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knitr License: Artistic-2.0 MD5sum: d4dbc895bd2de2dca145ad86d96a28c9 NeedsCompilation: no Package: AnnotationFilter Version: 1.16.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db License: Artistic-2.0 MD5sum: 8fa71403018268d536fcbc0c52e54a03 NeedsCompilation: no Package: AnnotationForge Version: 1.34.1 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, markdown, BiocStyle, knitr, BiocManager, BiocFileCache License: Artistic-2.0 MD5sum: f32a32e3bb7e148639efe09a8f7d6ff9 NeedsCompilation: no Package: AnnotationHub Version: 3.0.2 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, interactiveDisplayBase, httr, yaml, dplyr Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 1723427f6cad829e707fd3fb1f4a437a NeedsCompilation: yes Package: AnnotationHubData Version: 1.22.0 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 License: Artistic-2.0 MD5sum: 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1e64c5197247dc95d69669dbab02bccb NeedsCompilation: no Package: anota Version: 1.40.0 Depends: qvalue Imports: multtest, qvalue License: GPL-3 MD5sum: 0eea6a1fc6403ae1c87f69e917243cb8 NeedsCompilation: no Package: anota2seq Version: 1.14.0 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: 6c045e2428867c986bc6005ab1d15cbc NeedsCompilation: no Package: antiProfiles Version: 1.32.0 Depends: R (>= 3.0), matrixStats (>= 0.50.0), methods (>= 2.14), locfit (>= 1.5) Suggests: antiProfilesData, RColorBrewer License: Artistic-2.0 MD5sum: f2ea29f1a395958e04d62e14057ee127 NeedsCompilation: no Package: AnVIL Version: 1.4.1 Depends: R (>= 3.6), dplyr Imports: stats, utils, methods, futile.logger, jsonlite, httr, rapiclient (>= 0.1.3), tibble, tidyselect, tidyr, rlang, BiocManager Suggests: knitr, rmarkdown, testthat, withr, readr License: Artistic-2.0 MD5sum: 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License: Artistic License 2.0 MD5sum: 67a8ed79c0aa34f6e115f9c81aa6bc1b NeedsCompilation: yes Package: arrayMvout Version: 1.50.0 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: dfbae927c8d3594a1d74675ac0eb0a97 NeedsCompilation: no Package: arrayQuality Version: 1.70.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL MD5sum: 3d2cdf4eeafe03513a2d48607fc0662e NeedsCompilation: no Package: arrayQualityMetrics Version: 3.48.0 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 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Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testthat, utils, lifecycle LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: bb510740c2ed2e685ccb75f399c886a0 NeedsCompilation: yes Package: attract Version: 1.44.0 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: b72c05eb2a84e52125d421c9d08e4994 NeedsCompilation: no Package: AUCell Version: 1.14.0 Imports: data.table, graphics, grDevices, GSEABase, methods, mixtools, R.utils, shiny, stats, SummarizedExperiment, BiocGenerics, S4Vectors, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, rbokeh, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: 4ddecb61938427c577caeb9491a0bab2 NeedsCompilation: no Package: 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methods, utils, DelayedArray, BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat LinkingTo: Rcpp, beachmat Suggests: testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix License: GPL-3 MD5sum: e5f008179a2f3941cb13a2aa00210c45 NeedsCompilation: yes Package: BiocSklearn Version: 1.14.1 Depends: R (>= 4.0), reticulate, methods, SummarizedExperiment, knitr Imports: basilisk, Rcpp Suggests: testthat, restfulSE, HDF5Array, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: fcb7c754080f294dfa0d93c650a33f1d NeedsCompilation: no Package: BiocStyle Version: 2.20.2 Imports: bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils, yaml, BiocManager Suggests: BiocGenerics, RUnit, htmltools License: Artistic-2.0 MD5sum: 782fb5e050ffc389db227977f2aa57fd NeedsCompilation: no Package: biocthis Version: 1.2.0 Imports: BiocManager, fs, glue, rlang, styler, usethis (>= 2.0.1) Suggests: BiocStyle, covr, devtools, knitr, pkgdown, RefManageR, rmarkdown, sessioninfo, testthat, utils License: 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BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr, rmarkdown, covr, xml2, git2r License: AGPL-3 MD5sum: f08973024771b262763c2b905017dd95 NeedsCompilation: yes Package: bioDist Version: 1.64.0 Depends: R (>= 2.0), methods, Biobase,KernSmooth Suggests: locfit License: Artistic-2.0 MD5sum: 4f0d06bf8e817ec68bc2f60f0625ab47 NeedsCompilation: no Package: biomaRt Version: 2.48.3 Depends: methods Imports: utils, XML, AnnotationDbi, progress, stringr, httr, digest, BiocFileCache, rappdirs, xml2 Suggests: BiocStyle, knitr, rmarkdown, testthat, mockery License: Artistic-2.0 MD5sum: e1b8dd1277db4a59c93dd744dab43053 NeedsCompilation: no Package: biomformat Version: 1.20.0 Depends: R (>= 3.2), methods Imports: plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5 Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) License: GPL-2 MD5sum: 571c3ec839e5519bb8a2f0d63ed92010 NeedsCompilation: no Package: BioMM Version: 1.8.0 Depends: R (>= 3.6) Imports: 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gridExtra, org.Hs.eg.db, hgu133plus2.db, ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer License: GPL (>= 3) + file LICENSE MD5sum: 946a03e11707bf2bcf4351a3390b09f9 NeedsCompilation: yes Package: biosigner Version: 1.20.0 Depends: Biobase, ropls Imports: methods, e1071, MultiDataSet, randomForest Suggests: BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, omicade4, rmarkdown, testthat License: CeCILL MD5sum: 7aabe07f9ac432b7173f3c3444296270 NeedsCompilation: no Package: Biostrings Version: 2.60.2 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), GenomeInfoDb Imports: methods, utils, grDevices, graphics, stats, crayon, LinkingTo: S4Vectors, IRanges, XVector Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, 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0.23.19), IRanges (>= 1.99.28), GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21), SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>= 1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4), ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlang Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit License: Artistic-2.0 MD5sum: 83ad0eb484435c661f92f3fc661ed4f5 NeedsCompilation: yes Package: BiRewire Version: 3.24.0 Depends: igraph, slam, tsne, Matrix Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: 6ade1bd63fcd516a946b71888bfec2f9 NeedsCompilation: yes Package: biscuiteer Version: 1.6.0 Depends: R (>= 3.6), biscuiteerData, bsseq Imports: readr, qualV, Matrix, impute, HDF5Array, S4Vectors, Rsamtools, data.table, Biobase, GenomicRanges, BiocGenerics, VariantAnnotation, DelayedMatrixStats, SummarizedExperiment, GenomeInfoDb, Mus.musculus, 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Imports: grid, stats, grDevices, utils, circlize, viridis, RColorBrewer, ComplexHeatmap, SummarizedExperiment, pasilla Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl License: MIT + file LICENSE MD5sum: 2924fa0deced5f622dd30136e0e39bd1 NeedsCompilation: no Package: blima Version: 1.26.0 Depends: R(>= 3.3) Imports: beadarray(>= 2.0.0), Biobase(>= 2.0.0), Rcpp (>= 0.12.8), BiocGenerics, grDevices, stats, graphics LinkingTo: Rcpp Suggests: xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr License: GPL-3 MD5sum: cbd6964c97503a615dc5c40bfdbf207d NeedsCompilation: yes Package: BLMA Version: 1.16.0 Depends: ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel, Biobase, metafor, methods Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 758c53e5198d2f77d77318ebcc4be708 NeedsCompilation: no Package: BloodGen3Module Version: 1.0.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, ExperimentHub, methods, grid, graphics, stats, grDevices, 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NeedsCompilation: yes Package: BRGenomics Version: 1.4.0 Depends: R (>= 4.0), rtracklayer, GenomeInfoDb, S4Vectors Imports: GenomicRanges, parallel, IRanges, stats, Rsamtools, GenomicAlignments, DESeq2, SummarizedExperiment, utils, methods Suggests: BiocStyle, knitr, rmarkdown, testthat, apeglm, remotes, ggplot2, reshape2, Biostrings License: Artistic-2.0 MD5sum: 90909e392a5ced0c93fcaed7b527b3e3 NeedsCompilation: no Package: bridge Version: 1.56.0 Depends: R (>= 1.9.0), rama License: GPL (>= 2) MD5sum: 455738fee88083a39b6881c1e6191c6b NeedsCompilation: yes Package: BridgeDbR Version: 2.2.1 Depends: R (>= 3.3.0), rJava Imports: curl Suggests: BiocStyle, knitr, rmarkdown, testthat License: AGPL-3 MD5sum: 4bcfb4daf5033d9c0224f38445e73c6e NeedsCompilation: no Package: BrowserViz Version: 2.14.1 Depends: R (>= 3.5.0), jsonlite (>= 1.5), httpuv(>= 1.5.0) Imports: methods, BiocGenerics Suggests: RUnit, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 72c590ceea1534446a59a3b33b9395e0 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RUnit, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 50b1b1a560f8a69b5cd3afd14a8466c9 NeedsCompilation: no Package: BumpyMatrix Version: 1.0.1 Imports: utils, methods, Matrix, S4Vectors, IRanges Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 1eb71c420fb9ac68e0ea45c38518dc39 NeedsCompilation: no Package: BUS Version: 1.48.0 Depends: R (>= 2.3.0), minet Imports: stats, infotheo License: GPL-3 MD5sum: fcf872999125cf981e9112953fc1d1a0 NeedsCompilation: yes Package: BUScorrect Version: 1.10.0 Depends: R (>= 3.5.0) Imports: