4.6.1), matrixStats (>= 0.55.0), SummarizedExperiment (>= 1.14.1), stringr (>= 1.4.0), cluster (>= 2.1.0), grDevices (>= 4.0.4), methods, graphics, stats, utils Suggests: testthat (>= 2.1.0), knitr (>= 1.25), rmarkdown (>= 1.16), 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License: GPL-3 MD5sum: 2c428a3ae0480ee3228d4b24aae5022d Package: hdxmsqc Version: 1.2.0 Depends: R(>= 4.3), QFeatures, S4Vectors, Spectra Imports: dplyr, tidyr, ggplot2, BiocStyle, knitr, methods, grDevices, stats, MsCoreUtils Suggests: RColorBrewer, pheatmap, MASS, patchwork, testthat License: file LICENSE MD5sum: 1bfa3228955f3bf19e15b043e6959bcf Package: heatmaps Version: 1.30.0 Depends: R (>= 3.5.0) Imports: methods, grDevices, graphics, stats, Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage, RColorBrewer, BiocGenerics, GenomeInfoDb Suggests: BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 7f7d1f8447970e536d404feb1d9c9e56 Package: Heatplus Version: 3.14.0 Imports: graphics, grDevices, stats, RColorBrewer Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) MD5sum: ed29451d1e969c4c4735e9663c75cd3d Package: HelloRanges Version: 1.32.0 Depends: methods, BiocGenerics, S4Vectors (>= 0.17.39), IRanges (>= 2.13.12), 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(>= 0.9), IRanges, lifecycle, limma, magrittr, matrixStats, methods, MultiAssayExperiment, purrr, R6, Rdpack, rlang, S4Vectors, stats, tidyr, utils Suggests: BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown, statmod, testthat (>= 2.0), vdiffr License: Apache License 2.0 MD5sum: c862e376995abad47cee317d0f246fe9 Package: HERON Version: 1.4.0 Depends: R (>= 4.4.0), SummarizedExperiment (>= 1.1.6), GenomicRanges, IRanges, S4Vectors Imports: matrixStats, stats, data.table, harmonicmeanp, metap, cluster, spdep, Matrix, limma, methods Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 056a2011f0334c34d072d472f4832095 Package: HGC Version: 1.14.0 Depends: R (>= 4.1.0) Imports: Rcpp (>= 1.0.0), RcppEigen(>= 0.3.2.0), Matrix, RANN, ape, dendextend, ggplot2, mclust, patchwork, dplyr, grDevices, methods, stats LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 78a741aa14dbe5a61b826c16d534d05e Package: 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License: MIT + file LICENSE MD5sum: dcd40890921b0f32ec4942fffeb5a5ad Package: HiCBricks Version: 1.24.0 Depends: R (>= 3.6), utils, curl, rhdf5, R6, grid Imports: ggplot2, viridis, RColorBrewer, scales, reshape2, stringr, data.table, GenomeInfoDb, GenomicRanges, stats, IRanges, grDevices, S4Vectors, digest, tibble, jsonlite, BiocParallel, R.utils, readr, methods Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 1c6f506be869d7e59e6725df20a2d4b4 Package: HiCcompare Version: 1.28.0 Depends: R (>= 3.5.0), dplyr Imports: data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5 Suggests: knitr, rmarkdown, testthat, multiHiCcompare License: MIT + file LICENSE MD5sum: 0e03378756c88af08d4694644d0ca509 Package: HiCDCPlus Version: 1.14.0 Imports: Rcpp,InteractionSet,GenomicInteractions,bbmle,pscl,BSgenome,data.table,dplyr,tidyr,GenomeInfoDb,rlang,splines,MASS,GenomicRanges,IRanges,tibble,R.utils,Biostrings,rtracklayer,methods,S4Vectors LinkingTo: Rcpp Suggests: BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, RUnit, BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix, BiocFileCache, rappdirs Enhances: parallel License: GPL-3 MD5sum: b8a1add1b5d236846c6109a97a001546 Package: HiCDOC Version: 1.8.0 Depends: InteractionSet, GenomicRanges, SummarizedExperiment, R (>= 4.1.0) Imports: methods, zlibbioc, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools, pbapply, BiocParallel, BiocGenerics, grid, cowplot, gridExtra, data.table, multiHiCcompare, GenomeInfoDb LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5 License: LGPL-3 MD5sum: 336cb3dad30759011059b91b983aef16 Package: HiCExperiment Version: 1.6.0 Depends: R (>= 4.2) Imports: InteractionSet, strawr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5, Matrix, vroom, dplyr, stats Suggests: HiContacts, HiContactsData, BiocFileCache, rtracklayer, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 9b3ca91e5a28d121b60ad2207b021bc4 Package: HiContacts Version: 1.8.0 Depends: R (>= 4.2), HiCExperiment Imports: InteractionSet, SummarizedExperiment, GenomicRanges, IRanges, GenomeInfoDb, S4Vectors, methods, BiocGenerics, BiocIO, BiocParallel, RSpectra, Matrix, tibble, tidyr, dplyr, readr, stringr, ggplot2, ggrastr, scales, stats, utils Suggests: HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: a8842d016cd3fd012cd996616d446350 Package: hicVennDiagram Version: 1.4.0 Depends: R (>= 4.3.0) Imports: GenomeInfoDb, 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: 997463dc1eb996d3200ba528bb34139e Package: hierGWAS Version: 1.36.0 Depends: R (>= 3.2.0) Imports: fastcluster,glmnet, fmsb Suggests: BiocGenerics, RUnit, MASS License: GPL-3 MD5sum: 8400c69ad34c6999cdaad9d07d49bb0e Package: hierinf Version: 1.24.0 Depends: R (>= 3.6.0) Imports: fmsb, glmnet, methods, parallel, stats Suggests: knitr, MASS, testthat License: GPL-3 | file LICENSE MD5sum: f8e9e514ab52ae329137784a54d0427a Package: HilbertCurve Version: 2.0.0 Depends: R (>= 4.0.0), grid Imports: methods, utils, png, grDevices, circlize (>= 0.3.3), IRanges, GenomicRanges, polylabelr, Rcpp LinkingTo: Rcpp Suggests: knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0), markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown License: MIT + file LICENSE MD5sum: 33867513d842b461739d3eb14b290593 Package: HilbertVis Version: 1.64.0 Depends: R (>= 2.6.0), grid, lattice Suggests: IRanges, EBImage License: GPL (>= 3) MD5sum: 5b8537a39f27cc5c306a4b6f121dba04 Package: HiLDA Version: 1.20.0 Depends: R(>= 4.1), ggplot2 Imports: R2jags, abind, cowplot, grid, forcats, stringr, GenomicRanges, S4Vectors, XVector, Biostrings, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, BiocGenerics, tidyr, grDevices, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 657bb01aa611bcd6412c0b538a3f0090 Package: hipathia Version: 3.6.0 Depends: R (>= 4.1), igraph (>= 1.0.1), AnnotationHub(>= 2.6.5), MultiAssayExperiment(>= 1.4.9), SummarizedExperiment(>= 1.8.1) Imports: coin, stats, limma, grDevices, utils, graphics, preprocessCore, servr, DelayedArray, matrixStats, methods, S4Vectors, ggplot2, ggpubr, dplyr, tibble, visNetwork, reshape2, MetBrewer Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: f0422f1cd8733557b4831c4441f0c52d Package: HIPPO Version: 1.18.0 Depends: R (>= 3.6.0) Imports: ggplot2, graphics, stats, reshape2, gridExtra, Rtsne, umap, dplyr, rlang, magrittr, irlba, Matrix, SingleCellExperiment, ggrepel Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 561a8ce3f5c889362e0ec64bb4d5c43e Package: hiReadsProcessor Version: 1.42.0 Depends: R (>= 3.5.0), Biostrings, pwalign, GenomicAlignments, BiocParallel, hiAnnotator Imports: sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl, methods Suggests: knitr, testthat, markdown License: GPL-3 MD5sum: cbe5b5821c9a549c9929fe6216a92b34 Package: HIREewas Version: 1.24.0 Depends: R (>= 3.5.0) Imports: quadprog, gplots, grDevices, stats Suggests: BiocStyle, knitr, BiocGenerics License: GPL (>= 2) MD5sum: dff55de392757252661da05cdaa2337e Package: HiTC Version: 1.50.0 Depends: R (>= 2.15.0), methods, IRanges, GenomicRanges Imports: Biostrings, graphics, grDevices, 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ggplot2, grid, methods, stats, RANN, Rcpp (>= 1.0.9) LinkingTo: Rcpp Suggests: testthat (>= 3.0.0), BiocStyle License: GPL-3 + file LICENSE MD5sum: 0c3103517e242d83a2c545053d52e6fe Package: hopach Version: 2.66.0 Depends: R (>= 2.11.0), cluster, Biobase, methods Imports: graphics, grDevices, stats, utils, BiocGenerics License: GPL (>= 2) MD5sum: 1a89d2867519b30053b78379afe76110 Package: HPAanalyze Version: 1.24.0 Depends: R (>= 3.5.0) Imports: dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils, gridExtra Suggests: knitr, rmarkdown, markdown, devtools, BiocStyle License: GPL-3 + file LICENSE MD5sum: 2af4909e81313bc3cd3c0938947f2053 Package: hpar Version: 1.48.0 Depends: R (>= 3.5.0) Imports: utils, ExperimentHub Suggests: org.Hs.eg.db, GO.db, AnnotationDbi, knitr, BiocStyle, testthat, rmarkdown, dplyr, DT License: Artistic-2.0 MD5sum: 557411fffdd681cc2e606bc058c6df0c Package: HPiP Version: 1.12.0 Depends: R (>= 4.1) Imports: dplyr (>= 1.0.6), httr (>= 1.4.2), readr, tidyr, tibble, utils, stringr, magrittr, caret, corrplot, ggplot2, pROC, PRROC, igraph, graphics, stats, purrr, grDevices, protr, MCL Suggests: rmarkdown, colorspace, e1071, kernlab, ranger, SummarizedExperiment, Biostrings, randomForest, gprofiler2, gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools, knitr License: MIT + file LICENSE MD5sum: b1cfe00dd187eb254cff392e73880361 Package: HTSFilter Version: 1.46.0 Depends: R (>= 4.0.0) Imports: edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices, graphics, methods Suggests: EDASeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 41f46b4e6914a243e5b41492badcb4f2 Package: HuBMAPR Version: 1.0.4 Depends: R (>= 4.4.0) Imports: httr2, dplyr, tidyr, tibble, rjsoncons, rlang, utils, stringr, whisker, purrr Suggests: testthat (>= 3.0.0), knitr, ggplot2, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 8b19167488a8ee2e3cb064bca6860654 Package: HubPub Version: 1.14.0 Imports: available, usethis, biocthis, dplyr, aws.s3, fs, 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stats, stringr, scales, rlang, httr, openxlsx, htmltools, reshape2, reactable, msigdbr, kableExtra, rmarkdown, igraph, visNetwork, shiny, BiocStyle Suggests: tidyverse, devtools, testthat, knitr License: GPL-3 + file LICENSE MD5sum: 20fb862f1af81b1bd879ed2eaa57fcc9 Package: hyperdraw Version: 1.58.0 Depends: R (>= 2.9.0) Imports: methods, grid, graph, hypergraph, Rgraphviz, stats4 License: GPL (>= 2) MD5sum: 713159aa39d6ff1182ed95f3f23f5d4b Package: hypergraph Version: 1.78.0 Depends: R (>= 2.1.0), methods, utils, graph Suggests: BiocGenerics, RUnit License: Artistic-2.0 MD5sum: a098ff4f6a2a7394c2c72e5fa25a0fc7 Package: iASeq Version: 1.50.0 Depends: R (>= 2.14.1) Imports: graphics, grDevices License: GPL-2 MD5sum: 68f6a701ee2a2ad3ee27f9d4c2114796 Package: iasva Version: 1.24.0 Depends: R (>= 3.5), Imports: irlba, stats, cluster, graphics, SummarizedExperiment, BiocParallel Suggests: knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot, DescTools, RColorBrewer License: GPL-2 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TxDb.Dmelanogaster.UCSC.dm6.ensGene Suggests: knitr, rmarkdown, Rsubread (>= 1.29.0), testthat License: GPL-3 + file LICENSE MD5sum: 5970abeccc222d5dba9bd924da6ba5d7 Package: iCheck Version: 1.36.0 Depends: R (>= 3.2.0), Biobase, lumi, gplots Imports: stats, graphics, preprocessCore, grDevices, randomForest, affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest, scatterplot3d, utils License: GPL (>= 2) MD5sum: 5476a671d44b423ced39841f10319165 Package: iChip Version: 1.60.0 Depends: R (>= 2.10.0) Imports: limma License: GPL (>= 2) MD5sum: 80068585c0c1eded3b1f74534503448e Package: iClusterPlus Version: 1.42.0 Depends: R (>= 4.1.0), parallel Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: bbe9411bf05809c05254fcd7a5e18ad8 Package: iCNV Version: 1.26.0 Depends: R (>= 3.3.1), CODEX Imports: fields, ggplot2, truncnorm, tidyr, data.table, dplyr, grDevices, graphics, stats, utils, rlang Suggests: knitr, rmarkdown, WES.1KG.WUGSC License: GPL-2 MD5sum: 7e988179b06e9d42a141a3f742ddb042 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gplots, pheatmap, airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve (>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks License: MIT + file LICENSE MD5sum: 2b6457048f66b54dd75afc1ae295349b Package: interactiveDisplay Version: 1.44.0 Depends: R (>= 3.5.0), methods, BiocGenerics, grid Imports: interactiveDisplayBase (>= 1.7.3), shiny, RColorBrewer, ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi Suggests: RUnit, hgu95av2.db, knitr, GenomicRanges, SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer, metagenomeSeq, gplots, vegan, Biobase Enhances: rstudio License: Artistic-2.0 MD5sum: f5ee47212cd5ccd08a0e8bc554ee902a Package: interactiveDisplayBase Version: 1.44.0 Depends: R (>= 2.10), methods, BiocGenerics Imports: shiny, DT Suggests: knitr, markdown Enhances: rstudioapi License: Artistic-2.0 MD5sum: 25271662116a7a3b14d94410d6330af0 Package: InterCellar Version: 2.12.0 Depends: R (>= 4.1) Imports: config, golem, shiny, DT, shinydashboard, shinyFiles, shinycssloaders, data.table, fs, dplyr, tidyr, circlize, colourpicker, dendextend, factoextra, ggplot2, plotly, plyr, shinyFeedback, shinyalert, tibble, umap, visNetwork, wordcloud2, readxl, htmlwidgets, colorspace, signal, scales, htmltools, ComplexHeatmap, grDevices, stats, tools, utils, biomaRt, rlang, fmsb, igraph Suggests: testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, httr License: MIT + file LICENSE MD5sum: dae7e4c7cf8d251af2c0dd47ab2cca0f Package: IntEREst Version: 1.30.0 Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, SummarizedExperiment, edgeR, S4Vectors, GenomicFiles Imports: seqLogo, Biostrings, GenomicFeatures (>= 1.39.4), txdbmaker, IRanges, seqinr, graphics, grDevices, stats, utils, grid, methods, DBI, RMariaDB, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2 Suggests: clinfun, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-2 MD5sum: a4324e2581ed923bc10784e9d1727165 Package: IntramiRExploreR Version: 1.28.0 Depends: R (>= 3.4) Imports: igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats, utils, grDevices, graphics Suggests: gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat License: GPL-2 MD5sum: 942c90864098af9b2d1156d3413bac02 Package: IONiseR Version: 2.30.0 Depends: R (>= 3.4) Imports: rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2, methods, BiocGenerics, XVector, tibble, stats, BiocParallel, bit64, stringr, utils Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData License: MIT + file LICENSE MD5sum: b25bae71679f845dbdcc839e7305a8bd Package: iPAC Version: 1.50.0 Depends: R(>= 2.15), scatterplot3d, Biostrings, pwalign, multtest Imports: grDevices, graphics, stats, gdata License: GPL-2 MD5sum: 5fdc029c1c48019249fd4f7ae14bded0 Package: iPath Version: 1.12.0 Depends: R (>= 4.1), mclust, BiocParallel, survival Imports: Rcpp (>= 1.0.5), matrixStats, ggpubr, ggplot2, survminer, stats LinkingTo: Rcpp, RcppArmadillo Suggests: rmarkdown, BiocStyle, knitr License: GPL-2 MD5sum: a6ad60f70b785d4d52031c9f5d5ab520 Package: ipdDb Version: 1.24.0 Depends: R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1), AnnotationHub Imports: Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats, assertthat Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 58a01b99c59b4a1107a02c38d99cd50a Package: IRanges Version: 2.40.1 Depends: R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.39.2), S4Vectors (>= 0.43.2) Imports: stats4 LinkingTo: S4Vectors Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 2956d4de1e701150ff4364ea107a0f68 Package: ISAnalytics Version: 1.16.1 Depends: R (>= 4.4.0) Imports: utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs, lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools, grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib, DT Suggests: testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown, roxygen2, vegan, withr, extraDistr, ggalluvial, scales, gridExtra, R.utils, RefManageR, flexdashboard, circlize, plotly, gtools, eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr, future, doFuture, foreach, psych, data.table, Rcapture License: CC BY 4.0 MD5sum: 43af68128391aa369a17e88b2e62124c Package: iSEE Version: 2.18.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, listviewer, ComplexHeatmap, circlize, grid Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools, GenomicRanges License: MIT + file LICENSE MD5sum: d53af9dd5ef6d34d6c0de64b68befbf0 Package: iSEEde Version: 1.4.0 Depends: iSEE Imports: DESeq2, edgeR, methods, S4Vectors, shiny, SummarizedExperiment Suggests: airway, BiocStyle, covr, knitr, limma, org.Hs.eg.db, RefManageR, rmarkdown, scuttle, sessioninfo, statmod, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 47a6aa07a225a65535f657415205c08e Package: iSEEfier Version: 1.2.0 Imports: iSEE, iSEEu, methods, ggplot2, igraph, rlang, stats, SummarizedExperiment, SingleCellExperiment, visNetwork, BiocBaseUtils Suggests: knitr, rmarkdown, scater, scRNAseq, org.Mm.eg.db, scuttle, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 3994ac1f8e4d329e7678807f0a951003 Package: iSEEhex Version: 1.8.0 Depends: SummarizedExperiment, iSEE Imports: ggplot2, hexbin, methods, shiny Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), scRNAseq, scater License: Artistic-2.0 MD5sum: b1a931aee92046326ec6ea911c816e6e Package: iSEEhub Version: 1.8.0 Depends: SummarizedExperiment, SingleCellExperiment, ExperimentHub Imports: AnnotationHub, BiocManager, DT, iSEE, methods, rintrojs, S4Vectors, shiny, shinydashboard, shinyjs, utils Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), nullrangesData Enhances: BioPlex, biscuiteerData, bodymapRat, CLLmethylation, CopyNeutralIMA, curatedAdipoArray, curatedAdipoChIP, curatedMetagenomicData, curatedTCGAData, DMRcatedata, DuoClustering2018, easierData, emtdata, epimutacionsData, FieldEffectCrc, GenomicDistributionsData, GSE103322, GSE13015, GSE62944, HDCytoData, HMP16SData, HumanAffyData, imcdatasets, mcsurvdata, MetaGxBreast, MetaGxOvarian, MetaGxPancreas, MethylSeqData, muscData, NxtIRFdata, ObMiTi, quantiseqr, restfulSEData, RLHub, sesameData, SimBenchData, SingleCellMultiModal, SingleMoleculeFootprintingData, spatialDmelxsim, STexampleData, TabulaMurisData, TabulaMurisSenisData, TENxVisiumData, tissueTreg, VectraPolarisData, xcoredata License: Artistic-2.0 MD5sum: 0a0135e700bca6dd5ef978588829c139 Package: iSEEindex Version: 1.4.0 Depends: SummarizedExperiment, SingleCellExperiment Imports: BiocFileCache, DT, iSEE, methods, paws.storage, rintrojs, shiny, shinydashboard, shinyjs, stringr, urltools, utils Suggests: BiocStyle, covr, knitr, RefManageR, rmarkdown, markdown, scRNAseq, sessioninfo, testthat (>= 3.0.0), yaml License: Artistic-2.0 MD5sum: 9eeb34b0cad2e10d79456acb630f49b8 Package: iSEEpathways Version: 1.4.0 Depends: iSEE Imports: ggplot2, methods, S4Vectors, shiny, shinyWidgets, stats, SummarizedExperiment Suggests: airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr, org.Hs.eg.db, RefManageR, rmarkdown, scater, scuttle, sessioninfo, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 1a68b3ce15c069d8e177c8cfcc90357a Package: iSEEtree Version: 1.0.0 Depends: R (>= 4.4.0), iSEE Imports: grDevices, methods, miaViz, S4Vectors, shiny, mia, shinyWidgets, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, utils Suggests: biomformat, BiocStyle, knitr, MGnifyR, RefManageR, remotes, rmarkdown, scater, testthat (>= 3.0.0), vegan License: Artistic-2.0 MD5sum: 29fd92c248262c5bb91c8438cecbf1fd Package: iSEEu Version: 1.18.0 Depends: iSEE, iSEEhex Imports: methods, S4Vectors, IRanges, shiny, SummarizedExperiment, SingleCellExperiment, ggplot2 (>= 3.4.0), DT, stats, colourpicker, shinyAce Suggests: scRNAseq, scater, scran, airway, edgeR, AnnotationDbi, org.Hs.eg.db, GO.db, KEGGREST, knitr, igraph, rmarkdown, BiocStyle, htmltools, Rtsne, uwot, testthat (>= 2.1.0), covr License: MIT + file LICENSE MD5sum: 43f0a316564674102a8b062d65fb13fd Package: iSeq Version: 1.58.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: 1f4043e60f4b985930675add186fa096 Package: ISLET Version: 1.8.0 Depends: R(>= 4.2.0), Matrix, parallel, BiocParallel, SummarizedExperiment, BiocGenerics, lme4, nnls Imports: stats, methods, purrr, abind Suggests: BiocStyle, knitr, rmarkdown, htmltools, RUnit, dplyr License: GPL-2 MD5sum: 5802414b2c2fb4aeb313675e991a3305 Package: isobar Version: 1.52.0 Depends: R (>= 2.10.0), Biobase, stats, methods Imports: distr, plyr, biomaRt, ggplot2 Suggests: MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS License: LGPL-2 MD5sum: 7f556af435d3d189b2cb56ef93293544 Package: IsoBayes Version: 1.4.0 Depends: R (>= 4.3.0) Imports: methods, Rcpp, data.table, glue, stats, doParallel, parallel, doRNG, foreach, iterators, ggplot2, HDInterval, SummarizedExperiment, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 193fad08cf564a40d3348a995b445890 Package: IsoCorrectoR Version: 1.24.0 Depends: R (>= 3.5) Imports: dplyr, magrittr, methods, quadprog, readr, readxl, stringr, tibble, tools, utils, pracma, WriteXLS Suggests: IsoCorrectoRGUI, knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 14d29ed88e6363393630e97fc835d682 Package: IsoCorrectoRGUI Version: 1.22.0 Depends: R (>= 3.6) Imports: IsoCorrectoR, readxl, tcltk2, tcltk, utils Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: d83eb0e0439df9afb05597a8eb3ee38e Package: IsoformSwitchAnalyzeR Version: 2.6.0 Depends: R (>= 4.2), limma, DEXSeq, satuRn (>= 1.7.0), sva, ggplot2 (>= 3.3.5), pfamAnalyzeR Imports: methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>= 2.50.0), IRanges, GenomicRanges, RColorBrewer, rtracklayer, VennDiagram, DBI, grDevices, graphics, stats, utils, GenomeInfoDb, grid, tximport (>= 1.7.1), tximeta (>= 1.7.12), edgeR, futile.logger, stringr, dplyr, magrittr, readr, tibble, XVector, BiocGenerics, RCurl, Biobase, SummarizedExperiment, tidyr, S4Vectors, BiocParallel, pwalign Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, rmarkdown License: GPL (>= 2) MD5sum: e403b6b0b1156e08e98d19e37e8829c7 Package: ISoLDE Version: 1.34.0 Depends: R (>= 3.3.0),graphics,grDevices,stats,utils License: GPL (>= 2.0) MD5sum: ec0890a1213966a3ff9544700191d7e9 Package: isomiRs Version: 1.34.0 Depends: R (>= 4.4), SummarizedExperiment Imports: AnnotationDbi, BiocGenerics, Biobase, broom, cluster, cowplot, DEGreport, DESeq2, IRanges, dplyr, GenomicRanges, gplots, ggplot2, gtools, gridExtra, grid, grDevices, graphics, GGally, limma, methods, RColorBrewer, readr, reshape, rlang, stats, stringr, S4Vectors, tidyr, tibble Suggests: knitr, rmarkdown, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 5a49470b687d3dc88486fb6a9cccd565 Package: ITALICS Version: 2.66.0 Depends: R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser, pd.mapping50k.xba240 Imports: affxparser, DBI, GLAD, oligo, oligoClasses, stats Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp License: GPL-2 MD5sum: ff8480c68f32364835365e7999d9c801 Package: iterativeBMA Version: 1.64.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: 44eb471f5027668369be5b361613a424 Package: iterativeBMAsurv Version: 1.64.0 Depends: BMA, leaps, survival, splines Imports: graphics, grDevices, stats, survival, utils License: GPL (>= 2) MD5sum: f18551e71109ed7d3aa737b846ad1e3f Package: IVAS Version: 2.26.0 Depends: R (> 3.0.0),GenomicFeatures, ggplot2, Biobase Imports: doParallel, lme4, BiocGenerics, GenomicRanges, IRanges, foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, ggfortify, grDevices, methods, Matrix, BiocParallel,utils, stats Suggests: BiocStyle License: GPL-2 MD5sum: adb4a53a02f861911748f855871d4a9b Package: ivygapSE Version: 1.28.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: shiny, survival, survminer, hwriter, plotly, ggplot2, S4Vectors, graphics, stats, utils, UpSetR Suggests: knitr, png, limma, grid, DT, randomForest, digest, testthat, rmarkdown, BiocStyle, magick, statmod, codetools License: Artistic-2.0 MD5sum: 821397516c2f062e3912b650a0b82813 Package: IWTomics Version: 1.30.0 Depends: R (>= 3.5.0), GenomicRanges Imports: parallel,gtable,grid,graphics,methods,IRanges,KernSmooth,fda,S4Vectors,grDevices,stats,utils,tools Suggests: knitr License: GPL (>= 2) MD5sum: 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(>= 0.27.3), e1071, LiblineaR, graphics, grDevices, utils, apcluster LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors Suggests: SparseM, Biobase, BiocGenerics, knitr License: GPL (>= 2.1) MD5sum: d90bbdb7eef07c9cfbeb9664078e558b Package: KEGGgraph Version: 1.66.0 Depends: R (>= 3.5.0) Imports: methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz Suggests: RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) MD5sum: a3fe251068491a396ab57ff7568bb40b Package: KEGGlincs Version: 1.32.0 Depends: R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db (>= 3.3.0) Imports: AnnotationDbi,KEGGgraph,igraph,plyr,gtools,httr,RJSONIO,KEGGREST, methods,graphics,stats,utils, XML, grDevices Suggests: BiocManager (>= 1.20.3), knitr, graph License: GPL-3 MD5sum: 66757a71854835aacbbe3ed4943307b6 Package: keggorthology Version: 2.58.0 Depends: R (>= 2.5.0), hgu95av2.db, graph Imports: AnnotationDbi, DBI, grDevices, methods, tools, utils Suggests: RBGL,ALL License: 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OrgMassSpecR, protViz, S4Vectors, Spectra, testthat, mzR License: Apache License 2.0 MD5sum: beb3fd1423f5af6ecbe3f7b20769081a Package: LACE Version: 2.10.0 Depends: R (>= 4.2.0) Imports: curl, igraph, foreach, doParallel, sortable, dplyr, forcats, data.tree, graphics, grDevices, parallel, RColorBrewer, Rfast, stats, SummarizedExperiment, utils, purrr, stringi, stringr, Matrix, tidyr, jsonlite, readr, configr, DT, tools, fs, data.table, htmltools, htmlwidgets, bsplus, shinyvalidate, shiny, shinythemes, shinyFiles, shinyjs, shinyBS, shinydashboard, biomaRt, callr, logr, ggplot2, svglite Suggests: BiocGenerics, BiocStyle, testthat, knitr, rmarkdown License: file LICENSE MD5sum: 2d2a5cbadd7f32a474bc35471dfc132a Package: lapmix Version: 1.72.0 Depends: R (>= 2.6.0),stats Imports: Biobase, graphics, grDevices, methods, stats, tools, utils License: GPL (>= 2) MD5sum: 52f25290008cc1b2a10539ebf9f3169b Package: LBE Version: 1.74.0 Depends: stats Imports: graphics, stats, utils Suggests: qvalue License: GPL-2 MD5sum: 65a2b691182937fe131b274040b04460 Package: ldblock Version: 1.36.0 Depends: R (>= 3.5), methods, rlang Imports: BiocGenerics (>= 0.25.1), httr, Matrix Suggests: RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats, VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75, Rsamtools, GenomicFiles (>= 1.13.6) License: Artistic-2.0 MD5sum: c7a93a80760efcd3f8173ae678aa6ba8 Package: LEA Version: 3.18.0 Depends: R (>= 3.3.0), methods, stats, utils, graphics Suggests: knitr License: GPL-3 MD5sum: 0c8ee7240544f6e3730c03c33ee00027 Package: LedPred Version: 1.40.0 Depends: R (>= 3.2.0), e1071 (>= 1.6) Imports: akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl, ROCR, testthat License: MIT | file LICENSE MD5sum: c5dc3e6a75fed396c7f53c4bfb08ba4c Package: lefser Version: 1.16.0 Depends: SummarizedExperiment, R (>= 4.0.0) Imports: coin, MASS, ggplot2, S4Vectors, stats, methods, utils, dplyr, testthat, tibble, tidyr, forcats, stringr, ggtree Suggests: knitr, rmarkdown, curatedMetagenomicData, BiocStyle, phyloseq, pkgdown, covr, withr License: Artistic-2.0 MD5sum: 096e4c4f1650fe56ff0404ee9dfc51c6 Package: lemur Version: 1.4.0 Depends: R (>= 4.1) Imports: stats, utils, irlba, methods, SingleCellExperiment, SummarizedExperiment, rlang (>= 1.1.0), vctrs (>= 0.6.0), glmGamPoi (>= 1.12.0), BiocGenerics, S4Vectors, Matrix, DelayedMatrixStats, HDF5Array, MatrixGenerics, matrixStats, Rcpp, harmony (>= 1.2.0), limma, BiocNeighbors LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 75e90cc4fa43a63a4a1472132f511600 Package: les Version: 1.56.0 Depends: R (>= 2.13.2), methods, graphics, fdrtool Imports: boot, gplots, RColorBrewer Suggests: Biobase, limma Enhances: parallel License: GPL-3 MD5sum: 9857ddad2601ce9959bc1fdf0127d786 Package: levi Version: 1.24.0 Imports: DT(>= 0.4), RColorBrewer(>= 1.1-2), colorspace(>= 1.3-2), dplyr(>= 0.7.4), 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(>= 2) MD5sum: 3165f462f5e95c72d2368c7f7de60b3d Package: limpca Version: 1.2.0 Depends: R (>= 3.5.0) Imports: ggplot2, stringr, plyr, ggrepel, reshape2, grDevices, graphics, doParallel, parallel, dplyr, tibble, tidyr, ggsci, tidyverse, methods, stats, SummarizedExperiment, S4Vectors Suggests: BiocStyle, pander, rmarkdown, car, gridExtra, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: f5be1cdb0e04d0557e93dccab7e1de66 Package: lineagespot Version: 1.10.0 Imports: VariantAnnotation, MatrixGenerics, SummarizedExperiment, data.table, stringr, httr, utils Suggests: BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 514c64a9fabecfa21ddcef49f2390a1f Package: LinkHD Version: 1.20.0 Depends: R(>= 3.6.0), methods, ggplot2, stats Imports: scales, cluster, graphics, ggpubr, gridExtra, vegan, rio, MultiAssayExperiment, emmeans, reshape2, data.table Suggests: MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 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rmarkdown, igraph, reshape2, limma, License: MIT + file LICENSE MD5sum: 41ca5eed30243ef8ce068165838de74b Package: lipidr Version: 2.20.0 Depends: R (>= 3.6.0), SummarizedExperiment Imports: methods, stats, utils, data.table, S4Vectors, rlang, dplyr, tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD, magrittr Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, spelling, testthat License: MIT + file LICENSE MD5sum: 4dc964937d2049d315c08a62a2db2983 Package: LiquidAssociation Version: 1.60.