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rlang, stats, stringr, tibble, tidyr, tidyselect Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: cd5c631580905c989bcfd01506e10d96 NeedsCompilation: no Package: dir.expiry Version: 1.19.0 Imports: utils, filelock Suggests: rmarkdown, knitr, testthat, BiocStyle License: GPL-3 MD5sum: 13208ddb810de55bac342a6e300b5465 NeedsCompilation: no Package: DirichletMultinomial Version: 1.53.0 Depends: S4Vectors, IRanges Imports: stats4, methods, BiocGenerics Suggests: lattice, parallel, MASS, RColorBrewer, DT, knitr, rmarkdown, BiocStyle License: LGPL-3 MD5sum: d3cb91ef46b0cc8e1470048c173e3418 NeedsCompilation: yes Package: discordant Version: 1.35.0 Depends: R (>= 4.1.0) Imports: Rcpp, Biobase, stats, biwt, gtools, MASS, tools, dplyr, methods, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: f6cd60a6738fad13f9251d223f7457c5 NeedsCompilation: yes Package: DiscoRhythm Version: 1.27.0 Depends: R (>= 3.6.0) Imports: 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pheatmap, rmarkdown, testthat (>= 3.0.0), withr, airway Enhances: massdataset License: MIT + file LICENSE MD5sum: ed5f1fd3949cbbd5a91584e627aee725 NeedsCompilation: no Package: dominoSignal Version: 1.5.0 Depends: R(>= 4.2.0), Imports: biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid, igraph, Matrix, methods, plyr, stats, utils, magrittr, purrr, dplyr Suggests: knitr, patchwork, rmarkdown, Seurat, testthat, formatR, BiocFileCache, SingleCellExperiment License: GPL-3 | file LICENSE MD5sum: f818a52ac7681163e666b0832fcae72c NeedsCompilation: no Package: doppelgangR Version: 1.39.0 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: d6f187381a45fb289021785c3601d52f NeedsCompilation: no Package: Doscheda Version: 1.33.0 Depends: R (>= 3.4) Imports: methods, drc, stats, httr, jsonlite, 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forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils License: Artistic-2.0 MD5sum: 125ebe6a64c802ad0113199e27d95877 NeedsCompilation: no Package: GenomicTuples Version: 1.45.0 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), Seqinfo, S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, covr, GenomicAlignments, Biostrings, GenomeInfoDb License: Artistic-2.0 MD5sum: 741f14d409d9956e3d7e84f44edfb04d NeedsCompilation: yes Package: GenProSeq Version: 1.15.0 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: e0ada07e38d3ecf2260ecedff197c90a NeedsCompilation: no Package: GeoDiff Version: 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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: 211f7acec31c157ccb088f118f1d47d1 NeedsCompilation: no Package: GlobalAncova Version: 4.29.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: ec14ba8f2c3040ff59ba41c12daf1236 NeedsCompilation: yes Package: globalSeq Version: 1.39.0 Depends: R (>= 3.0.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 MD5sum: 76715066ad400a15abfd506679acd6b0 NeedsCompilation: no Package: globaltest Version: 5.65.0 Depends: methods, survival Imports: Biobase, AnnotationDbi, annotate, graphics Suggests: vsn, golubEsets, KEGGREST, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart, mstate License: GPL (>= 2) MD5sum: f1991cb535f841135e73d59f1387bdc7 NeedsCompilation: no Package: GmicR Version: 1.25.0 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: 70f351edfca89c9ef12a591228d174c8 NeedsCompilation: no Package: GMRP Version: 1.39.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: 42539a1abff03145d4154fa57bbb1ade NeedsCompilation: no Package: GNET2 Version: 1.27.0 Depends: R (>= 3.6) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment,dplyr,igraph, grDevices, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 MD5sum: 8c6a4f7a88c7d56a2a9b97d69431668c 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Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat License: GPL-3 MD5sum: 7c46ca7a3845feb770b83d789293d55c NeedsCompilation: yes Package: goProfiles Version: 1.73.