gplots, methods, grDevices, stats, SummarizedExperiment Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 769fd235046b9b7840ab1ce165099982 NeedsCompilation: yes Package: BUSpaRse Version: 1.6.1 Depends: R (>= 3.6) Imports: AnnotationDbi, AnnotationFilter, biomaRt, BiocGenerics, Biostrings, BSgenome, dplyr, ensembldb, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, IRanges, magrittr, Matrix, methods, plyranges, Rcpp, S4Vectors, stats, stringr, tibble, tidyr, utils, zeallot LinkingTo: Rcpp, RcppArmadillo, RcppProgress, BH Suggests: knitr, rmarkdown, testthat, BiocStyle, TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86 License: BSD_2_clause + file LICENSE MD5sum: a82009b4f7d9aa56416fb5017e081019 NeedsCompilation: yes Package: CAEN Version: 1.0.0 Depends: R (>= 4.1) Imports: stats,PoiClaClu,SummarizedExperiment,methods Suggests: knitr,rmarkdown License: GPL-2 MD5sum: 7edb7daa0585d3aea9201e8c6dc4a349 NeedsCompilation: no Package: CAFE Version: 1.28.0 Depends: R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio Imports: affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 4bb462d696b914d4fe34d26c6de8a6c0 NeedsCompilation: no Package: CAGEfightR Version: 1.12.0 Depends: R (>= 3.5), GenomicRanges (>= 1.30.1), rtracklayer (>= 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SummarizedExperiment, utils, vegan, VGAM Suggests: BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 2f1b075e0872267fc821a90189a3f5f0 NeedsCompilation: no Package: calm Version: 1.6.0 Imports: mgcv, stats, graphics Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: b076f5c4ecb6b8f768816776c22bb254 NeedsCompilation: no Package: CAMERA Version: 1.48.0 Depends: R (>= 2.1.0), methods, Biobase, xcms (>= 1.13.5) Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph Suggests: faahKO, RUnit, BiocGenerics Enhances: Rmpi, snow License: GPL (>= 2) MD5sum: 7b6e0ef39f4c9312bd0ebf80a2d5adef NeedsCompilation: yes Package: canceR Version: 1.26.0 Depends: R (>= 3.4), tcltk, tcltk2, cgdsr Imports: GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart, survival, Biobase, phenoTest, circlize, plyr, graphics, stats, utils, grDevices Suggests: testthat (>= 0.10.0), R.rsp License: GPL-2 MD5sum: 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gtools, GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors (>= 0.9.25), sqldf, survival, VGAM Enhances: parallel License: GPL (>= 2) MD5sum: 2f4e512c301672e60ab3d0781a69305f NeedsCompilation: yes Package: CATALYST Version: 1.16.2 Depends: R (>= 4.0), SingleCellExperiment Imports: circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot, data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel, ggridges, graphics, grDevices, grid, gridExtra, magrittr, Matrix, matrixStats, methods, nnls, purrr, RColorBrewer, reshape2, Rtsne, SummarizedExperiment, S4Vectors, scales, scater, stats Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot License: GPL (>= 2) MD5sum: 26f23531e16e1f4658fdb8050888969a NeedsCompilation: no Package: Category Version: 2.58.0 Depends: methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix Imports: utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db License: Artistic-2.0 MD5sum: 72b174edd876b795bb77cd3a9e4846df NeedsCompilation: no Package: categoryCompare Version: 1.36.0 Depends: R (>= 2.10), Biobase, BiocGenerics (>= 0.13.8), Imports: AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1), GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29), methods, grDevices, utils Suggests: knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter License: GPL-2 MD5sum: 8edbc2df0fd32ca7a37092c09590a373 NeedsCompilation: no Package: CausalR Version: 1.24.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 361104a2c5c80477a48f793a05f0a9d1 NeedsCompilation: no Package: cbaf Version: 1.14.0 Depends: R (>= 3.5.0) Imports: BiocFileCache, RColorBrewer, cgdsr, genefilter, gplots, grDevices, stats, utils, openxlsx Suggests: 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Imports: stats, S4Vectors, utils, methods, Matrix, SummarizedExperiment, SingleCellExperiment, Rtsne, graphics, grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp, Rdpack (>= 0.7) LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 630e8984c10f23498c6a4d207a708678 NeedsCompilation: yes Package: ccmap Version: 1.18.0 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: 1ab5bd227f78704f2b272b1362c04652 NeedsCompilation: no Package: CCPROMISE Version: 1.18.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: ae77835ff40d3572a4c76adc9e49597b NeedsCompilation: no Package: ccrepe Version: 1.28.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat License: MIT + file LICENSE MD5sum: 74136774f8a95c9278fef03507c324c9 NeedsCompilation: no Package: celaref Version: 1.10.0 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: ac3e928a5ad206ecc2c2a4b97fc9e9b4 NeedsCompilation: no Package: celda Version: 1.8.1 Depends: R (>= 4.0) 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, SingleCellExperiment, dbscan, DelayedArray, stringr, Matrix, ComplexHeatmap, multipanelfigure, circlize LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, M3DExampleData, TENxPBMCData, singleCellTK License: MIT + file LICENSE MD5sum: 3f5bf2a70d361085d3d5d13c3099a2db NeedsCompilation: yes Package: CellaRepertorium Version: 1.2.0 Depends: R (>= 4.0) Imports: dplyr, tibble, stringr, Biostrings, Rcpp, reshape2, methods, rlang (>= 0.3), purrr, Matrix, S4Vectors, BiocGenerics, tidyr, forcats, progress, stats, utils LinkingTo: Rcpp Suggests: testthat, readr, knitr, rmarkdown, ggplot2, BiocStyle, ggdendro, broom, lme4, RColorBrewer, SingleCellExperiment, scater, broom.mixed, cowplot License: GPL-3 MD5sum: 38e2c328a5909121a1051692686d19cd NeedsCompilation: yes Package: cellbaseR Version: 1.16.0 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: 4fef813c71599e936d0f8d532b85daf6 NeedsCompilation: no Package: CellBench Version: 1.8.0 Depends: R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils Imports: 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: 1e84294773bede7b35af0d6279ba0fe7 NeedsCompilation: no Package: cellHTS2 Version: 2.56.0 Depends: R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid Imports: GSEABase, Category, stats4, BiocGenerics Suggests: ggplot2 License: Artistic-2.0 MD5sum: a6b27848f0d4b869b9fb9b4e02d86762 NeedsCompilation: no Package: CelliD Version: 1.0.0 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: 2e85faa191b38954cbe24470643780e2 NeedsCompilation: yes Package: cellity Version: 1.20.0 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: 188cdc4549d56ebb0f31aeb887f1a002 NeedsCompilation: no Package: CellMapper Version: 1.18.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 MD5sum: 2841613fc2967ee425434f5aa551b7d7 NeedsCompilation: no Package: cellmigRation Version: 1.0.0 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, 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1.22.0 Depends: R (>= 3.3), topGO Imports: topicmodels, slam, maptpx, igraph, xtable, gplots Suggests: BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db, Biobase, tools License: Artistic-2.0 MD5sum: ed5ee3d7719c42b05416c74bb62b6141 NeedsCompilation: no Package: CEMiTool Version: 1.16.0 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: cde0a4dab48f5abc51804a9dc1171e68 NeedsCompilation: no Package: censcyt Version: 1.0.0 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: 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LinkingTo: BH, Rcpp Suggests: ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager, rmarkdown Enhances: ChemmineR (>= 2.13.0) License: file LICENSE MD5sum: ea2abea0c081f05f9ebecfdd0bb58b6a NeedsCompilation: yes Package: ChemmineR Version: 3.44.0 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 LinkingTo: Rcpp, BH Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png,rmarkdown, BiocManager Enhances: ChemmineOB License: Artistic-2.0 MD5sum: ba81826e7515f382c4c4bc72c5925130 NeedsCompilation: yes Package: CHETAH Version: 1.8.0 Depends: R (>= 3.6), ggplot2, SingleCellExperiment Imports: gplots, shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr License: file LICENSE MD5sum: 9e65b54e247ca639bc223b1b03901624 NeedsCompilation: no Package: ChIC Version: 1.12.0 Depends: spp, R (>= 3.6) Imports: ChIC.data (>= 1.11.1), caTools, methods, GenomicRanges, IRanges, parallel, progress, randomForest, caret, grDevices, stats, utils, graphics, S4Vectors, BiocGenerics, genomeIntervals, Rsamtools License: GPL-2 MD5sum: 92265bc933fea1af0f407cb373a5c4ea NeedsCompilation: no Package: Chicago Version: 1.20.0 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: 28fff879ee82bf7e9f014e07bde6264b NeedsCompilation: no Package: chimeraviz Version: 1.18.0 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: d8b1b19903fc4af4b3b286fba7970b06 NeedsCompilation: no Package: ChIPanalyser Version: 1.14.0 Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb Suggests: BSgenome.Dmelanogaster.UCSC.dm3,knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 66cfb57702c44322091eb950403d8e83 NeedsCompilation: no Package: ChIPComp Version: 1.22.0 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: 3da2d99cb5120a8b65a4c0e301f016d0 NeedsCompilation: yes Package: chipenrich 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GenomicFeatures, ggplot2, gplots, graphics, grDevices, gtools, methods, plotrix, dplyr, parallel, magrittr, RColorBrewer, rtracklayer, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, tibble License: Artistic-2.0 MD5sum: 18ff9e8b1a10956aac8584306dbe8cf2 