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>= 3) MD5sum: b73b8998be73a2990cfe4c05e0205da8 Package: lisaClust Version: 1.14.4 Depends: R (>= 4.0) Imports: ggplot2, class, concaveman, grid, BiocParallel, spatstat.explore, spatstat.geom, BiocGenerics, S4Vectors, methods, spicyR, purrr, stats, data.table, dplyr, tidyr, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, pheatmap, spatstat.random, testthat Suggests: BiocStyle, knitr, rmarkdown, SpatialDatasets, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: b459953629148578bbe32ad69ae1bcb8 Package: lmdme Version: 1.48.0 Depends: R (>= 2.14.1), pls, stemHypoxia Imports: stats, methods, limma Enhances: parallel License: GPL (>= 2) MD5sum: 977673fa558eef0d9c965c6dd1deaa55 Package: loci2path Version: 1.26.0 Depends: R (>= 3.5.0) Imports: pheatmap, wordcloud, RColorBrewer, data.table, methods, grDevices, stats, graphics, GenomicRanges, BiocParallel, S4Vectors Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: d5462648e649e1e6fdcf74f4a8a68cce Package: logicFS Version: 2.26.0 Depends: LogicReg, mcbiopi, survival Imports: graphics, methods, stats Suggests: genefilter, siggenes License: LGPL (>= 2) MD5sum: 4cf9432257c069f2e6be83853ffb8d68 Package: LOLA Version: 1.36.0 Depends: R (>= 3.5.0) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, reshape2, utils, stats, methods Suggests: parallel, testthat, knitr, BiocStyle, rmarkdown Enhances: simpleCache, qvalue, ggplot2 License: GPL-3 MD5sum: 5c0896f8c7750314e0fc7b144e69f99a Package: LoomExperiment Version: 1.24.0 Depends: R (>= 3.5.0), S4Vectors, SingleCellExperiment, SummarizedExperiment, methods, rhdf5, BiocIO Imports: DelayedArray, GenomicRanges, HDF5Array, Matrix, stats, stringr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown, reticulate License: Artistic-2.0 MD5sum: aa60bf13cfbf4600b7da4fbbe5f2a0fd Package: LPE Version: 1.80.0 Depends: R (>= 2.10) Imports: stats License: LGPL MD5sum: 4f2c3d22538e54821170609eae385d59 Package: lpNet Version: 2.38.0 Depends: lpSolve, KEGGgraph License: Artistic License 2.0 MD5sum: c42cf2aa1f199fec0d66e51def3e3665 Package: lpsymphony Version: 1.34.0 Depends: R (>= 3.0.0) Suggests: BiocStyle, knitr, testthat Enhances: slam License: EPL MD5sum: b7b6a466f95663a9b302744f9bf74955 Package: LRBaseDbi Version: 2.16.0 Depends: R (>= 3.5.0) Imports: methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase 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Imports: S4Vectors, Biobase, scran, dplyr, ggplot2 Suggests: nnls, knitr, testthat, rmarkdown, BiocStyle, GenomicRanges, limma, ExperimentHub, AnnotationHub, DelayedMatrixStats, BisqueRNA, DelayedArray License: Artistic-2.0 MD5sum: b16c55a8f41a5262c8a1574d01f0368d Package: LymphoSeq Version: 1.34.0 Depends: R (>= 3.3), LymphoSeqDB Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq, RColorBrewer, circlize, grid, utils, stats, ggtree, msa, Biostrings, phangorn, stringdist, UpSetR Suggests: knitr, pheatmap, wordcloud, rmarkdown License: Artistic-2.0 MD5sum: 3fed23bae29369c2ff46e28aae1c5fb3 Package: M3C Version: 1.28.0 Depends: R (>= 3.5.0) Imports: ggplot2, Matrix, doSNOW, cluster, parallel, foreach, doParallel, matrixcalc, Rtsne, corpcor, umap Suggests: knitr, rmarkdown License: AGPL-3 MD5sum: d778f7ab77d2115b72a404c554ff52fd Package: M3Drop Version: 1.32.0 Depends: R (>= 3.4), numDeriv Imports: RColorBrewer, gplots, bbmle, statmod, grDevices, graphics, stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods, scater Suggests: ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat, Biobase License: GPL (>= 2) MD5sum: 6b15f148bf34f85edc4d624e3c9a507d Package: m6Aboost Version: 1.12.0 Depends: S4Vectors, adabag, GenomicRanges, R (>= 4.1) Imports: dplyr, rtracklayer, BSgenome, Biostrings, utils, methods, IRanges, ExperimentHub Suggests: knitr, rmarkdown, bookdown, testthat, BiocStyle, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: 08db0fdb5e3db6f3c04edf614fb38d9d Package: Maaslin2 Version: 1.20.0 Depends: R (>= 3.6) Imports: robustbase, biglm, pcaPP, edgeR, metagenomeSeq, pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap, logging, data.table, lmerTest, hash, optparse, grDevices, stats, utils, glmmTMB, MASS, cplm, pscl, lme4, tibble Suggests: knitr, testthat (>= 2.1.0), rmarkdown, markdown License: MIT + file LICENSE MD5sum: 48f19c15c989d9dc34d1ca2ade1f50fa Package: Macarron Version: 1.10.0 Depends: R (>= 4.2.0), SummarizedExperiment Imports: BiocParallel, DelayedArray, WGCNA, ff, data.table, dynamicTreeCut, Maaslin2, plyr, stats, psych, xml2, httr, RJSONIO, logging, methods, utils Suggests: knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown, markdown License: MIT + file LICENSE MD5sum: afe57611792f0cb19eef499205483f12 Package: maCorrPlot Version: 1.76.0 Depends: lattice Imports: graphics, grDevices, lattice, stats License: GPL (>= 2) MD5sum: 61dd28e57fb1f5ba728b6395a86e2fb2 Package: MACSQuantifyR Version: 1.20.0 Imports: readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel, methods, stats, latticeExtra, lattice, rmarkdown, png, grid, gridExtra, prettydoc, rvest, xml2 Suggests: knitr, testthat, R.utils, spelling License: Artistic-2.0 MD5sum: b7e01dac62c000434a317df2f040d9fe Package: MACSr Version: 1.14.0 Depends: R (>= 4.1.0) Imports: utils, reticulate, S4Vectors, methods, basilisk, ExperimentHub, AnnotationHub Suggests: testthat, knitr, rmarkdown, BiocStyle, MACSdata License: 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knitr, mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment, rmarkdown, S4Vectors, curl License: MIT + file LICENSE MD5sum: c061c9669dec8954a98635cc693e6432 Package: MAGAR Version: 1.14.0 Depends: R (>= 4.1), HDF5Array, RnBeads, snpStats, crlmm Imports: doParallel, igraph, bigstatsr, rjson, plyr, data.table, UpSetR, reshape2, jsonlite, methods, ff, argparse, impute, RnBeads.hg19, RnBeads.hg38, utils, stats Suggests: gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil, rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools, BiocGenerics, BiocManager License: GPL-3 MD5sum: 84c4a286836403f0381ca4d6f9275fe2 Package: MAGeCKFlute Version: 2.9.0 Depends: R (>= 4.1) Imports: Biobase, gridExtra, ggplot2, ggrepel, grDevices, grid, reshape2, stats, utils, DOSE, clusterProfiler, pathview, enrichplot, msigdbr, depmap Suggests: biomaRt, BiocStyle, dendextend, graphics, knitr, pheatmap, png, scales, sva, BiocManager License: GPL (>= 3) MD5sum: 202d20da3a37fd63e028feefc439422c Package: magpie Version: 1.6.0 Depends: R (>= 4.3.0) Imports: utils, rtracklayer, Matrix, matrixStats, stats, S4Vectors, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi, aod, BiocParallel, DESeq2, openxlsx, RColorBrewer, reshape2, TRESS Suggests: knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset, BiocGenerics, BiocStyle License: MIT + file LICENSE MD5sum: 10ce590633e1ec3c92637fb97fbddc7a Package: magrene Version: 1.8.0 Depends: R (>= 4.2.0) Imports: utils, stats, BiocParallel Suggests: BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo, testthat (>= 3.0.0) License: GPL-3 MD5sum: 72bcd1e0a784074e5a229f5682343570 Package: MAI Version: 1.12.0 Depends: R (>= 3.5.0) Imports: caret, parallel, doParallel, foreach, e1071, future.apply, future, missForest, pcaMethods, tidyverse, stats, utils, methods, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 5d24f5f0917b4a26aa7e36e1b82a84a1 Package: 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MASS,affy,limma,gcrma,ROC,class,e1071,caret,hgu133plus2.db,ROCR,AnnotationDbi,LungCancerACvsSCCGEO Suggests: parallel License: GPL-2 MD5sum: 7f21623123573345b3a94ba6ccf9484b Package: mapscape Version: 1.30.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), base64enc (>= 0.1-3), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 6f8bfbad0fbd263d98c885276f38afc0 Package: mariner Version: 1.6.0 Depends: R (>= 4.2.0) Imports: methods, S4Vectors, BiocGenerics, BiocManager, GenomicRanges, InteractionSet, data.table, stats, rlang, glue, assertthat, plyranges, magrittr, dbscan, purrr, progress, GenomeInfoDb, strawr (>= 0.0.91), DelayedArray, HDF5Array, abind, BiocParallel, IRanges, SummarizedExperiment, rhdf5, plotgardener, RColorBrewer, colourvalues, utils, grDevices, graphics, grid Suggests: knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub, marinerData License: GPL-3 MD5sum: e87c27cff6c6a45cbaed70693edfbb49 Package: marr Version: 1.16.0 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IRanges, methods, BiocGenerics, parallel, data.table Suggests: testthat, knitr, rmarkdown, BiocStyle, AnnotationHub License: MIT + file LICENSE MD5sum: 43ba77738d15acfbbfdce9c6b81b163e Package: maSigPro Version: 1.78.0 Depends: R (>= 2.3.1) Imports: Biobase, graphics, grDevices, venn, mclust, stats, MASS License: GPL (>= 2) MD5sum: 73e96f946a244107028007d1137f883c Package: maskBAD Version: 1.50.0 Depends: R (>= 2.10), gcrma (>= 2.27.1), affy Suggests: hgu95av2probe, hgu95av2cdf License: GPL (>= 2) MD5sum: 847c8f3bc139a07ee23607d26a506218 Package: MassArray Version: 1.58.0 Depends: R (>= 2.10.0), methods Imports: graphics, grDevices, stats, utils License: GPL (>= 2) MD5sum: 7094360dfd4ec300d1787d12897f4a55 Package: massiR Version: 1.42.0 Depends: cluster, gplots, diptest, Biobase, R (>= 3.0.2) Suggests: biomaRt, RUnit, BiocGenerics License: GPL-3 MD5sum: 8797190584a6dd1913e76e5ede6af94e Package: MassSpecWavelet Version: 1.72.1 Suggests: signal, waveslim, BiocStyle, knitr, rmarkdown, 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Homo.sapiens Imports: biomaRt, fgsea, GenomicFeatures, GenomicRanges, ggplot2, graphics, grDevices, Gviz, IRanges, limma, methods, parallel, S4Vectors, stats, SummarizedExperiment, utils Suggests: Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k, knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit License: GPL-2 MD5sum: 9bb53509f6c14357462f81a16cbc81f8 Package: mdp Version: 1.26.0 Depends: R (>= 4.0) Imports: ggplot2, gridExtra, grid, stats, utils Suggests: testthat, knitr, rmarkdown, fgsea, BiocManager License: GPL-3 MD5sum: 413e7ba5789616112302db5ccec0b4a3 Package: mdqc Version: 1.68.0 Depends: R (>= 2.2.1), cluster, MASS License: LGPL (>= 2) MD5sum: 08bd689ce939f9c63b736089394539b6 Package: MDTS Version: 1.26.0 Depends: R (>= 3.5.0) Imports: GenomicAlignments, GenomicRanges, IRanges, Biostrings, DNAcopy, Rsamtools, parallel, stringr Suggests: testthat, knitr License: Artistic-2.0 MD5sum: f8e9ee34ab14b196242f4e91bd88a688 Package: MEAL Version: 1.36.0 Depends: R (>= 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forcats, testthat (>= 2.1.0), knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1), rmarkdown, covr License: MIT + file LICENSE MD5sum: 9b353d80c05f66eeb7a0a3ed16ca6abd Package: Mergeomics Version: 1.34.0 Depends: R (>= 3.0.1) Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 272217259dabac3073d2751b96679e44 Package: MeSHDbi Version: 1.42.0 Depends: R (>= 3.0.1) Imports: methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase Suggests: testthat License: Artistic-2.0 MD5sum: b97d40cd3e5cd520a0f5cf5460e0368a Package: meshes Version: 1.32.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, DOSE, enrichplot, GOSemSim (>= 2.31.2), methods, utils, AnnotationHub, MeSHDbi, yulab.utils (>= 0.1.5) Suggests: knitr, rmarkdown, prettydoc License: Artistic-2.0 MD5sum: 70efe2d39c900418ec7cb144307f289a Package: meshr Version: 2.12.0 Depends: R (>= 4.1.0) Imports: markdown, rmarkdown, BiocStyle, knitr, methods, stats, utils, fdrtool, MeSHDbi, Category, S4Vectors, BiocGenerics, RSQLite License: 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(>= 4.0) Imports: dplyr (>= 1.0), methods, mgcv, caret, S4Vectors, stats, utils, rlang, graphics, matrixStats, tidyr Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 3534105b7b04c464f5d30efe58c2bc3c Package: metabinR Version: 1.8.0 Depends: R (>= 4.3) Imports: methods, rJava Suggests: BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: 555856259f10c92d44025d90b04c7483 Package: MetaboAnnotation Version: 1.10.1 Depends: R (>= 4.0.0) Imports: BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics, methods, S4Vectors, Spectra (>= 1.13.2), BiocParallel, SummarizedExperiment, QFeatures, AnnotationHub, graphics, CompoundDb Suggests: testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, microbenchmark, mzR Enhances: RMariaDB, RSQLite License: Artistic-2.0 MD5sum: 46a28119da5a0ce4d796e5029189ceba Package: MetaboCoreUtils Version: 1.14.0 Depends: R (>= 4.0) Imports: utils, MsCoreUtils, BiocParallel, methods, stats Suggests: BiocStyle, testthat, knitr, rmarkdown, robustbase License: Artistic-2.0 MD5sum: 860c088097756edf1fbe16a174dbb6fe Package: metabolomicsWorkbenchR Version: 1.16.0 Depends: R (>= 4.0) Imports: data.table, httr, jsonlite, methods, MultiAssayExperiment, struct, SummarizedExperiment, utils Suggests: BiocStyle, covr, knitr, HDF5Array, httptest, rmarkdown, structToolbox, testthat, pmp, grid, png License: GPL-3 MD5sum: e1ba80ee373080775039f1b2d71a865c Package: metabomxtr Version: 1.40.0 Depends: methods,Biobase Imports: optimx, Formula, plyr, multtest, BiocParallel, ggplot2 Suggests: xtable, reshape2 License: GPL-2 MD5sum: 7d4b0f9714f22092de5e13a48668a4e0 Package: MetaboSignal Version: 1.36.0 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: 5bc77d9aa27d2e8319c010b3c98b949d Package: metaCCA Version: 1.34.0 Suggests: knitr License: MIT + file LICENSE MD5sum: 151423e933268624293aaab023fbc78e Package: MetaCyto Version: 1.28.0 Depends: R (>= 3.4) Imports: flowCore (>= 1.4),tidyr (>= 0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices, graphics, stats, utils Suggests: knitr, dplyr, rmarkdown License: GPL (>= 2) MD5sum: c0cbe38b13773db278a35d5859984de5 Package: metagene2 Version: 1.22.0 Depends: R (>= 4.0), R6 (>= 2.0), GenomicRanges, BiocParallel Imports: rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges, ggplot2, Rsamtools, purrr, data.table, methods, dplyr, magrittr, reshape2 Suggests: BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: a6504ac91fda908be9cc2440d344bfd6 Package: metagenomeSeq Version: 1.47.0 Depends: R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer Imports: parallel, matrixStats, foreach, Matrix, gplots, graphics, grDevices, stats, utils, Wrench Suggests: annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW License: Artistic-2.0 MD5sum: 307ead57470a2e8de7ac22be471fa70e Package: metahdep Version: 1.64.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 MD5sum: 0ca5a0c93704947ee937d795b5f4d900 Package: MetaNeighbor Version: 1.26.0 Depends: R(>= 3.5) Imports: grDevices, graphics, methods, stats (>= 3.4), utils (>= 3.4), Matrix (>= 1.2), matrixStats (>= 0.54), beanplot (>= 1.2), gplots (>= 3.0.1), RColorBrewer (>= 1.1.2), SummarizedExperiment (>= 1.12), SingleCellExperiment, igraph, dplyr, tidyr, tibble, ggplot2 Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2), UpSetR License: MIT + file LICENSE MD5sum: b438930001f56b8506a2529b23b6ebdf Package: MetaPhOR Version: 1.8.0 Depends: R (>= 4.2.0) Imports: utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats, clusterProfiler, RecordLinkage, RCy3 Suggests: BiocStyle, knitr, rmarkdown, kableExtra License: Artistic-2.0 MD5sum: 1f79b2b90d44fe87d1de6a19097358c9 Package: metapod Version: 1.14.0 Imports: Rcpp LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: f7dfb55ce2836d5120a0892bd4592946 Package: metapone Version: 1.12.0 Depends: R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea, ggplot2, ggrepel Imports: methods Suggests: rmarkdown, knitr License: Artistic-2.0 MD5sum: ca18d2f4ed1e1c1f00b7f003f07a4213 Package: metaSeq Version: 1.46.0 Depends: R (>= 2.13.0), NOISeq, snow, Rcpp License: Artistic-2.0 MD5sum: e707df89c8146742fa03d1a505e1de8b Package: metaseqR2 Version: 1.18.0 Depends: R (>= 4.0.0), DESeq2, limma, locfit, splines Imports: ABSSeq, Biobase, BiocGenerics, BiocParallel, biomaRt, Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter, 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: 909107be4074ce686952f538e6048e96 Package: MetCirc Version: 1.36.0 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: 005c1196acaca7ddfb98c9b3834023f6 Package: methimpute Version: 1.28.0 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: 35f051768fe4bcad04f0aedef23e9911 Package: methInheritSim Version: 1.28.0 Depends: R (>= 3.5.0) Imports: methylKit, GenomicRanges, GenomeInfoDb, parallel, BiocGenerics, S4Vectors, methods, stats, IRanges, msm Suggests: BiocStyle, knitr, rmarkdown, RUnit, methylInheritance License: Artistic-2.0 MD5sum: 09d71f9902724ec1764e2d6467f354b5 Package: methodical Version: 1.1.0 Depends: GenomicRanges, ggplot2, R (>= 4.2.0), SummarizedExperiment Imports: BiocParallel, Biostrings, BSgenome, cowplot, data.table, DelayedArray, dplyr, ExperimentHub, foreach, GenomeInfoDb, HDF5Array, IRanges, R.utils, RcppRoll, rhdf5, rtracklayer, S4Vectors, scales, tibble, tidyr Suggests: AnnotationHub, annotatr, BiocStyle, BSgenome.Athaliana.TAIR.TAIR9, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, DESeq2, knitr, methrix, rmarkdown, TumourMethData License: GPL (>= 3) MD5sum: d805bb8ccf69e40076d69a89b589921e Package: MethPed Version: 1.34.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 MD5sum: caa53885a09a10357a0f93a19dbb1cfb Package: methrix Version: 1.20.0 Depends: R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment Imports: rtracklayer, DelayedArray, HDF5Array, BSgenome, DelayedMatrixStats, parallel, methods, ggplot2, S4Vectors, matrixStats, graphics, stats, utils, GenomicRanges, IRanges Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 85e21404486f97c1d793f0cf85718f0b Package: MethTargetedNGS Version: 1.38.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign Imports: utils, graphics, stats License: Artistic-2.0 MD5sum: c678800fa21e3c9068f5599e7f615c72 Package: MethylAid Version: 1.40.0 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: 57bfb5611e4abbc2c23c4e3650de2ca6 Package: methylCC Version: 1.20.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: GPL-3 MD5sum: 1be2736748c02043e9e8e73eb4ef255d Package: methylclock Version: 1.12.0 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: c9083eb1c9dcc0ff71b8961fd81ef23c Package: methylGSA Version: 1.24.0 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: 071c68f18cab23d54a45c970d013190f Package: methyLImp2 Version: 1.2.0 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: 4ed4d2fefcdf307f0ce375878fbb242d Package: methylInheritance Version: 1.30.0 Depends: R (>= 3.5) Imports: methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors, methods, parallel, ggplot2, gridExtra, rebus Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim License: Artistic-2.0 MD5sum: 5dc118e8fdce7d9d7d11cff0c59707f3 Package: methylKit Version: 1.32.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.18.1), methods Imports: IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>= 0.13.13), GenomeInfoDb, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager License: Artistic-2.0 MD5sum: b34e49ea7949c0eeefba39350bc0f195 Package: MethylMix Version: 2.36.0 Depends: R (>= 3.2.0) Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown License: GPL-2 MD5sum: 9ce767d82acb0ce68be33b68bab2cbad Package: methylMnM Version: 1.44.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: bda212847952609db3c8a43534439962 Package: methylPipe Version: 1.40.0 Depends: R (>= 3.5.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) MD5sum: 718d6da3ff67b05f4b8f6b36aa8c12e7 Package: methylscaper Version: 1.14.0 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: 77085e776c43d6cdb58f6462960d7f2a Package: MethylSeekR Version: 1.46.0 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), graphics (>= 2.15.2), grDevices (>= 2.15.2), parallel (>= 2.15.2), stats (>= 2.15.2), utils (>= 2.15.2) Suggests: BSgenome.Hsapiens.UCSC.hg18 License: GPL (>= 2) MD5sum: cf17d3a71ab514d5edd6e5685b0c1e16 Package: methylSig Version: 1.18.0 Depends: R (>= 3.6) Imports: bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, GenomeInfoDb, GenomicRanges, methods, parallel, stats, S4Vectors Suggests: BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr License: GPL-3 MD5sum: d75d364436a8e8f8fba05f3924582639 Package: methylumi Version: 2.52.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio, GenomicFeatures Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 MD5sum: dfa3856842221619f35d0b62e4b53f50 Package: MetID Version: 1.24.0 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: f9101a05ca42f5a88f72f52b269b814f Package: MetNet Version: 1.24.0 Depends: R (>= 4.0), S4Vectors (>= 0.28.1), SummarizedExperiment (>= 1.20.0) Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), corpcor (>= 1.6.10), dplyr (>= 1.0.3), ggplot2 (>= 3.3.3), GeneNet (>= 1.2.15), GENIE3 (>= 1.7.0), methods (>= 3.5), parmigene (>= 1.0.2), psych (>= 2.1.6), rlang (>= 0.4.10), stabs (>= 0.6), stats (>= 3.6), tibble (>= 3.0.5), tidyr (>= 1.1.2) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1), Spectra (>= 1.4.1), MsCoreUtils (>= 1.6.0) License: GPL (>= 3) MD5sum: 20ae416a9e5bac11cb1154c979764112 Package: mfa Version: 1.28.0 Depends: R (>= 3.4.0) Imports: methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack, MCMCglmm, coda, magrittr, tibble, Biobase LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: 6236dd0f505dd0cf4247c6e3c28b6aaf Package: Mfuzz Version: 2.66.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 MD5sum: 3eb3562244fd1b5dacdcfd2cd8c17322 Package: MGFM Version: 1.40.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 MD5sum: 748d6bf49bc250df6c7448fa33f397e8 Package: MGFR Version: 1.32.0 Depends: R (>= 3.5) Imports: biomaRt, annotate License: GPL-3 MD5sum: 0080d11c5729496d8d6380ea0c10ab49 Package: MGnifyR Version: 1.2.0 Depends: R(>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment, SummarizedExperiment, BiocGenerics Imports: mia, ape, dplyr, httr, methods, plyr, reshape2, S4Vectors, urltools, utils, tidyjson Suggests: biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2, BiocStyle, miaViz, vegan, scater, phyloseq, magick License: Artistic-2.0 | file LICENSE MD5sum: edef99db2e7256de4c0446e4b406933d Package: mgsa Version: 1.54.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: 2a79892dcb67532402f7fa5171301afa Package: mia Version: 1.14.0 Depends: R (>= 4.0), MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment (>= 1.99.3) Imports: ape, BiocGenerics, BiocParallel, Biostrings, bluster, DECIPHER, decontam, DelayedArray, DelayedMatrixStats, DirichletMultinomial, dplyr, IRanges, MASS, MatrixGenerics, mediation, methods, rbiom, rlang, S4Vectors, scater, scuttle, stats, tibble, tidyr, utils, vegan Suggests: ade4, BiocStyle, biomformat, dada2, knitr, miaViz, microbiomeDataSets, NMF, patchwork, phyloseq, reldist, rhdf5, rmarkdown, stringr, testthat, topicdoc, topicmodels, yaml License: Artistic-2.0 | file LICENSE MD5sum: 112c5d3e54b458441592f0c8fb933687 Package: miaSim Version: 1.12.0 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: 8f0d73e5c64724f081e9ab9739f86b62 Package: miaViz Version: 1.14.0 Depends: R (>= 4.0), SummarizedExperiment, TreeSummarizedExperiment, mia (>= 1.13.0), ggplot2, ggraph (>= 2.0) Imports: methods, stats, S4Vectors, BiocGenerics, BiocParallel, DelayedArray, scater, ggtree, ggnewscale, viridis, tibble, tidytext, tidytree, tidygraph, rlang, purrr, tidyr, dplyr, ape, DirichletMultinomial, ggrepel, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, bluster, ComplexHeatmap, circlize License: Artistic-2.0 | file LICENSE MD5sum: 1dc42730ba3ccaf7bf5c7a23809c4141 Package: MiChip Version: 1.60.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: 81cb607439d13ba782f64cc8fc913be0 Package: microbiomeDASim Version: 1.20.0 Depends: R (>= 3.6.0) Imports: graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase Suggests: testthat (>= 2.1.0), knitr, devtools License: MIT + file LICENSE MD5sum: 70ebf0590bd465007031f5b910e9cc28 Package: microbiomeExplorer Version: 1.16.0 Depends: shiny, magrittr, metagenomeSeq, Biobase Imports: shinyjs (>= 2.0.0), shinydashboard, shinycssloaders, shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer, dplyr, tidyr, purrr, rlang, knitr, readr, DT (>= 0.12.0), biomformat, tools, stringr, vegan, matrixStats, heatmaply, car, broom, limma, reshape2, tibble, forcats, lubridate, methods, plotly (>= 4.9.1) Suggests: V8, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: a970b70b5e2d85ca2f07994179b73f78 Package: microbiomeMarker Version: 1.11.0 Depends: R (>= 4.1.0) Imports: dplyr, phyloseq, magrittr, purrr, MASS, utils, ggplot2, tibble, rlang, stats, coin, ggtree, tidytree, methods, IRanges, tidyr, patchwork, ggsignif, metagenomeSeq, DESeq2, edgeR, BiocGenerics, Biostrings, yaml, biomformat, S4Vectors, Biobase, ComplexHeatmap, ANCOMBC, caret, limma, ALDEx2, multtest, plotROC, vegan, pROC, BiocParallel Suggests: testthat, covr, glmnet, Matrix, kernlab, e1071, ranger, knitr, rmarkdown, BiocStyle, withr License: GPL-3 MD5sum: e8ab332ff33dd55ef15479e6117024c0 Package: MicrobiomeProfiler Version: 1.12.0 Depends: R (>= 4.2.0) Imports: clusterProfiler (>= 4.5.2), config, DT, enrichplot, golem, gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader, htmltools, ggplot2, graphics, stats, utils, yulab.utils Suggests: rmarkdown, knitr, testthat (>= 3.0.0), prettydoc License: GPL-2 MD5sum: 0f86f1f6d2556d20901b62838684a672 Package: MicrobiotaProcess Version: 1.18.0 Depends: R (>= 4.0.0) Imports: ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>= 1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table, ggfun (>= 0.1.1) Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager License: GPL (>= 3.0) MD5sum: ffcb0ccfab7994629391495739d44bfc Package: microRNA Version: 1.64.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: a7dd3313e12666c0bbe53932ee740317 Package: microSTASIS Version: 1.6.0 Depends: R (>= 4.2.0) Imports: BiocParallel, ggplot2, ggside, grid, rlang, stats, stringr, TreeSummarizedExperiment Suggests: BiocStyle, gghighlight, knitr, rmarkdown, methods, RefManageR, sessioninfo, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0) License: GPL-3 MD5sum: 7bda4c3d2f59944116ec6b9820f0fd69 Package: MICSQTL Version: 1.4.0 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: 32619ac1ec642d817eb90fe01c86bb21 Package: miloR Version: 2.2.0 Depends: R (>= 4.0.0), edgeR Imports: BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>= 1.3-0), MatrixGenerics, S4Vectors, stats, stringr, methods, igraph, irlba, utils, cowplot, BiocParallel, BiocSingular, limma, ggplot2, tibble, matrixStats, ggraph, gtools, SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices, Rcpp, pracma, numDeriv LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppML Suggests: testthat, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, MASS, curl, scRNAseq, graphics, sparseMatrixStats License: GPL-3 + file LICENSE MD5sum: b38b39f43b7c387256a69788bf1c91ae Package: mimager Version: 1.30.0 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: e1efdeae3c85e5b5d31dc684ba076025 Package: mina Version: 1.14.0 Depends: R (>= 4.0.0) Imports: methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory, foreach, ggplot2, parallel, parallelDist, reshape2, plyr, biganalytics, stringr, Hmisc, utils LinkingTo: Rcpp, RcppParallel, RcppArmadillo Suggests: knitr, rmarkdown Enhances: doMC License: GPL MD5sum: d73844d7bce3a0fefa42b2f221e8f644 Package: MineICA Version: 1.46.