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: c42391cdd74a30e29bcc14213b8a1e11 NeedsCompilation: no Package: GOSemSim Version: 2.37.0 Depends: R (>= 4.2.0) Imports: AnnotationDbi, DBI, digest, GO.db, methods, rlang, R.utils, stats, utils, yulab.utils (>= 0.2.1) LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, readr, rmarkdown, testthat, tidyr, tidyselect, ROCR License: Artistic-2.0 MD5sum: 588b173c361f1103ee329f009ba7e8cc NeedsCompilation: yes Package: goSorensen Version: 1.13.0 Depends: R (>= 4.4) Imports: clusterProfiler, goProfiles, org.Hs.eg.db, parallel, stats, stringr Suggests: BiocManager, BiocStyle, knitr, rmarkdown, org.At.tair.db, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcSakai.eg.db, org.EcK12.eg.db, org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Pt.eg.db, org.Xl.eg.db, GO.db, ggplot2, ggrepel, DT, magick License: GPL-3 MD5sum: dc61f999e6dfaf8b1ac20366ab6123e4 NeedsCompilation: no Package: goSTAG Version: 1.35.0 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 8adfab713bde24a69e906c84385b4270 NeedsCompilation: no Package: GOstats Version: 2.77.0 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: 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Suggests: testthat (>= 2.1.0), knitr (>= 1.25), rmarkdown (>= 1.16), prettydoc (>= 0.3.0), httr (>= 1.4.1), S4Vectors (>= 0.22.1), BiocStyle (>= 2.15.8) License: GPL-3 MD5sum: d861b8aac4162085ca297d226111d14f NeedsCompilation: no Package: gypsum Version: 1.7.0 Imports: utils, httr2, jsonlite, parallel, filelock, rappdirs Suggests: knitr, rmarkdown, testthat, BiocStyle, digest, jsonvalidate, DBI, RSQLite, S4Vectors, methods License: MIT + file LICENSE MD5sum: 0d7316ac9b8a5b9cc04fb8a0eae99f41 NeedsCompilation: no Package: h5mread Version: 1.3.0 Depends: R (>= 4.5), methods, rhdf5, BiocGenerics, SparseArray Imports: stats, tools, rhdf5filters, S4Vectors, IRanges, S4Arrays LinkingTo: Rhdf5lib, S4Vectors Suggests: BiocParallel, ExperimentHub, TENxBrainData, HDF5Array, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: edf9c4fb164dc1b8b08dd14fb42c1c6b NeedsCompilation: yes Package: h5vc Version: 2.45.0 Depends: grid, gridExtra, ggplot2 Imports: rhdf5, reshape, S4Vectors, 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Seurat, SeuratObject, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix, markdown License: file LICENSE MD5sum: 9bc6dfaadd82740e901d404e2c49cf44 NeedsCompilation: yes Package: MOGAMUN Version: 1.21.0 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: knitr, markdown License: GPL-3 + file LICENSE MD5sum: 67f1eb270dafc86dd8cba0ca423d1332 NeedsCompilation: no Package: mogsa Version: 1.45.0 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: 3e7846b0d6606e9325621d5a0e1f1303 NeedsCompilation: no Package: MOMA Version: 1.23.0 Depends: R (>= 4.0) Imports: circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics, grid, grDevices, magrittr, methods, MKmisc, MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr, reshape2, rlang, stats, stringr, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, viper License: GPL-3 MD5sum: 07cf68913e5578426c213263f2a1a374 NeedsCompilation: no Package: monocle Version: 2.39.0 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: 450081298502d1eee67bba7acdc50ab2 NeedsCompilation: yes Package: MoonlightR Version: 1.37.0 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: ca958bd09db867ca4ca6d60f1365dbd4 NeedsCompilation: no Package: mosaics Version: 2.49.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, Seqinfo, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: f428f263bff1d70321f759186b3ed0c5 NeedsCompilation: yes Package: mosbi Version: 1.17.0 Depends: R (>= 4.1) Imports: Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust, isa2, QUBIC, akmbiclust, RColorBrewer LinkingTo: Rcpp, BH, RcppParallel Suggests: knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0) License: AGPL-3 + file LICENSE MD5sum: 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vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID (>= 1.5.2), digest, lattice, ggplot2, scales, MASS, Rcpp LinkingTo: Rcpp Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.43.3), magick, msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, XML, shiny, magrittr, SummarizedExperiment, Spectra License: Artistic-2.0 MD5sum: 27d26d5cd333891e24a77f3cb2b4402f NeedsCompilation: yes Package: MSnID Version: 1.45.0 Depends: R (>= 2.10), Rcpp Imports: MSnbase (>= 1.12.1), mzID (>= 1.3.5), R.cache, foreach, doParallel, parallel, methods, iterators, data.table, Biobase, ProtGenerics, reshape2, dplyr, mzR, BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics, Biostrings, purrr, rlang, stringr, tibble, AnnotationHub, AnnotationDbi, xtable License: Artistic-2.0 MD5sum: 148b7533db691e447baec7c8366ec58e NeedsCompilation: no Package: mspms Version: 1.3.0 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sessioninfo, rmarkdown, testthat, tidyverse, plotly, MsDataHub, MSnbase, matrixStats, MsCoreUtils, covr