NeedsCompilation: no Package: chipseq Version: 1.42.0 Depends: R (>= 2.10), 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 License: Artistic-2.0 MD5sum: d43c8958c7a40bd29f4b240dac4b9484 NeedsCompilation: yes Package: ChIPseqR Version: 1.46.0 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: 82429a53bd78744bc963f8b44068da79 NeedsCompilation: yes Package: ChIPsim Version: 1.46.0 Depends: Biostrings (>= 2.29.2) Imports: IRanges, XVector, Biostrings, ShortRead, graphics, methods, stats, utils Suggests: actuar, zoo License: GPL (>= 2) MD5sum: 397e67464730cb61853794f52aa5645a NeedsCompilation: no Package: ChIPXpress Version: 1.36.0 Depends: R (>= 2.10), ChIPXpressData Imports: Biobase, GEOquery, frma, affy, bigmemory, biganalytics Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 9807da3d4fc190a70c26b750991c3144 NeedsCompilation: no Package: chopsticks Version: 1.58.0 Imports: graphics, stats, utils, methods, survival Suggests: hexbin License: GPL-3 MD5sum: e87fe726ffe3e0a240dab8600097849e NeedsCompilation: yes Package: chromDraw Version: 2.22.0 Depends: R (>= 3.0.0) Imports: Rcpp (>= 0.11.1), GenomicRanges (>= 1.17.46) LinkingTo: Rcpp License: GPL-3 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stringdist, 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, Sushi, forcats, Rcpp, coop, matrixTests, DelayedArray LinkingTo: Rcpp Suggests: testthat, knitr, markdown, rmarkdown, BiocStyle, Signac, future License: GPL-3 MD5sum: ff2ee0ea1f13a255fcc3d9827e88cb4b NeedsCompilation: yes Package: chromstaR Version: 1.18.0 Depends: R (>= 3.3), 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: 6fbb3dba2abcf6d4e13157eef75dc6e9 NeedsCompilation: yes Package: chromswitch Version: 1.14.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.26.4) Imports: cluster (>= 2.0.6), Biobase (>= 2.36.2), BiocParallel (>= 1.8.2), dplyr (>= 0.5.0), gplots(>= 3.0.1), graphics, grDevices, IRanges (>= 2.4.8), lazyeval (>= 0.2.0), matrixStats (>= 0.52), magrittr (>= 1.5), methods, NMF (>= 0.20.6), rtracklayer (>= 1.36.4), S4Vectors (>= 0.23.19), stats, tidyr (>= 0.6.3) Suggests: BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3), GenomeInfoDb (>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3), testthat License: MIT + file LICENSE MD5sum: 36c3eaee85a16400486a338bd1bccc8b NeedsCompilation: no Package: chromVAR Version: 1.14.0 Depends: R (>= 3.4) Imports: IRanges, GenomeInfoDb, GenomicRanges, ggplot2, nabor, BiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools, S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats, utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment, RColorBrewer, BSgenome LinkingTo: Rcpp, RcppArmadillo Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr License: MIT + file LICENSE MD5sum: df45ce98b934b87ce7f2e6fd22a7e781 NeedsCompilation: yes Package: CHRONOS Version: 1.20.0 Depends: R (>= 3.5) Imports: XML, RCurl, RBGL, parallel, foreach, doParallel, openxlsx, igraph, circlize, graph, stats, utils, grDevices, graphics, methods, biomaRt, rJava Suggests: RUnit, BiocGenerics, knitr License: GPL-2 MD5sum: 62c92eced247aa9d363dc075e6d1c948 NeedsCompilation: no Package: cicero Version: 1.10.1 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, rmarkdown, rtracklayer (>= 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eulerr, foreach, doParallel, 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 License: MIT + file LICENSE MD5sum: f52c7fd88e3475eea17199908b34e589 NeedsCompilation: yes Package: combi Version: 1.4.0 Depends: R (>= 3.5.0) Imports: ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix, BB, reshape2, alabama, cobs, Biobase, vegan, grDevices, graphics, methods, SummarizedExperiment Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: f60c30036e3a7f9bced73fdd1cdd943f NeedsCompilation: no Package: coMET Version: 1.24.0 Depends: R (>= 3.7.0), grid, utils, biomaRt, Gviz, psych Imports: colortools, hash,grDevices, gridExtra, rtracklayer, IRanges, S4Vectors, GenomicRanges, stats, corrplot Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 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License: MIT + file LICENSE MD5sum: 2d88881dfec5c93b4917e025e825a1dd NeedsCompilation: no Package: CONFESS Version: 1.20.0 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: 5423a7f0339ee95fb91344e3ecf17223 NeedsCompilation: no Package: consensus Version: 1.10.0 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: 4493b38da76218f75dbc2291e966ccc9 NeedsCompilation: no Package: ConsensusClusterPlus Version: 1.56.0 Imports: Biobase, ALL, graphics, stats, utils, cluster License: GPL-2 MD5sum: 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SummarizedExperiment, tibble, XML (>= 3.98.1.17), readxl (>= 1.3.1) Suggests: knitr, rmarkdown, lydata, org.Hs.eg.db, testthat, tximportData License: MIT + file LICENSE MD5sum: 15b23ba1aca4e9ef3853f3213d96f13a NeedsCompilation: no Package: CSAR Version: 1.44.0 Depends: R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 MD5sum: 6a2968c445a2b0b152c6e4f5fde8ee77 NeedsCompilation: yes Package: csaw Version: 1.26.0 Depends: GenomicRanges, SummarizedExperiment Imports: Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, metapod, utils LinkingTo: Rhtslib, zlibbioc, Rcpp Suggests: AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager License: GPL-3 MD5sum: 138378af65a80e9d09c57fdc0e7fa85e NeedsCompilation: yes Package: CSSP Version: 1.30.0 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SingleCellExperiment, methods Imports: S4Vectors, BiocParallel, HDF5Array, DelayedArray, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5 Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat, shinytest License: GPL (>= 2) MD5sum: aa2375e4b8d82d978d06754d4d59c3cf NeedsCompilation: no Package: CytoML Version: 2.4.0 Depends: R (>= 3.5.0) Imports: cytolib(>= 2.3.9), flowCore (>= 1.99.10), flowWorkspace (>= 4.1.8), openCyto (>= 1.99.2), XML, data.table, jsonlite, RBGL, Rgraphviz, Biobase, methods, graph, graphics, utils, base64enc, plyr, dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, lattice, stats, corpcor, RUnit, tibble, RcppParallel, xml2 LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1), flowWorkspace Suggests: testthat, flowWorkspaceData , knitr, parallel License: file LICENSE License_restricts_use: yes MD5sum: 21bf73aa629cae06bd45f6ae6b7eb3c6 NeedsCompilation: yes Package: CytoTree Version: 1.2.0 Depends: R (>= 4.0), igraph Imports: FlowSOM, Rtsne, ggplot2, destiny, gmodels, flowUtils, Biobase, Matrix, flowCore, sva, matrixStats, methods, mclust, prettydoc, RANN(>= 2.5), Rcpp (>= 0.12.0), BiocNeighbors, cluster, pheatmap, scatterpie, umap, scatterplot3d, limma, stringr, grDevices, grid, stats LinkingTo: Rcpp Suggests: BiocGenerics, knitr, RColorBrewer, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 96f3edfd49f1d4155e1b42d672c1674b NeedsCompilation: yes Package: dada2 Version: 1.20.0 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: 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DaMiRseq Version: 2.4.3 Depends: R (>= 3.4), 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: 0452ae1e29276486edb6439d6f9dc571 NeedsCompilation: no Package: DAPAR Version: 1.24.8 Depends: R (>= 4.1.0) Imports: Biobase, MSnbase, tibble, RColorBrewer,stats,preprocessCore, Cairo,png, lattice,reshape2,gplots,pcaMethods,ggplot2, limma,knitr,tmvtnorm,norm,impute, stringr, grDevices, graphics, openxlsx, utils, cp4p (>= 0.3.5), scales, Matrix, vioplot, imp4p (>= 1.1), forcats, methods, DAPARdata (>= 1.22.2), siggenes, graph, lme4, readxl, highcharter, clusterProfiler, dplyr, tidyr,AnnotationDbi, tidyverse, vsn, FactoMineR, factoextra, multcomp, purrr, visNetwork, foreach, parallel, doParallel, igraph, dendextend, Mfuzz, apcluster, diptest, cluster Suggests: BiocGenerics, testthat, BiocStyle License: Artistic-2.0 MD5sum: cbb5442b2ee3f0c2de0465d87c9d64ed NeedsCompilation: no Package: DART Version: 1.40.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: f98cb3db55121e31639563fa499e465f NeedsCompilation: no Package: dasper Version: 1.2.0 Depends: R (>= 4.0) Imports: basilisk, BiocFileCache, BiocParallel, data.table, dplyr, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, magrittr, megadepth, methods, plyranges, readr, reticulate, S4Vectors, stringr, SummarizedExperiment, tidyr Suggests: BiocStyle, covr, testthat, GenomicState, ggplot2, ggpubr, ggrepel, grid, knitcitations, knitr, recount, rmarkdown, sessioninfo, rtracklayer, tibble License: Artistic-2.0 MD5sum: 07a4332113458a5634d46752ad6c8257 NeedsCompilation: no Package: dcanr Version: 1.8.0 Depends: R (>= 3.6.0) Imports: igraph, foreach, plyr, stringr, reshape2, methods, Matrix, graphics, stats, RColorBrewer, circlize, doRNG Suggests: EBcoexpress, testthat, EBarrays, GeneNet, COSINE, mclust, minqa, SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle, edgeR Enhances: parallel, doSNOW, doParallel License: GPL-3 MD5sum: 1bdda7118a9c6e896f94efc007c415ce NeedsCompilation: no Package: dce Version: 1.0.0 Depends: R (>= 4.1) Imports: stats, methods, assertthat, graph, pcalg, purrr, tidyverse, Matrix, ggraph, tidygraph, ggplot2, rlang, expm, MASS, CombinePValue, edgeR, epiNEM, igraph, metap, mnem, naturalsort, ppcor, glm2, graphite, reshape2, dplyr, glue, Rgraphviz, harmonicmeanp, org.Hs.eg.db, logger Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, cowplot, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment License: GPL-3 MD5sum: 84a72ddae24812ca80b5c3af07d9cd2b NeedsCompilation: no Package: dcGSA Version: 1.20.