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply Enhances: doMC License: GPL-2 MD5sum: 451f5b3eef691e4beabf3eb648545614 Package: minet Version: 3.64.0 Imports: infotheo License: Artistic-2.0 MD5sum: 63ea0363ab1b67a98bddfa64f287d5bb Package: minfi Version: 1.52.1 Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges, SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>= 1.1.9) Imports: S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray (>= 0.15.16), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools License: Artistic-2.0 MD5sum: 76949a11ec3ab089f26de11b9dfd243b Package: MinimumDistance Version: 1.50.0 Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1) Imports: methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: 13ac97aec115edf30d3e95845cf2001c Package: MiPP Version: 1.78.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: f2b2ab05dd12147cdbea3d335021bd8f Package: miQC Version: 1.14.0 Depends: R (>= 3.5.0) Imports: SingleCellExperiment, flexmix, ggplot2, splines Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 31649bc1dca427b6c22edec426a1ae48 Package: MIRA Version: 1.28.0 Depends: R (>= 3.5) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: e7ac815382948b72083fa5da72a7923c Package: MiRaGE Version: 1.48.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: BiocGenerics, S4Vectors, AnnotationDbi, BiocManager Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL MD5sum: 07f1ec8ff51f26f5e294a37b2fbaf2bc Package: miRBaseConverter Version: 1.30.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown License: GPL (>= 2) MD5sum: ba51b045b8ee6d49d10ba8a271116839 Package: miRcomp Version: 1.36.0 Depends: R (>= 3.2), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: b75b5455e0d315afb69065a7fb447f19 Package: mirIntegrator Version: 1.36.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: d9e6c47a7535826046f7158193d8d50c Package: MIRit Version: 1.2.0 Depends: MultiAssayExperiment, R (>= 4.4.0) Imports: AnnotationDbi, BiocFileCache, BiocParallel, DESeq2, edgeR, fgsea, genekitr, geneset, ggplot2, ggpubr, graph, graphics, graphite, grDevices, httr, limma, methods, Rcpp, Rgraphviz (>= 2.44.0), rlang, stats, utils LinkingTo: Rcpp Suggests: BiocStyle, biomaRt, BSgenome.Hsapiens.UCSC.hg38, GenomicRanges, ggrepel, ggridges, Gviz, gwasrapidd, knitr, MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 994e6d509ff93277d157c855aa7a7e5b Package: miRLAB Version: 1.36.0 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: 0e7c36c5436d9f44805014a073ee612e Package: miRNAmeConverter Version: 1.34.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 3ccf6a1e9f996c8204b9bc0d3ebd9188 Package: miRNApath Version: 1.66.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: 4767f31e632eb689b0a739cee6e356be Package: miRNAtap Version: 1.40.0 Depends: R (>= 3.3.0), AnnotationDbi Imports: DBI, RSQLite, stringr, sqldf, plyr, methods Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat License: GPL-2 MD5sum: e4a9e57b96942f3bc026fe79f9263a1b Package: miRSM Version: 2.2.0 Depends: R (>= 4.4.0) Imports: WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL, fabia, NMF, biclust, iBBiG, BicARE, isa2, s4vd, BiBitR, rqubic, Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero, ppclust, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE, MatrixCorrelation, energy Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: b7297da1b1ca7d083d57a139c7a0d296 Package: miRspongeR Version: 2.10.0 Depends: R (>= 4.4.0) Imports: corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, linkcomm, utils, Rcpp, org.Hs.eg.db, foreach, doParallel Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: a45029488bd93363ae53f528b24149bc Package: mirTarRnaSeq Version: 1.14.0 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: 0c68629b35ac3b64e56e5f586b1cfa35 Package: missMethyl Version: 1.40.0 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICv2anno.20a1.hg38 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICv2manifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub License: GPL-2 MD5sum: cb61a705a2ddb0629e8df36f24542018 Package: missRows Version: 1.26.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: efda3d9dea7f10024e856b55e3378893 Package: mitch Version: 1.18.4 Depends: R (>= 4.4) Imports: stats, grDevices, graphics, utils, MASS, plyr, reshape2, parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r, kableExtra Suggests: stringi, testthat (>= 2.1.0), HGNChelper, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: CC BY-SA 4.0 + file LICENSE MD5sum: a995787c8f7aafa621e4a2365a5954a2 Package: mitoClone2 Version: 1.12.0 Depends: R (>= 4.1.0) Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2 LinkingTo: Rhtslib (>= 1.13.1) Suggests: knitr, rmarkdown, Biostrings, testthat License: GPL-3 MD5sum: 9d7158eb25234478a80bcc254679a064 Package: mixOmics Version: 6.30.0 Depends: R (>= 4.4.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, ggrepel, BiocParallel, utils, gsignal, rgl Suggests: BiocStyle, knitr, rmarkdown, testthat, microbenchmark, magick License: GPL (>= 2) MD5sum: 7c498be857690af979c62fee34d905db Package: MLInterfaces Version: 1.86.0 Depends: R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4, tools, grDevices, graphics, stats, magrittr, SummarizedExperiment Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, BiocStyle, knitr, testthat Enhances: parallel License: LGPL MD5sum: 31af707d2a4a09fb228c04a15a85dc2e Package: MLSeq Version: 2.24.0 Depends: caret, ggplot2 Imports: testthat, VennDiagram, pamr, methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, e1071, kernlab License: GPL (>= 2) MD5sum: 37e7a3968b8bd6f38d02bf4484671099 Package: MMDiff2 Version: 1.34.0 Depends: R (>= 3.5.0), Rsamtools, Biobase Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 MD5sum: 7c9613d94befdcef1565c4b338b4838a Package: MMUPHin Version: 1.20.0 Depends: R (>= 3.6) Imports: Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr, stringr, cowplot, utils, stats, grDevices Suggests: testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter License: MIT + file LICENSE MD5sum: 62e507d7cfb658f08b5a8e08643bfd99 Package: mnem Version: 1.22.0 Depends: R (>= 4.1) Imports: cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071, ggplot2, wesanderson LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle License: GPL-3 MD5sum: d8b050c65aaf9fc83f6cd12ffe7afcd0 Package: moanin Version: 1.14.0 Depends: R (>= 4.0), SummarizedExperiment, topGO, stats Imports: S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics, methods, grDevices, reshape2, NMI, zoo, ClusterR, splines, matrixStats Suggests: testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: dbb3bbc28acd4fa31adc0266fbd38618 Package: mobileRNA Version: 1.2.0 Depends: R (>= 4.3.0) Imports: dplyr, tidyr, ggplot2, BiocGenerics, DESeq2, edgeR, ggrepel, grDevices, pheatmap, utils, tidyselect, progress, RColorBrewer, GenomicRanges, rtracklayer, data.table, SimDesign, scales, IRanges, stats, methods, Biostrings, reticulate, S4Vectors, GenomeInfoDb, SummarizedExperiment, rlang, bioseq, grid Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: a8fd5547b49a4b68ceb7c062dd0d5977 Package: MODA Version: 1.32.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: cfd29b7bd55ce1a9e16213fd84a072f9 Package: ModCon Version: 1.14.0 Depends: data.table, parallel, utils, stats, R (>= 4.1) Suggests: testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny, shinyFiles, shinydashboard, shinyjs License: GPL-3 + file LICENSE MD5sum: 0946fd60908bc7b68eac8730ccca0d84 Package: Modstrings Version: 1.22.0 Depends: R (>= 3.6), Biostrings (>= 2.51.5) Imports: methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: a0d9a5f1edce04596db7671786c3d564 Package: MOFA2 Version: 1.16.0 Depends: R (>= 4.0) Imports: rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods, RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array, grDevices, stats, magrittr, forcats, utils, corrplot, DelayedArray, Rtsne, uwot, basilisk, stringi Suggests: knitr, testthat, Seurat, SeuratObject, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown License: file LICENSE MD5sum: ef9bd855b1d70c76a2fe69477fe217ea Package: MOGAMUN Version: 1.16.0 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: knitr, markdown License: GPL-3 + file LICENSE MD5sum: 4ae1973cb39b634f209fb05cd232c516 Package: mogsa Version: 1.40.0 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: be8eeb3d70586ca9fae6742102c2c77a Package: MoleculeExperiment Version: 1.6.0 Depends: R (>= 2.10) Imports: SpatialExperiment, Matrix, purrr, data.table, dplyr (>= 1.1.1), magrittr, rjson, utils, methods, terra, ggplot2, rlang, cli, EBImage, rhdf5, BiocParallel, S4Vectors, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: b12abd75cc893ca57e9c3f58e7c2a888 Package: MOMA Version: 1.18.0 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: d098a53ca37bb865eceefbdace0bbe26 Package: monocle Version: 2.34.0 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: 2a0f0309bc543c3ac61a20acc5b1ffdb Package: Moonlight2R Version: 1.4.0 Depends: R (>= 4.3), 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 Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), devtools, roxygen2, png License: GPL-3 MD5sum: 00ca012b7af7f8b61869b89d2870d334 Package: MoonlightR Version: 1.32.0 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: 67a3e484e2bef08ee6df48cfb63a4c3c Package: mosaics Version: 2.44.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: 7cd0f74b1654f9b0b68d665cf162c6bf Package: mosbi Version: 1.12.0 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: f8e43bbf27ce419cf2851073b5b1e0e7 Package: MOSClip Version: 1.0.0 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: 608507544a67e3c93397072ea8e23b91 Package: mosdef Version: 1.2.0 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: 23365cafa0ba4ad48c0297925e64c6c2 Package: MOSim Version: 2.2.0 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: b85ca6edc057beda271e81f29d2af2ce Package: Motif2Site Version: 1.10.0 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: d43b370706072c19f095dcee4913c6e5 Package: motifbreakR Version: 2.20.0 Depends: R (>= 4.4.0), grid, MotifDb Imports: methods, grDevices, stringr, parallel, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment, pwalign, DT, bsicons, BiocFileCache, biomaRt, bslib, shiny, vroom Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Hsapiens.UCSC.hg38 License: GPL-2 MD5sum: d26de187891b7aa6d56f2deff6b6173d Package: motifcounter Version: 1.30.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: e54a03ca964e8116ae53f5b79215c319 Package: MotifDb Version: 1.48.0 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: aa56ba03d3deb2a9541a1cdaca1325e6 Package: motifTestR Version: 1.2.1 Depends: Biostrings, GenomicRanges, ggplot2 (>= 3.5.0), R (>= 4.3.0), Imports: GenomeInfoDb, graphics, harmonicmeanp, IRanges, matrixStats, methods, parallel, patchwork, rlang, S4Vectors, stats, universalmotif Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, extraChIPs, ggdendro, knitr, MotifDb, rmarkdown, rtracklayer, testthat (>= 3.0.0) License: GPL-3 MD5sum: a5143aaa5fb3cbd8751a68fb74885c97 Package: MouseFM Version: 1.16.0 Depends: R (>= 4.0.0) Imports: httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales, gtools, tidyr, data.table, jsonlite, rlist, GenomeInfoDb, methods, biomaRt, stats, IRanges Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 71903ca515cb0dae4218ccd3c4293069 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methods, parallel, plyranges, Rbowtie, reticulate, rtracklayer, stats, stringi, tidyr, tidyselect, utils Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, knitr, magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL-2 MD5sum: 77847387caaefed3a132937ecb52ea04 Package: MultiDataSet Version: 1.34.0 Depends: R (>= 4.1), Biobase Imports: BiocGenerics, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman, limma Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment License: file LICENSE MD5sum: f234c1bf5bf1809597791cdc562d4a80 Package: multiGSEA Version: 1.16.2 Depends: R (>= 4.0.0) Imports: magrittr, graphite, AnnotationDbi, metaboliteIDmapping, dplyr, fgsea, metap, rappdirs, rlang, methods Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: GPL-3 MD5sum: 991446bfd60039b223923735d5aae2f9 Package: multiHiCcompare Version: 1.24.0 Depends: R (>= 4.0.0) Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: db862d2e0edf47dbedf342bdfecd27b6 Package: MultiMed Version: 2.28.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE MD5sum: ab68066b267fd678ff3558c334fbde82 Package: multiMiR Version: 1.28.0 Depends: R (>= 3.4) Imports: stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 2.0), methods, BiocGenerics, AnnotationDbi, dplyr, Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) License: MIT + file 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ScaledMatrix, beachmat, scuttle, metapod, scran, batchelor, uwot Suggests: testthat, knitr, BiocStyle, rmarkdown, scater, bluster, DropletUtils, scRNAseq License: GPL-3 MD5sum: 9914e1ab37bd337cca13fb2ab6d777dc Package: MungeSumstats Version: 1.14.1 Depends: R(>= 4.1) Imports: magrittr, data.table, utils, R.utils, dplyr, stats, GenomicRanges, IRanges, GenomeInfoDb, BSgenome, Biostrings, stringr, VariantAnnotation, googleAuthR, httr, jsonlite, methods, parallel, rtracklayer(>= 1.59.1), RCurl Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, Rsamtools, MatrixGenerics, badger, BiocParallel, GenomicFiles License: Artistic-2.0 MD5sum: 91544fbe69c5764996e884b460a9909a Package: muscat Version: 1.20.0 Depends: R (>= 4.4) Imports: BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, rlang, S4Vectors, scales, scater, scuttle, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition, viridis Suggests: BiocStyle, countsimQC, ExperimentHub, iCOBRA, knitr, patchwork, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, stageR, testthat, UpSetR License: GPL-3 MD5sum: 452a5ebc2f5ca7af24e787e870eb0a81 Package: muscle Version: 3.48.0 Depends: Biostrings License: Unlimited MD5sum: 890af93d09c9e9ae7ef7cdefd4df7141 Package: musicatk Version: 2.0.0 Depends: R (>= 4.4.0), NMF Imports: SummarizedExperiment, VariantAnnotation, Biostrings, base, methods, magrittr, tibble, tidyr, gtools, gridExtra, MCMCprecision, MASS, matrixTests, data.table, dplyr, rlang, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, S4Vectors, uwot, ggplot2, stringr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, decompTumor2Sig, topicmodels, ggrepel, plotly, utils, factoextra, cluster, ComplexHeatmap, philentropy, maftools, shiny, stringi, tidyverse, ggpubr, Matrix (>= 1.6.1), scales, conclust Suggests: TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard, shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr, shinyWidgets, cowplot, withr License: LGPL-3 MD5sum: 30662c00dec61e0c81cb4c29aa5b3330 Package: MVCClass Version: 1.80.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: a7e5a9b686adf43637dee9dd8f40bf7a Package: MWASTools Version: 1.30.0 Depends: R (>= 3.5.0) Imports: glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra, igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST, ComplexHeatmap, stats, utils Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: CC BY-NC-ND 4.0 MD5sum: d3b14b7246e9b93d3431a6980e8ab15d Package: mygene Version: 1.42.0 Depends: R (>= 3.2.1), GenomicFeatures, txdbmaker Imports: methods, utils, stats, httr (>= 0.3), jsonlite (>= 0.9.7), Hmisc, sqldf, plyr, S4Vectors Suggests: BiocStyle License: Artistic-2.0 MD5sum: 001561ee10d6ba23ee507ddf2b30b245 Package: myvariant Version: 1.36.0 Depends: R (>= 3.2.1), VariantAnnotation Imports: httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, GenomeInfoDb Suggests: BiocStyle License: Artistic-2.0 MD5sum: 3ac6ab8492ec140534baf7ba005320b1 Package: mzID Version: 1.44.0 Depends: methods Imports: XML, plyr, parallel, doParallel, foreach, iterators, ProtGenerics Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 5e99922f9f866f9d0f750eb4330f370d Package: mzR Version: 2.40.0 Depends: R (>= 4.0.0), Rcpp (>= 0.10.1), methods, utils Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3), ncdf4 LinkingTo: Rcpp, Rhdf5lib (>= 1.1.4) Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown License: Artistic-2.0 MD5sum: 7f9356d9d855719db590b6ee29bf93e6 Package: NADfinder Version: 1.30.0 Depends: R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, S4Vectors, SummarizedExperiment Imports: graphics, methods, baseline, signal, GenomicAlignments, GenomeInfoDb, rtracklayer, limma, trackViewer, stats, utils, Rsamtools, metap, EmpiricalBrownsMethod,ATACseqQC, corrplot, csaw Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager, rmarkdown License: GPL (>= 2) MD5sum: c16f0999573f39fd6d1918d8949adada Package: NanoMethViz Version: 3.2.0 Depends: R (>= 4.0.0), methods, ggplot2 (>= 3.4.0) Imports: cpp11 (>= 0.2.5), readr, cli, S4Vectors, SummarizedExperiment, BiocSingular, bsseq, forcats, assertthat, AnnotationDbi, Rcpp, dplyr, dbscan, e1071, fs, GenomicRanges, Biostrings, ggrastr, glue, graphics, IRanges, limma (>= 3.44.0), patchwork, purrr, rlang, R.utils, Rsamtools, scales (>= 1.2.0), stats, stringr, tibble, tidyr, utils, withr, zlibbioc LinkingTo: Rcpp Suggests: BiocStyle, DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>= 1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm39.refGene, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0), covr License: Apache License (>= 2.0) MD5sum: afc65eef015630681c38f6c4eac0ca87 Package: NanoStringDiff Version: 1.36.0 Depends: Biobase Imports: matrixStats, methods, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle License: GPL MD5sum: b89bbcb4472b230db20cff1e8d178dbf Package: NanoStringNCTools Version: 1.14.0 Depends: R (>= 3.6), Biobase, S4Vectors, ggplot2 Imports: BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes, grDevices, IRanges, methods, pheatmap, RColorBrewer, stats, utils Suggests: biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf License: MIT MD5sum: 14c186d55b19601ff1d9a89a4e22a1c1 Package: 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rmarkdown License: GPL-2 MD5sum: 5706c10a7279a7be1509b468f58c7696 Package: ncRNAtools Version: 1.16.0 Imports: httr, xml2, utils, methods, grDevices, ggplot2, IRanges, GenomicRanges, S4Vectors Suggests: knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics License: GPL-3 MD5sum: 2ea2df1a722c45aee7cc769ca3b02b51 Package: ndexr Version: 1.28.0 Depends: RCX Imports: httr, jsonlite, plyr, tidyr Suggests: BiocStyle, testthat, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 52bdc656c1c4d79dd7a435587e0b2a76 Package: nearBynding Version: 1.16.0 Depends: R (>= 4.0) Imports: R.utils, matrixStats, plyranges, transport, Rsamtools, S4Vectors, grDevices, graphics, rtracklayer, dplyr, GenomeInfoDb, methods, GenomicRanges, utils, stats, magrittr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, ggplot2, gplots, BiocGenerics, rlang Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: a6e9a4df37d47da977240cebe1902467 Package: Nebulosa Version: 1.16.0 Depends: R (>= 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RcppParallel, parallel, grDevices, graphics, stats, utils, dynamicTreeCut, WGCNA, impute, colorspace, methods, BiocStyle, R.utils LinkingTo: Rcpp, RcppParallel Suggests: knitr, rmarkdown License: GPL-3 OS_type: unix MD5sum: ac32d58d45d7db085780af39b88d94b1 Package: nethet Version: 1.38.0 Imports: glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network, ggplot2, grDevices, graphics, stats, utils Suggests: knitr, xtable, BiocStyle, testthat License: GPL-2 MD5sum: d0db3f23a4763de7d0283a6c4b5f0aee Package: NetPathMiner Version: 1.42.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 6a6cfbf2c2a0dd1c4f4ca2401b1b644b Package: netprioR Version: 1.32.0 Depends: methods, graphics, R(>= 3.3) Imports: stats, Matrix, dplyr, doParallel, foreach, parallel, sparseMVN, ggplot2, gridExtra, pROC Suggests: knitr, BiocStyle, pander License: GPL-3 MD5sum: 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stats Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr License: GPL-3 MD5sum: ba8dcafccb8413647a0abd4b7ab00bf2 Package: ngsReports Version: 2.8.0 Depends: R (>= 4.2.0), BiocGenerics, ggplot2 (>= 3.5.0), patchwork (>= 1.1.1), tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro, grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate, methods, plotly (>= 4.9.4), reshape2, rlang, rmarkdown, scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo Suggests: BiocStyle, Cairo, DT, knitr, pander, readr, testthat, truncnorm License: LGPL-3 MD5sum: edbdcdc5e70cdd7e9402ea790ef1f53b Package: nipalsMCIA Version: 1.4.2 Depends: R (>= 4.3.0) Imports: ComplexHeatmap, dplyr, fgsea, ggplot2 (>= 3.0.0), graphics, grid, methods, MultiAssayExperiment, SummarizedExperiment, pracma, rlang, RSpectra, scales, stats Suggests: BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0) License: GPL-3 MD5sum: bdaba49dfd7bd119dadaec4c321ff8b6 Package: nnNorm Version: 2.70.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: 2113701df8be7b95768096ac84b9cfa3 Package: nnSVG Version: 1.10.0 Depends: R (>= 4.2) Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat License: MIT + file LICENSE MD5sum: 2a8343ea613e5ced2acf4d2605a71943 Package: NOISeq Version: 2.50.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 MD5sum: 4ed30e5470c0082d9e2944530100f178 Package: NoRCE Version: 1.18.0 Depends: R (>= 4.2.0) Imports: KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,stringr,GenomeInfoDb, S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl, dbplyr,utils,ggplot2,igraph,stats,reshape2,readr, GO.db,zlibbioc, biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi 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, methods,markdown License: MIT + file LICENSE MD5sum: 1052cac9e75f685ba4a9a3f26908f04f Package: normalize450K Version: 1.34.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 74ad804eacfe11ea99d29c487b0f7d62 Package: NormalyzerDE Version: 1.24.0 Depends: R (>= 4.1.0) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, utils, 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npGSEA Version: 1.42.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: 68fd5becbd159352711ebf23f84b841f Package: NTW Version: 1.56.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 MD5sum: 7f17e586e1ec334d71269f97d04e2c81 Package: nucleoSim Version: 1.34.0 Imports: stats, IRanges, S4Vectors, graphics, methods Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: e96d7f221b1b8b844fa935aa4e9a7060 Package: nucleR Version: 2.38.0 Depends: R (>= 3.5.0), methods Imports: Biobase, BiocGenerics, Biostrings, GenomeInfoDb, GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr, ggplot2, magrittr, parallel, stats, utils, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat License: LGPL (>= 3) MD5sum: 332a484910129c1c7e2c464e0a18a7fd Package: nuCpos Version: 1.24.0 Depends: R (>= 4.2.0) 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multtest (>= 1.7.3), graphics, grDevices, stats, interp License: LGPL MD5sum: 12c2af35ae106dcd0054b193e7a783cb Package: octad Version: 1.8.0 Depends: R (>= 4.2.0), magrittr, dplyr, ggplot2, edgeR, RUVSeq, DESeq2, limma, rhdf5, foreach, Rfast, octad.db, stats, httr, qpdf, ExperimentHub, AnnotationHub, Biobase, S4Vectors Imports: EDASeq, GSVA, data.table, htmlwidgets, plotly, reshape2, grDevices, utils Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: ca7596731160e1be146e0ab1f3037437 Package: odseq Version: 1.34.0 Depends: R (>= 3.2.3) Imports: msa (>= 1.2.1), kebabs (>= 1.4.1), mclust (>= 5.1) Suggests: knitr(>= 1.11) License: MIT + file LICENSE MD5sum: ca80a8291b431a1c01fb007119438ac4 Package: OGRE Version: 1.10.0 Depends: R (>= 4.2.0), S4Vectors Imports: GenomicRanges, methods, data.table, assertthat, ggplot2, Gviz, IRanges, AnnotationHub, grDevices, stats, GenomeInfoDb, shiny, shinyFiles, DT, rtracklayer, shinydashboard, shinyBS,tidyr Suggests: testthat (>= 3.0.0), knitr (>= 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SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>= 1.23.2), foreach, BiocManager, utils, S4Vectors (>= 0.9.25), RSQLite, DBI, ff Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, VanillaICE, crlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) MD5sum: 6cc901f8c98e8927fd99edf478b2d113 Package: OLIN Version: 1.84.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 MD5sum: 35405e3a56a5b165e67a0b95c28b8479 Package: OLINgui Version: 1.80.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: GPL-2 MD5sum: a177738839b3cccb5ce664a628e5a68b Package: omada Version: 1.8.0 Depends: pdfCluster (>= 1.0-3), kernlab (>= 0.9-29), R 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matrixStats, rmarkdown, shiny, stats, vegan, zCompositions License: MIT + file LICENSE MD5sum: 2912f94f438648d7fb95b4598914ff72 Package: omicRexposome Version: 1.28.0 Depends: R (>= 3.5.0), Biobase Imports: stats, utils, grDevices, graphics, methods, rexposome, limma, sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet, SmartSVA, isva, parallel, SummarizedExperiment, stringr Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata License: MIT + file LICENSE MD5sum: 8c5af76dc949cd570f51b45add4ae971 Package: OmicsMLRepoR Version: 1.0.0 Depends: R (>= 4.4.0) Imports: dplyr, stringr, rols, tidyr, methods, stats, tibble, data.tree, jsonlite, plyr, BiocFileCache, readr, DiagrammeR, rlang, lubridate Suggests: arrow, knitr, BiocStyle, curatedMetagenomicData, testthat (>= 3.0.0), cBioPortalData License: Artistic-2.0 MD5sum: 494aef65f057e443ba0d574d9a65d957 Package: OMICsPCA Version: 1.24.0 Depends: R (>= 3.5.0), OMICsPCAdata Imports: HelloRanges, fpc, stats, MultiAssayExperiment, pdftools, methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown, kableExtra, rtracklayer, IRanges, GenomeInfoDb, reshape2, ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR, PerformanceAnalytics, tidyr, data.table, cluster, magick Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: b98293b961f3e0ef0706b164dd102768 Package: omicsPrint Version: 1.26.0 Depends: R (>= 3.5), MASS Imports: methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 2) MD5sum: e76f3fc345c1d76f1985c9838a411cca Package: omicsViewer Version: 1.10.0 Depends: R (>= 4.2) Imports: survminer, survival, fastmatch, reshape2, stringr, beeswarm, grDevices, DT, shiny, shinythemes, shinyWidgets, plotly, networkD3, httr, matrixStats, RColorBrewer, Biobase, fgsea, openxlsx, psych, shinybusy, ggseqlogo, htmlwidgets, graphics, grid, stats, utils, methods, shinyjs, curl, flatxml, ggplot2, S4Vectors, SummarizedExperiment, RSQLite, Matrix, shinycssloaders, ROCR, drc Suggests: BiocStyle, knitr, rmarkdown, unittest License: GPL-2 MD5sum: a1de06f4b7d14ecaaa16c00079db6ab1 Package: Omixer Version: 1.16.0 Depends: R (>= 4.0.0) Imports: dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr, tidyselect, grid, stats, stringr Suggests: knitr, rmarkdown, BiocStyle, magick, testthat License: MIT + file LICENSE MD5sum: 8061a2a35d305c6410e317d3b49140f6 Package: OmnipathR Version: 3.14.0 Depends: R(>= 4.0) Imports: checkmate, crayon, curl, digest, dplyr(>= 1.1.0), httr, igraph, jsonlite, later, logger, lubridate, magrittr, progress, purrr, rappdirs, readr(>= 2.0.0), readxl, rlang, rmarkdown, RSQLite, R.utils, rvest, stats, stringi, stringr, tibble, tidyr, tidyselect, tools, utils, vctrs, withr, XML, xml2, yaml, zip Suggests: BiocStyle, bookdown, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, R.matlab, sigmajs, smoof, supraHex, testthat License: MIT + file LICENSE MD5sum: 678c3c523d26691c0a72b8231e431968 Package: ompBAM Version: 1.10.0 Imports: utils, Rcpp Suggests: RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis, desc, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: ae6eb245ad8537b4071ca4b65c90b28e Package: omXplore Version: 1.0.0 Depends: R (>= 4.4.0), methods Imports: shiny, MSnbase, PSMatch, SummarizedExperiment, MultiAssayExperiment, shinyBS, shinyjs, shinyjqui, DT, RColorBrewer, gplots, highcharter, visNetwork, tibble, grDevices, stats, utils, htmlwidgets, vioplot, graphics, FactoMineR, dendextend, dplyr, factoextra, tidyr Suggests: knitr, rmarkdown, BiocStyle, testthat, Matrix, graph License: Artistic-2.0 MD5sum: c06e3a1732353b49efddca077b115da0 Package: oncomix Version: 1.28.