License: Artistic-2.0 MD5sum: bde913d9b44e970ece8ed558876e0808 NeedsCompilation: no Package: MsQuality Version: 1.11.0 Depends: R (>= 4.2.0) Imports: BiocParallel (>= 1.32.0), ggplot2 (>= 3.3.5), htmlwidgets (>= 1.5.3), methods (>= 4.2.0), msdata (>= 0.32.0), MsExperiment (>= 0.99.0), plotly (>= 4.9.4.1), ProtGenerics (>= 1.24.0), rlang (>= 1.1.1), rmzqc (>= 0.7.0), shiny (>= 1.6.0), shinydashboard (>= 0.7.1), Spectra (>= 1.13.2), stats (>= 4.2.0), stringr (>= 1.4.0), tibble (>= 3.1.4), tidyr (>= 1.1.3), utils (>= 4.2.0) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), dplyr (>= 1.0.5), knitr (>= 1.11), mzR (>= 2.32.0), rmarkdown (>= 2.7), S4Vectors (>= 0.29.17), testthat (>= 2.2.1) License: GPL-3 MD5sum: e49a9e4158ec35f0c174dfcc5c6ee9bc NeedsCompilation: no Package: MSstats Version: 4.19.0 Depends: R (>= 4.0) Imports: MSstatsConvert, data.table, checkmate, MASS, htmltools, 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grDevices, MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp, Biostrings, checkmate, ggrepel, plotly, htmltools LinkingTo: Rcpp Suggests: knitr, rmarkdown, tinytest, covr, mockery, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: f691ae1f753375bcbc3e6af95daa38c2 NeedsCompilation: yes Package: MSstatsQC Version: 2.29.0 Depends: R (>= 3.5.0) Imports: dplyr,plotly,ggplot2,ggExtra, stats,grid, MSnbase, qcmetrics Suggests: knitr,rmarkdown, testthat, RforProteomics License: Artistic License 2.0 MD5sum: b78f1d19f89fd380e06fa63eac5b62c1 NeedsCompilation: no Package: MSstatsQCgui Version: 1.31.0 Imports: shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid Suggests: knitr License: Artistic License 2.0 MD5sum: 0168d168f96740aa5461073bec3d7d29 NeedsCompilation: no Package: MSstatsResponse Version: 1.1.0 Depends: R (>= 4.5.0) Imports: BiocParallel, ggplot2, dplyr, stats, parallel, data.table Suggests: MSstats, MSstatsTMT, tidyverse, boot, purrr, gridExtra, knitr, rmarkdown, BiocStyle, 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2.27.0 Depends: R (>= 3.5.0), methods, Seqinfo, GenomicRanges (>= 1.61.1), Biostrings (>= 2.77.2) Imports: utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), bitops, BiocParallel, stats LinkingTo: Rhtslib (>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, VariantAnnotation, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr License: Artistic-2.0 | file LICENSE MD5sum: 230f2f814ac617a81c3af0d780af439c NeedsCompilation: yes Package: rsbml Version: 2.69.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils Imports: BiocGenerics, graph, utils License: Artistic-2.0 MD5sum: e559fd8b8e6c8a921eb630f75de51964 NeedsCompilation: yes Package: rScudo Version: 1.27.0 Depends: R (>= 3.6) Imports: methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, 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RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 3e62286e0523cb6456af3da11a6ecb65 NeedsCompilation: no Package: RTopper Version: 1.57.0 Depends: R (>= 2.12.0), Biobase Imports: limma, multtest Suggests: org.Hs.eg.db, KEGGREST, GO.db License: GPL (>= 3) + file LICENSE MD5sum: 00c7908268460873c56b454d1a4e5db3 NeedsCompilation: no Package: Rtpca Version: 1.21.0 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: c9840e24da8e17631fa1d11770d1d18f NeedsCompilation: no Package: rTRM Version: 1.49.0 Depends: R (>= 2.10), igraph (>= 1.0) Imports: methods, AnnotationDbi, DBI, RSQLite Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 84e56df6af5d776e5ed18391c41c05d0 NeedsCompilation: no Package: runibic 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BiocParallel, torch (>= 0.3.0), coro, igraph, Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival Suggests: knitr, rmarkdown, BiocStyle License: LGPL MD5sum: ff6255d53d05c6acb7ea108cacb01253 NeedsCompilation: no Package: scFeatureFilter Version: 1.31.0 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: a18143499a21e3db95bd40d20d478081 NeedsCompilation: no Package: scHiCcompare Version: 1.3.0 Depends: R (>= 4.5.0) Imports: grDevices, graphics, stats, utils, dplyr, ggplot2, gtools, HiCcompare, lattice, mclust, mice, miceadds, ranger, rstatix, tidyr, rlang, data.table, BiocParallel Suggests: knitr, rmarkdown, testthat, BiocStyle, DT, gridExtra License: MIT + file LICENSE MD5sum: 7bef8d97dc989485e264a5f8f78b2e5c NeedsCompilation: no 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Biobase Imports: affy, limma, lattice, ggplot2 Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr, testthat License: Artistic-2.0 MD5sum: a95447e139776475c4ec5bf4d55b0ba3 NeedsCompilation: yes Package: weaver Version: 1.77.0 Depends: R (>= 2.5.0), digest, tools, utils, codetools Suggests: codetools License: GPL-2 MD5sum: 569130ce3ddc107a877d9d99d31cad05 NeedsCompilation: no Package: webbioc Version: 1.83.0 Depends: R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma, qvalue Imports: multtest, qvalue, stats, utils, BiocManager License: GPL (>= 2) MD5sum: 0067aee4e5c0a3c4323c9135b150b64d NeedsCompilation: no Package: weitrix Version: 1.23.0 Depends: R (>= 3.6), SummarizedExperiment Imports: methods, utils, stats, grDevices, assertthat, S4Vectors, DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics, limma, topconfects, dplyr, purrr, ggplot2, rlang, scales, reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl Suggests: knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR, EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, ComplexHeatmap, patchwork, testthat (>= 2.1.0) License: LGPL-2.1 | file LICENSE MD5sum: dfae48cc58804afb453d3c3009a9dc2f NeedsCompilation: no Package: widgetTools Version: 1.89.0 Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: 8b2582d70e7bc352de68ed2fdeeee32c NeedsCompilation: no Package: wpm Version: 1.21.0 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: 6fc8ba41206daaecbeb5299afb5b4c5d NeedsCompilation: no Package: Wrench Version: 1.29.0 Depends: R (>= 3.5.0) Imports: limma, matrixStats, locfit, stats, graphics Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR License: Artistic-2.0 MD5sum: 8ddd693196e1b4115d67148988999f3e NeedsCompilation: no Package: XAItest Version: 1.3.0 Depends: R (>= 3.5.0) Imports: limma, randomForest, kernelshap, caret, lime, DT, methods, SummarizedExperiment, ggplot2 Suggests: knitr, ggforce, shapr (>= 1.0.1), airway, xgboost, BiocGenerics, RUnit, S4Vectors License: MIT + file LICENSE MD5sum: 4eee60fd169ecd17d10419012b4dbb6e NeedsCompilation: no Package: xcms Version: 4.9.0 Depends: R (>= 4.1.0), BiocParallel (>= 1.8.0) Imports: MSnbase (>= 2.33.3), mzR (>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics (>= 1.37.1), lattice, MassSpecWavelet (>= 1.66.0), S4Vectors, IRanges, SummarizedExperiment, MsCoreUtils (>= 1.19.2), MsFeatures, MsExperiment (>= 1.5.4), Spectra (>= 1.16.1), progress, RColorBrewer, MetaboCoreUtils (>= 1.11.2), data.table 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, rhdf5 Enhances: Rgraphviz, rgl License: GPL (>= 2) + file LICENSE MD5sum: 8f1991de74a527bf30864d39ce535b20 NeedsCompilation: yes Package: xcore Version: 1.15.0 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 (>= 2.0.1), xcoredata License: GPL-2 MD5sum: 80d1b4af0ce891246515fb8fbb38c616 NeedsCompilation: no Package: XDE Version: 2.57.0 Depends: R (>= 2.10.0), Biobase (>= 2.5.5) Imports: BiocGenerics, genefilter, graphics, grDevices, gtools, methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta, siggenes Suggests: MASS, RUnit Enhances: coda License: LGPL-2 MD5sum: fe6ab0b97e398cb3ee98e4c2238c29dc NeedsCompilation: yes Package: Xeva Version: 1.27.0 Depends: R (>= 3.6) Imports: methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2, scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid, nlme, PharmacoGx, downloader Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 470adf68760cebf173979d39bf52853c NeedsCompilation: no Package: XINA Version: 1.29.0 Depends: R (>= 3.5) Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 73a8471b726e53170c60276f4983bbd6 NeedsCompilation: no Package: xmapbridge Version: 1.69.0 Depends: R (>= 2.0), methods Suggests: RUnit, RColorBrewer License: LGPL-3 MD5sum: 02d82da8f9012ee31e79c50e5a75a1ac NeedsCompilation: no Package: XVector Version: 0.51.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.43.8) Imports: methods, utils, stats, tools, BiocGenerics, S4Vectors, IRanges LinkingTo: S4Vectors, IRanges Suggests: Biostrings, drosophila2probe, RUnit License: Artistic-2.0 MD5sum: 2505a567a52cc4bf696f557e15a8fd59 NeedsCompilation: yes Package: yamss Version: 1.37.0 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: 7ea5a4f343d21a58b83e8c77b085ef3b NeedsCompilation: no Package: zFPKM Version: 1.33.0 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: 8e4217115336a816cc1a36a8b5a14fc1 NeedsCompilation: no Package: zitools Version: 1.5.0 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: 03e5e1ec7cdb736165ef876d022ae8df NeedsCompilation: no