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: 82aadb34484631987b7a8ac2062ba829 NeedsCompilation: no Package: ddCt Version: 1.48.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: RUnit License: LGPL-3 MD5sum: 28790fa3bfed64f83cef15a48b386f20 NeedsCompilation: no Package: ddPCRclust Version: 1.12.0 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: fc72ecedd74a5349756efe23e34a7dd0 NeedsCompilation: no Package: dearseq Version: 1.4.0 Depends: R (>= 3.6.0) Imports: CompQuadForm, ggplot2, KernSmooth, matrixStats, methods, parallel, pbapply, stats, statmod Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr License: GPL-2 | file LICENSE MD5sum: b0c0828bea8f7737358dec0ca3155b3a NeedsCompilation: no Package: debCAM Version: 1.10.0 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: 7123accf3a3735a530f6dda097fc10c1 NeedsCompilation: no Package: debrowser Version: 1.20.1 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: 501243e26cd9048b0789201ab52897c2 NeedsCompilation: no Package: DECIPHER Version: 2.20.0 Depends: R (>= 3.5.0), Biostrings (>= 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dplyr, GSVA, magrittr, Matrix, purrr, rlang, speedglm, stats, stringr, tibble, tidyr, tidyselect, viper, withr Suggests: BiocStyle, covr, knitr, pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo, testthat License: GPL-3 MD5sum: 839daedb272bf0444bb11463bbe70330 NeedsCompilation: no Package: DeepBlueR Version: 1.18.0 Depends: R (>= 3.3), XML, RCurl Imports: GenomicRanges, data.table, stringr, diffr, dplyr, methods, rjson, utils, R.utils, foreach, withr, rtracklayer, GenomeInfoDb, settings, filehash Suggests: knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr, RColorBrewer, matrixStats License: GPL (>= 2.0) MD5sum: 587ed5c34f8eef9523cc078a9d934ef1 NeedsCompilation: no Package: DeepPINCS Version: 1.0.2 Depends: keras, tensorflow, R (>= 4.1) Imports: CatEncoders, matlab, rcdk, stringdist, tokenizers, webchem, purrr, ttgsea, PRROC, reticulate, stats Suggests: knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: f90cccb077ff206d4241f219fb60d531 NeedsCompilation: no Package: deepSNV 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LGPL (>= 3) MD5sum: aa4d4eda6d86fcf9b6b05689891a8ca5 NeedsCompilation: yes Package: DEGraph Version: 1.44.0 Depends: R (>= 2.10.0), R.utils Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph License: GPL-3 MD5sum: d76bef855a9f02c439417e67c48989be NeedsCompilation: no Package: DEGreport Version: 1.28.0 Depends: R (>= 3.6.0) Imports: utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, lasso2, magrittr, Nozzle.R1, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE MD5sum: 83052fb100579c58c49429a5dfbbb9ab NeedsCompilation: no Package: DEGseq Version: 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rmarkdown, shiny License: LGPL MD5sum: 050d351fb103eb5b12f36266abe9d1c4 NeedsCompilation: yes Package: EBSEA Version: 1.20.0 Depends: R (>= 4.0.0) Imports: DESeq2, graphics, stats, EmpiricalBrownsMethod Suggests: knitr, rmarkdown License: GPL-2 MD5sum: c9213bc13f17c856620b611159817061 NeedsCompilation: no Package: EBSeq Version: 1.32.0 Depends: blockmodeling, gplots, testthat, R (>= 3.0.0) License: Artistic-2.0 MD5sum: 19f459f3de57052ccfde1233b2160675 NeedsCompilation: no Package: EBSeqHMM Version: 1.26.0 Depends: EBSeq License: Artistic-2.0 MD5sum: 0da1eaba0ddb29ecd1f87222e1ea5c90 NeedsCompilation: no Package: ecolitk Version: 1.64.0 Depends: R (>= 2.10) Imports: Biobase, graphics, methods Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy License: GPL (>= 2) MD5sum: f9a34386b1ca4880f92546d9a75faa07 NeedsCompilation: no Package: EDASeq Version: 2.26.1 Depends: Biobase (>= 2.15.1), ShortRead (>= 1.11.42) Imports: methods, graphics, BiocGenerics, IRanges (>= 1.13.9), aroma.light, 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Suggests: knitr, rmarkdown Enhances: doMC, multicore License: Artistic-2.0 MD5sum: 08443b9702c260df0415fbaa54d3eb7f NeedsCompilation: no Package: flowPeaks Version: 1.38.0 Depends: R (>= 2.12.0) Enhances: flowCore License: Artistic-1.0 MD5sum: e9f07b362494a00a5ab14351da420cbf NeedsCompilation: yes Package: flowPloidy Version: 1.18.0 Imports: flowCore, car, caTools, knitr, rmarkdown, minpack.lm, shiny, methods, graphics, stats, utils Suggests: flowPloidyData, testthat License: GPL-3 MD5sum: 9d7c100bdb9b4ad1df7f901e9286e970 NeedsCompilation: no Package: flowPlots Version: 1.40.0 Depends: R (>= 2.13.0), methods Suggests: vcd License: Artistic-2.0 MD5sum: 422de928885d653973b33babc12b1812 NeedsCompilation: no Package: FlowRepositoryR Version: 1.23.0 Depends: R (>= 3.2) Imports: XML, RCurl, tools, utils, jsonlite Suggests: RUnit, BiocGenerics, flowCore, methods License: Artistic-2.0 MD5sum: 0718e29c9f61615b249a342c6adacca0 NeedsCompilation: no Package: FlowSOM Version: 2.0.0 Depends: R (>= 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stats, cluster, utils, KernSmooth, lattice, ks, RColorBrewer, rrcov Suggests: xtable, testthat, openCyto Enhances: RBGL,graph License: Artistic-2.0 MD5sum: 8396614b53bfc338bd1ba5562e039cfa NeedsCompilation: no Package: flowTime Version: 1.16.1 Depends: R (>= 3.4), flowCore Imports: utils, dplyr (>= 1.0.0), tibble, magrittr, plyr, rlang Suggests: knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, stats, flowClust, openCyto, flowStats, ggcyto License: Artistic-2.0 MD5sum: b16c4e26f6b48cd1910f68415998efca NeedsCompilation: no Package: flowTrans Version: 1.44.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 MD5sum: 348699f440d4bd44be6d2221cc411a51 NeedsCompilation: no Package: flowUtils Version: 1.56.0 Depends: R (>= 2.2.0) Imports: Biobase, graph, methods, stats, utils, corpcor, RUnit, XML, flowCore (>= 1.32.0) Suggests: gatingMLData License: Artistic-2.0 MD5sum: dd39163bd7144dfd7c2ee6ca882a04fa 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LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib (>= 2.3.7),Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1) Suggests: testthat, flowWorkspaceData (>= 2.23.2), knitr, ggcyto, parallel, CytoML, openCyto License: file LICENSE License_restricts_use: yes MD5sum: 7c871faaf53cfca2e0d10ee9b6e81189 NeedsCompilation: yes Package: fmcsR Version: 1.34.0 Depends: R (>= 2.10.0), ChemmineR, methods Imports: RUnit, methods, ChemmineR, BiocGenerics, parallel Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap,rmarkdown License: Artistic-2.0 MD5sum: b938405424e87121ae4b87d823fc2a18 NeedsCompilation: yes Package: fmrs Version: 1.2.0 Depends: R (>= 4.0.0) Imports: methods, survival, stats Suggests: BiocGenerics, testthat, knitr, utils License: GPL (>= 3) MD5sum: 65c15515082a303aa26587a03a494da2 NeedsCompilation: yes Package: fobitools Version: 1.0.0 Depends: R (>= 4.1) Imports: clisymbols, crayon, dplyr, fgsea, ggplot2, ggraph, magrittr, ontologyIndex, purrr, RecordLinkage, stringr, textclean, tictoc, tidygraph, tidyr, vroom Suggests: BiocStyle, covr, ggrepel, kableExtra, knitr, metabolomicsWorkbenchR, POMA, rmarkdown, rvest, SummarizedExperiment, testthat (>= 2.3.2), tidyverse License: GPL-3 MD5sum: 571db4ec49549003ef7759653818ddf0 NeedsCompilation: no Package: FoldGO Version: 1.10.0 Depends: R (>= 4.0) Imports: topGO (>= 2.30.1), ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), stats, methods Suggests: knitr, rmarkdown, devtools, kableExtra License: GPL-3 MD5sum: 686728ba47a787737b7283e54df9c68a NeedsCompilation: no Package: FRASER Version: 1.4.0 Depends: BiocParallel, data.table, Rsamtools, SummarizedExperiment Imports: AnnotationDbi, BBmisc, Biobase, BiocGenerics, biomaRt, BSgenome, cowplot, DelayedArray (>= 0.5.11), DelayedMatrixStats, extraDistr, generics, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges, grDevices, ggplot2, ggrepel, HDF5Array, matrixStats, methods, OUTRIDER, pcaMethods, pheatmap, plotly, PRROC, RColorBrewer, rhdf5, Rsubread, R.utils, S4Vectors, stats, tibble, tools, utils, VGAM LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, covr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, License: MIT + file LICENSE MD5sum: 554a5ead744a51a5e0f834d475b02e7e NeedsCompilation: yes Package: frenchFISH Version: 1.4.0 Imports: utils, MCMCpack, NHPoisson Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: a65d618d00555195248eeaa508fc7652 NeedsCompilation: no Package: FRGEpistasis Version: 1.28.0 Depends: R (>= 2.15), MASS, fda, methods, stats Imports: utils License: GPL-2 MD5sum: 6f9efdfdb9287727bb23ff7dba6d5ce4 NeedsCompilation: no Package: frma Version: 1.44.0 Depends: R (>= 2.10.0), Biobase (>= 2.6.0) Imports: Biobase, MASS, DBI, affy, methods, oligo, oligoClasses, preprocessCore, utils, BiocGenerics Suggests: hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: e469fc86ed9a0935437ed932d3dd3ad0 NeedsCompilation: no Package: frmaTools Version: 1.44.0 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igraph, graph, RBGL, GO.db, org.Hs.eg.db, org.Mm.eg.db, GOSemSim, GEOquery, AnnotationDbi, Biobase, BiocFileCache, matrixStats Suggests: org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Dr.eg.db, org.Ce.eg.db, org.At.tair.db, org.EcK12.eg.db, org.Bt.eg.db, org.Cf.eg.db, org.Ag.