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: 58b6772cb4742c7e87d87c4fcf1db117 Package: oncoscanR Version: 1.8.0 Depends: R (>= 4.2), IRanges (>= 2.30.0), GenomicRanges (>= 1.48.0), magrittr Imports: readr, S4Vectors, methods, utils Suggests: testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 4e4e58233db49e65596722786d8b8e94 Package: OncoScore Version: 1.34.0 Depends: R (>= 4.1.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: 206e5d54c841d3deb1857397d924c970 Package: OncoSimulR Version: 4.7.7 Depends: R (>= 3.5.0) Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel, stringr LinkingTo: Rcpp Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander License: GPL (>= 3) MD5sum: 15eebc443b53f504a000b06579a91ea3 Package: 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Package: oposSOM Version: 2.24.0 Depends: R (>= 4.0.0), igraph (>= 1.0.0) Imports: fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt, Biobase, RcppParallel, Rcpp, methods, graph, XML, png, RCurl LinkingTo: RcppParallel, Rcpp License: GPL (>= 2) MD5sum: 1ceded05b3aaafeae9d073f25a4021fd Package: oppar Version: 1.34.0 Depends: R (>= 3.3) Imports: Biobase, methods, GSEABase, GSVA Suggests: knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel License: GPL-2 MD5sum: 22f072cb9ad04fe58e68886e9faf8564 Package: oppti Version: 1.20.0 Depends: R (>= 3.5) Imports: limma, stats, reshape, ggplot2, grDevices, RColorBrewer, pheatmap, knitr, methods, devtools, parallelDist, Suggests: markdown License: MIT MD5sum: 21048078c29350e5f3de4972cf646885 Package: optimalFlow Version: 1.18.0 Depends: dplyr, optimalFlowData, rlang (>= 0.4.0) Imports: transport, parallel, Rfast, robustbase, dbscan, randomForest, foreach, graphics, doParallel, stats, flowMeans, rgl, ellipse Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: 65644c53473e6c6500563dc7e8845746 Package: OPWeight Version: 1.28.0 Depends: R (>= 3.4.0), Imports: graphics, qvalue, MASS, tibble, stats, Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat License: Artistic-2.0 MD5sum: df5f482dbec1d82da0fb64df021e50d5 Package: OrderedList Version: 1.78.0 Depends: R (>= 3.6.1), Biobase, twilight Imports: methods License: GPL (>= 2) MD5sum: 3c432ad30febf1dee405f13fcbdf3992 Package: ORFhunteR Version: 1.14.0 Depends: Biostrings, rtracklayer, Peptides Imports: Rcpp (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg38, data.table, stringr, randomForest, xfun, stats, utils, parallel, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown License: MIT License MD5sum: f090ea8b601d23195152de7292fc4a10 Package: ORFik Version: 1.26.1 Depends: R (>= 4.1.0), IRanges (>= 2.17.1), GenomicRanges (>= 1.35.1), GenomicAlignments (>= 1.19.0) Imports: AnnotationDbi (>= 1.45.0), Biostrings (>= 2.51.1), biomaRt, biomartr (>= 1.0.7), BiocFileCache, BiocGenerics (>= 0.29.1), BiocParallel (>= 1.19.0), BSgenome, cowplot (>= 1.0.0), data.table (>= 1.11.8), DESeq2 (>= 1.24.0), fst (>= 0.9.2), GenomeInfoDb (>= 1.15.5), GenomicFeatures (>= 1.31.10), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), httr (>= 1.3.0), jsonlite, methods (>= 3.6.0), R.utils, Rcpp (>= 1.0.0), Rsamtools (>= 1.35.0), rtracklayer (>= 1.43.0), stats, SummarizedExperiment (>= 1.14.0), S4Vectors (>= 0.21.3), tools, txdbmaker, utils, XML, xml2 (>= 1.2.0), withr LinkingTo: Rcpp Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 5aa585b7218b80e2f7d2673e3f9667a9 Package: OrganismDbi Version: 1.48.0 Depends: R (>= 2.14.0), BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.39.4) Imports: methods, utils, stats, DBI, BiocManager, Biobase, graph, RBGL, S4Vectors, IRanges, GenomicRanges (>= 1.31.13), txdbmaker Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr License: Artistic-2.0 MD5sum: 22667bb0e475de45d6f12ba13399760a Package: Organism.dplyr Version: 1.34.0 Depends: R (>= 3.4), dplyr (>= 0.7.0), AnnotationFilter (>= 1.1.3) Imports: RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges, GenomicFeatures, AnnotationDbi, rlang, methods, tools, utils, BiocFileCache, DBI, dbplyr, tibble Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, magick, BiocStyle, ggplot2 License: Artistic-2.0 MD5sum: 8e94bf665c9119dae120643d153d32e9 Package: orthogene Version: 1.12.0 Depends: R (>= 4.1) Imports: dplyr, methods, stats, utils, Matrix, jsonlite, homologene, gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr, patchwork, DelayedArray, grr, repmis, ggtree, tools Suggests: rworkflows, 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phantasusLite, XML Suggests: testthat, BiocStyle, knitr, rmarkdown, org.Hs.eg.db, org.Mm.eg.db License: MIT + file LICENSE MD5sum: 8c1d7055014ac01beb06be2c55b9cece Package: phantasusLite Version: 1.4.0 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: 794f88da44a0a3477204c45ad4c28bf3 Package: PharmacoGx Version: 3.10.0 Depends: R (>= 3.6), CoreGx Imports: BiocGenerics, Biobase, S4Vectors, SummarizedExperiment, MultiAssayExperiment, BiocParallel, ggplot2, RColorBrewer, magicaxis, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table, checkmate, boot, coop LinkingTo: Rcpp Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils License: GPL (>= 3) MD5sum: bd51f481852d719b04b4377533cf9155 Package: PhenoGeneRanker Version: 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Package: phenoTest Version: 1.54.0 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: 8ef678c78f7692880fe41af62eece0cf Package: PhenStat Version: 2.42.0 Depends: R (>= 3.5.0) Imports: SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf, knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4, graphics, grDevices, utils, stats Suggests: RUnit, BiocGenerics License: file LICENSE MD5sum: 996744cb6dc9b5633d408315bd9e0ec2 Package: philr Version: 1.32.0 Imports: ape, phangorn, tidyr, ggplot2, ggtree, methods Suggests: testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq, SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr, mia License: GPL-3 MD5sum: ddd7406d3db6550bd510423db2dc1f7b Package: PhIPData Version: 1.14.0 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: b418603824ad1141d965d73b6e085740 Package: phosphonormalizer Version: 1.30.0 Depends: R (>= 4.0) Imports: plyr, stats, graphics, matrixStats, methods Suggests: knitr, rmarkdown, testthat Enhances: MSnbase License: GPL (>= 2) MD5sum: 9474c53b1dde7a7e27a810dfee632447 Package: PhosR Version: 1.16.0 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: 18862a55c60f2cbadf2cd31c8170413d Package: PhyloProfile Version: 1.20.4 Depends: R (>= 4.4.0) Imports: ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, dplyr, DT, energy, ExperimentHub, extrafont, fastcluster, ggplot2, gridExtra, pbapply, plotly, RColorBrewer, RCurl, scattermore, shiny, shinyBS, shinycssloaders, shinyFiles, shinyjs, stringr, tsne, umap, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat, OmaDB License: MIT + file LICENSE MD5sum: e2cb0e26182519952cec80f3148e3fb1 Package: piano Version: 2.22.0 Depends: R (>= 3.5) Imports: BiocGenerics, Biobase, gplots, igraph, relations, marray, fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard, visNetwork, scales, grDevices, graphics, stats, utils, methods Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: b99d1833a863a990170402e6e02eda3f Package: pickgene Version: 1.78.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: ffd3cdad09407f04ee479893671215f4 Package: PICS Version: 2.50.0 Depends: R (>= 3.0.0) Imports: utils, stats, graphics, grDevices, methods, IRanges, GenomicRanges, Rsamtools, GenomicAlignments Suggests: rtracklayer, parallel, knitr License: Artistic-2.0 MD5sum: a223981842c099245d0dd8ceeede635b Package: Pigengene Version: 1.32.0 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: 59bc85381e0cf44bd1257ae9ef13debb Package: PING Version: 2.50.0 Depends: R(>= 3.5.0) Imports: methods, PICS, graphics, grDevices, stats, Gviz, fda, BSgenome, stats4, BiocGenerics, IRanges, GenomicRanges, S4Vectors Suggests: parallel, ShortRead, rtracklayer License: Artistic-2.0 MD5sum: ab95ab7572a26c2f11ca217124ec2f02 Package: pipeComp Version: 1.16.0 Depends: R (>= 4.1) Imports: BiocParallel, S4Vectors, ComplexHeatmap, SingleCellExperiment, SummarizedExperiment, Seurat, matrixStats, Matrix, cluster, aricode, methods, utils, dplyr, grid, scales, scran, viridisLite, clue, randomcoloR, ggplot2, cowplot, intrinsicDimension, scater, knitr, reshape2, stats, Rtsne, uwot, circlize, RColorBrewer Suggests: BiocStyle, rmarkdown License: GPL MD5sum: 1116dd9e8a3078138ad3eebc73dd42a5 Package: pipeFrame Version: 1.22.0 Depends: R (>= 4.0.0), Imports: BSgenome, digest, visNetwork, magrittr, methods, Biostrings, GenomeInfoDb, parallel, stats, utils, rmarkdown Suggests: BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: 751b79943386134cbb006b1b350b2238 Package: PIPETS Version: 1.2.0 Depends: R (>= 4.4.0) Imports: dplyr, utils, stats, GenomicRanges, BiocGenerics, methods Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: cc974053ce11f3608d2a402078f2d255 Package: Pirat Version: 1.0.1 Depends: R (>= 4.4.0), BiocManager (>= 1.3.20) Imports: basilisk (>= 1.18.0), reticulate, progress, ggplot2, MASS, invgamma, grDevices, stats, graphics, SummarizedExperiment, S4Vectors Suggests: knitr, BiocStyle License: GPL-2 MD5sum: 37fe88a57559e56d059f085c3b54b6ff Package: PIUMA Version: 1.2.0 Depends: R (>= 4.3), ggplot2 Imports: cluster, umap, tsne, kernlab, vegan, dbscan, igraph, scales, Hmisc, patchwork, grDevices, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat, rmarkdown License: GPL-3 + file LICENSE MD5sum: 14d91f6ec7e04f9220d144fb6ac057ac Package: planet Version: 1.14.0 Depends: R (>= 4.3) Imports: methods, tibble, magrittr, dplyr Suggests: ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr, rmarkdown License: GPL-2 MD5sum: 3d07bcb15988677e447085a801477a23 Package: planttfhunter Version: 1.6.0 Depends: R (>= 4.2.0) Imports: Biostrings, SummarizedExperiment, utils, methods Suggests: BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 363fe3795448d31f4561af974cc6c72f Package: plasmut Version: 1.4.0 Depends: R (>= 4.3.0) Imports: tibble, stats, dplyr Suggests: knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf, BiocStyle, biocViews, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 75dba570095be0e37f114d9a0569618b Package: plgem Version: 1.78.0 Depends: R (>= 2.10) Imports: utils, Biobase (>= 2.5.5), MASS, methods License: GPL-2 MD5sum: 9f6f5a64cca6de9e665b671f2215bef9 Package: plier Version: 1.76.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) MD5sum: e2cb4425a62b91b23044bac973863bcd Package: plotgardener Version: 1.12.0 Depends: R (>= 4.1.0) Imports: curl, data.table, dplyr, GenomeInfoDb, GenomicRanges, glue, grDevices, grid, ggplotify, IRanges, methods, plyranges, purrr, Rcpp, RColorBrewer, rhdf5, rlang, stats, strawr, tools, utils, withr LinkingTo: Rcpp Suggests: AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene License: MIT + file LICENSE MD5sum: 5651105e2201229c309cad7d7a63997e Package: plotGrouper Version: 1.24.0 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) 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Artistic-2.0 MD5sum: 43fbc7efc9dd4256ffc7afbf7d3398f0 Package: plyxp Version: 1.0.0 Depends: R (>= 4.4.0) Imports: dplyr, purrr, rlang, SummarizedExperiment, tidyr, tidyselect, vctrs, tibble, pillar, cli, glue, S7, S4Vectors, utils, methods Suggests: devtools, knitr, rmarkdown, testthat, airway, IRanges, here License: MIT + file LICENSE MD5sum: dfdf9838bcf3110b7275d9b6ff6fdc3f Package: pmm Version: 1.38.0 Depends: R (>= 2.10) Imports: lme4, splines License: GPL-3 MD5sum: 9429522bf43326c4120d16e253e88a00 Package: PoDCall Version: 1.14.0 Depends: R (>= 4.4) Imports: ggplot2, gridExtra, mclust, diptest, rlist, shiny, DT, LaplacesDemon, purrr, shinyjs, readr, grDevices, stats, utils Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 53b84f1ad9bcc967c9398debc252696c Package: podkat Version: 1.38.0 Depends: R (>= 3.5.0), methods, Rsamtools (>= 1.99.1), GenomicRanges Imports: Rcpp (>= 0.11.1), parallel, stats (>= 4.3.0), graphics, grDevices, utils, Biobase, BiocGenerics, 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eb21c3524a869f71c2c3a0e783abd39c Package: pqsfinder Version: 2.22.0 Depends: R (>= 3.5.0), Biostrings Imports: Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods LinkingTo: Rcpp, BH (>= 1.78.0) Suggests: BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi License: BSD_2_clause + file LICENSE MD5sum: 82fbca2fae205aef4933ccb716c5b7ff Package: pram Version: 1.22.0 Depends: R (>= 3.6) Imports: methods, BiocParallel, tools, utils, data.table (>= 1.11.8), GenomicAlignments (>= 1.16.0), rtracklayer (>= 1.40.6), BiocGenerics (>= 0.26.0), GenomeInfoDb (>= 1.16.0), GenomicRanges (>= 1.32.0), IRanges (>= 2.14.12), Rsamtools (>= 1.32.3), S4Vectors (>= 0.18.3) Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 3) MD5sum: 670e58663447f1572d9cef7756196b92 Package: prebs Version: 1.46.0 Depends: R (>= 2.14.0), GenomicAlignments, affy, RPA Imports: parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges, Biobase, 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2.1.0) License: Apache License (== 2.0) | file LICENSE MD5sum: 09afcfc089a1db277c1d16fc9f438ba3 Package: projectR Version: 1.22.0 Depends: R (>= 4.0.0) Imports: methods, cluster, stats, limma, NMF, ROCR, ggalluvial, RColorBrewer, dplyr, fgsea, reshape2, viridis, scales, Matrix, MatrixModels, msigdbr, ggplot2, cowplot, ggrepel, umap, tsne Suggests: BiocStyle, CoGAPS, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap, gplots, SeuratObject License: GPL (== 2) MD5sum: 1f154985fbeef5fb8ccf0ad82f74e4bd Package: pRoloc Version: 1.46.0 Depends: R (>= 3.5), MSnbase (>= 1.19.20), MLInterfaces (>= 1.67.10), methods, Rcpp (>= 0.10.3), BiocParallel Imports: stats4, Biobase, mclust (>= 4.3), caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS, knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools, plyr, ggplot2, biomaRt, utils, grDevices, graphics LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, rmarkdown, pRolocdata (>= 1.43.2), roxygen2, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape, magick License: GPL-2 MD5sum: 4e16ed52d6805e7c8d8e1651e77b6675 Package: pRolocGUI Version: 2.16.0 Depends: methods, R (>= 3.1.0), pRoloc (>= 1.27.6), Biobase, MSnbase (>= 2.1.11) Imports: shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics, utils, ggplot2, shinydashboardPlus (>= 2.0.0), colourpicker, shinyhelper, shinyWidgets, shinyjs, colorspace, stats, grDevices, grid, BiocGenerics, shinydashboard Suggests: pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown, testthat (>= 3.0.0) License: GPL-2 MD5sum: c099f261929c5f99881ba1ce492f8553 Package: PROMISE Version: 1.58.0 Depends: R (>= 3.1.0), Biobase, GSEABase Imports: Biobase, GSEABase, stats License: GPL (>= 2) MD5sum: 485d84c82406b20c7dcd74b54aaabba3 Package: PRONE Version: 1.0.0 Depends: R (>= 4.4.0), SummarizedExperiment Imports: dplyr, magrittr, data.table, RColorBrewer, ggplot2, S4Vectors, ComplexHeatmap, stringr, NormalyzerDE, tibble, limma, MASS, edgeR, matrixStats, preprocessCore, stats, gtools, methods, ROTS, ComplexUpset, tidyr, purrr, circlize, gprofiler2, plotROC, MSnbase, UpSetR, dendsort, vsn, Biobase, reshape2, POMA, ggtext, scales, DEqMS Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, DT License: GPL (>= 3) MD5sum: c83016e254b6b2e0345e7eaf432ee98a Package: PROPER Version: 1.38.0 Depends: R (>= 3.3) Imports: edgeR Suggests: BiocStyle,DESeq2,DSS,knitr License: GPL MD5sum: 70976d786d0e71a890b1245d88c5ec2f Package: PROPS Version: 1.27.0 Imports: bnlearn, reshape2, sva, stats, utils, Biobase Suggests: knitr, rmarkdown License: GPL-2 MD5sum: c924a73ea26009f82585b42d884e2755 Package: Prostar Version: 1.38.1 Depends: R (>= 4.4.0) Imports: DAPAR (>= 1.35.1), DAPARdata (>= 1.30.0), rhandsontable, data.table, shiny, shinyBS, shinyAce, highcharter, htmlwidgets, webshot, shinythemes, later, shinycssloaders, future, promises, shinyjqui, tibble, ggplot2, gplots, shinyjs, vioplot, Biobase, DT, R.utils, RColorBrewer, XML, colourpicker, gtools, markdown, rclipboard, sass, shinyTree, shinyWidgets Suggests: BiocStyle, BiocManager, testthat, knitr License: Artistic-2.0 MD5sum: 1fa037576945ac643e47fdcb945f4322 Package: proteinProfiles Version: 1.46.0 Depends: R (>= 2.15.2) Imports: graphics, stats Suggests: testthat License: GPL-3 MD5sum: 73af5d3eb87e193ea12a286ab5702978 Package: ProteoDisco Version: 1.12.0 Depends: R (>= 4.1.0), Imports: BiocGenerics (>= 0.38.0), BiocParallel (>= 1.26.0), Biostrings (>= 2.60.1), checkmate (>= 2.0.0), cleaver (>= 1.30.0), dplyr (>= 1.0.6), GenomeInfoDb (>= 1.28.0), GenomicFeatures (>= 1.44.0), GenomicRanges (>= 1.44.0), IRanges (>= 2.26.0), methods (>= 4.1.0), ParallelLogger (>= 2.0.1), plyr (>= 1.8.6), rlang (>= 0.4.11), S4Vectors (>= 0.30.0), tibble (>= 3.1.2), tidyr (>= 1.1.3), VariantAnnotation (>= 1.36.0), XVector (>= 0.32.0), Suggests: 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License: Artistic-2.0 MD5sum: 2e18d80cde241554774337238458d82f Package: psygenet2r Version: 1.37.1 Depends: R (>= 3.4) Imports: stringr, RCurl, igraph, ggplot2, reshape2, grid, parallel, biomaRt, BgeeDB, topGO, Biobase, labeling, GO.db Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: e9059fc9f2139d1a84ab47da14b833a3 Package: puma Version: 3.48.0 Depends: R (>= 3.2.0), oligo (>= 1.32.0),graphics,grDevices, methods, stats, utils, mclust, oligoClasses Imports: Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses Suggests: pumadata, affydata, snow, limma, ROCR,annotate License: LGPL MD5sum: 22a5d82a15451082fb41897264b2f544 Package: PureCN Version: 2.12.0 Depends: R (>= 3.5.0), DNAcopy, VariantAnnotation (>= 1.14.1) Imports: GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer, S4Vectors, data.table, grDevices, graphics, stats, utils, SummarizedExperiment, GenomeInfoDb, GenomicFeatures, Rsamtools, Biobase, Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra, futile.logger, VGAM, tools, methods, mclust, rhdf5, Matrix Suggests: BiocParallel, BiocStyle, PSCBS, R.utils, TxDb.Hsapiens.UCSC.hg19.knownGene, covr, knitr, optparse, org.Hs.eg.db, jsonlite, markdown, rmarkdown, testthat Enhances: genomicsdb (>= 0.0.3) License: Artistic-2.0 MD5sum: f72b67a760451a18e47a8b162aa86bb2 Package: pvac Version: 1.54.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) MD5sum: deb9d879989db2fcdb45da54c06434b4 Package: pvca Version: 1.46.0 Depends: R (>= 2.15.1) Imports: Matrix, Biobase, vsn, stats, lme4 Suggests: golubEsets License: LGPL (>= 2.0) MD5sum: f8e46532b1621b89d568df0d5929daa2 Package: Pviz Version: 1.40.0 Depends: R(>= 3.0.0), Gviz(>= 1.7.10) Imports: biovizBase, Biostrings, GenomicRanges, IRanges, data.table, methods Suggests: knitr, pepDat License: Artistic-2.0 MD5sum: b5f3a94f1a449c4b6f181146bc86e22c Package: pwalign Version: 1.2.0 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(>= 1.7.2), igraph, grDevices, plotly, tidyr, tidyselect, reshape2 Suggests: SingleCellExperiment, MsDataHub (>= 1.3.3), Matrix, HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap License: Artistic-2.0 MD5sum: ba70f85cafbe82d069386a276a1debec Package: qmtools Version: 1.10.0 Depends: R (>= 4.2.0), SummarizedExperiment Imports: rlang, ggplot2, patchwork, heatmaply, methods, MsCoreUtils, stats, igraph, VIM, scales, grDevices, graphics, limma Suggests: Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute, imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: d1893eed6d28a17a3d070ca48f8bd962 Package: qpcrNorm Version: 1.64.0 Depends: methods, Biobase, limma, affy License: LGPL (>= 2) MD5sum: e7da1320100adf4a651af0fca12ef839 Package: qpgraph Version: 2.40.0 Depends: R (>= 3.5) Imports: methods, parallel, Matrix (>= 1.5-0), grid, annotate, graph (>= 1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm, qtl, Rgraphviz Suggests: RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats License: GPL (>= 2) MD5sum: e63a5342fac898256bacc8ff11a84f01 Package: qPLEXanalyzer Version: 1.24.0 Depends: R (>= 4.0), Biobase, MSnbase Imports: assertthat, BiocGenerics, Biostrings, dplyr (>= 1.0.0), ggdendro, ggplot2, graphics, grDevices, IRanges, limma, magrittr, preprocessCore, purrr, RColorBrewer, readr, rlang, scales, stats, stringr, tibble, tidyr, tidyselect, utils Suggests: patchwork, knitr, qPLEXdata, rmarkdown, statmod, testthat, UniProt.ws, vdiffr License: GPL-2 MD5sum: 7a5a2a9eadf03fd9f8464073dd8288e1 Package: qsea Version: 1.32.0 Depends: R (>= 4.3) Imports: Biostrings, graphics, gtools, methods, stats, utils, HMMcopy, rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges, 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DEFormats, DESeq2, GenomeInfoDb, GenomicRanges, knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR, rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment, utils Suggests: BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot (>= 1.29.1), sessioninfo, DT, edgeR, ggbio (>= 1.35.2), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker License: Artistic-2.0 MD5sum: ddaba2af1e5f6e553ea085c63cde5d8d Package: regsplice Version: 1.32.0 Imports: glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats, pbapply, utils, methods Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 4463ac2c89e8694e7c5f8a6337c09b11 Package: regutools Version: 1.18.0 Depends: R (>= 4.0) Imports: AnnotationDbi, AnnotationHub, Biostrings, DBI, GenomicRanges, Gviz, IRanges, RCy3, RSQLite, S4Vectors, methods, stats, utils, BiocFileCache Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr License: Artistic-2.0 MD5sum: 25256edf6124a82e63aab9fc05663de3 Package: REMP Version: 1.30.0 Depends: R (>= 3.6), SummarizedExperiment(>= 1.1.6), minfi (>= 1.22.0) Imports: readr, rtracklayer, graphics, stats, utils, methods, settings, BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel, doParallel, parallel, foreach, caret, kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db, impute, iterators Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC License: GPL-3 MD5sum: 5b365d1bb263d04ce63b78c25996cbc4 Package: Repitools Version: 1.52.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.8.0) Imports: parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, BSgenome (>= 1.47.3), gplots, grid, MASS, gsmoothr, edgeR (>= 3.4.0), DNAcopy, Rsolnp, cluster Suggests: ShortRead, BSgenome.Hsapiens.UCSC.hg18 License: LGPL (>= 2) MD5sum: ae606f9d6db9ecfd7ad4681d386cefae Package: ReportingTools Version: 2.46.0 Depends: methods, knitr, utils Imports: Biobase,hwriter,Category,GOstats,limma(>= 3.17.5),lattice,AnnotationDbi,edgeR, annotate,PFAM.db, GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils, DESeq2(>= 1.3.41), ggplot2, ggbio, IRanges Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db, rmarkdown, markdown License: Artistic-2.0 MD5sum: 6cb6f33a0bfa661c92fd7d383586118f Package: RepViz Version: 1.22.0 Depends: R (>= 3.5.1), GenomicRanges (>= 1.30.0), Rsamtools (>= 1.34.1), IRanges (>= 2.14.0), biomaRt (>= 2.36.0), S4Vectors (>= 0.18.0), graphics, grDevices, utils Suggests: rmarkdown, knitr, testthat License: GPL-3 MD5sum: fcebea8cdd498ef3da36854b2e18a47b Package: ResidualMatrix Version: 1.16.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular License: GPL-3 MD5sum: c6d7551e20d9e1b36edda49f4acc4d76 Package: RESOLVE Version: 1.8.0 Depends: R (>= 4.1.0) Imports: Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5, data.table, GenomeInfoDb, GenomicRanges, glmnet, ggplot2, gridExtra, IRanges, lsa, MutationalPatterns, nnls, parallel, reshape2, S4Vectors, RhpcBLASctl Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 4aee9b458018829b7d419a1aeee5d002 Package: retrofit Version: 1.6.0 Depends: R (>= 4.2), Rcpp LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2, corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl License: GPL-3 MD5sum: 9458806864969f52caeaa41be1454fc0 Package: ReUseData Version: 1.6.0 Imports: Rcwl, RcwlPipelines, BiocFileCache, S4Vectors, stats, tools, utils, methods, jsonlite, yaml, basilisk Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle License: GPL-3 MD5sum: ca2d12ebb729f43d5580861ead812f30 Package: rexposome Version: 1.28.0 Depends: R (>= 3.5), Biobase Imports: methods, utils, stats, lsr, FactoMineR, stringr, circlize, corrplot, ggplot2, ggridges, reshape2, pryr, S4Vectors, imputeLCMD, scatterplot3d, glmnet, gridExtra, grid, Hmisc, gplots, gtools, scales, lme4, grDevices, graphics, ggrepel, mice Suggests: mclust, flexmix, testthat, BiocStyle, knitr, formatR, rmarkdown License: MIT + file LICENSE MD5sum: 6b09fea9ee023f0eda94283a88846eb5 Package: rfaRm Version: 1.18.0 Imports: httr, stringi, rsvg, magick, data.table, Biostrings, utils, rvest, xml2, IRanges, S4Vectors, jsonlite Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics, RUnit License: GPL-3 MD5sum: 038d6c3076a529ad9fb937e2bdc1a703 Package: Rfastp Version: 1.16.0 Imports: Rcpp, rjson, ggplot2, reshape2 LinkingTo: Rcpp, Rhtslib, zlibbioc Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: ca98249593c3ce6a03af0de98b4832e6 Package: rfPred Version: 1.44.0 Depends: R (>= 3.5.0), methods Imports: utils, GenomeInfoDb, data.table, IRanges, GenomicRanges, parallel, Rsamtools Suggests: BiocStyle License: GPL (>= 2) MD5sum: ec7b7bd7920a00e0c69ed9a497b6f32e Package: rGADEM Version: 2.54.0 Depends: R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo Imports: Biostrings, GenomicRanges, methods, graphics, seqLogo Suggests: BSgenome.Hsapiens.UCSC.hg19, rtracklayer License: Artistic-2.0 MD5sum: 0a76402e9c593dc8d540b77347fc2f45 Package: rGenomeTracks Version: 1.12.0 Depends: R (>= 4.1.0), Imports: imager, reticulate, methods, rGenomeTracksData Suggests: rmarkdown, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 5c257b672cb7718cc4c7b30c09be0392 Package: RgnTX Version: 1.8.0 Depends: R (>= 4.2.0) Imports: GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, graphics, IRanges, methods, regioneR, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 7db9882660ccc22b10974b4a93ec6408 Package: rgoslin Version: 1.10.0 Imports: Rcpp (>= 1.0.3), dplyr LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra, BiocManager, stringr, stringi, ggplot2, tibble, lipidr License: MIT + file LICENSE MD5sum: e9f219efd3fab20e71fb753839dbaf06 Package: RGraph2js Version: 1.34.0 Imports: utils, whisker, rjson, digest, graph Suggests: RUnit, BiocStyle, BiocGenerics, xtable, sna License: GPL-2 MD5sum: 5ab7f6e5401d98ec06ffffa8771d0416 Package: Rgraphviz Version: 2.50.0 Depends: R (>= 2.6.0), methods, utils, graph, grid Imports: stats4, graphics, grDevices Suggests: RUnit, BiocGenerics, XML License: EPL MD5sum: b812b35a2eb56f55d8d48135bc298e9d Package: rGREAT Version: 2.8.0 Depends: R (>= 4.0.0), GenomicRanges, IRanges, methods Imports: graphics, rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats, GlobalOptions, shiny, DT, GenomicFeatures, digest, GO.db, progress, circlize, AnnotationDbi, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, RColorBrewer, S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp LinkingTo: Rcpp Suggests: testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db Enhances: BioMartGOGeneSets, UniProtKeywords License: MIT + file LICENSE MD5sum: 2d6e3d944e842b70b8e783a386c3c23b Package: RGSEA Version: 1.40.0 Depends: R(>= 2.10.0) Imports: BiocGenerics Suggests: BiocStyle, GEOquery, knitr, RUnit License: GPL (>= 3) MD5sum: 3cafe001490abb031022a41d66d66757 Package: rgsepd Version: 1.38.0 Depends: R (>= 4.2.0), DESeq2, goseq (>= 1.28) Imports: gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, AnnotationDbi Suggests: boot, tools, BiocGenerics, knitr, xtable License: GPL-3 MD5sum: 72851f87e2d34752ec137639961163db Package: rhdf5 Version: 2.50.1 Depends: R (>= 4.0.0), methods Imports: Rhdf5lib (>= 1.13.4), rhdf5filters (>= 1.15.5) LinkingTo: Rhdf5lib Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr, ggplot2, mockery, BiocParallel License: Artistic-2.0 MD5sum: e9ca43a793cff4a64423d9d2c3f92b9a Package: rhdf5client Version: 1.28.0 Depends: R (>= 3.6), methods, DelayedArray Imports: httr, rjson, utils, data.table Suggests: knitr, testthat, BiocStyle, DT, rmarkdown License: Artistic-2.0 MD5sum: 2060d5a52723aff055658fa77e1ba59c Package: rhdf5filters Version: 1.18.0 LinkingTo: Rhdf5lib Suggests: BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.47.7) License: BSD_2_clause + file LICENSE MD5sum: 8e5d4fb7186b04c3f8af61b5ab560db2 