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Pt.eg.db, org.Pf.plasmo.db, org.Mmu.eg.db, org.Ss.eg.db, org.Xl.eg.db, testthat, pryr, knitr, rmarkdown, prettydoc, ggplot2, kableExtra, profvis, reshape2 License: MIT + file LICENSE MD5sum: 701fc46ae79289d4c314abb2873b8cb1 NeedsCompilation: no Package: GAprediction Version: 1.18.0 Depends: R (>= 3.3) Imports: glmnet, stats, utils, Matrix Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: f18abfea6e9c8270875f41bc70dbce65 NeedsCompilation: no Package: garfield Version: 1.20.0 Suggests: knitr License: GPL-3 MD5sum: dfce0c090510b7af183487a54b5dadf1 NeedsCompilation: yes Package: GARS Version: 1.12.0 Depends: R (>= 3.5), ggplot2, cluster Imports: DaMiRseq, MLSeq, stats, 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1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: 0b4e06d3d0208e643418cc48eb9f3f41 NeedsCompilation: no Package: genbankr Version: 1.20.0 Depends: methods Imports: BiocGenerics, IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), GenomicFeatures (>= 1.31.5), Biostrings, VariantAnnotation, rtracklayer, S4Vectors (>= 0.17.28), GenomeInfoDb, Biobase Suggests: RUnit, rentrez, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: cffa22acf248d889d4725ffc0e57e61b NeedsCompilation: no Package: GeneAccord Version: 1.10.0 Depends: R (>= 3.5) Imports: biomaRt, caTools, dplyr, ggplot2, graphics, grDevices, gtools, ggpubr, magrittr, maxLik, RColorBrewer, reshape2, stats, tibble, utils Suggests: assertthat, BiocStyle, devtools, knitr, rmarkdown, testthat License: file LICENSE MD5sum: d4fb31c743ecd6b2592b90541142dd02 NeedsCompilation: no Package: geneAttribution Version: 1.18.0 Imports: 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Depends: R (>= 3.3), methods Imports: igraph, snow, ape, grDevices, graphics, stats, utils, data.table Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: 2f248f65322d91bbc9aa7d7981755e31 NeedsCompilation: no Package: geneplotter Version: 1.70.0 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 License: Artistic-2.0 MD5sum: 3cebdd28df88565dc31a3e0d03c76023 NeedsCompilation: no Package: geneRecommender Version: 1.64.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: 89008ca69a800e78e66f6dcfc31f3046 NeedsCompilation: no Package: GeneRegionScan Version: 1.48.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), 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GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.41.5), 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, BiocStyle License: Artistic-2.0 MD5sum: 620d245c87edd17f00b589bd3661040b NeedsCompilation: yes Package: GenomicDataCommons Version: 1.16.0 Depends: R (>= 3.4.0), magrittr Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, SummarizedExperiment, S4Vectors, tibble Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools License: Artistic-2.0 MD5sum: a3e66a51579b75e25df9ea96adc2a989 NeedsCompilation: no Package: GenomicDistributions Version: 1.0.0 Depends: R (>= 4.0), IRanges, GenomicRanges Imports: data.table, ggplot2, reshape2, methods, utils, Biostrings, Suggests: AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown Enhances: BSgenome, extrafont, ensembldb, GenomicFeatures License: BSD_2_clause + file LICENSE MD5sum: c87f17315d1283d946a0108561b6bd6f NeedsCompilation: no Package: GenomicFeatures Version: 1.44.2 Depends: BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29), IRanges (>= 2.13.23), GenomeInfoDb (>= 1.25.7), GenomicRanges (>= 1.31.17), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl, XVector (>= 0.19.7), Biostrings (>= 2.47.6), BiocIO, rtracklayer (>= 1.51.5), biomaRt (>= 2.17.1), Biobase (>= 2.15.1) Suggests: RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 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XML, Biobase, BiocManager, BiocFileCache, IRanges (>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub, rhdf5, DelayedArray, HDF5Array Suggests: RUnit, BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5, SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard License: Artistic-2.0 MD5sum: 8a95a891e0b7f595aebe6f2cc452906a NeedsCompilation: no Package: GenomicSuperSignature Version: 1.0.1 Depends: R (>= 4.0), SummarizedExperiment Imports: ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable 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: 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BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, S4Vectors, stats, utils Suggests: BiocStyle, GSE62944, knitr, rmarkdown License: Artistic-2.0 MD5sum: ab9e4124b0208a90cba53a3c343a6bb2 NeedsCompilation: no Package: GSEAlm Version: 1.52.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: 512767e6b0906042f4bd6384f07de72f NeedsCompilation: no Package: GSEAmining Version: 1.2.0 Depends: R (>= 4.0) Imports: dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud, stringr, gridExtra, rlang, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat License: GPL-3 | file LICENSE MD5sum: 53edb681143aedb193a2ffe9c6499cae NeedsCompilation: no Package: gsean Version: 1.12.0 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, knitr, plotly, RANKS, WGCNA, 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utils, grid, methods, DBI, RMySQL, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2 Suggests: clinfun, knitr, BSgenome.Hsapiens.UCSC.hg19 License: GPL-2 MD5sum: 49725658571c118ce7ca30b2405fac89 NeedsCompilation: no Package: InterMineR Version: 1.14.1 Depends: R (>= 3.4.1) Imports: Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, igraph, httr, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, methods Suggests: BiocStyle, Gviz, knitr, rmarkdown, GeneAnswers, GO.db, org.Hs.eg.db License: LGPL MD5sum: 97052789bf1e59a46470865e3c8333db NeedsCompilation: no Package: IntramiRExploreR Version: 1.14.1 Depends: R (>= 3.4) Imports: igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats, utils, grDevices, graphics Suggests: RDAVIDWebService, gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat License: GPL-2 MD5sum: 0fc2029d8fa83f258ac36fa94d51a7bf NeedsCompilation: no Package: inveRsion Version: 1.40.0 Depends: methods, haplo.stats Imports: graphics, methods, utils License: 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tidyr, tibble Suggests: knitr, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 0d43608d670381601c169b985a776343 NeedsCompilation: no Package: ITALICS Version: 2.52.0 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: 65a7dcef71307fa88012532aacde7366 NeedsCompilation: no Package: iterativeBMA Version: 1.50.0 Depends: BMA, leaps, Biobase (>= 2.5.5) License: GPL (>= 2) MD5sum: ec48084033cc956a1d4ec31cc512453f NeedsCompilation: no Package: iterativeBMAsurv Version: 1.50.0 Depends: BMA, leaps, survival, splines Imports: graphics, grDevices, stats, survival, utils License: GPL (>= 2) MD5sum: b65f06f38db46353488199a4ac9f79fd NeedsCompilation: no Package: iterClust Version: 1.14.0 Depends: R (>= 3.4.1) Imports: Biobase, cluster, stats, methods Suggests: tsne, 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sfsmisc, progress, utils Suggests: rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, downloader, R.utils, doParallel, reshape2, JASPAR2020, TFBSTools, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr, jpeg, sesame, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 MD5sum: e2ef11a1eb3c509519c10e4589727fd3 NeedsCompilation: no Package: methrix Version: 1.6.0 Depends: R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment Imports: rtracklayer, DelayedArray, HDF5Array, BSgenome, DelayedMatrixStats, parallel, methods, ggplot2, matrixStats, graphics, stats, utils, GenomicRanges, IRanges Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: fe3845bddb1814ecc3d4775db9a00ad4 NeedsCompilation: no Package: MethTargetedNGS Version: 1.24.0 Depends: R (>= 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MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: e80b4f434c1c4d8e9b0e469aa2e2a1d6 NeedsCompilation: no Package: methylCC Version: 1.6.0 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: knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: CC BY 4.0 MD5sum: 38b105da59d89428535ed1f1ae9e1240 NeedsCompilation: no Package: methylGSA Version: 1.10.0 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: d737ec8552755c04780709a69ac9dc8a NeedsCompilation: no Package: methylInheritance Version: 1.16.0 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: a3b00c49542bfbff118446b76dbde5ea NeedsCompilation: no Package: methylKit Version: 1.18.0 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: 18d2329199dd6e51af592930c8ae59dd NeedsCompilation: yes Package: MethylMix Version: 2.22.0 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: 2db0a87d1ca9b89e683624042a1c8713 NeedsCompilation: no Package: methylMnM Version: 1.30.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: c27bb054aa2f8e0c1e63be01423c2c63 NeedsCompilation: yes Package: methylPipe Version: 1.26.0 Depends: R (>= 3.2.0), 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: 5752a0296587863bf07777795b0f64e2 NeedsCompilation: yes Package: methylscaper Version: 1.0.1 Depends: R (>= 4.1.0) Imports: shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment Suggests: knitr, rmarkdown, devtools License: GPL-2 MD5sum: 3bea4e2fd7e6e2cda71eaedd50c3c058 NeedsCompilation: no Package: MethylSeekR Version: 1.32.0 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: 416e9aca89ff66e0e70b56e49d03414e NeedsCompilation: no Package: methylSig Version: 1.4.0 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: 672d1cde07bfaec6bd7d2257bc14743e NeedsCompilation: no Package: methylumi Version: 2.38.0 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 Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, methyAnalysis, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 MD5sum: 414501b1e8fa6c6386723328d5c664c5 NeedsCompilation: no Package: MetID Version: 1.10.0 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: 869d4e6f598bae15429654e00e3b2ffa NeedsCompilation: no Package: MetNet Version: 1.10.0 Depends: R (>= 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tkWidgets Suggests: marray License: GPL-2 MD5sum: f77dd8af3a2e27011f3952d3c855b8cf NeedsCompilation: no Package: MGFM Version: 1.26.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 MD5sum: 27447a5d51d607e8b1daa9011b453120 NeedsCompilation: no Package: MGFR Version: 1.18.0 Depends: R (>= 3.5) Imports: biomaRt, annotate License: GPL-3 MD5sum: 9fa0cdd66b9e9083ef718bf3a40b8e37 NeedsCompilation: no Package: mgsa Version: 1.40.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: 5b12edb853e1765fcc8f516aff935a8b NeedsCompilation: yes Package: mia Version: 1.0.8 Depends: R (>= 4.1), SummarizedExperiment, SingleCellExperiment, TreeSummarizedExperiment (>= 1.99.3) Imports: methods, stats, utils, MASS, ape, decontam, vegan, BiocGenerics, S4Vectors, IRanges, Biostrings, DECIPHER, BiocParallel, DelayedArray, DelayedMatrixStats, scuttle, scater, DirichletMultinomial, rlang, dplyr, tibble, tidyr Suggests: testthat, knitr, patchwork, BiocStyle, yaml, phyloseq, dada2, stringr, biomformat, reldist, ade4, microbiomeDataSets, rmarkdown License: Artistic-2.0 | file LICENSE MD5sum: 7c9226a22fcceb91ba691c4af036bc4c NeedsCompilation: no Package: miaViz Version: 1.0.1 Depends: R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment, mia (>= 0.99), ggplot2, ggraph (>= 2.0) Imports: methods, stats, S4Vectors, BiocGenerics, BiocParallel, DelayedArray, scater, ggtree, ggnewscale, viridis, tibble, tidytree, tidygraph, rlang, purrr, tidyr, dplyr, ape, DirichletMultinomial Suggests: knitr, rmarkdown, BiocStyle, testthat, patchwork, microbiomeDataSets License: Artistic-2.0 | file LICENSE MD5sum: 5ed31ae14843adc8f4eb365ab5c09e6b NeedsCompilation: no Package: MiChip Version: 1.46.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: 31ded3a49c080a0e7a76fa62258402c6 NeedsCompilation: no Package: microbiome Version: 1.14.0 Depends: R (>= 3.6.0), phyloseq, ggplot2 Imports: dplyr, reshape2, Rtsne, scales, stats, tibble, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE MD5sum: 228d381c68d58a8ead919e2dc7b21f16 NeedsCompilation: no Package: microbiomeDASim Version: 1.6.0 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: a507cf92a6f6af523fd3053aa502d804 NeedsCompilation: no Package: microbiomeExplorer Version: 1.2.0 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: f516d38629730d783d88adc40751ee84 NeedsCompilation: no Package: MicrobiotaProcess Version: 1.4.4 Depends: R (>= 4.0.0) Imports: ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.3.5), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, picante, plyr, DECIPHER, randomForest, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, corrr, ggupset, ggVennDiagram, gghalves, ggalluvial, forcats, pillar, cli, phyloseq, aplot, ggnewscale, ggside, ggtreeExtra License: GPL (>= 3.0) MD5sum: 0cbf3a641ffc595f5247fead7381a18d NeedsCompilation: no Package: microRNA Version: 1.50.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: 199c6fdbd3065917df2645fe70242905 NeedsCompilation: yes Package: midasHLA Version: 1.0.0 Depends: R (>= 4.1), MultiAssayExperiment (>= 1.8.3) Imports: assertthat (>= 0.2.0), broom (>= 0.5.1), dplyr (>= 0.8.0.1), formattable (>= 0.2.0.1), HardyWeinberg (>= 1.6.3), kableExtra (>= 1.1.0), knitr (>= 1.21), magrittr (>= 1.5), methods, stringi (>= 1.2.4), rlang (>= 0.3.1), S4Vectors (>= 0.20.1), stats, SummarizedExperiment (>= 1.12.0), tibble (>= 2.0.1), utils, qdapTools (>= 1.3.3) Suggests: broom.mixed (>= 0.2.4), cowplot (>= 1.0.0), devtools (>= 2.0.1), ggplot2 (>= 3.1.0), ggpubr (>= 0.2.5), rmarkdown, seqinr (>= 3.4-5), survival (>= 2.43-3), testthat (>= 2.0.1), tidyr (>= 1.1.2) License: MIT + file LICENCE MD5sum: b6bf40d69c1dde3c8afd3292e164ff35 NeedsCompilation: no Package: MIGSA Version: 1.16.0 Depends: R (>= 3.4), methods, BiocGenerics Imports: AnnotationDbi, Biobase, BiocParallel, compiler, data.table, edgeR, futile.logger, ggdendro, ggplot2, GO.db, GOstats, graph, graphics, grDevices, grid, GSEABase, ismev, jsonlite, limma, matrixStats, org.Hs.eg.db, RBGL, reshape2, Rgraphviz, stats, utils, vegan Suggests: BiocStyle, breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, knitr, mGSZ, MIGSAdata, RUnit License: GPL (>= 2) MD5sum: 16b8ebbdde22ef9b2f3eebdae9882347 NeedsCompilation: no Package: miloR Version: 1.0.0 Depends: R (>= 4.0.0), edgeR Imports: BiocNeighbors, SingleCellExperiment, Matrix (>= 1.3-0), S4Vectors, stats, stringr, methods, igraph, irlba, cowplot, BiocParallel, BiocSingular, limma, ggplot2, tibble, matrixStats, ggraph, gtools, SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices Suggests: testthat, MASS, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, BiocStyle, MouseGastrulationData, magick, RCurl, curl, graphics License: GPL-3 + file LICENSE MD5sum: dcf68be268133fb88791cb95df62eec1 NeedsCompilation: no Package: mimager Version: 1.16.0 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: eb58c7979fa3e766b7584aa4267aebf0 NeedsCompilation: no Package: MIMOSA Version: 1.30.0 Depends: R (>= 3.0.2), MASS, plyr, reshape, Biobase, ggplot2 Imports: methods, Formula, data.table, pracma, MCMCpack, coda, modeest, testthat, Rcpp, scales, dplyr, tidyr, rlang LinkingTo: Rcpp, RcppArmadillo Suggests: parallel, knitr License: MIT + file LICENSE MD5sum: cfc8965ed26241b73e5e9b37e0d60e0e NeedsCompilation: yes Package: mina Version: 1.0.0 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: 52eaea105165b8ee48155bf34aa5476e NeedsCompilation: yes Package: 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org.Hs.eg.db Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 6abf4d0343deede79ba0f9ab5f515522 NeedsCompilation: yes Package: mirTarRnaSeq Version: 1.0.0 Depends: R (>= 4.1.0) Imports: purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap, reshape2, corrplot, grDevices, graphics, stats, utils, data.table, R.utils Suggests: BiocStyle, knitr, rmarkdown, R.cache License: MIT MD5sum: e65fcab6f3da1f406e7539b0987a25b1 NeedsCompilation: no Package: missMethyl Version: 1.26.1 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, 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 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tidyr, VariantTools, magrittr, methods, grDevices, graphics, stats, utils, stringr, data.table Suggests: testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle, MMAPPR2data License: GPL-3 OS_type: unix MD5sum: 4e7811bdab26aef7553eda91de37d931 NeedsCompilation: no Package: MMDiff2 Version: 1.20.0 Depends: R (>= 3.3), 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: c2a5883fb9ed8982c4739bfd752dee56 NeedsCompilation: no Package: MMUPHin Version: 1.6.2 Depends: R (>= 3.6) Imports: Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr, cowplot, utils, stats, grDevices Suggests: testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter License: MIT + file LICENSE MD5sum: 4fc674258bcd52e0fbafaa893cefb858 NeedsCompilation: no Package: 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stringi Suggests: knitr, testthat, Seurat, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown, data.table, tidyverse, BiocStyle, Matrix License: GPL (>= 2) + file LICENSE MD5sum: c179e9c976d2633e5f3d8210102df1a0 NeedsCompilation: yes Package: MOGAMUN Version: 1.2.1 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: BiocStyle, knitr, rmarkdown, markdown License: GPL-3 + file LICENSE MD5sum: bca30f71429e10202f229f113c45136e NeedsCompilation: no Package: mogsa Version: 1.26.0 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: 14016f6e6de2f3d6e121a894c9d3fb69 NeedsCompilation: no Package: MOMA Version: 1.4.0 Depends: R (>= 4.0) Imports: circlize, cluster, ComplexHeatmap, dplyr, ggplot2, 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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 License: GPL (>= 3) MD5sum: 70615486888da4c4d4c7623b0679119e NeedsCompilation: no Package: mosaics Version: 2.30.0 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: d0c48eccc3bd7614462a2b0638dd08d7 NeedsCompilation: yes Package: MOSim Version: 1.6.0 Depends: R (>= 3.6) Imports: HiddenMarkov, zoo, methods, matrixStats, dplyr, stringi, lazyeval, rlang, stats, utils, purrr, scales, stringr, tibble, tidyr, ggplot2, Biobase, IRanges, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 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cd7e9be5e4fa53657e418c25271d9fd5 NeedsCompilation: yes Package: MSnID Version: 1.26.0 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: 48e1af3bb36cca32e6a75ee317b025a2 NeedsCompilation: no Package: MSPrep Version: 1.2.0 Depends: R (>= 4.0) Imports: SummarizedExperiment, S4Vectors, pcaMethods (>= 1.24.0), VIM, crmn, preprocessCore, sva, dplyr (>= 0.7), tidyr, tibble (>= 1.2), magrittr, rlang, stats, stringr, methods, ddpcr, missForest Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 1.0.2) License: GPL-3 MD5sum: 190a17cbcd4341cdf19084523aaf384e NeedsCompilation: no Package: msPurity Version: 1.18.0 Depends: Rcpp Imports: plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite, uuid, jsonlite Suggests: testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL License: GPL-3 + file LICENSE MD5sum: 94f0f8b7c583e99e971f20cf35f7de6a NeedsCompilation: no Package: msqrob2 Version: 1.0.0 Depends: R (>= 4.1), QFeatures (>= 1.1.2) Imports: stats, methods, lme4, purrr, BiocParallel, Matrix, MASS, limma, SummarizedExperiment, codetools Suggests: multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata, MSnbase, matrixStats, MsCoreUtils