Package: Rhdf5lib Version: 1.28.0 Depends: R (>= 4.2.0) Suggests: BiocStyle, knitr, rmarkdown, tinytest, mockery License: Artistic-2.0 MD5sum: ff6e53ddad24f62af494fba2ae2571f7 Package: rhinotypeR Version: 1.0.0 Depends: R (>= 4.4.0) Imports: Biostrings Suggests: knitr, rmarkdown, BiocManager, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 99e7eb309f5510dcc6f73cd817bcc2bd Package: Rhisat2 Version: 1.22.0 Depends: R (>= 4.4.0) Imports: txdbmaker, SGSeq, GenomicRanges, methods, utils Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 Archs: x64 MD5sum: a7fa1196abda2778abc10e22486f1205 Package: Rhtslib Version: 3.2.0 Imports: tools, zlibbioc LinkingTo: zlibbioc Suggests: knitr, rmarkdown, BiocStyle License: LGPL (>= 2) MD5sum: cb482a0b3751ae23be0b81f3a6ca0a69 Package: RiboCrypt Version: 1.12.0 Depends: R (>= 3.6.0), ORFik (>= 1.13.12) Imports: bslib, BiocGenerics, BiocParallel, Biostrings, data.table, dplyr, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, httr, IRanges, jsonlite, knitr, markdown, NGLVieweR, plotly, rlang, RCurl, shiny, shinycssloaders, shinyhelper, shinyjqui, stringr Suggests: testthat, rmarkdown, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 3ff63a5c531256043db10f445a0cd593 Package: RiboDiPA Version: 1.14.0 Depends: R (>= 4.1), Rsamtools, GenomicFeatures, GenomicAlignments Imports: Rcpp (>= 1.0.2), graphics, stats, data.table, elitism, methods, S4Vectors, IRanges, GenomicRanges, matrixStats, reldist, doParallel, foreach, parallel, qvalue, DESeq2, ggplot2, BiocFileCache, BiocGenerics, txdbmaker LinkingTo: Rcpp Suggests: knitr, rmarkdown License: LGPL (>= 3) MD5sum: 890534ad790f5b07d69e34efcecd2a12 Package: RiboProfiling Version: 1.36.0 Depends: R (>= 3.5.0), Biostrings Imports: BiocGenerics, GenomeInfoDb, GenomicRanges, IRanges, reshape2, GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments, ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment License: GPL-3 MD5sum: a07d068464ad160802995119c9debfc3 Package: ribor Version: 1.18.0 Depends: R (>= 3.6.0) Imports: dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors, tidyr, tools, yaml Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: acd55d821c124bee728c8152ad386f0a Package: riboSeqR Version: 1.40.0 Depends: R (>= 3.0.2), methods, GenomicRanges, abind Imports: Rsamtools, IRanges, S4Vectors, baySeq, GenomeInfoDb, seqLogo Suggests: BiocStyle, RUnit, BiocGenerics License: GPL-3 MD5sum: a827a834547d7646891d23fc2086cc19 Package: ribosomeProfilingQC Version: 1.18.0 Depends: R (>= 4.0), GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq, GenomicAlignments, GenomicFeatures, GenomeInfoDb, IRanges, methods, motifStack, rtracklayer, Rsamtools, RUVSeq, Rsubread, S4Vectors, XVector, ggplot2, ggfittext, scales, ggrepel, utils, cluster, stats, graphics, grid, txdbmaker, ggExtra Suggests: RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10, edgeR, DESeq2, limma, ashr, testthat, rmarkdown, vsn, Biobase License: GPL (>= 3) + file LICENSE MD5sum: ff5cefb907f983e6781c970e6ad790be Package: rifi Version: 1.10.0 Depends: R (>= 4.2) Imports: car, cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, graphics, grDevices, grid, methods, nls2, nnet, rlang, S4Vectors, scales, stats, stringr, SummarizedExperiment, tibble, rtracklayer, reshape2, utils Suggests: DescTools, devtools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: b938221af76be968774e7cb38305a6da Package: rifiComparative Version: 1.6.0 Depends: R (>= 4.2) Imports: cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2, ggrepel, graphics, grDevices, grid, methods, nnet, rlang, S4Vectors, scales, stats, stringr, tibble, rtracklayer, utils, writexl, DTA, LSD, reshape2, devtools, SummarizedExperiment Suggests: DescTools, knitr, rmarkdown, BiocStyle License: GPL-3 + file LICENSE MD5sum: 029d0440d65e86cf389449d69c9efcf3 Package: RImmPort Version: 1.34.0 Imports: plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools, utils, RSQLite Suggests: knitr License: GPL-3 MD5sum: 8f57bc2abbf95929bd71cec8c9862ade Package: RITAN Version: 1.30.0 Depends: R (>= 4.0), Imports: graphics, methods, stats, utils, grid, gridExtra, reshape2, gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL, linkcomm, dynamicTreeCut, gsubfn, hash, png, sqldf, igraph, BgeeDB, knitr, RITANdata, GenomicFeatures, ensembldb, AnnotationFilter, EnsDb.Hsapiens.v86 Suggests: rmarkdown, BgeeDB License: file LICENSE MD5sum: e301fd68a284adc37175508c634090ed Package: RIVER Version: 1.30.0 Depends: R (>= 3.3.2) Imports: glmnet, pROC, ggplot2, graphics, stats, Biobase, methods, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools License: GPL (>= 2) MD5sum: 7ea3510066ff53c2d5decbd3c1da2e1a Package: RJMCMCNucleosomes Version: 1.30.0 Depends: R (>= 3.5.0), IRanges, GenomicRanges Imports: Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb, S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit License: Artistic-2.0 MD5sum: 407a424001789ab70b5f62c4738ee2c4 Package: RLassoCox Version: 1.14.0 Depends: R (>= 4.1), glmnet Imports: Matrix, igraph, survival, stats Suggests: 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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: a8ee860493ea5f46c4bb08ce848c4abc Package: roar Version: 1.42.0 Depends: R (>= 3.0.1) Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, GenomicAlignments (>= 0.99.4), rtracklayer, GenomeInfoDb Suggests: RNAseqData.HNRNPC.bam.chr14, testthat License: GPL-3 MD5sum: c301b1bbc83ddcf68aa7ddd8da63a048 Package: roastgsa Version: 1.4.0 Depends: R (>= 4.3.0) Imports: parallel, grDevices, graphics, utils, stats, methods, grid, RColorBrewer, gplots, ggplot2, limma, Biobase Suggests: BiocStyle, knitr, rmarkdown, GSEABenchmarkeR, EnrichmentBrowser, preprocessCore, DESeq2 License: GPL-3 MD5sum: 7bed419441b341321bd5102c44b81c3d Package: ROC Version: 1.82.0 Depends: R (>= 1.9.0), utils, methods Imports: knitr Suggests: rmarkdown, Biobase, BiocStyle License: Artistic-2.0 MD5sum: 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rvest, S4Vectors (>= 0.23.10), stats, stringr, SummarizedExperiment, TCGAutils (>= 1.9.4), utils Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown License: GPL-2 MD5sum: f692e728834cd358cf7c746b24627ae5 Package: RTN Version: 2.30.0 Depends: R (>= 3.6.3), methods, Imports: RedeR, minet, viper, mixtools, snow, stats, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr, pheatmap, grDevices, graphics, utils Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 5afac2d33bb31e822229cf8db5218cb6 Package: RTNduals Version: 1.30.0 Depends: R(>= 3.6.3), RTN(>= 2.14.1), methods Imports: graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: c9b5cdc3a21349bbb87cfb467c99fe36 Package: RTNsurvival Version: 1.30.0 Depends: R(>= 3.6.3), RTN(>= 2.14.1), RTNduals(>= 1.14.1), methods Imports: survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test Suggests: Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 4ff7cd7e703ca3445304aace5987cb96 Package: RTopper Version: 1.52.0 Depends: R (>= 2.12.0), Biobase Imports: limma, multtest Suggests: org.Hs.eg.db, KEGGREST, GO.db License: GPL (>= 3) + file LICENSE MD5sum: 42745b1bdde56d42b1c003fc627f5808 Package: Rtpca Version: 1.16.0 Depends: R (>= 4.0.0), stats, dplyr, tidyr Imports: Biobase, methods, ggplot2, pROC, fdrtool, splines, utils, tibble Suggests: knitr, BiocStyle, TPP, testthat, rmarkdown License: GPL-3 MD5sum: 86dcedaf373d7082b5ea8735313c518c Package: rtracklayer Version: 1.66.0 Depends: R (>= 3.5.0), methods, GenomicRanges (>= 1.37.2) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.35.3), S4Vectors (>= 0.23.18), IRanges (>= 2.13.13), XVector (>= 0.19.7), GenomeInfoDb (>= 1.15.2), Biostrings (>= 2.47.6), zlibbioc, curl, httr, Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), BiocIO, tools, restfulr 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GENLIB, gRain, snpStats, kinship2, methods, stats, utils, R.utils Suggests: knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation License: GPL-2 MD5sum: ec97ea5a009366de8584b8de984848ec Package: rWikiPathways Version: 1.26.0 Imports: httr, utils, XML, rjson, data.table, RCurl, dplyr, tidyr, readr, stringr, purrr, lubridate Suggests: testthat, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 105309ef650cc35086b18be412578c05 Package: S4Arrays Version: 1.6.0 Depends: R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>= 0.45.2), S4Vectors, IRanges Imports: stats, crayon LinkingTo: S4Vectors Suggests: BiocParallel, SparseArray (>= 0.0.4), DelayedArray, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 3aa0a21df2492287cc8314082ce62ca2 Package: S4Vectors Version: 0.44.0 Depends: R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>= 0.37.0) Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 1be41da5261184d5bdfda0a080ea3eb3 Package: safe Version: 3.46.0 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: GPL (>= 2) MD5sum: 1a12a7809019113d46613df1698056a2 Package: sagenhaft Version: 1.76.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: ad68a6ac75156c712dfc08423762f431 Package: SAIGEgds Version: 2.6.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.28.0), SeqArray (>= 1.43.7), Rcpp Imports: methods, stats, utils, Matrix, RcppParallel, CompQuadForm, survey LinkingTo: Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0) Suggests: parallel, markdown, rmarkdown, crayon, SNPRelate, RUnit, knitr, ggmanh, BiocGenerics License: GPL-3 MD5sum: 61d7372385e295b9d0d03f4c35322058 Package: sampleClassifier Version: 1.30.0 Depends: R (>= 4.0), MGFM, MGFR, annotate Imports: e1071, ggplot2, stats, utils Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db License: Artistic-2.0 MD5sum: d4f0acc60567cc7d1ed0d99c47fe5f7d Package: SamSPECTRAL Version: 1.60.0 Depends: R (>= 3.3.3) Imports: methods License: GPL (>= 2) MD5sum: 2dc8695f5bd331b7a35473f35c5cb3e0 Package: sangeranalyseR Version: 1.16.0 Depends: R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER, parallel, reshape2, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle, logger Suggests: testthat (>= 2.1.0) License: GPL-2 MD5sum: cc5f71de7ec1cada97e7be88ee4bc665 Package: sangerseqR Version: 1.42.0 Depends: R (>= 3.5.0), Biostrings, pwalign, stringr Imports: methods, shiny Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 MD5sum: 2bd4b04a1216e27521c76d70cd074c3d Package: SANTA Version: 2.42.0 Depends: R (>= 4.1), igraph Imports: graphics, Matrix, methods, stats Suggests: BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db, markdown, rmarkdown, RUnit License: GPL (>= 2) MD5sum: b5dacd4abfe5e3c3775f41d1a7b6985e Package: SARC Version: 1.4.0 Depends: R (>= 4.3), RaggedExperiment, GenomicRanges Imports: tidyverse, utils, reshape2, DescTools, metap, multtest, plyranges, data.table, scales, RColorBrewer, grid, gtable, gridExtra, GenomicFeatures, stats, ggplot2, plotly, IRanges Suggests: knitr, kableExtra, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, Homo.sapiens, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, GenomicAlignments License: GPL-3 MD5sum: 664bec1dc13edf55b00d891aca3199ab Package: sarks Version: 1.18.0 Depends: R (>= 4.0) Imports: rJava, Biostrings, IRanges, utils, stats, cluster, binom Suggests: RUnit, BiocGenerics, ggplot2 License: BSD_3_clause + file LICENSE MD5sum: 9db0d7c0f2e309b0d777774b93aef615 Package: saseR Version: 1.2.0 Depends: R (>= 4.3.0) Imports: ASpli, S4Vectors, BiocGenerics, GenomicFeatures, MASS, PRROC, SummarizedExperiment, edgeR, pracma, precrec, BiocParallel, DESeq2, DEXSeq, data.table, limma, methods, GenomicRanges, GenomicAlignments, rrcov, MatrixGenerics, stats, IRanges, knitr, dplyr, igraph, parallel License: Artistic-2.0 MD5sum: a750611873669c10bc4cff90bfc43d3b Package: satuRn Version: 1.14.0 Depends: R (>= 4.1) Imports: locfdr, SummarizedExperiment, BiocParallel, limma, pbapply, ggplot2, boot, Matrix, stats, methods, graphics Suggests: knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray License: Artistic-2.0 MD5sum: 80d247f9446ac1b7a5c02d886ea0c8cb Package: SBGNview Version: 1.20.0 Depends: R (>= 3.6), pathview, SBGNview.data Imports: Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph, rmarkdown, knitr, SummarizedExperiment, AnnotationDbi, httr, KEGGREST, bookdown Suggests: testthat, gage License: AGPL-3 MD5sum: 85f81af7afa847ce4fe5c774d205fda6 Package: 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Package: scanMiR Version: 1.12.0 Depends: R (>= 4.0) Imports: Biostrings, pwalign, GenomicRanges, IRanges, data.table, BiocParallel, methods, GenomeInfoDb, S4Vectors, ggplot2, stats, stringi, utils, graphics, grid, seqLogo, cowplot Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: ac43b9efd96d1b9ca4738a82d431b630 Package: scanMiRApp Version: 1.12.0 Depends: R (>= 4.0), scanMiR Imports: AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel, Biostrings, data.table, digest, DT, ensembldb, fst, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs, rtracklayer, S4Vectors, scanMiRData, shiny, shinycssloaders, shinydashboard, shinyjqui, stats, utils, txdbmaker, waiter Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-3 MD5sum: 1dc27712fbd1eab5111cf3a11031fd61 Package: scAnnotatR Version: 1.12.0 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: 2a41a5d624e3e44724c568b7d77dfbce Package: SCAN.UPC Version: 2.48.0 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva Imports: utils, methods, MASS, tools, IRanges Suggests: pd.hg.u95a License: MIT MD5sum: 125d2a12dfa977d668cfe6bc82de1704 Package: SCANVIS Version: 1.20.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file LICENSE MD5sum: f21bc9086660ac49aa9b4267a1e1dc82 Package: SCArray Version: 1.14.0 Depends: R (>= 3.5.0), gdsfmt (>= 1.36.0), methods, DelayedArray (>= 0.31.5) Imports: S4Vectors, utils, Matrix, SparseArray (>= 1.5.13), BiocParallel, DelayedMatrixStats, SummarizedExperiment, SingleCellExperiment, BiocSingular Suggests: BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown, rmarkdown, rhdf5, HDF5Array License: GPL-3 MD5sum: 4d97d4e31be7e992ceff772d243277cb Package: SCArray.sat Version: 1.6.0 Depends: methods, SCArray (>= 1.13.1), SeuratObject (>= 5.0), Seurat (>= 5.0) Imports: S4Vectors, utils, stats, BiocGenerics, BiocParallel, gdsfmt, DelayedArray, BiocSingular, SummarizedExperiment, Matrix Suggests: future, RUnit, knitr, markdown, rmarkdown, BiocStyle License: GPL-3 MD5sum: 478d48d818bead35a013bd90f367acb9 Package: scatterHatch Version: 1.12.0 Depends: R (>= 4.1) Imports: grid, ggplot2, plyr, spatstat.geom, stats, grDevices Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 4b9bbf1402edfec5f3783fffb8f81e98 Package: scBFA Version: 1.20.0 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: c36edf6011b330e77d6aa1678a021d2e Package: SCBN Version: 1.24.0 Depends: R (>= 3.5.0) Imports: stats Suggests: knitr,rmarkdown,BiocStyle,BiocManager License: GPL-2 MD5sum: 057ffe676b1455a824bb1c5e2a77ef0b Package: scBubbletree Version: 1.8.0 Depends: R (>= 4.2.0) Imports: reshape2, BiocParallel, ape, scales, Seurat, ggplot2, ggtree, patchwork, proxy, methods, stats, base, utils, dplyr Suggests: BiocStyle, knitr, testthat, cluster, SingleCellExperiment License: GPL-3 + file LICENSE MD5sum: beccbcf1dcb628bbfa564789e4f53746 Package: scCB2 Version: 1.16.0 Depends: R (>= 3.6.0) Imports: SingleCellExperiment, SummarizedExperiment, Matrix, methods, utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel, iterators, foreach, Seurat Suggests: testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 110514f10fd8ccf2670dd59561779520 Package: scClassify Version: 1.18.0 Depends: R (>= 4.0) Imports: S4Vectors, limma, ggraph, igraph, methods, cluster, minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix, ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo Suggests: knitr, rmarkdown, BiocStyle, pkgdown License: GPL-3 MD5sum: 004c455e5fc797bb806a9ffa1fd769a0 Package: sccomp Version: 1.10.0 Depends: R (>= 4.2.0) Imports: instantiate (>= 0.2.3), callr, fs, stats, SeuratObject, SingleCellExperiment, parallel, dplyr, tidyr, purrr, magrittr, rlang, tibble, boot, lifecycle, stats, tidyselect, utils, ggplot2, ggrepel, patchwork, forcats, readr, scales, stringr, glue, withr, digest Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), markdown, knitr, loo, prettydoc, tidyseurat, tidySingleCellExperiment, bayesplot, posterior License: GPL-3 MD5sum: e8c4ce508b14d99c892ac960c30367fd Package: scDataviz Version: 1.16.0 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: 51e057c557d7e14f1f734c6b013c2d34 Package: scDblFinder Version: 1.20.0 Depends: R (>= 4.0), SingleCellExperiment Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost, stats, utils, MASS, IRanges, GenomicRanges, GenomeInfoDb, Rsamtools, rtracklayer Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans License: GPL-3 + file LICENSE MD5sum: 5c37fe9460edf39aeccb48630856dd44 Package: scDD Version: 1.30.0 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: 012493e1bf2cf179d470973200ef7d5e Package: scDDboost Version: 1.8.0 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: 3ec58cc053975c2031eb2aea441d92f4 Package: scde Version: 2.34.0 Depends: R (>= 3.0.0), flexmix Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown License: GPL-2 MD5sum: 441175da2dba631794940de2f3fd4dd7 Package: scDesign3 Version: 1.4.0 Depends: R (>= 4.3.0) Imports: dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist, SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm, parallel, pbmcapply, rvinecopulib, umap, ggplot2, irlba, viridis, BiocParallel, matrixStats, Matrix, sparseMVN, coop Suggests: mvnfast, igraph, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle License: MIT + file LICENSE MD5sum: 90c572a4d09b294498352313fd04e978 Package: scDiagnostics Version: 1.0.0 Depends: R (>= 4.4.0) Imports: SingleCellExperiment, methods, isotree, ggplot2, ggridges, SummarizedExperiment, ranger, transport, speedglm, cramer, rlang, bluster, patchwork Suggests: AUCell, BiocStyle, knitr, Matrix, rmarkdown, scran, scRNAseq, SingleR, celldex, scuttle, scater, dplyr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 314721257a33f88f411baba16a41286a Package: scDotPlot Version: 1.0.0 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: a35245fd3274e320725e6031bee0d164 Package: scds Version: 1.22.0 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: 41549ffded7d7b882f8f79f19529590e Package: SCFA Version: 1.16.0 Depends: R (>= 4.0) Imports: matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph, Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival Suggests: knitr, rmarkdown, BiocStyle License: LGPL MD5sum: 753a9f604078aace66232332c82a5252 Package: scFeatureFilter Version: 1.26.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods Suggests: testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE MD5sum: c3416f257b3c1dc7ffbb73f8dd2b38cb Package: scFeatures Version: 1.6.0 Depends: R (>= 4.2.0) Imports: DelayedArray, DelayedMatrixStats, EnsDb.Hsapiens.v79, EnsDb.Mmusculus.v79, GSVA, ape, glue, dplyr, ensembldb, gtools, msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom, tidyr, AUCell, BiocParallel, rmarkdown, methods, stats, cli, SingleCellSignalR, MatrixGenerics, Seurat, DT Suggests: knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler License: GPL-3 MD5sum: 330e91c9e894fe9e3da5d8f8e0905069 Package: scGPS Version: 1.20.0 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: b17fac68238ecc4a166b5e3b89128320 Package: schex Version: 1.20.0 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: cf53ae58c750a73bbfc248d9f4b2c282 Package: scHOT Version: 1.18.0 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: 881a6cf1bd0c72808a9c00e83b0f614d Package: scider Version: 1.4.0 Depends: R (>= 4.3) Imports: SpatialExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, sf, lwgeom, ggplot2, stats, pheatmap, plotly, shiny, igraph, janitor, knitr, methods, utils, rlang, isoband, S4Vectors, grDevices Suggests: edgeR, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 91b0dc4d71518f07bf3605bedf4c5f04 Package: scifer Version: 1.8.1 Imports: dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra, tibble, scales, rlang, flowCore, methods, basilisk, reticulate, here, utils, basilisk.utils Suggests: BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0) Enhances: parallel License: MIT + file LICENSE MD5sum: 205b3cf6415b881ddfda6da3ff7041af Package: scmap Version: 1.28.0 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: d8605c461c0766ac4ab4c194acffc52a Package: scMerge Version: 1.22.0 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: da01e44a73ccd838f112e9170d03e5eb Package: scMET Version: 1.8.0 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: 9dc0558ab223e1436693f74aed569be9 Package: scmeth Version: 1.26.0 Depends: R (>= 3.5.0) Imports: knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes License: GPL-2 MD5sum: 8bd31f18d15a4d1e677ea2b463312f4e Package: scMitoMut Version: 1.2.0 Depends: R (>= 4.3.0) Imports: data.table, Rcpp, magrittr, plyr, stringr, utils, stats, methods, ggplot2, pheatmap, zlibbioc, RColorBrewer, rhdf5, readr, parallel, grDevices LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils License: Artistic-2.0 MD5sum: e9be0c5a32f892a782d5ac5d52a5fe4d Package: scMultiSim Version: 1.2.0 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: bba6467cc50e84160455c6381415a5d5 Package: SCnorm Version: 1.28.0 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: bf9668c8b851f01f73fe54ef1be49b22 Package: scone Version: 1.30.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment, DelayedMatrixStats, sparseMatrixStats Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData License: Artistic-2.0 MD5sum: b94d877c0dd468f41bbcc6fc148ec615 Package: Sconify Version: 1.26.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 45317659d3b1c1339b080c2386b2fbb3 Package: SCOPE Version: 1.18.0 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: f62c2f981e797a29a8db0c323393da4b Package: scoreInvHap Version: 1.28.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: b476d10fed37f2b9d27b809d5aacdaff Package: scoup Version: 1.0.0 Depends: R (>= 4.4), Matrix Imports: Biostrings, methods Suggests: BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat (>= 3.0.0), yaml License: GPL (>= 2) MD5sum: c4383aa6b28feb5ffd2033a54e5999c9 Package: scPCA Version: 1.20.0 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: 94488d23a58680d9b40e1f47394fc2b9 Package: scPipe Version: 2.6.0 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), zlibbioc, 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: 44add625927c7dc44ae827e259bba33d Package: scran Version: 1.34.0 Depends: SingleCellExperiment, scuttle Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, MatrixGenerics, S4Arrays, DelayedArray, BiocSingular, bluster, metapod, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, DelayedMatrixStats, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, pheatmap, scater License: GPL-3 MD5sum: a89159950152657a3c335c62f41b63d8 Package: scrapper Version: 1.0.3 Imports: methods, Rcpp, beachmat (>= 2.21.6), DelayedArray, BiocNeighbors (>= 1.99.0), igraph, parallel LinkingTo: Rcpp, assorthead, beachmat, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, MatrixGenerics, sparseMatrixStats, Matrix, scRNAseq License: MIT + file LICENSE MD5sum: 9f6360cb411175f821e715aea5b9624a Package: scReClassify Version: 1.12.0 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: a4f202944dc50107b555c0f423b653f6 Package: scRecover Version: 1.22.0 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: b7519283d60c17ac1a6415966f9aa70a Package: screenCounter Version: 1.6.0 Depends: S4Vectors, SummarizedExperiment Imports: Rcpp, zlibbioc, BiocParallel LinkingTo: Rcpp Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 450c22a5b2c8e89b7e0e6ac19fe6e7c1 Package: ScreenR Version: 1.8.0 Depends: R (>= 4.2) Imports: methods (>= 4.0), rlang (>= 0.4), stringr (>= 1.4), limma (>= 3.46), patchwork (>= 1.1), tibble (>= 3.1.6), scales (>= 1.1.1), ggvenn (>= 0.1.9), purrr (>= 0.3.4), ggplot2 (>= 3.3), stats, tidyr (>= 1.2), magrittr (>= 1.0), dplyr (>= 1.0), edgeR (>= 3.32), tidyselect (>= 1.1.2) Suggests: rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0), BiocStyle (>= 2.22.0), covr (>= 3.5) License: MIT + file LICENSE MD5sum: 162652a45d17f93cb669c8adb1251d9f Package: scRepertoire Version: 2.2.1 Depends: ggplot2, R (>= 4.0) Imports: assertthat, cubature, dplyr, evmix, ggalluvial, ggdendro, ggraph, grDevices, igraph, iNEXT, methods, plyr, quantreg, Rcpp, reshape2, rjson, rlang, S4Vectors, SeuratObject, SingleCellExperiment, stats, stringr, stringdist, SummarizedExperiment, tidygraph, truncdist, utils, VGAM, hash, purrr, lifecycle LinkingTo: Rcpp Suggests: BiocManager, BiocStyle, circlize, knitr, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0), vdiffr License: MIT + file LICENSE MD5sum: 85c59a40ca3d9f1938f8b2bc1b7a69fd Package: scRNAseqApp Version: 1.6.0 Depends: R (>= 4.3.0) Imports: bibtex, bslib, circlize, ComplexHeatmap, colourpicker, data.table, DBI, DT, GenomicRanges, GenomeInfoDb, ggdendro, ggforce, ggplot2, ggrepel, ggridges, grDevices, grid, gridExtra, htmltools, IRanges, jsonlite, magrittr, methods, patchwork, plotly, RColorBrewer, RefManageR, rhdf5, Rsamtools, RSQLite, rtracklayer, S4Vectors, scales, scrypt, Seurat, SeuratObject, shiny, shinyhelper, shinymanager, slingshot, SingleCellExperiment, sortable, stats, tools, xfun, xml2, utils Suggests: rmarkdown, knitr, testthat, BiocStyle Enhances: celldex, future, SingleR, SummarizedExperiment, tricycle License: GPL-3 MD5sum: 46b93081b26521c492324caed0d8d539 Package: scruff Version: 1.24.0 Depends: R (>= 4.0) Imports: data.table, GenomicAlignments, GenomicFeatures, txdbmaker, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread, parallelly Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 7f27ac7d4105040d73e123dad5a50653 Package: scry Version: 1.18.0 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: cd8df33a65ad4a3ad0428d23b60703f5 Package: scShapes Version: 1.12.0 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: d3758a662ff9182a1f9620b496aa99d4 Package: scTensor Version: 2.16.0 Depends: R (>= 4.1.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8), abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics, stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2 Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens, AnnotationHub License: Artistic-2.0 MD5sum: 49350b340bc2f27b6fbd0a882620038a Package: scTGIF Version: 1.20.0 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: 036dc309226c4f5aebaf7657e96398d7 Package: scTHI Version: 1.18.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 3803acfa1ae01a7411e588c705d4c6e7 Package: scTreeViz Version: 1.12.0 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: 8679d3c4564ee9873a197c265277589a Package: scuttle Version: 1.16.0 Depends: SingleCellExperiment Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays, MatrixGenerics, SparseArray, DelayedArray, beachmat LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, sparseMatrixStats, DelayedMatrixStats, scran License: GPL-3 MD5sum: d2c8e9ec0dabd36245a334b9a5c2bbd1 Package: scviR Version: 1.6.0 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: b79edd6bb98997404d86d6bdefe11e4b Package: SDAMS Version: 1.26.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: a2bd12dfb376078c8ed164318ab5c6d6 Package: seahtrue Version: 1.0.0 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 (>= 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Imports: Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: 233637a74dd65c248154801388cdba4e Package: selectKSigs Version: 1.18.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: e2ec91647d0af6b8300b2d60133baa00 Package: SELEX Version: 1.38.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: 50bc8b794e46ac6f1d68652482e3800b Package: SemDist Version: 1.40.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) MD5sum: 766918e5ef3957bd0127f2e35eb4716e Package: semisup Version: 1.30.0 Depends: R (>= 3.0.0) Imports: VGAM Suggests: knitr, testthat, SummarizedExperiment License: GPL-3 MD5sum: 3e84b877fb2a0638a1494618138794e3 Package: seq2pathway Version: 1.38.0 Depends: R (>= 3.6.2) Imports: nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data License: GPL-2 MD5sum: 0480e89c3565458ae992cf4880909a9a Package: seqArchR Version: 1.10.0 Depends: R (>= 4.2.0) Imports: utils, graphics, cvTools (>= 0.3.2), MASS, Matrix, methods, stats, cluster, matrixStats, fpc, cli, prettyunits, reshape2 (>= 1.4.3), reticulate (>= 1.22), BiocParallel, Biostrings, grDevices, ggplot2 (>= 3.1.1), ggseqlogo (>= 0.1) Suggests: cowplot, hopach (>= 2.42.0), BiocStyle, knitr (>= 1.22), rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>= 0.3.0) License: GPL-3 | file LICENSE MD5sum: 443b4d629b0146638d7ed0cd53b8ba7c Package: seqArchRplus Version: 1.6.0 Depends: R (>= 4.2), GenomicRanges, IRanges, S4Vectors Imports: BiocParallel, Biostrings, BSgenome, ChIPseeker, cli, clusterProfiler, cowplot, factoextra, GenomeInfoDb, ggplot2, ggimage, graphics, grDevices, gridExtra, heatmaps, magick, methods, RColorBrewer, scales, seqArchR, seqPattern, stats, utils Suggests: BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr (>= 2.0.2), covr, knitr (>= 1.22), org.Dm.eg.db, pdftools, rmarkdown (>= 1.12), slickR, TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun License: GPL-3 MD5sum: 63604924b31bfe7917b159f6d6ced465 Package: SeqArray Version: 1.46.1 Depends: R (>= 3.5.0), gdsfmt (>= 1.31.1) Imports: methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors LinkingTo: gdsfmt Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, markdown, rmarkdown, Rsamtools, VariantAnnotation License: GPL-3 MD5sum: d7b83d7e5e4447704cb021a5b3163dfa Package: seqCAT Version: 1.28.0 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE MD5sum: 54726c942150ebe281b3e6446697de6f Package: seqcombo Version: 1.28.0 Depends: R (>= 3.4.0) Imports: ggplot2, grid, igraph, utils, yulab.utils Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble License: Artistic-2.0 MD5sum: 50bb974a11163c879dbc0b68a290e31e Package: SeqGate Version: 1.16.0 Depends: S4Vectors, SummarizedExperiment, GenomicRanges Imports: stats, methods, BiocManager Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown License: GPL (>= 2.0) MD5sum: fc1b4b4e12e0e59656236bb2defffe10 Package: SeqGSEA Version: 1.46.0 Depends: Biobase, doParallel, DESeq2 Imports: methods, biomaRt Suggests: GenomicRanges License: GPL (>= 3) MD5sum: 697abf102b0a19ca5bccf4652e84cd9c Package: seq.hotSPOT Version: 1.6.0 Depends: R (>= 3.5.0) Imports: R.utils, hash, stats, base, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 64a4d59615d2587d292cd8f9aa58f420 Package: seqLogo Version: 1.72.0 Depends: R (>= 4.2), methods, grid Imports: stats4, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: LGPL (>= 2) MD5sum: 5a880209cfd2401da757ed7eafcb8c27 Package: seqPattern Version: 1.38.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 MD5sum: fa619fa446f2639770b11825062163a6 Package: seqsetvis Version: 1.26.0 Depends: R (>= 4.3), ggplot2 Imports: cowplot, data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, ggplotify, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, scales, stats, UpSetR Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: b7f93ced00df894c39c314723b447b2c Package: SeqSQC Version: 1.28.0 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: 16741c5e9b42a6da31384d1eeb481250 Package: seqTools Version: 1.40.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 876721c64303e7028e6aa17173f54a55 Package: SeqVarTools Version: 1.44.0 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: f6c807fa152e8212fe92b0d933bc81d4 Package: sesame Version: 1.24.0 Depends: R (>= 4.3.0), sesameData Imports: graphics, BiocParallel, utils, methods, stringr, readr, tibble, MASS, wheatmap (>= 0.2.0), GenomicRanges, IRanges, grid, preprocessCore, S4Vectors, ggplot2, BiocFileCache, GenomeInfoDb, stats, SummarizedExperiment, dplyr, reshape2 Suggests: scales, BiocManager, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals License: MIT + file LICENSE MD5sum: 4e0348e6086caf88e43080ef53a130f5 Package: SEtools Version: 1.20.0 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: 19584ed52f279452aa3ec39cdbbf34d0 Package: sevenbridges Version: 1.36.0 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: d40e27ea1feb2b9967bade98bf31276f Package: sevenC Version: 1.26.0 Depends: R (>= 3.5), InteractionSet (>= 1.2.0) Imports: rtracklayer (>= 1.34.1), BiocGenerics (>= 0.22.0), GenomeInfoDb (>= 1.12.2), GenomicRanges (>= 1.28.5), IRanges (>= 2.10.3), S4Vectors (>= 0.14.4), readr (>= 1.1.0), purrr (>= 0.2.2), data.table (>= 1.10.4), boot (>= 1.3-20), methods (>= 3.4.1) Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr License: GPL-3 MD5sum: 6451075703397b676bd6d0cf583c77b7 Package: SGCP Version: 1.6.0 Depends: R (>= 4.2.0) Imports: ggplot2, expm, caret, plyr, dplyr, GO.db, annotate, SummarizedExperiment, genefilter, GOstats, RColorBrewer, xtable, Rgraphviz, reshape2, openxlsx, ggridges, DescTools, org.Hs.eg.db, methods, grDevices, stats, RSpectra, graph Suggests: knitr, rmarkdown, BiocManager, devtools, BiocStyle License: GPL-3 MD5sum: e43539d90442b0094de8f5559c5ff8ab Package: SGSeq Version: 1.40.0 Depends: R (>= 4.0), IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), Rsamtools (>= 1.31.2), SummarizedExperiment, methods Imports: AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>= 2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>= 1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19), grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7), stats Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown License: Artistic-2.0 MD5sum: b1c027892ee7ead18175993c2477451e Package: SharedObject Version: 1.20.0 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, Rcpp Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 4c92f29cdce39e04ae6081cdc66626a6 Package: shinyepico Version: 1.14.0 Depends: R (>= 4.3.0) Imports: DT (>= 0.15.0), data.table (>= 1.13.0), doParallel (>= 1.0.0), dplyr (>= 1.0.9), foreach (>= 1.5.0), GenomicRanges (>= 1.38.0), ggplot2 (>= 3.3.0), gplots (>= 3.0.0), heatmaply (>= 1.1.0), limma (>= 3.42.0), minfi (>= 1.32.0), plotly (>= 4.9.2), reshape2 (>= 1.4.0), rlang (>= 1.0.2), rmarkdown (>= 2.3.0), rtracklayer (>= 1.46.0), shiny (>= 1.5.0), shinyWidgets (>= 0.5.0), shinycssloaders (>= 0.3.0), shinyjs (>= 1.1.0), shinythemes (>= 1.1.0), statmod (>= 1.4.0), tidyr (>= 1.2.0), zip (>= 2.1.0) Suggests: knitr (>= 1.30.0), mCSEA (>= 1.10.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, testthat, minfiData, BiocStyle License: AGPL-3 + file LICENSE MD5sum: c445fdb8382571da2f1e7c840e39c03d Package: shiny.gosling Version: 1.2.0 Imports: htmltools, jsonlite, rlang, shiny, shiny.react, fs, digest, rjson Suggests: config, covr, knitr, lintr, mockery (>= 0.4.3), rcmdcheck, rmarkdown, sessioninfo, spelling, testthat (>= 3.0.0), GenomicRanges, VariantAnnotation, StructuralVariantAnnotation, biovizBase, ggbio License: LGPL-3 MD5sum: 44139dbff8620877ab21ac4cb172d07f Package: shinyMethyl Version: 1.42.0 Imports: Biobase, BiocGenerics, graphics, grDevices, htmltools, MatrixGenerics, methods, minfi, RColorBrewer, shiny, stats, utils Suggests: shinyMethylData, minfiData, BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 4a461132c7df6016c9aa4bcdd33bddf9 Package: ShortRead Version: 1.64.0 Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), pwalign, hwriter, methods, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi, knitr License: Artistic-2.0 MD5sum: 5ecd77de15337b6ba80d58151a1b384b Package: SIAMCAT Version: 2.10.0 Depends: R (>= 4.2.0), mlr3, phyloseq Imports: beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot, lmerTest, mlr3learners, mlr3tuning, paradox, lgr Suggests: BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr License: GPL-3 MD5sum: 227fd452cd67431b3918daf8429f1bd0 Package: SICtools Version: 1.36.0 Depends: R (>= 3.0.0), methods, Rsamtools (>= 1.18.1), doParallel (>= 1.0.8), Biostrings (>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges (>= 1.22.4), IRanges (>= 2.4.8) Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 5bb3ba259e1d2cb3699c452c59d58a4c Package: SigCheck Version: 2.38.0 Depends: R (>= 4.0.0), MLInterfaces, Biobase, e1071, BiocParallel, survival Imports: graphics, stats, utils, methods Suggests: BiocStyle, breastCancerNKI, qusage License: Artistic-2.0 MD5sum: ad343b8b3284151dc864a1ae8196f977 Package: sigFeature Version: 1.24.0 Depends: R (>= 3.5.0) Imports: biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer, Matrix, SparseM, graphics, stats, utils, SummarizedExperiment, BiocParallel, methods Suggests: RUnit, BiocGenerics, knitr, rmarkdown License: GPL (>= 2) MD5sum: bc98a4c34dc4a50c313b98f90cef98f3 Package: SigFuge Version: 1.44.0 Depends: R (>= 3.5.0), GenomicRanges Imports: ggplot2, matlab, reshape, sigclust Suggests: org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle License: GPL-3 MD5sum: a062c2aaa0a8c9c433b88a0bf3fbabf0 Package: siggenes Version: 1.80.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: 270cbb13e762e5044effec9dd0b70b74 Package: sights Version: 1.32.0 Depends: R(>= 3.3) Imports: MASS(>= 7.3), qvalue(>= 2.2), ggplot2(>= 2.0), reshape2(>= 1.4), lattice(>= 0.2), stats(>= 3.3) Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx License: GPL-3 | file LICENSE MD5sum: ebdc902404f0dfecde765d2efdffeab8 Package: signatureSearch Version: 1.20.0 Depends: R(>= 4.2.0), Rcpp, SummarizedExperiment, org.Hs.eg.db Imports: AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array, magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, utils, reshape2, visNetwork, BiocParallel, fastmatch, reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray, BiocGenerics, tibble LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, signatureSearchData, DT License: Artistic-2.0 MD5sum: 085632bc44b2c0ca49dc25a52da6f8cc Package: signeR Version: 2.8.0 Depends: R (>= 3.0.2), VariantAnnotation, NMF Imports: BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat, survivalAnalysis, future, VGAM, MASS, kknn, glmnet, e1071, randomForest, ada, future.apply, ggplot2, pROC, pheatmap, RColorBrewer, listenv, reshape2, scales, survminer, dplyr, ggpubr, cowplot, tibble, readr, shiny, shinydashboard, shinycssloaders, shinyWidgets, bsplus, DT, magrittr, tidyr, BiocFileCache, proxy, rtracklayer, BSgenome LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown License: GPL-3 MD5sum: e1b348b16affcf93a369f81f1dee1fa7 Package: signifinder Version: 1.7.0 Depends: R (>= 4.3.0) Imports: AnnotationDbi, BiocGenerics, ComplexHeatmap, consensusOV, cowplot, DGEobj.utils, dplyr, ensembldb, ggplot2, ggridges, GSVA, IRanges, magrittr, matrixStats, maxstat, methods, openair, org.Hs.eg.db, patchwork, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, sparrow, SpatialExperiment, stats, SummarizedExperiment, survival, survminer, viridis Suggests: BiocStyle, edgeR, grid, kableExtra, knitr, limma, testthat (>= 3.0.0) License: AGPL-3 MD5sum: ae22524b15b4abc77eede161445fe22f Package: SigsPack Version: 1.20.0 Depends: R (>= 3.6) Imports: quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0), VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb, GenomicRanges, rtracklayer, SummarizedExperiment, graphics, stats, utils Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: aaae2ba7629b6493f212ca5ec2aecfaf Package: sigsquared Version: 1.38.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: f9ca0e67017a7b20560e8478941756c8 Package: SIM Version: 1.76.0 Depends: R (>= 3.5), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) MD5sum: 979eea280168224572c53e73070e5f8c Package: SIMAT Version: 1.38.0 Depends: R (>= 3.5.0), Rcpp (>= 0.11.3) Imports: mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: ebb0f1a0191a3ee6207af262299a47e4 Package: SimBu Version: 1.8.0 Imports: basilisk, BiocParallel, data.table, dplyr, ggplot2, tools, Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer, RCurl, reticulate, sparseMatrixStats, SummarizedExperiment, tidyr Suggests: curl, knitr, matrixStats, rmarkdown, Seurat (>= 5.0.0), SeuratObject (>= 5.0.0), testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: f151df81b043c9b3fca925588f5face7 Package: SIMD Version: 1.24.0 Depends: R (>= 3.5.0) Imports: edgeR, statmod, methylMnM, stats, utils Suggests: BiocStyle, knitr,rmarkdown License: GPL-3 MD5sum: 3dd4af4b1f10954555b8aaa28883da14 Package: SimFFPE Version: 1.18.0 Depends: Biostrings Imports: dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods Suggests: BiocStyle License: LGPL-3 MD5sum: 2c7341648e5f2ab6956c43e14c863d7e Package: similaRpeak Version: 1.38.0 Depends: R6 (>= 2.0) Imports: stats Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 281ce1507caf2d9b351ee33311f9dd43 Package: SIMLR Version: 1.32.0 Depends: R (>= 4.1.0), Imports: parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra LinkingTo: Rcpp Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph License: file LICENSE MD5sum: 1042d44c5f0092bbe24de2176ff538b5 Package: simona Version: 1.4.0 Depends: R (>= 4.1.0) Imports: methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions, igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize, ComplexHeatmap, grDevices, stats, utils, shiny LinkingTo: Rcpp Suggests: knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC, AnnotationDbi, Matrix, DiagrammeR, ragg, png, InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment, AnnotationHub, jsonlite License: MIT + file LICENSE MD5sum: 82c3d512ab209eb0f37cf481c6c465d9 Package: simPIC Version: 1.2.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, Matrix, stats, SummarizedExperiment, actuar, rlang, S4Vectors, methods, scales, scuttle Suggests: ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 6e9f559f8b31111300104d20785e464b Package: simpleSeg Version: 1.8.0 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: 3276d85b29bebf2c78f30a44d033b54f Package: simplifyEnrichment Version: 2.0.0 Depends: R (>= 4.0.0) 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: f054a711953a0a0dcf9fcac5f0e7ce67 Package: sincell Version: 1.38.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: GPL (>= 2) MD5sum: 90e669c94bef098281409ceee5e8c98f Package: single Version: 1.10.0 Depends: R (>= 4.0) Imports: Biostrings, BiocGenerics, dplyr, GenomicAlignments,IRanges, methods, reshape2, rlang, Rsamtools, stats, stringr, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: cee8b7d1fbb26775ccb7076bb0e251e3 Package: SingleCellAlleleExperiment Version: 1.2.0 Depends: R (>= 4.4.0), SingleCellExperiment Imports: SummarizedExperiment, BiocParallel, DelayedArray, methods, utils, Matrix, S4Vectors, stats Suggests: scaeData, knitr, rmarkdown, BiocStyle, scran, scater, scuttle, ggplot2, patchwork, org.Hs.eg.db, AnnotationDbi, DropletUtils, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 54ba7de8cea644587e2c6677da1118db Package: SingleCellExperiment Version: 1.28.1 Depends: SummarizedExperiment Imports: methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne License: GPL-3 MD5sum: 1bfbb9016054a656a56959c2f680a114 Package: SingleCellSignalR Version: 1.18.0 Depends: R (>= 4.0) Imports: BiocManager, circlize, limma, igraph, gplots, grDevices, edgeR, data.table, pheatmap, stats, Rtsne, graphics, stringr, foreach, multtest, scran, utils, Suggests: knitr, rmarkdown License: GPL-3 MD5sum: b375a4f7582262030619dea2dbb37d6a Package: singleCellTK Version: 2.15.2 Depends: R (>= 4.0), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase Imports: ape, anndata, AnnotationHub, batchelor, BiocParallel, celldex, colourpicker, colorspace, cowplot, cluster, ComplexHeatmap, data.table, DelayedMatrixStats, DESeq2, dplyr, DT, ExperimentHub, ensembldb, fields, ggplot2, ggplotify, ggrepel, ggtree, gridExtra, grid, GSVA (>= 1.50.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix (>= 1.6-1), matrixStats, methods, msigdbr, multtest, plotly, plyr, ROCR, Rtsne, S4Vectors, scater, scMerge (>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, stringr, SoupX, sva, reshape2, shinyalert, circlize, enrichR (>= 3.2), celda, shinycssloaders, DropletUtils, scds (>= 1.2.0), reticulate (>= 1.14), tools, tximport, tidyr, eds, withr, GSEABase, R.utils, zinbwave, scRNAseq (>= 2.0.2), TENxPBMCData, yaml, rmarkdown, magrittr, scDblFinder, metap, VAM (>= 0.5.3), tibble, rlang, TSCAN, TrajectoryUtils, scuttle, utils, stats, zellkonverter, tidyr Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony, SeuratObject, optparse License: MIT + file LICENSE MD5sum: 14bcc20e1ae64f0e44d5799de769687c Package: SingleMoleculeFootprinting Version: 2.0.0 Depends: R (>= 4.4.1) Imports: BiocGenerics, Biostrings, BSgenome, dplyr, GenomeInfoDb, GenomicRanges, ggpointdensity, ggplot2, ggrepel, grDevices, IRanges, Matrix, parallel, patchwork, plyr, plyranges, QuasR, RColorBrewer, rlang, S4Vectors, stats, stringr, tibble, tidyr, tidyverse, viridis Suggests: BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr, qs, rmarkdown, readr, SingleMoleculeFootprintingData, testthat (>= 3.0.0) License: GPL-3 MD5sum: 1d811e2061d5c7784262e9c38627546c Package: SingleR Version: 2.8.0 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocSingular, BiocNeighbors, stats, utils, Rcpp, beachmat (>= 2.21.1), parallel LinkingTo: Rcpp, beachmat, assorthead, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scater, scran, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 MD5sum: fc6a763a7c89cde7f404c27c4916df24 Package: singscore Version: 1.26.0 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: 7935d2e665d69abb496159fbb8ec8aad Package: SiPSiC Version: 1.6.0 Depends: Matrix, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle License: file LICENSE MD5sum: 0cdf36ad24754ccd3c39bdba7a7a5dc5 Package: sitadela Version: 1.14.0 Depends: R (>= 4.1.0) Imports: Biobase, BiocGenerics, biomaRt, Biostrings, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, methods, parallel, Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, txdbmaker, utils Suggests: BiocStyle, BSgenome, knitr, rmarkdown, RMySQL, RUnit License: Artistic-2.0 MD5sum: 6aed8aaf4cf00cbb23cd44b9c3d70c70 Package: sitePath Version: 1.22.0 Depends: R (>= 4.1) 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: a577f87bee0001e9c28d4c6e7e915e18 Package: sizepower Version: 1.76.0 Depends: stats License: LGPL MD5sum: f6ea70d2b8d263c3c6831d1b2e3b24dd Package: sketchR Version: 1.2.0 Imports: basilisk, Biobase, DelayedArray, dplyr, ggplot2, methods, reticulate, rlang, scales, stats Suggests: rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle, scran, scater, SingleR, celldex, cowplot, SummarizedExperiment, beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment License: MIT + file LICENSE MD5sum: 3c782f8c0e95774451fa82f58b7d59f5 Package: skewr Version: 1.38.0 Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports: minfi, S4Vectors (>= 0.19.1), RColorBrewer Suggests: GEOquery, knitr, minfiData License: GPL-2 MD5sum: cdcd04111f0d7be93707c443016319e1 Package: slingshot Version: 2.14.0 Depends: R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils Imports: graphics, grDevices, igraph, matrixStats, methods, S4Vectors, SingleCellExperiment, SummarizedExperiment Suggests: BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr License: Artistic-2.0 MD5sum: 74c48da12c1a8d14714cee2469f22fde Package: SLqPCR Version: 1.72.0 Depends: R(>= 2.4.0) Imports: stats Suggests: RColorBrewer License: GPL (>= 2) MD5sum: 0db2e797a429e7bc114510535cc7a585 Package: SMAD Version: 1.22.0 Depends: R (>= 3.6.0), RcppAlgos Imports: magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: eaf445dc42d6412fa46505deb08f4d24 Package: smartid Version: 1.2.0 Depends: R (>= 4.4) Imports: dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools, sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater, splatter, testthat (>= 3.0.0), tidytext, UpSetR License: MIT + file LICENSE MD5sum: 9a924f7c9379bfce13605989240ca73b Package: SMITE Version: 1.34.0 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: eba39bc12e95f9e3d2d50a1c2c557667 Package: smoothclust Version: 1.2.0 Depends: R (>= 4.4.0) Imports: SpatialExperiment, SummarizedExperiment, sparseMatrixStats, spdep, methods, utils Suggests: BiocStyle, knitr, STexampleData, scuttle, scran, scater, ggspavis, testthat License: MIT + file LICENSE MD5sum: 03982619e7b332d93faacdc7d984a0a7 Package: SNAGEE Version: 1.46.0 Depends: R (>= 2.6.0), SNAGEEdata Suggests: ALL, hgu95av2.db Enhances: parallel License: Artistic-2.0 MD5sum: 3ef56e87816de4bb6987e9b1f4b1c222 Package: snapcount Version: 1.18.0 Depends: R (>= 4.0.0) Imports: R6, httr, rlang, purrr, jsonlite, assertthat, data.table, Matrix, magrittr, methods, stringr, stats, IRanges, GenomicRanges, SummarizedExperiment Suggests: BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: bebe8b871fdd0d4060bea47595204924 Package: snifter Version: 1.16.0 Depends: R (>= 4.0.0) Imports: basilisk, reticulate, irlba, stats, assertthat Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) License: GPL-3 MD5sum: 036732c8133cf4829f4922d7d19b10d6 Package: snm Version: 1.54.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL MD5sum: b8c3e45bae4e99ee0782d9a1e72e4801 Package: SNPediaR Version: 1.32.0 Depends: R (>= 3.0.0) Imports: RCurl, jsonlite Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: edfeb214f4acfc86f806981aee5f981c Package: SNPhood Version: 1.36.0 Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, data.table, checkmate Imports: DESeq2, cluster, ggplot2, lattice, GenomeInfoDb (>= 1.34.8), BiocParallel, VariantAnnotation, BiocGenerics, IRanges, methods, SummarizedExperiment, RColorBrewer, Biostrings, grDevices, gridExtra, stats, grid, utils, reshape2, scales, S4Vectors Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot License: LGPL (>= 3) MD5sum: e314ab61f8423f3073cf783bc57e36f1 Package: SNPRelate Version: 1.40.0 Depends: R (>= 2.15), gdsfmt (>= 1.8.3) Imports: methods LinkingTo: gdsfmt Suggests: parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS, BiocGenerics Enhances: SeqArray (>= 1.12.0) License: GPL-3 MD5sum: 95ee0f71fe000a52c5a85e084e196835 Package: snpStats Version: 1.56.0 Depends: R(>= 2.10.0), survival, Matrix, methods Imports: graphics, grDevices, stats, utils, BiocGenerics, zlibbioc Suggests: hexbin License: GPL-3 MD5sum: 165f54a75166800cdf3fb82b8da62b84 Package: soGGi Version: 1.38.0 Depends: R (>= 3.5.0), BiocGenerics, SummarizedExperiment Imports: methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, GenomicAlignments, rtracklayer, preprocessCore, chipseq, BiocParallel Suggests: testthat, BiocStyle, knitr License: GPL (>= 3) MD5sum: 2586f41f0f26761c6203da79ffbd9939 Package: SOMNiBUS Version: 1.14.2 Depends: R (>= 4.1.0) Imports: Matrix, mgcv, stats, VGAM, IRanges, GenomeInfoDb, GenomicRanges, rtracklayer, S4Vectors, BiocManager, annotatr, yaml, utils, bsseq, reshape2, data.table, ggplot2, tidyr, Suggests: BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, License: MIT + file LICENSE MD5sum: d7e91107a37036e510933f4c551af542 Package: SpaceMarkers Version: 1.2.1 Depends: R (>= 4.4.0) Imports: matrixStats, matrixTests, rstatix, spatstat.explore, spatstat.geom, ape, hdf5r, jsonlite, Matrix, qvalue, stats, utils, methods Suggests: data.table, devtools, dplyr, ggplot2, hrbrthemes, knitr, RColorBrewer, cowplot, readbitmap, rjson, rmarkdown, BiocStyle, testthat (>= 3.0.0), viridis, CoGAPS Enhances: BiocParallel License: MIT + file LICENSE MD5sum: 93d3df36f88ddfe80fb16d251f51ce84 Package: SpacePAC Version: 1.44.0 Depends: R(>= 2.15),iPAC Suggests: RUnit, BiocGenerics, rgl License: GPL-2 MD5sum: 0f57010076a3df4302e09fe8caaa4313 Package: Spaniel Version: 1.20.0 Depends: R (>= 4.0) Imports: Seurat, SingleCellExperiment, SummarizedExperiment, dplyr, methods, ggplot2, scater (>= 1.13), scran, igraph, shiny, jpeg, magrittr, utils, S4Vectors, DropletUtils, jsonlite, png Suggests: knitr, rmarkdown, testthat, devtools License: MIT + file LICENSE MD5sum: 4698e3c897a47ba0fbfb80265720a473 Package: SpaNorm Version: 1.0.0 Depends: R (>= 4.4) Imports: edgeR, ggplot2, Matrix, matrixStats, methods, rlang, scran, SeuratObject, SingleCellExperiment, SpatialExperiment, stats, SummarizedExperiment, S4Vectors, utils Suggests: testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown, covr, BiocStyle, Seurat, patchwork, ggforce, ggnewscale License: GPL (>= 3) MD5sum: c70da3288b2a03d28a98b12f255e0e75 Package: sparrow Version: 1.12.0 Depends: R (>= 4.0) Imports: babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet, checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>= 1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>= 2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix, methods, plotly (>= 4.9.0), stats, utils, viridis Suggests: AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr, PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot License: MIT + file LICENSE MD5sum: 1fd25c573abbf60317e2d547706a6c9f Package: SparseArray Version: 1.6.0 Depends: R (>= 4.3.0), methods, Matrix, BiocGenerics (>= 0.43.1), MatrixGenerics (>= 1.11.1), S4Vectors (>= 0.43.2), S4Arrays (>= 1.5.11) Imports: utils, stats, matrixStats, IRanges, XVector LinkingTo: S4Vectors, IRanges, XVector Suggests: HDF5Array, ExperimentHub, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 3c5fe8c2a411f96491b8252dbecf5c09 Package: sparseMatrixStats Version: 1.18.0 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: 73ad13bc4946fb6992cc3e70cc585c45 Package: sparsenetgls Version: 1.24.0 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: 22a2e3a151e58e670ee996dba9ef55aa Package: SparseSignatures Version: 2.16.0 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: 3ff24c10744f5a2cd37c303fd377eb50 Package: spaSim Version: 1.8.0 Depends: R (>= 4.2.0) Imports: ggplot2, methods, stats, dplyr, spatstat.geom, spatstat.random, SpatialExperiment, SummarizedExperiment, RANN Suggests: RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown License: Artistic-2.0 MD5sum: ae9a540a0f921dae818a43ddd2fd3a66 Package: SpatialCPie Version: 1.22.0 Depends: R (>= 3.6) Imports: colorspace (>= 1.3-2), data.table (>= 1.12.2), digest (>= 0.6.21), dplyr (>= 0.7.6), ggforce (>= 0.3.0), ggiraph (>= 0.5.0), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), grid (>= 3.5.1), igraph (>= 1.2.2), lpSolve (>= 5.6.13), methods (>= 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logNormReg (>= 0.4) Suggests: testthat, knitr, rmarkdown, qpdf, Seurat License: MIT + file LICENSE MD5sum: 1763889b8c2011d6d56f5fee018dc60c Package: SpatialExperiment Version: 1.16.0 Depends: methods, SingleCellExperiment Imports: rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils License: GPL-3 MD5sum: 840ae7b4f7511e7eecc4fcd7ddb27c43 Package: SpatialFeatureExperiment Version: 1.8.4 Depends: R (>= 4.2.0) Imports: Biobase, BiocGenerics, BiocNeighbors, BiocParallel, data.table, DropletUtils, EBImage, grDevices, lifecycle, Matrix, methods, rjson, rlang, S4Vectors, sf, sfheaders, SingleCellExperiment, SpatialExperiment, spatialreg, spdep (>= 1.1-7), SummarizedExperiment, stats, terra, utils, zeallot Suggests: arrow, BiocStyle, dplyr, knitr, RBioFormats, rhdf5, rmarkdown, scater, sfarrow, SFEData (>= 1.5.3), Seurat, SeuratObject, sparseMatrixStats, testthat (>= 3.0.0), tidyr, Voyager (>= 1.7.2), withr, xml2 License: Artistic-2.0 MD5sum: 9f67cc2562f4c96637645cf95ab9f2cd Package: spatialHeatmap Version: 2.12.1 Depends: R (>= 3.5.0) Imports: data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid, gridExtra, igraph, methods, Matrix, rsvg, shiny, grDevices, graphics, ggplotify, parallel, reshape2, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2 Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend, DT, dynamicTreeCut, flashClust, gplots, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, scater, scuttle, scran, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, xlsx, yaml License: Artistic-2.0 MD5sum: 6101adace3f96118c64ea7dfe98cd95f Package: SpatialOmicsOverlay Version: 1.6.0 Depends: R (>= 4.1.0) Imports: S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML, scattermore, dplyr, pbapply, data.table, readxl, magick, grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats, utils, methods, ggtext, tools, RBioFormats Suggests: knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf License: MIT MD5sum: 0ab086201cfeb57d54cb4a3fbcc16ad7 Package: spatialSimGP Version: 1.0.0 Depends: R (>= 4.4) Imports: SpatialExperiment, MASS, SummarizedExperiment Suggests: testthat (>= 3.0.0), STexampleData, ggplot2, knitr License: MIT + file LICENSE MD5sum: a33141aadb72cc812cac7c5d524d6e6e Package: speckle Version: 1.6.0 Depends: R (>= 4.2.0) Imports: limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods, stats, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 1150e96aaa1c2557179971a1051bd4f8 Package: specL Version: 1.40.0 Depends: R (>= 4.1), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.7), RSQLite (>= 1.1), seqinr (>= 3.3) Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) License: GPL-3 MD5sum: 4ee4294addd2b2f66cfb3bf2e88b358d Package: SpeCond Version: 1.60.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) MD5sum: 7e6de68c098395564a9e5c6453df0bf6 Package: Spectra Version: 1.16.0 Depends: R (>= 4.0.0), S4Vectors, BiocParallel Imports: ProtGenerics (>= 1.37.1), methods, IRanges, MsCoreUtils (>= 1.7.5), graphics, grDevices, stats, tools, utils, fs, BiocGenerics, MetaboCoreUtils Suggests: testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick License: Artistic-2.0 MD5sum: 4f5a2c2478b206edfd92d72bdf74d927 Package: SpectralTAD Version: 1.22.0 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: 1741d5f2ef3e3b150a675337acafda91 Package: SpectraQL Version: 1.0.0 Depends: R (>= 4.4.0), ProtGenerics (>= 1.25.1) Imports: Spectra (>= 1.5.6), MsCoreUtils, methods Suggests: testthat, msdata (>= 0.19.3), roxygen2, rmarkdown, knitr, S4Vectors, BiocStyle, mzR License: Artistic-2.0 MD5sum: 01ff6fb2f9775134265d28f62a802806 Package: SPEM Version: 1.46.0 Depends: R (>= 2.15.1), Rsolnp, Biobase, methods License: GPL-2 MD5sum: 43de683e4700d1709c1353c31b1f8e79 Package: SPIA Version: 2.58.0 Depends: R (>= 2.14.0), graphics, KEGGgraph Imports: graphics Suggests: graph, Rgraphviz, hgu133plus2.db License: file LICENSE License_restricts_use: yes MD5sum: 079c42f23e92ca69409aae2da33183f1 Package: SPIAT Version: 1.8.0 Depends: R (>= 4.2.0), SpatialExperiment (>= 1.8.0) Imports: apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3), gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3), RANN (>= 2.6.1), pracma (>= 2.2.5), dbscan (>= 1.1-5), mmand (>= 1.5.4), tibble (>= 2.1.3), grDevices, stats, utils, vroom, dittoSeq, spatstat.geom, methods, spatstat.explore, raster, sp, SummarizedExperiment, rlang Suggests: BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown, testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap, elsa License: Artistic-2.0 + file LICENSE MD5sum: d794845f189a7c4ffb00970a4794219c Package: spicyR Version: 1.18.0 Depends: R (>= 4.1) Imports: ggplot2, concaveman, BiocParallel, spatstat.explore, spatstat.geom, lmerTest, S4Vectors, methods, pheatmap, rlang, grDevices, stats, data.table, dplyr, tidyr, scam, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, ggforce, ClassifyR, tibble, magrittr, cli, survival, ggthemes, ggh4x, coxme, ggnewscale Suggests: SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: d7fd9dc8c844f2cab3b38583fd74ae2d Package: spikeLI Version: 2.66.0 Imports: graphics, grDevices, stats, utils License: GPL-2 MD5sum: 511b95468b10a9af6801abe41412fa43 Package: spiky Version: 1.12.0 Depends: Rsamtools, GenomicRanges, R (>= 3.6.0) Imports: stats, scales, bamlss, methods, tools, IRanges, Biostrings, GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome, S4Vectors, graphics, ggplot2, utils Suggests: covr, testthat, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager License: GPL-2 MD5sum: 423a726c35d7ea4e20b62e97917609a0 Package: spillR Version: 1.2.0 Depends: R (>= 4.3.0), SummarizedExperiment, CATALYST Imports: dplyr, tibble, tidyselect, stats, ggplot2, tidyr, spatstat.univar, S4Vectors, parallel Suggests: knitr, rmarkdown, cowplot, testthat (>= 3.0.0), BiocStyle, hexbin License: LGPL-3 MD5sum: 80adcbf3c88acfd159a75f687c54dac5 Package: spkTools Version: 1.62.0 Depends: R (>= 2.7.0), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), graphics, grDevices, gtools, methods, RColorBrewer, stats, utils Suggests: xtable License: GPL (>= 2) MD5sum: 276e090ced861d8352c5d89b13de96a0 Package: splatter Version: 1.30.0 Depends: R (>= 4.0), SingleCellExperiment Imports: BiocGenerics, BiocParallel, checkmate (>= 2.0.0), crayon, edgeR, fitdistrplus, grDevices, locfit, matrixStats, methods, rlang, S4Vectors, scuttle, stats, SummarizedExperiment, utils, withr Suggests: BASiCS (>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), igraph, IRanges, knitr, limSolve, lme4, magick, mfa, phenopath, preprocessCore, progress, pscl, rmarkdown, scales, scater (>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave License: GPL-3 + file LICENSE MD5sum: fbf5ac4e278b4380af8511d6f811cd43 Package: SpliceWiz Version: 1.8.0 Depends: R (>= 3.5.0), NxtIRFdata Imports: ompBAM, methods, stats, utils, tools, parallel, scales, magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2, AnnotationHub, RSQLite, BiocFileCache, BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray, DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges, HDF5Array, htmltools, IRanges, patchwork, pheatmap, progress, plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment, S4Vectors, shiny, shinyFiles, shinyWidgets, shinydashboard, stringi, rhandsontable, DT, grDevices, heatmaply, matrixStats, RColorBrewer, rvest, httr LinkingTo: ompBAM, Rcpp, RcppProgress Suggests: knitr, rmarkdown, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, AnnotationDbi, fgsea, Rsubread License: MIT + file LICENSE MD5sum: b41783ea50218c14175f437fee5fd252 Package: SplicingFactory Version: 1.14.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, methods, stats Suggests: testthat, knitr, rmarkdown, ggplot2, tidyr License: GPL-3 + file LICENSE MD5sum: 5f443d798ce1a352f8f5605262d6d397 Package: SplicingGraphs Version: 1.46.0 Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22), Rgraphviz (>= 2.3.7) Imports: methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>= 0.17.5), BiocParallel, IRanges (>= 2.21.2), GenomeInfoDb, GenomicRanges (>= 1.23.21), Rsamtools, graph Suggests: igraph, Gviz, txdbmaker, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit License: Artistic-2.0 MD5sum: 8b8d0f8e03d3ff38a6831bed5b9007d7 Package: splineTimeR Version: 1.34.0 Depends: R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines, GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs Suggests: knitr License: GPL-3 MD5sum: 2ae62a43a30367d9362f9046311aab53 Package: splots Version: 1.72.0 Imports: grid, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI, dplyr, ggplot2 License: LGPL MD5sum: d7ce9506440819a6d8410e8f1734ae42 Package: SPONGE Version: 1.28.0 Depends: R (>= 3.6) Imports: Biobase, stats, ppcor, logging, foreach, doRNG, data.table, MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse, caret, dplyr, biomaRt, randomForest, ggridges, cvms, ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr, stringr, tidyr Suggests: testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, digest, doParallel, bigmemory, GSVA License: GPL (>= 3) MD5sum: 1cc5480faf8a74c02530c84445bcf6be Package: spoon Version: 1.2.0 Depends: R (>= 4.4) Imports: SpatialExperiment, BRISC, nnSVG, BiocParallel, Matrix, methods, SummarizedExperiment, stats, utils, scuttle Suggests: testthat, STexampleData, knitr License: MIT + file LICENSE MD5sum: 60763fdbe8983a847896751c361b8a0b Package: SpotClean Version: 1.8.0 Depends: R (>= 4.2.0), Imports: stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment, SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap, rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling License: GPL-3 MD5sum: efd27054c0e05880010b9c9069e9b5da Package: SPOTlight Version: 1.10.0 Depends: R (>= 4.1) Imports: ggplot2, NMF, Matrix, matrixStats, nnls, SingleCellExperiment, sparseMatrixStats, stats Suggests: BiocStyle, colorBlindness, DelayedArray, DropletUtils, ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg, knitr, methods, png, rmarkdown, scater, scatterpie, scran, SpatialExperiment, SummarizedExperiment, S4Vectors, TabulaMurisSenisData, TENxVisiumData, testthat License: GPL-3 MD5sum: 04bd8cfb24499a6b07cdd15ebba3a47f Package: SpotSweeper Version: 1.2.0 Depends: R (>= 4.3.0) Imports: SpatialExperiment, SummarizedExperiment, BiocNeighbors, SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco, grDevices Suggests: knitr, BiocStyle, rmarkdown, scuttle, STexampleData, ggpubr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 544e2515e19068a0eba1d723cacca7ee Package: spqn Version: 1.18.0 Depends: R (>= 4.0), ggplot2, ggridges, SummarizedExperiment, BiocGenerics Imports: graphics, stats, utils, matrixStats Suggests: BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3), RUnit License: Artistic-2.0 MD5sum: 2014325802a0499f003840ee4122be90 Package: SPsimSeq Version: 1.16.0 Depends: R (>= 4.0) Imports: stats, methods, SingleCellExperiment, fitdistrplus, graphics, edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils Suggests: knitr, rmarkdown, LSD, testthat, BiocStyle License: GPL-2 MD5sum: 2c8e76dd8fc9d9173b227df22e6e3e55 Package: SQLDataFrame Version: 1.20.0 Depends: DelayedArray, S4Vectors Imports: stats, utils, methods, BiocGenerics, RSQLite, duckdb, DBI Suggests: knitr, rmarkdown, BiocStyle, testthat MD5sum: 25488fa9682c1d50ecbb6d05de8aad1d Package: squallms Version: 1.0.0 Depends: R (>= 3.5.0) Imports: xcms, MSnbase, MsExperiment, RaMS, dplyr, tidyr, tibble, ggplot2, shiny, plotly, data.table, caret, stats, graphics, utils, keys Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a5238b6021d64dec2de66b3d9f4b7576 Package: sRACIPE Version: 1.22.0 Depends: R (>= 3.6.0),SummarizedExperiment, methods, Rcpp Imports: ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork, gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices, stats, utils, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown, tinytest, doFuture License: MIT + file LICENSE MD5sum: d73d5ced2459ad20c84a9be9ddac9339 Package: SRAdb Version: 1.68.1 Depends: RSQLite, graph, RCurl Imports: R.utils Suggests: Rgraphviz License: Artistic-2.0 MD5sum: c5dfc04d6ad12c3a8b38864dd92f91c3 Package: srnadiff Version: 1.25.0 Depends: R (>= 3.6) Imports: Rcpp (>= 0.12.8), stats, methods, devtools, S4Vectors, GenomeInfoDb, rtracklayer, SummarizedExperiment, IRanges, GenomicRanges, DESeq2, edgeR, Rsamtools, GenomicFeatures, GenomicAlignments, grDevices, Gviz, BiocParallel, BiocManager, BiocStyle LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocManager, BiocStyle License: GPL-3 MD5sum: c2d58b305f9724301f3b7e4c0af0248c Package: sscu Version: 2.36.0 Depends: R (>= 3.3) Imports: Biostrings (>= 2.36.4), seqinr (>= 3.1-3), BiocGenerics (>= 0.16.1) Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 10468813311de313950980200f7f29c1 Package: sSeq Version: 1.44.0 Depends: R (>= 3.0), caTools, RColorBrewer License: GPL (>= 3) MD5sum: ccffcf9fdcfab095f789e6f0e3b5e612 Package: ssize Version: 1.80.0 Depends: gdata, xtable License: LGPL MD5sum: 7edf6f8aeedca5fbb4bda0b83e8c7532 Package: sSNAPPY Version: 1.10.0 Depends: R (>= 4.3.0), ggplot2 Imports: dplyr (>= 1.1), magrittr, rlang, stats, graphite, tibble, ggraph, igraph, reshape2, org.Hs.eg.db, SummarizedExperiment, edgeR, methods, ggforce, pheatmap, utils, stringr, gtools, tidyr Suggests: BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools, knitr, pander, patchwork, rmarkdown, spelling, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: e976b2ed6d8b64aaeaaa1b5097deb5dc Package: ssPATHS Version: 1.20.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: ROCR, dml, MESS Suggests: ggplot2, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 5486f055be5528123f3ca71729a08201 Package: ssrch Version: 1.22.0 Depends: R (>= 3.6), methods Imports: shiny, DT, utils Suggests: knitr, testthat, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: e61c517e64e02c2ba7f4de13e9ebfb71 Package: ssviz Version: 1.40.0 Depends: R (>= 3.5.0), methods, Rsamtools, Biostrings, reshape, ggplot2, RColorBrewer, stats Suggests: knitr License: GPL-2 MD5sum: 8ca5d4c136f777ef3d303312afe907b8 Package: StabMap Version: 1.0.0 Depends: R (>= 4.4.0), Imports: igraph, slam, BiocNeighbors, Matrix, MASS, abind, SummarizedExperiment, methods, MatrixGenerics, BiocGenerics, BiocSingular, BiocParallel Suggests: scran, scater, knitr, UpSetR, gridExtra, SingleCellMultiModal, BiocStyle, magrittr, testthat (>= 3.0.0), purrr, sparseMatrixStats License: GPL-2 MD5sum: 5ad7912306c2c28d777d9e544ff59e64 Package: stageR Version: 1.28.0 Depends: R (>= 3.4), SummarizedExperiment Imports: methods, stats Suggests: knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma, DEXSeq, testthat License: GNU General Public License version 3 MD5sum: e130f068e2e6ce1554eecad9870a210b Package: standR Version: 1.10.0 Depends: R (>= 4.1) Imports: dplyr, SpatialExperiment (>= 1.5.2), SummarizedExperiment, SingleCellExperiment, edgeR, rlang, readr, tibble, ggplot2, tidyr, ruv, limma, patchwork, S4Vectors, Biobase, BiocGenerics, grDevices, stats, methods, ggalluvial, mclustcomp, RUVSeq Suggests: knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr, ggrepel, cluster, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a9dc6c8ac0c6fe69e1b15d36ae10e191 Package: STATegRa Version: 1.42.0 Depends: R (>= 2.10) Imports: Biobase, gridExtra, ggplot2, methods, stats, grid, MASS, calibrate, gplots, edgeR, limma, foreach, affy Suggests: RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>= 1.3), roxygen2, doSNOW License: GPL-2 MD5sum: c210ca2df9701a7a3732813d933d99ef Package: Statial Version: 1.8.0 Depends: R (>= 4.1.0) Imports: BiocParallel, spatstat.geom, concaveman, data.table, spatstat.explore, dplyr, tidyr, SingleCellExperiment, tibble, stringr, tidyselect, ggplot2, methods, stats, SummarizedExperiment, S4Vectors, plotly, purrr, ranger, magrittr, limma, SpatialExperiment, cluster, treekoR Suggests: BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR, ggsurvfit, lisaClust, survival License: GPL-3 MD5sum: 2f8f1bbd58584b9bc82a902d7d0f0de3 Package: statTarget Version: 1.36.0 Depends: R (>= 3.6.0) Imports: randomForest,plyr,pdist,ROC,utils,grDevices,graphics,rrcov,stats, pls,impute Suggests: testthat, BiocStyle, knitr, rmarkdown License: LGPL (>= 3) MD5sum: 2a0656eae9ce387bf16bad3dfcd950cf Package: STdeconvolve Version: 1.9.0 Depends: R (>= 4.1) Imports: topicmodels, BiocParallel, Matrix, methods, mgcv, ggplot2, scatterpie, viridis, slam, stats, clue, liger, reshape2, graphics, grDevices, utils Suggests: knitr, BiocStyle, rmarkdown, testthat, rcmdcheck, gplots, gridExtra, hash, dplyr, parallel License: GPL-3 MD5sum: 12c9b0c851af3b2cbc3b5a2bb0589971 Package: stepNorm Version: 1.78.0 Depends: R (>= 1.8.0), marray, methods Imports: marray, MASS, methods, stats License: LGPL MD5sum: cef94527b142c1b15590ea9852c11eb3 Package: stJoincount Version: 1.8.0 Depends: R (>= 4.2.0) Imports: graphics, stats, dplyr, magrittr, sp, raster, spdep, ggplot2, pheatmap, grDevices, Seurat, SpatialExperiment, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 0926080f105c009e2ff2c283cbbd44e8 Package: strandCheckR Version: 1.24.0 Imports: dplyr, magrittr, GenomeInfoDb, GenomicAlignments, GenomicRanges, IRanges, Rsamtools, S4Vectors, grid, BiocGenerics, ggplot2, reshape2, stats, gridExtra, TxDb.Hsapiens.UCSC.hg38.knownGene, methods, stringr, rmarkdown Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 38d110fea6c6c7f9620cb10d24557ec3 Package: Streamer Version: 1.52.0 Imports: methods, graph, RBGL, parallel, BiocGenerics Suggests: RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz License: Artistic-2.0 MD5sum: bc9595e6b1ce4f01d4bfed238bd73cdc Package: STRINGdb Version: 2.18.0 Depends: R (>= 2.14.0) Imports: png, sqldf, plyr, igraph, httr, methods, RColorBrewer, gplots, hash, plotrix Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: b652fefc7b469d6305622f4bcea05b33 Package: struct Version: 1.18.0 Depends: R (>= 4.0) Imports: methods,ontologyIndex, datasets, graphics, stats, utils, knitr, SummarizedExperiment, S4Vectors, rols Suggests: testthat, rstudioapi, rmarkdown, covr, BiocStyle, openxlsx, ggplot2, magick License: GPL-3 MD5sum: e4db55c27a7ce95e8bb34b5e0ff838ca Package: Structstrings Version: 1.22.1 Depends: R (>= 4.0), S4Vectors (>= 0.27.12), 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2.1.0), roxygen2, rmarkdown, tidyverse, knitr, ggbio, biovizBase, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, License: GPL-3 + file LICENSE MD5sum: 0ccb62f330827c6033ebb17ca93a9e9f Package: SubCellBarCode Version: 1.22.0 Depends: R (>= 3.6) Imports: Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra, networkD3, ggrepel, graphics, stats, org.Hs.eg.db, AnnotationDbi Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 1a0cd66e902625234fd321bffd5dee53 Package: subSeq Version: 1.36.0 Depends: R (>= 3.2) Imports: data.table, dplyr, tidyr, ggplot2, magrittr, qvalue (>= 1.99), digest, Biobase Suggests: limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr License: MIT + file LICENSE MD5sum: 45b01c4607c9f66deef41c65172b3bb6 Package: SUITOR Version: 1.8.0 Depends: R (>= 4.2.0) Imports: stats, utils, graphics, ggplot2, BiocParallel Suggests: devtools, MutationalPatterns, RUnit, BiocManager, BiocGenerics, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 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SummarizedExperiment, pheatmap, survival, survminer, clustvarsel, stats, utils Suggests: maftools, scales, knitr, rmarkdown License: Artistic-2.0 MD5sum: bf40c55f18ecff8cbe71361f43cf4d48 Package: sva Version: 3.54.0 Depends: R (>= 3.2), mgcv, genefilter, BiocParallel Imports: matrixStats, stats, graphics, utils, limma, edgeR Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat License: Artistic-2.0 MD5sum: 76f889a8b93f734b586089bf7fddb348 Package: svaNUMT Version: 1.12.0 Depends: GenomicRanges, rtracklayer, VariantAnnotation, StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>= 4.0) Imports: assertthat, stringr, dplyr, methods, rlang, GenomeInfoDb, S4Vectors, GenomicFeatures, pwalign Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges, SummarizedExperiment, rmarkdown License: GPL-3 + file LICENSE MD5sum: 8ee4287eae84c3f5d5e6db8ce2b97154 Package: 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DT, stats Suggests: systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocGenerics, Biostrings, methods License: Artistic-2.0 MD5sum: 29c8e745bb9f86e7b530cfc7e520b9df Package: tadar Version: 1.4.0 Depends: GenomicRanges, ggplot2, R (>= 4.4.0) Imports: BiocGenerics, GenomeInfoDb, Gviz, IRanges, MatrixGenerics, methods, rlang, Rsamtools, S4Vectors, stats, VariantAnnotation Suggests: BiocStyle, covr, knitr, limma, rmarkdown, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: 8f23ccf548485eb8f6e939a4ae0e1e08 Package: TADCompare Version: 1.16.0 Depends: R (>= 4.0) Imports: dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2, tidyr, ggpubr, RColorBrewer, reshape2, cowplot Suggests: BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, SpectralTAD, magick, qpdf License: MIT + file LICENSE MD5sum: 2ed62406ab9f00695c16bcf074eb83c3 Package: tanggle Version: 1.12.0 Depends: R (>= 4.1), ggplot2 (>= 2.2.0), ggtree Imports: ape (>= 5.0), phangorn (>= 2.5), 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License: MIT + file LICENSE MD5sum: 5dabddbc2b7efcca991f7ee9bd589dcf Package: TCC Version: 1.46.0 Depends: R (>= 3.0), methods, DESeq2, edgeR, ROC Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: 2693c0afc7032f05f9a6d9e17c71edea Package: TCGAutils Version: 1.26.0 Depends: R (>= 4.2.0) Imports: AnnotationDbi, BiocGenerics, BiocBaseUtils, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment (>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2 Suggests: AnnotationHub, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 6c55e5683b16e807af3221b3ff09bad6 Package: TCseq Version: 1.30.0 Depends: R 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GenomicFeatures, BiocStyle, hues, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 5c16dfeab4488fca829b3e4ea1b8c06c Package: tidyFlowCore Version: 1.0.0 Depends: R (>= 4.3) Imports: Biobase, dplyr, flowCore, ggplot2, methods, purrr, rlang, stats, stringr, tibble, tidyr Suggests: BiocStyle, HDCytoData, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 6bcfcb12af6fe348dc4fcf397efabca9 Package: tidyomics Version: 1.2.0 Depends: R (>= 4.2) Imports: tidySummarizedExperiment, tidySingleCellExperiment, tidyseurat, tidybulk, plyranges, nullranges, purrr, rlang, stringr, cli, utils Suggests: tidyr, dplyr, tibble, ggplot2, mockr (>= 0.2.0), knitr (>= 1.41), rmarkdown (>= 2.20), testthat (>= 3.1.6) License: MIT + file LICENSE MD5sum: 97709ee94d0d5476157445ee72f3c2e6 Package: tidysbml Version: 1.0.0 Depends: R (>= 4.4.0) Imports: xml2, methods Suggests: rmarkdown, knitr, BiocStyle, biomaRt, RCy3, testthat (>= 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Suggests: BiocStyle, testthat, knitr, markdown, scater, igraph, cowplot, DropletUtils, tidySummarizedExperiment License: GPL (>= 3) MD5sum: 0cb5875075e21d8461473fec5efbbf97 Package: tidySummarizedExperiment Version: 1.16.0 Depends: R (>= 4.3.0), SummarizedExperiment, ttservice (>= 0.4.0) Imports: dplyr, tibble (>= 3.0.4), magrittr, tidyr, ggplot2, rlang, purrr, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, stats, pkgconfig Suggests: BiocStyle, testthat, knitr, markdown, rmarkdown, plotly License: GPL-3 MD5sum: 92730762556972e6b8d01a6e2b5e57d2 Package: tidytof Version: 1.0.0 Depends: R (>= 4.3) Imports: doParallel, dplyr, flowCore, foreach, ggplot2, ggraph, glmnet, methods, parallel, purrr, readr, recipes, rlang, stringr, survival, tidygraph, tidyr, tidyselect, yardstick, Rcpp, tibble, stats, utils, RcppHNSW LinkingTo: Rcpp Suggests: ConsensusClusterPlus, Biobase, broom, covr, diffcyt, emdist, FlowSOM, forcats, ggrepel, HDCytoData, knitr, markdown, philentropy, rmarkdown, Rtsne, statmod, SummarizedExperiment, testthat (>= 3.0.0), lmerTest, lme4, ggridges, spelling, scattermore, preprocessCore, SingleCellExperiment, Seurat, SeuratObject, embed, rsample, BiocGenerics License: MIT + file LICENSE MD5sum: d46be2ea8f88908d8ce958a309affdb4 Package: tigre Version: 1.60.0 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, AnnotationDbi, gplots, graphics, grDevices, stats, utils, annotate, DBI, RSQLite Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager License: AGPL-3 MD5sum: 77be4bae9bd3be45b03cc77527f22e9d Package: TileDBArray Version: 1.16.0 Depends: SparseArray (>= 1.5.20), DelayedArray (>= 0.31.7) Imports: methods, tiledb, S4Vectors Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat License: MIT + file LICENSE MD5sum: 0890bb768508d6527aa14238819edbc7 Package: tilingArray Version: 1.84.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 MD5sum: ff6865bcd0b0a5b4036e8ca2762c3c58 Package: timecourse Version: 1.78.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL MD5sum: a71a8adf0d3ac75451e0b489c9373c1e Package: timeOmics Version: 1.18.0 Depends: mixOmics, R (>= 4.0) Imports: dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr, ggrepel, lmtest, plyr, checkmate Suggests: BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse, igraph, gplots License: GPL-3 MD5sum: f8440b686522b9387a7339c8d53fe87f Package: timescape Version: 1.30.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), stringr (>= 1.0.0), dplyr (>= 0.4.3), gtools (>= 3.5.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: cd09371809d378187881eeb9a571fa4f Package: TIN Version: 1.38.0 Depends: R (>= 2.12.0), data.table, impute, aroma.affymetrix Imports: WGCNA, squash, stringr Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 31ba9105ac8117e726d99b373218f29b Package: TissueEnrich Version: 1.26.0 Depends: R (>= 3.5), ggplot2 (>= 2.2.1), SummarizedExperiment (>= 1.6.5), GSEABase (>= 1.38.2) Imports: dplyr (>= 0.7.3), tidyr (>= 0.8.0), stats Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 525fa4efd02cf12468b2b65580b7a812 Package: TitanCNA Version: 1.44.0 Depends: R (>= 3.5.1) Imports: BiocGenerics (>= 0.31.6), IRanges (>= 2.6.1), GenomicRanges (>= 1.24.3), VariantAnnotation (>= 1.18.7), foreach (>= 1.4.3), GenomeInfoDb (>= 1.8.7), data.table (>= 1.10.4), dplyr (>= 0.5.0), License: GPL-3 MD5sum: a3188c9867c94c12a7957e3d7616e1f7 Package: tkWidgets Version: 1.84.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 MD5sum: cb3941f5a1b85e90bad4c74eef9eea34 Package: tLOH Version: 1.14.0 Depends: R (>= 4.2) Imports: scales, stats, utils, ggplot2, data.table, purrr, dplyr, VariantAnnotation, GenomicRanges, MatrixGenerics, bestNormalize, depmixS4, naniar, stringr Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 4588e6c6c333be904c80c26b046542e1 Package: TMixClust Version: 1.28.0 Depends: R (>= 3.4) Imports: gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel, flexclust, grDevices, graphics, Biobase, SPEM Suggests: rmarkdown, knitr, BiocStyle, testthat License: GPL (>= 2) MD5sum: 0eda754b552f4d552b50ab0f905750a0 Package: TMSig Version: 1.0.0 Depends: R (>= 4.4.0), limma Imports: circlize, ComplexHeatmap, data.table, grDevices, grid, GSEABase, Matrix, methods, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: 2403bea7178cb86fd3dd9703c7af85ca Package: TnT Version: 1.28.0 Depends: R (>= 3.4), GenomicRanges Imports: methods, stats, utils, grDevices, htmlwidgets, jsonlite, data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr Suggests: GenomicFeatures, shiny, BiocManager, rmarkdown, testthat License: AGPL-3 MD5sum: 35cdb261b036211764cc910b87acd53b Package: TOAST Version: 1.20.0 Depends: R (>= 3.6), EpiDISH, limma, nnls, quadprog Imports: stats, methods, SummarizedExperiment, corpcor, doParallel, parallel, ggplot2, tidyr, GGally Suggests: BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix License: GPL-2 MD5sum: b6225f10646d2454195fbe649eff6655 Package: tomoda Version: 1.16.0 Depends: R (>= 4.0.0) Imports: methods, stats, grDevices, reshape2, Rtsne, umap, RColorBrewer, ggplot2, ggrepel, SummarizedExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 79b25f5438afcde6193be0a79c0ca35d Package: tomoseqr Version: 1.10.0 Depends: R (>= 4.2) Imports: grDevices, graphics, animation, tibble, dplyr, stringr, purrr, methods, shiny, BiocFileCache, readr, tools, plotly, ggplot2 Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: ea772518f342feeb68571c5e9088efb6 Package: TOP Version: 1.6.0 Depends: R (>= 3.5.0) Imports: assertthat, caret, ClassifyR, directPA, doParallel, dplyr, ggnewscale, ggplot2, ggraph, ggrepel, ggthemes, glmnet, Hmisc, igraph, latex2exp, limma, magrittr, methods, plotly, pROC, purrr, reshape2, stats, stringr, survival, tibble, tidygraph, tidyr, statmod Suggests: knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData, ggbeeswarm, ggsci, survminer, tidyverse License: GPL-3 MD5sum: be4c652a52212d5a318e5aadc753f6a4 Package: topconfects Version: 1.22.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, assertthat, ggplot2 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: 8fb8763e710a14b30784a4718114a580 Package: topdownr Version: 1.28.0 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 (>= 2.3.10), PSMatch (>= 1.6.0), ggplot2 (>= 2.2.1), mzR (>= 2.27.5) Suggests: topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat, BiocStyle, xml2 License: GPL (>= 3) MD5sum: 8b412652e9d5e384236ef808c844eb2b Package: topGO Version: 2.58.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.6), graph (>= 1.14.0), Biobase (>= 2.0.0), GO.db (>= 2.3.0), AnnotationDbi (>= 1.7.19), SparseM (>= 0.73) Imports: lattice, matrixStats, DBI Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest License: LGPL MD5sum: 4a77cfe0023cce9ad15fdb6ef020b070 Package: ToxicoGx Version: 2.10.0 Depends: R (>= 4.1), CoreGx Imports: SummarizedExperiment, BiocGenerics, S4Vectors, Biobase, BiocParallel, ggplot2, tibble, dplyr, caTools, downloader, magrittr, methods, reshape2, 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: 2114d9c10c35c7cf4772efcadcd2567c Package: TPP2D Version: 1.22.0 Depends: R (>= 3.6.0), stats, utils, dplyr, methods Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl, parallel, MASS, BiocParallel, limma Suggests: knitr, testthat, rmarkdown, BiocStyle License: GPL-3 MD5sum: db71a9b88da76a49cd2ef5c54fb32031 Package: TPP Version: 3.34.0 Depends: R (>= 3.4), Biobase, dplyr, magrittr, tidyr Imports: biobroom, broom, data.table, doParallel, foreach, futile.logger, ggplot2, grDevices, gridExtra, grid, knitr, limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr, purrr, RColorBrewer, RCurl, reshape2, rmarkdown, splines, stats, stringr, tibble, utils, VennDiagram, VGAM Suggests: BiocStyle, testthat License: Artistic-2.0 MD5sum: dbffbd82c0b75aa2d90d93574138b8a2 Package: tpSVG Version: 1.2.0 Depends: mgcv, R (>= 4.4) Imports: stats, BiocParallel, MatrixGenerics, methods, SingleCellExperiment, SummarizedExperiment, SpatialExperiment Suggests: BiocStyle, knitr, nnSVG, rmarkdown, scran, scuttle, STexampleData, escheR, ggpubr, colorspace, BumpyMatrix, sessioninfo, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: b582ac64a8d0570bdc53a63f68e481c9 Package: tracktables Version: 1.40.0 Depends: R (>= 3.5.0) Imports: IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base, stringr, RColorBrewer, methods Suggests: knitr, BiocStyle License: GPL (>= 3) MD5sum: bd03420a8963b743f4b39f393464447e Package: trackViewer Version: 1.42.0 Depends: R (>= 3.5.0), grDevices, methods, GenomicRanges, grid Imports: GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, InteractionSet, utils, rhdf5, strawr, txdbmaker Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack License: GPL (>= 2) MD5sum: f8098e15bdafd4805c9713164cb57f04 Package: tradeSeq Version: 1.20.0 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: c2ec82c215618f24e3dcff763ca8a732 Package: TrajectoryGeometry Version: 1.14.0 Depends: R (>= 4.1) Imports: pracma, rgl, ggplot2, stats, methods Suggests: dplyr, knitr, RColorBrewer, rmarkdown License: MIT + file LICENSE MD5sum: 71d490bad3de88e924a49e54b53f028f Package: TrajectoryUtils Version: 1.14.0 Depends: SingleCellExperiment Imports: methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 4d8067ac785178fd3f654481f9f52975 Package: transcriptogramer Version: 1.28.0 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: 68c7c20248a660d2ea675dd0bd36e069 Package: transcriptR Version: 1.34.0 Depends: R (>= 3.5.0), methods Imports: BiocGenerics, caret, chipseq, e1071, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2, Rsamtools, rtracklayer, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat License: GPL-3 MD5sum: afa1b41a6a02b213b181a373e6db6422 Package: transformGamPoi Version: 1.12.0 Imports: glmGamPoi, DelayedArray, Matrix, MatrixGenerics, SummarizedExperiment, HDF5Array, methods, utils, Rcpp LinkingTo: Rcpp Suggests: testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: c7096af0dd81111d8b2d43b76dfb37df Package: transite Version: 1.24.0 Depends: R (>= 3.5) Imports: BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils LinkingTo: Rcpp (>= 1.0.4.8) Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: e7aa4a7265e1c48b0df59f19dd6eddd5 Package: tRanslatome Version: 1.44.0 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: c8562b11bc57c9cb1e50457abb45d13f Package: transmogR Version: 1.2.0 Depends: Biostrings, GenomicRanges Imports: BSgenome, dplyr, GenomeInfoDb, GenomicFeatures, ggplot2 (>= 3.5.0), IRanges, jsonlite, matrixStats, methods, parallel, rlang, scales, stats, S4Vectors, SummarizedExperiment, VariantAnnotation, vroom Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, ComplexUpset, extraChIPs, InteractionSet, knitr, rmarkdown, rtracklayer, testthat (>= 3.0.0) License: GPL-3 MD5sum: 62790413343d398dc365bda6a7235098 Package: transomics2cytoscape Version: 1.16.0 Imports: RCy3, KEGGREST, dplyr, purrr, tibble, pbapply Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 03e36d35dbbbdf34111b340dc083175d Package: TransView Version: 1.50.0 Depends: methods, GenomicRanges Imports: BiocGenerics, S4Vectors (>= 0.9.25), IRanges, zlibbioc, gplots LinkingTo: Rhtslib (>= 1.99.1) Suggests: RUnit, pasillaBamSubset, BiocManager License: GPL-3 MD5sum: 1691ba7f566ac7f0ff44c4ef8dbd7b45 Package: traseR Version: 1.36.0 Depends: R (>= 3.5.0), GenomicRanges, IRanges, BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL MD5sum: 39755890d0fc07202ce114c0ace4e3d9 Package: traviz Version: 1.12.0 Depends: R (>= 4.0) Imports: ggplot2, viridis, mgcv, SingleCellExperiment, slingshot, princurve, Biobase, methods, RColorBrewer, SummarizedExperiment, grDevices, graphics, rgl Suggests: scater, dplyr, testthat (>= 3.0.0), covr, S4Vectors, rmarkdown, knitr License: MIT + file LICENSE MD5sum: 41f1009fbb664e2f72dfe47729813825 Package: TreeAndLeaf Version: 1.18.0 Depends: R(>= 4.0) Imports: RedeR(>= 1.40.4), igraph, ape Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer License: Artistic-2.0 MD5sum: fb3db74e47be2cc3f81cffcc6a1311ec Package: treeclimbR Version: 1.2.0 Depends: R (>= 4.4.0) Imports: TreeSummarizedExperiment (>= 1.99.0), edgeR, methods, SummarizedExperiment, S4Vectors, dirmult, dplyr, tibble, tidyr, ape, diffcyt, ggnewscale, ggplot2 (>= 3.4.0), viridis, ggtree, stats, utils, rlang Suggests: knitr, rmarkdown, scales, testthat (>= 3.0.0), BiocStyle License: Artistic-2.0 MD5sum: 6cc2cb1bf885e5a95bc19b8ce5a6ae7a Package: treeio Version: 1.30.0 Depends: R (>= 3.6.0) Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble, tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6) Suggests: Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml License: Artistic-2.0 MD5sum: 384844281c8e99e8f3bc8d87870e37df Package: treekoR Version: 1.14.0 Depends: R (>= 4.1) Imports: stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2, hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt, edgeR, lme4, multcomp Suggests: knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0) License: GPL-3 MD5sum: 772c8c23f07411ce947d74afae7996df Package: TreeSummarizedExperiment Version: 2.14.0 Depends: R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18), Biostrings Imports: methods, BiocGenerics, utils, ape, rlang, dplyr, SummarizedExperiment, BiocParallel, IRanges, treeio Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: fd513060631797bbe94a67a7e2290ef7 Package: TREG Version: 1.10.0 Depends: R (>= 4.2), SummarizedExperiment Imports: Matrix, purrr, rafalib Suggests: BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap, sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0), tibble, tidyr, SingleCellExperiment License: Artistic-2.0 MD5sum: 4b8b272fe70daf56e184280eb789df96 Package: Trendy Version: 1.28.0 Depends: R (>= 3.4) Imports: stats, utils, graphics, grDevices, segmented, gplots, parallel, magrittr, BiocParallel, DT, S4Vectors, SummarizedExperiment, methods, shiny, shinyFiles Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL-3 MD5sum: d198fa99443dfc6f7047d494b39a0f4a Package: TRESS Version: 1.12.0 Depends: R (>= 4.1.0), parallel, S4Vectors Imports: utils, rtracklayer, Matrix, matrixStats, stats, methods, graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools, AnnotationDbi Suggests: knitr, rmarkdown,BiocStyle License: GPL-3 + file LICENSE MD5sum: 97a6c762a21f4c2cb1640dbd6715cd42 Package: tricycle Version: 1.14.0 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: 10937c92126ce37db831ab824a2dbe5e Package: trigger Version: 1.52.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 MD5sum: f8ffe12fe0edcbc291da845d9673d360 Package: trio Version: 3.44.0 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1) Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 MD5sum: e0741721dbcddd02762cc7584c774cbc Package: triplex Version: 1.46.0 Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27), XVector (>= 0.11.6), Biostrings (>= 2.39.10) Imports: methods, grid, GenomicRanges LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer License: BSD_2_clause + file LICENSE MD5sum: 99b498bc7d417d26c0c1cfd2ef1bbd93 Package: tripr Version: 1.12.0 Depends: shiny (>= 1.6.0), shinyBS Imports: shinyjs, shinyFiles, plyr, data.table, DT, stringr, stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices, graphics, stats, utils, vegan Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr Enhances: parallel License: MIT + file LICENSE MD5sum: 6f3fcb329ca7ad10bdb103d44323045d Package: tRNA Version: 1.24.0 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: c8cbc55f566baa3f3bf3eb7a2f9ccb72 Package: tRNAdbImport Version: 1.24.0 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: 6d8c043e00206a5fb57b44f6781b5c29 Package: tRNAscanImport Version: 1.26.0 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, stringr, BiocGenerics, Biostrings, Structstrings, S4Vectors, IRanges, XVector, GenomeInfoDb, rtracklayer, BSgenome, Rsamtools Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 + file LICENSE MD5sum: 811c9eb9c9ae611b3e8a28898ed39118 Package: TRONCO Version: 2.38.0 Depends: R (>= 4.1.0), Imports: bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick License: GPL-3 MD5sum: cdf5936e4dd69101290e3bd471af3ac5 Package: TSAR Version: 1.4.0 Depends: R (>= 4.3.0) Imports: dplyr (>= 1.0.7), ggplot2 (>= 3.3.5), ggpubr (>= 0.4.0), magrittr (>= 2.0.3), mgcv (>= 1.8.38), readxl (>= 1.4.0), stringr (>= 1.4.0), tidyr (>= 1.1.4), utils (>= 4.3.1), shiny (>= 1.7.4.1), plotly (>= 4.10.2), shinyjs (>= 2.1.0), jsonlite (>= 1.8.7), rhandsontable (>= 0.3.8), openxlsx (>= 4.2.5.2), shinyWidgets (>= 0.7.6), minpack.lm (>= 1.2.3) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 1dd4711aa797986795f151c95e17518d Package: TSCAN Version: 1.44.0 Depends: R (>= 4.4.0), SingleCellExperiment, TrajectoryUtils Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, SparseArray (>= 1.5.23), DelayedArray (>= 0.31.9), S4Vectors Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor License: GPL (>= 2) MD5sum: f090485e7ca03c6404503a4c6d7c39d0 Package: ttgsea Version: 1.14.0 Depends: keras Imports: tm, text2vec, tokenizers, textstem, stopwords, data.table, purrr, DiagrammeR, stats Suggests: fgsea, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: 7292bb9712ec37e888ee8a8c771a1f31 Package: TTMap Version: 1.28.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 MD5sum: c167d665ab4698c043f4387003063448 Package: TurboNorm Version: 1.54.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata, hgu95av2cdf License: LGPL MD5sum: a26d5d6598d013de1b22c1eddb444019 Package: TVTB Version: 1.32.0 Depends: R (>= 3.4), methods, utils, stats Imports: AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel, Biostrings, ensembldb, GenomeInfoDb, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges (>= 2.21.6), reshape2, Rsamtools, S4Vectors (>= 0.25.14), SummarizedExperiment, VariantAnnotation (>= 1.19.9) Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander License: Artistic-2.0 MD5sum: 74deb90dd49a7d173b69c9b70cfab9e4 Package: tweeDEseq Version: 1.52.0 Depends: R (>= 4.3.0) Imports: Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn, grDevices, graphics, stats, utils LinkingTo: Rcpp Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) MD5sum: 0d164c0362b4953f2eb222d702a2d842 Package: twilight Version: 1.82.0 Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, grDevices, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) MD5sum: bacd4bff52b07e9fd3d54693998ae20b Package: twoddpcr Version: 1.30.0 Depends: R (>= 3.4) Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 0e62e31f080555fb0ecc5ab64b0fbf11 Package: txcutr Version: 1.12.0 Depends: R (>= 4.1.0) Imports: AnnotationDbi, GenomicFeatures, txdbmaker, IRanges, GenomicRanges, BiocGenerics, Biostrings, S4Vectors, rtracklayer, BiocParallel, stats, methods, utils Suggests: RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown, testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 MD5sum: 12e72229e6f3ea60630cb6302fe5c124 Package: txdbmaker Version: 1.2.1 Depends: BiocGenerics, S4Vectors, GenomeInfoDb (>= 1.39.9), GenomicRanges, GenomicFeatures Imports: methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>= 2.0), IRanges, UCSC.utils, AnnotationDbi, Biobase, BiocIO, rtracklayer, biomaRt (>= 2.59.1) Suggests: RMariaDB, mirbase.db, ensembldb, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 78d506a4388eb71fed1bac3e9f96db4e Package: tximeta Version: 1.24.0 Imports: SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, txdbmaker, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, tools, utils, methods, Matrix Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, fishpond, edgeR, limma, devtools License: GPL-2 MD5sum: 54b2afb8242326d1eda13b3f14f2699c Package: tximport Version: 1.34.0 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds License: LGPL (>= 2) MD5sum: fe9e1a154cc4b47e8217ba9ff49c22df Package: UCell Version: 2.10.1 Depends: R(>= 4.3.0) Imports: methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel, BiocNeighbors, SingleCellExperiment, SummarizedExperiment Suggests: scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: 7ba78752aaeeb313ae7b7da191c080ba Package: UCSC.utils Version: 1.2.0 Imports: methods, stats, httr, jsonlite, S4Vectors Suggests: DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 9633d28768a397cde007ede9b2aa3856 Package: Ularcirc Version: 1.24.0 Depends: R (>= 3.4.0) Imports: AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments, Organism.dplyr, plotgardener, R.utils, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, yaml Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: 4082d09aad65bced1e5db6959e25bc48 Package: UMI4Cats Version: 1.16.0 Depends: R (>= 4.0.0), SummarizedExperiment Imports: magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, magrittr, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats, org.Hs.eg.db, annotate, TxDb.Hsapiens.UCSC.hg19.knownGene, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat License: Artistic-2.0 MD5sum: 2a0ed8e1eb88efbcb1b1f1b44d3ba219 Package: uncoverappLib Version: 1.16.0 Imports: markdown, shiny, shinyjs, shinyBS, shinyWidgets,shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx, condformat, stringr, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache,rappdirs, TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils,S4Vectors, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, processx, Rsamtools, GenomicRanges Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: 03207b6e419248114c8fdf3ec8279fd3 Package: UNDO Version: 1.48.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 61de8d36b66e07c00acd514e15195f7d Package: unifiedWMWqPCR Version: 1.42.0 Depends: methods Imports: BiocGenerics, limma, stats, graphics License: GPL (>= 2) MD5sum: 595c73bd1a5fa56b887b9a9b4c1e4883 Package: UniProt.ws Version: 2.46.1 Depends: BiocGenerics, methods, RSQLite, utils Imports: AnnotationDbi, BiocFileCache, BiocBaseUtils, httr, httpcache, jsonlite, progress, rjsoncons Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: ea8a10b423627da13977b15b0e5eec49 Package: Uniquorn Version: 2.26.0 Depends: R (>= 3.5) Imports: stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation, data.table Suggests: testthat, knitr, rmarkdown, BiocGenerics License: Artistic-2.0 MD5sum: be27aaf2426c4e6df6de201b4bf62adc Package: universalmotif Version: 1.24.2 Depends: R (>= 3.5.0) Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid, MatrixGenerics LinkingTo: Rcpp, RcppThread Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio Enhances: PWMEnrich, rGADEM License: GPL-3 MD5sum: a2305f6696dabd8bab5f42cf00f8d06a Package: updateObject Version: 1.10.0 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: 1e0d775366e364f2ad5099b32cda7a52 Package: UPDhmm Version: 1.2.0 Depends: R (>= 4.3.0) Imports: HMM, utils, VariantAnnotation, GenomicRanges, S4Vectors, IRanges, stats Suggests: knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown, karyoploteR, regioneR, dplyr License: MIT + file LICENSE MD5sum: 7d615ab40723cfd0ccbf8bdd9c795dbc Package: uSORT Version: 1.32.0 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: 8191182af683f7fd549aa4780d105d1d Package: VAExprs Version: 1.12.0 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: e55111a61e16f0b3c40c2b35c0ce1da5 Package: VanillaICE Version: 1.68.0 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: 0f1137d28b8d7ceb4003e93400682f6d Package: VarCon Version: 1.14.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: f316c13ce1539a0bbaa974c8a84a4697 Package: variancePartition Version: 1.36.2 Depends: R (>= 4.3.0), ggplot2, limma (>= 3.62.1), BiocParallel Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0), iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack, rlang, lme4 (>= 1.1.33), grDevices, graphics, Biobase, methods, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, cowplot, Rfast, zenith, statmod, BiocGenerics, r2glmm, readr License: GPL-2 MD5sum: 0b09857ab5e3ba8a1a92fc8ece999a1e Package: VariantAnnotation Version: 1.52.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5), Rsamtools (>= 2.19.1) Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.57.2), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome (>= 1.47.3), GenomicFeatures (>= 1.31.3) LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0) Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr, magick, jsonlite, httr, rjsoncons License: Artistic-2.0 MD5sum: ba08c8146a704614cf13424dc0eba3de Package: VariantFiltering Version: 1.42.0 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, Biostrings (>= 2.33.11), GenomeInfoDb (>= 1.3.6), GenomicRanges (>= 1.19.13), SummarizedExperiment, GenomicFeatures, Rsamtools (>= 1.17.8), BSgenome, GenomicScores (>= 1.0.0), Gviz, 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: 2a2d510a6b1b0c681450371fd30e5e83 Package: VariantTools Version: 1.48.0 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: ba51fa2b64b65fe660828f2345984831 Package: VaSP Version: 1.18.0 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) MD5sum: 37ee6de59b9991decceeb09e12037418 Package: vbmp Version: 1.74.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: 46d146361c47e01246fd42ea54b6be6c Package: VCFArray Version: 1.22.0 Depends: R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28) Imports: tools, GenomicRanges, VariantAnnotation (>= 1.29.3), GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 4849f70b5f1681cf9937c4f382565abe Package: VDJdive Version: 1.8.0 Depends: R (>= 4.2) Imports: BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix, methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils LinkingTo: Rcpp Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: 3ddd9ccceac25467edce7db72b7d1868 Package: VegaMC Version: 3.44.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods License: GPL-2 MD5sum: 4e12526db7c37e9f24dd3a2badb9b834 Package: velociraptor Version: 1.16.0 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: fed339f4c0c82a15bfe066c5e5f7848f Package: veloviz Version: 1.12.0 Depends: R (>= 4.1) Imports: Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics, stats LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 3e2f6cc0f5df1552891175c272f9500f Package: VennDetail Version: 1.22.0 Imports: utils, grDevices, stats, methods, dplyr, purrr, tibble, magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger Suggests: knitr, rmarkdown, testthat, markdown License: GPL-2 MD5sum: b54d8ecb1c8cbeb05a56de7b99e3fef2 Package: VERSO Version: 1.16.0 Depends: R (>= 4.1.0) Imports: utils, data.tree, ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: b16796f3b24f0a14adf164004f3b2e12 Package: vidger Version: 1.26.0 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: b03c00640daa049f9195f1036f14bad9 Package: viper Version: 1.40.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: fb2644cdcf48363bea49024d30b3e55f Package: ViSEAGO Version: 1.19.0 Depends: R (>= 3.6) Imports: data.table, AnnotationDbi, AnnotationForge, biomaRt, dendextend, DiagrammeR, DT, dynamicTreeCut, fgsea, GOSemSim, ggplot2, GO.db, grDevices, heatmaply, htmlwidgets, igraph, methods, plotly, processx, topGO, RColorBrewer, R.utils, scales, stats, UpSetR, utils Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr, rmarkdown, corrplot, remotes, BiocManager MD5sum: ab722d882a6646d6aa35cda4c94791ec Package: VisiumIO Version: 1.2.0 Depends: R (>= 4.4.0), TENxIO Imports: BiocBaseUtils, BiocGenerics, BiocIO (>= 1.15.1), jsonlite, methods, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment Suggests: arrow, BiocStyle, knitr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: 6daa0d6f2031ebbc84aad4ee3b2bcb85 Package: vissE Version: 1.14.0 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: 5b3a6dfda80a47419c94daec4a7e7277 Package: Voyager Version: 1.8.1 Depends: R (>= 4.2.0), SpatialFeatureExperiment (>= 1.7.3) Imports: BiocParallel, bluster, DelayedArray, ggnewscale, ggplot2 (>= 3.4.0), grDevices, grid, lifecycle, Matrix, matrixStats, memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, spdep, stats, SummarizedExperiment, terra, utils, zeallot Suggests: arrow, automap, BiocSingular, BiocStyle, cowplot, data.table, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, xml2 License: Artistic-2.0 MD5sum: 5bb7669a4b7e3ee87b21b2117fef5c63 Package: VplotR Version: 1.16.0 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown License: GPL (>= 3) MD5sum: d0001bcfb77320043e5e3b3efcdbc969 Package: vsclust Version: 1.8.0 Depends: R (>= 4.2.0) Imports: matrixStats, limma, parallel, shiny, qvalue, grDevices, stats, MultiAssayExperiment, graphics LinkingTo: Rcpp Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, clusterProfiler License: GPL-2 MD5sum: 7005f80954f3b3f2b75d004766e5a567 Package: vsn Version: 3.74.0 Depends: R (>= 4.0.0), methods, Biobase Imports: affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat License: Artistic-2.0 MD5sum: d98f47c58c26e6818b8c2d8b003f1c66 Package: vtpnet Version: 0.46.0 Depends: R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach Suggests: MotifDb, VariantAnnotation, Rgraphviz License: Artistic-2.0 MD5sum: 330dcab45e2ed52658e9660e2a4fd56e Package: 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org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0) License: LGPL-2.1 | file LICENSE MD5sum: 44432274dd00194b8a13818aadcc2b83 Package: widgetTools Version: 1.84.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: 9c1721bf59fd7cab93e27d810fd1ff59 Package: wiggleplotr Version: 1.30.0 Depends: R (>= 3.6) Imports: dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer, cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter License: Apache License 2.0 MD5sum: 8374b15ebb973a48e53ed0db0fae167f Package: wpm Version: 1.16.0 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: 80b83bd5327722465dd6b118333105e6 Package: wppi Version: 1.14.0 Depends: R(>= 4.1) Imports: dplyr, igraph, logger, methods, magrittr, Matrix, OmnipathR(>= 2.99.8), progress, purrr, rlang, RCurl, stats, tibble, tidyr Suggests: knitr, testthat, rmarkdown License: MIT + file LICENSE MD5sum: 8f4f40b3bfe1f454f67d5f5485115523 Package: Wrench Version: 1.24.0 Depends: R (>= 3.5.0) Imports: limma, matrixStats, locfit, stats, graphics Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR License: Artistic-2.0 MD5sum: 39be1350a56e40126729590c0f37d8e0 Package: xcms Version: 4.4.0 Depends: R (>= 4.0.0), BiocParallel (>= 1.8.0) Imports: MSnbase (>= 2.29.3), mzR (>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics (>= 1.37.1), lattice, MassSpecWavelet (>= 1.66.0), S4Vectors, IRanges, SummarizedExperiment, MsCoreUtils (>= 1.15.5), MsFeatures, MsExperiment (>= 1.5.4), Spectra (>= 1.15.7), progress, RColorBrewer, MetaboCoreUtils (>= 1.11.2) Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>= 0.25.1), ncdf4, testthat (>= 3.1.9), pander, rmarkdown, MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal, mgcv Enhances: Rgraphviz, rgl License: GPL (>= 2) + file LICENSE MD5sum: 117fbf47dd9fd9bf4461713a0dd80569 Package: xcore Version: 1.10.0 Depends: R (>= 4.2) Imports: DelayedArray (>= 0.18.0), edgeR (>= 3.34.1), foreach (>= 1.5.1), GenomicRanges (>= 1.44.0), glmnet (>= 4.1.2), IRanges (>= 2.26.0), iterators (>= 1.0.13), magrittr (>= 2.0.1), Matrix (>= 1.3.4), methods (>= 4.1.1), MultiAssayExperiment (>= 1.18.0), stats, S4Vectors (>= 0.30.0), utils Suggests: AnnotationHub (>= 3.0.2), BiocGenerics (>= 0.38.0), BiocParallel (>= 1.28), BiocStyle (>= 2.20.2), data.table (>= 1.14.0), devtools (>= 2.4.2), doParallel (>= 1.0.16), ExperimentHub (>= 2.2.0), knitr (>= 1.37), pheatmap (>= 1.0.12), proxy (>= 0.4.26), ridge (>= 3.0), rmarkdown (>= 2.11), rtracklayer (>= 1.52.0), testthat (>= 3.0.0), usethis 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BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 021cd8aa95980269806e93b886c3d018 Package: XINA Version: 1.24.0 Depends: R (>= 3.5) Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 9503dab6eb89eb65a520dd71747d71a8 Package: xmapbridge Version: 1.64.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 MD5sum: 86ced8c2993059ddcbbc85030462f859 Package: XNAString Version: 1.14.0 Depends: R (>= 4.1) Imports: utils, Biostrings, pwalign, BSgenome, data.table, GenomicRanges, IRanges, methods, Rcpp, stringi, S4Vectors, future.apply, stringr, formattable, stats LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, BSgenome.Hsapiens.UCSC.hg38, pander License: GPL-2 MD5sum: 0b9854c5e84e6d7062b15ca4478ccd36 Package: XVector Version: 0.46.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9) Imports: methods, utils, tools, zlibbioc, BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 MD5sum: dbf35fd1e98ceb9d5c993dd342730dc0 Package: yamss Version: 1.32.0 Depends: R (>= 4.3.0), methods, BiocGenerics (>= 0.15.3), SummarizedExperiment Imports: IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table, grDevices, limma Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat License: Artistic-2.0 MD5sum: 9ae4c1d660a26557b185510fc02142dd Package: YAPSA Version: 1.32.0 Depends: R (>= 4.0.0), GenomicRanges, ggplot2, grid Imports: limSolve, SomaticSignatures, VariantAnnotation, GenomeInfoDb, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, doParallel, parallel, PMCMRplus, ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings, BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: bdf155e8ea2ca24308334507bac62b2d Package: yarn Version: 1.32.0 Depends: Biobase Imports: biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro Suggests: knitr, rmarkdown, testthat (>= 0.8) License: Artistic-2.0 MD5sum: d98d3a2a2de97b38565f08653ae48dee Package: zellkonverter Version: 1.16.0 Imports: basilisk, cli, DelayedArray, Matrix, methods, reticulate, S4Vectors, SingleCellExperiment (>= 1.11.6), SummarizedExperiment, utils Suggests: anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rhdf5 (>= 2.45.1), rmarkdown, scRNAseq, spelling, testthat, withr License: MIT + file LICENSE MD5sum: 21c2783b52f37c4ea1cf0fdcaf6950d1 Package: zenith Version: 1.8.0 Depends: R (>= 4.2.0), limma, methods Imports: variancePartition (>= 1.26.0), EnrichmentBrowser (>= 2.22.0), GSEABase (>= 1.54.0), msigdbr (>= 7.5.1), Rfast, ggplot2, tidyr, reshape2, progress, utils, Rdpack, stats Suggests: BiocStyle, BiocGenerics, knitr, pander, rmarkdown, tweeDEseqCountData, edgeR, kableExtra, RUnit License: Artistic-2.0 MD5sum: ac5ed1d074e7e3faad42adad6e9d0e7f Package: zFPKM Version: 1.28.0 Depends: R (>= 3.4.0) Imports: checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment Suggests: knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 02db7d99e5fe1fba34cceb0473a8c026 Package: zinbwave Version: 1.28.0 Depends: R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment Imports: BiocParallel, softImpute, stats, genefilter, edgeR, Matrix Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, sparseMatrixStats License: Artistic-2.0 MD5sum: b34230907b2f935c42d7911a42f9a8c7 Package: zitools Version: 1.0.0 Depends: R (>= 4.4.0), methods Imports: phyloseq, pscl, ggplot2, MatrixGenerics, SummarizedExperiment, stats, VGAM, matrixStats, tidyr, tibble, dplyr, DESeq2, reshape2, RColorBrewer, magrittr, BiocGenerics, graphics, utils Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), tidyverse, microbiome License: BSD_3_clause + file LICENSE MD5sum: 98c7f3e14febdefcfa1a24b5000816fe Package: zlibbioc Version: 1.52.0 Suggests: BiocStyle, knitr License: Artistic-2.0 + file LICENSE MD5sum: 084f8cb914833e76644cf6a8741fdbf9 Package: ZygosityPredictor Version: 1.6.0 Depends: R (>= 4.3.0) Imports: GenomicAlignments, GenomicRanges, Rsamtools, IRanges, VariantAnnotation, DelayedArray, dplyr, stringr, purrr, tibble, methods, knitr, igraph, readr, stats, magrittr, rlang Suggests: rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: b7da4a8298fb01011e19c854bd686a85