License: Artistic-2.0 MD5sum: 120e1d0f66e3561a6640d6e26e672351 NeedsCompilation: no Package: MSstats Version: 4.0.1 Depends: R (>= 4.0) Imports: MSstatsConvert, data.table, checkmate, MASS, limma, lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel, gplots, marray, stats, grDevices, graphics, methods LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, MSstatsBioData, tinytest, covr, markdown License: Artistic-2.0 MD5sum: 4a8db1098019f4195d19dd75580c7b66 NeedsCompilation: yes Package: MSstatsConvert Version: 1.2.2 Depends: R (>= 4.0) Imports: data.table, log4r, methods, checkmate, utils, stringi Suggests: tinytest, covr, knitr, rmarkdown License: Artistic-2.0 MD5sum: 7aa2ecb0ad3622a92e6037e6443de6aa NeedsCompilation: no Package: MSstatsLOBD Version: 1.0.0 Depends: R (>= 4.0) Imports: minpack.lm, ggplot2, utils, stats, grDevices LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr License: Artistic-2.0 MD5sum: 82a7e9ec14f26b7fe9959796595881ab NeedsCompilation: no Package: MSstatsPTM Version: 1.2.4 Depends: R (>= 4.0) Imports: dplyr, gridExtra, stringr, stats, ggplot2, grDevices, MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp, Biostrings, checkmate, ggrepel LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, tinytest, covr License: Artistic-2.0 MD5sum: ffa6cc81d7e3fb35b738167a8d778be3 NeedsCompilation: yes Package: MSstatsQC Version: 2.10.0 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: a52fb8e075ac03f3c5fe904d5e81bb73 NeedsCompilation: no Package: MSstatsQCgui Version: 1.12.0 Imports: shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid Suggests: knitr License: Artistic License 2.0 MD5sum: e7b201324c1e3fb248ea82c1db4c7774 NeedsCompilation: no Package: MSstatsSampleSize Version: 1.6.0 Depends: R (>= 3.6) Imports: ggplot2, BiocParallel, caret, gridExtra, reshape2, stats, utils, grDevices, graphics, MSstats Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: ee7aebbb949ecf3c342966a022cd59f4 NeedsCompilation: no Package: MSstatsTMT Version: 2.0.1 Depends: R (>= 4.0) Imports: limma, lme4, lmerTest, methods, data.table, stats, utils, ggplot2, grDevices, graphics, MSstats, MSstatsConvert, checkmate Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: fed248cc945797df7b7473eefaa061cc NeedsCompilation: no Package: MSstatsTMTPTM Version: 1.1.2 Depends: R (>= 4.0) Imports: dplyr, gridExtra, stringr, reshape2, stats, utils, ggplot2, grDevices, graphics, MSstatsTMT, Rcpp LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, testthat, MSstats, covr License: Artistic-2.0 MD5sum: 85291fa2ab550bcb46fca3d8387b5d6f NeedsCompilation: yes Package: Mulcom Version: 1.42.0 Depends: R (>= 2.10), Biobase Imports: graphics, grDevices, stats, methods, fields License: GPL-2 MD5sum: 763041df2e7bd75334840c33425b0cc5 NeedsCompilation: yes Package: MultiAssayExperiment Version: 1.18.0 Depends: R (>= 4.0.0), SummarizedExperiment (>= 1.3.81) Imports: methods, GenomicRanges (>= 1.25.93), BiocGenerics, S4Vectors (>= 0.23.19), IRanges, Biobase, stats, tidyr, utils Suggests: BiocStyle, HDF5Array (>= 1.19.17), knitr, maftools (>= 2.7.10), rmarkdown, R.rsp, RaggedExperiment, UpSetR, survival, survminer, testthat License: Artistic-2.0 MD5sum: cf09a85c83a09eec33c7f6bd11937f90 NeedsCompilation: no Package: MultiBaC Version: 1.2.0 Imports: Matrix, ggplot2, MultiAssayExperiment, ropls, graphics, methods Suggests: knitr, rmarkdown, BiocStyle, devtools License: GPL-3 MD5sum: 9636ac1e92336cd0e5c1cffc6681ce5d NeedsCompilation: no Package: multiClust Version: 1.22.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) MD5sum: 28e3f180c1465c3fb8549cf5b56c4632 NeedsCompilation: no Package: multicrispr Version: 1.2.0 Depends: R (>= 4.0) Imports: assertive, BiocGenerics, Biostrings, BSgenome, CRISPRseek, data.table, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, grid, karyoploteR, magrittr, 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: aa8e1de803e595dadec4ce56d103e89f NeedsCompilation: no Package: MultiDataSet Version: 1.20.2 Depends: R (>= 3.3), 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: b9746709458f271e8775016e0d15f1e0 NeedsCompilation: no Package: multiGSEA Version: 1.2.0 Depends: R (>= 4.0.0) Imports: magrittr, graphite, AnnotationDbi, 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, metaboliteIDmapping, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: GPL-3 MD5sum: f2de73b3ba4ff7fe26eea3c67fab048e NeedsCompilation: no Package: multiHiCcompare Version: 1.10.0 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: 3b43dc6a642dbfcbaea2086b23e5b1aa NeedsCompilation: no Package: MultiMed Version: 2.14.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE MD5sum: 52ad7abdfcfe9ef02e928c48c0eed0c4 NeedsCompilation: no Package: multiMiR Version: 1.14.0 Depends: R (>= 3.4) Imports: stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 1.2), methods, BiocGenerics, AnnotationDbi, dplyr, Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) License: MIT + file LICENSE MD5sum: d44c483d7a56e6a6f24497b6126ea1e6 NeedsCompilation: no Package: multiOmicsViz Version: 1.16.0 Depends: R (>= 3.3.2) Imports: methods, parallel, doParallel, foreach, grDevices, graphics, utils, SummarizedExperiment, stats Suggests: BiocGenerics License: LGPL MD5sum: c1ed278c6ea46a1fb572b15bcc818423 NeedsCompilation: no Package: multiscan Version: 1.52.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) MD5sum: 8ad053d5e4758334aef82fa5bcd55a62 NeedsCompilation: yes Package: multiSight Version: 1.0.0 Depends: R (>= 4.1) Imports: golem, config, R6, shiny, shinydashboard, DT, dplyr, stringr, anyLib, caret, biosigner, mixOmics, stats, DESeq2, clusterProfiler, rWikiPathways, ReactomePA, enrichplot, ppcor, metap, infotheo, igraph, networkD3, easyPubMed, utils, htmltools, rmarkdown Suggests: org.Mm.eg.db, rlang, markdown, attempt, processx, testthat, knitr, BiocStyle License: CeCILL + file LICENSE MD5sum: 903c0a71470ee6108097a70ec4722543 NeedsCompilation: no Package: multtest Version: 2.48.0 Depends: R (>= 2.10), methods, BiocGenerics, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL MD5sum: d4f80c2a5f634474baabf6a2949d0cee NeedsCompilation: yes Package: mumosa Version: 1.0.0 Depends: SingleCellExperiment Imports: stats, utils, methods, igraph, Matrix, BiocGenerics, BiocParallel, IRanges, S4Vectors, DelayedArray, DelayedMatrixStats, SummarizedExperiment, BiocNeighbors, BiocSingular, ScaledMatrix, beachmat, scuttle, metapod, scran, batchelor, uwot Suggests: testthat, knitr, BiocStyle, rmarkdown, scater, bluster, DropletUtils, scRNAseq License: GPL-3 MD5sum: f0634894f977edc4c6c25ad0d805244f NeedsCompilation: no Package: MungeSumstats Version: 1.0.1 Depends: R(>= 4.0) Imports: data.table, utils, stats, GenomicRanges, BSgenome, Biostrings Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, methods, BiocGenerics, IRanges, GenomeInfoDb, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr License: Artistic-2.0 MD5sum: a2193d5bce710d51f1b37564c4f408b4 NeedsCompilation: no Package: muscat Version: 1.6.0 Depends: R (>= 4.1) Imports: BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, S4Vectors, scales, scater, scuttle, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition, viridis Suggests: BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr, phylogram, RColorBrewer, reshape2, rmarkdown, testthat, UpSetR License: GPL (>= 2) MD5sum: 5aa2fde7deab2108da8be2fd68309f5c NeedsCompilation: no Package: muscle Version: 3.34.0 Depends: Biostrings License: Unlimited MD5sum: 80e33f3375e463548c9b454bc8fae64a NeedsCompilation: yes Package: musicatk Version: 1.2.0 Depends: R (>= 4.0.0), NMF Imports: SummarizedExperiment, VariantAnnotation, cowplot, Biostrings, base, methods, magrittr, tibble, tidyr, gtools, gridExtra, maftools, 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, deconstructSigs, decompTumor2Sig, topicmodels, ggrepel, withr, plotly, utils, factoextra, cluster, ComplexHeatmap, stringi, philentropy Suggests: testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr License: LGPL-3 MD5sum: 116f9420b6fa593e8a181eea3fed7514 NeedsCompilation: no Package: MutationalPatterns Version: 3.2.0 Depends: R (>= 4.1.0), GenomicRanges (>= 1.24.0), NMF (>= 0.20.6) Imports: stats, S4Vectors, BiocGenerics (>= 0.18.0), BSgenome (>= 1.40.0), VariantAnnotation (>= 1.18.1), dplyr (>= 0.8.3), tibble(>= 2.1.3), purrr (>= 0.3.2), tidyr (>= 1.0.0), stringr (>= 1.4.0), magrittr (>= 1.5), ggplot2 (>= 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NeedsCompilation: no Package: mygene Version: 1.28.0 Depends: R (>= 3.2.1), GenomicFeatures, Imports: httr (>= 0.3), jsonlite (>= 0.9.7), S4Vectors, Hmisc, sqldf, plyr Suggests: BiocStyle License: Artistic-2.0 MD5sum: 77e918071eb64f7c39be68263114e16b NeedsCompilation: no Package: myvariant Version: 1.22.0 Depends: R (>= 3.2.1), VariantAnnotation Imports: httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, GenomeInfoDb Suggests: BiocStyle License: Artistic-2.0 MD5sum: 9207d50915788a45250de445cef1eff8 NeedsCompilation: no Package: mzID Version: 1.30.0 Depends: methods Imports: XML, plyr, parallel, doParallel, foreach, iterators, ProtGenerics Suggests: knitr, testthat License: GPL (>= 2) MD5sum: a0320028ef68c5af16fb96445d1691ed NeedsCompilation: no Package: mzR Version: 2.26.1 Depends: Rcpp (>= 0.10.1), methods, utils Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3), ncdf4 LinkingTo: Rcpp, zlibbioc, Rhdf5lib (>= 1.1.4) Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle 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Suggests: DSS, Mus.musculus, Homo.sapiens, knitr, rmarkdown, testthat (>= 3.0.0), covr License: Apache License (>= 2.0) MD5sum: 107e640b3875c91a43a6d9e8d0d0fd08 NeedsCompilation: yes Package: NanoStringDiff Version: 1.22.0 Depends: Biobase Imports: matrixStats, methods, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle License: GPL MD5sum: 5cf7ce325dc2e10bbf34eb625ba3d72c NeedsCompilation: yes Package: NanoStringNCTools Version: 1.0.0 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: Artistic-2.0 MD5sum: 2c0626ed05ee3b61291276aeb7bea2ee NeedsCompilation: no Package: NanoStringQCPro Version: 1.24.0 Depends: R (>= 3.2), methods Imports: AnnotationDbi (>= 1.26.0), org.Hs.eg.db (>= 2.14.0), Biobase (>= 2.24.0), knitr (>= 1.12), NMF (>= 0.20.5), RColorBrewer (>= 1.0-5), png (>= 0.1-7) Suggests: 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knitr, rmarkdown License: GPL-3 OS_type: unix MD5sum: 9a55d628d66cb919e831613c2b73abc6 NeedsCompilation: yes Package: netboxr Version: 1.4.0 Depends: R (>= 4.0.0), igraph (>= 1.2.4.1), parallel Imports: RColorBrewer, DT, stats, clusterProfiler, data.table, gplots, jsonlite, plyr Suggests: paxtoolsr, BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, cgdsr License: LGPL-3 + file LICENSE MD5sum: a8f6d785cfc8baaac48e2f8b59698752 NeedsCompilation: no Package: netDx Version: 1.4.3 Depends: R (>= 3.6) Imports: ROCR,pracma,ggplot2,RCy3,glmnet,igraph,reshape2,parallel,stats,utils,MultiAssayExperiment,graphics,grDevices,methods,BiocFileCache,GenomicRanges,bigmemory,doParallel,foreach,combinat,rappdirs,GenomeInfoDb,S4Vectors,IRanges,RColorBrewer, scater, netSmooth, clusterExperiment,Rtsne,httr Suggests: curatedTCGAData, TCGAutils, rmarkdown, testthat, knitr, BiocStyle License: MIT + file LICENSE MD5sum: e59b857f6f8b34b2bf7440dae57c8f3d NeedsCompilation: no Package: nethet Version: 1.24.0 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R (>= 4.0) Imports: KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices, 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, License: MIT + file LICENSE MD5sum: b07977581a6126fe92188375444e1967 NeedsCompilation: no Package: normalize450K Version: 1.20.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: d30aa9f580e5d4882fef887ba69dadb3 NeedsCompilation: no Package: NormalyzerDE Version: 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OmnipathR Version: 3.0.4 Depends: R(>= 4.0) Imports: checkmate, curl, digest, dplyr, httr, igraph, jsonlite, later, logger, magrittr, progress, purrr, rappdirs, readr(>= 2.0.0), readxl, rlang, stats, stringr, tibble, tidyr, tidyselect, tools, utils, xml2, yaml Suggests: BiocStyle, dnet, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, rmarkdown, smoof, testthat License: MIT + file LICENSE MD5sum: 4e5b472c1b825ff6f63afbaad32bcb03 NeedsCompilation: no Package: oncomix Version: 1.14.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: e2b85ab88d3da2b37a7ffa4f9bc2a794 NeedsCompilation: no Package: OncoScore Version: 1.20.0 Depends: R (>= 4.0.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: cd82348e51d24682b418a704b035f455 NeedsCompilation: no Package: OncoSimulR 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Imports: Biobase, S4Vectors, methods, AnnotationDbi, stats, utils, BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT, igraph Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, celldex, rmarkdown License: Artistic-2.0 MD5sum: 2eaff23b5e46079dcc8556218248b024 NeedsCompilation: no Package: openCyto Version: 2.4.0 Depends: R (>= 3.5.0) Imports: methods,Biobase,BiocGenerics,gtools,flowCore(>= 1.99.17),flowViz,ncdfFlow(>= 2.11.34),flowWorkspace(>= 3.99.1),flowStats(>= 3.99.1),flowClust(>= 3.11.4),MASS,clue,plyr,RBGL,graph,data.table,ks,RColorBrewer,lattice,rrcov,R.utils LinkingTo: Rcpp Suggests: flowWorkspaceData, knitr, testthat, utils, tools, parallel, ggcyto, CytoML License: Artistic-2.0 MD5sum: 282fbbe81bc93e51e015daed41339f94 NeedsCompilation: yes Package: openPrimeR Version: 1.14.0 Depends: R (>= 4.0.0) Imports: Biostrings (>= 2.38.4), XML (>= 3.98-1.4), scales (>= 0.4.0), reshape2 (>= 1.4.1), seqinr (>= 3.3-3), IRanges (>= 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9f0ee90d606d74fd9fe124710dae776a NeedsCompilation: no Package: OpenStats Version: 1.4.0 Depends: nlme Imports: MASS, jsonlite, Hmisc, methods, knitr, AICcmodavg, car, rlist, summarytools, graphics, stats, utils Suggests: rmarkdown License: GPL (>= 2) MD5sum: 82ebe92e3a3ff7ddd4ec18d6d997b78e NeedsCompilation: no Package: oposSOM Version: 2.10.0 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: 74e2df039bc1488e80de39e9054ac298 NeedsCompilation: yes Package: oppar Version: 1.20.0 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: a8ca8e369a68a3a250d7f62a050841fc NeedsCompilation: yes Package: oppti Version: 1.6.0 Depends: R (>= 3.6) Imports: limma, stats, reshape, ggplot2, grDevices, RColorBrewer, pheatmap, knitr, methods, devtools License: MIT MD5sum: e18167dc449a0de2329cc5976c2f1a4b NeedsCompilation: no Package: optimalFlow Version: 1.4.0 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: 475cf1b1aecd720ed01c80ab556ec8b4 NeedsCompilation: no Package: OPWeight Version: 1.14.0 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: 7d3703c2c8bb899fa4ab0b32438a6a8a NeedsCompilation: no Package: OrderedList Version: 1.64.0 Depends: R (>= 3.6.1), Biobase, twilight Imports: methods License: GPL (>= 2) MD5sum: 3eb5dec3e409d7e30d5bca4d273b311b NeedsCompilation: no Package: ORFhunteR Version: 1.0.0 Depends: Biostrings, 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rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: f789694a425293bc33571ed824759892 NeedsCompilation: yes Package: Organism.dplyr Version: 1.20.0 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, BiocStyle, ggplot2 License: Artistic-2.0 MD5sum: d9a7c3f8d62287487956d14a03b618ba NeedsCompilation: no Package: OrganismDbi Version: 1.34.0 Depends: R (>= 2.14.0), methods, BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.39.4) Imports: Biobase, BiocManager, GenomicRanges (>= 1.31.13), graph, IRanges, RBGL, DBI, S4Vectors (>= 0.9.25), stats Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB License: Artistic-2.0 MD5sum: ca8131a15bb425762a7d616d8930735a NeedsCompilation: no Package: OSAT Version: 1.40.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 MD5sum: e94e281d75d84abf0d150453dcba150d NeedsCompilation: no Package: Oscope Version: 1.22.0 Depends: EBSeq, cluster, testthat, BiocParallel Suggests: BiocStyle License: Artistic-2.0 MD5sum: 71842c132082eddf777d421f4167756c NeedsCompilation: no Package: OTUbase Version: 1.42.0 Depends: R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>= 1.23.15), Biobase, vegan Imports: Biostrings License: Artistic-2.0 MD5sum: 9a8bd816b62eefb83617f61cf39195f4 NeedsCompilation: no Package: OUTRIDER Version: 1.10.0 Depends: R (>= 3.6), BiocParallel, GenomicFeatures, SummarizedExperiment, data.table, methods Imports: BBmisc, BiocGenerics, DESeq2 (>= 1.16.1), generics, GenomicRanges, ggplot2, grDevices, heatmaply, pheatmap, graphics, IRanges, matrixStats, plotly, plyr, pcaMethods, PRROC, RColorBrewer, Rcpp, reshape2, S4Vectors, scales, splines, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr License: MIT + file LICENSE MD5sum: 0b5e8fd042687740dc2f65a2b3bfb0b0 NeedsCompilation: yes Package: OVESEG Version: 1.8.0 Depends: R (>= 3.6) Imports: stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales License: GPL-2 MD5sum: d2f7ad4b460a34ccb224669ed23a56bf NeedsCompilation: yes Package: PAA Version: 1.26.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.6) Imports: e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR, sva LinkingTo: Rcpp Suggests: BiocStyle, RUnit, BiocGenerics, vsn License: BSD_3_clause + file LICENSE MD5sum: 69512b90d3428d9ff591506d007af5f8 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Depends: R (>= 4.0) Imports: GenomicRanges, igraph, motifmatchr, stats, utils, grDevices, graphics Suggests: bcellViper, BSgenome.Hsapiens.UCSC.hg19, JASPAR2018, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, TFBSTools, GenomicFeatures, annotate License: GPL-2 MD5sum: 9659c74fd408d7ac85a7befb7cddf60f NeedsCompilation: no Package: PAIRADISE Version: 1.8.0 Depends: R (>= 3.6), nloptr Imports: SummarizedExperiment, S4Vectors, stats, methods, abind, BiocParallel Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: ea773c2dc96e801dd5c804e53d95e743 NeedsCompilation: no Package: paircompviz Version: 1.30.0 Depends: R (>= 2.10), Rgraphviz Imports: Rgraphviz Suggests: multcomp, reshape, rpart, plyr, xtable License: GPL (>= 3.0) MD5sum: b1e2aa280841b1a48becacae4d5b12e7 NeedsCompilation: no Package: pandaR Version: 1.24.0 Depends: R (>= 3.0.0), methods, Biobase, BiocGenerics, Imports: matrixStats, igraph, ggplot2, grid, reshape, plyr, RUnit, hexbin Suggests: knitr 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License: MIT + file LICENSE MD5sum: 5404bfd70ec3290894c7fcf4c214f763 NeedsCompilation: no Package: PDATK Version: 1.0.2 Depends: R (>= 4.1), SummarizedExperiment Imports: data.table, MultiAssayExperiment, ConsensusClusterPlus, igraph, ggplotify, matrixStats, RColorBrewer, clusterRepro, CoreGx, caret, survminer, methods, S4Vectors, BiocGenerics, survival, stats, plyr, dplyr, MatrixGenerics, BiocParallel, rlang, piano, scales, survcomp, genefu, ggplot2, switchBox, reportROC, pROC, verification, utils Suggests: testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr, HDF5Array License: MIT + file LICENSE MD5sum: 46112ea3f208daf127a203c98d66e7b7 NeedsCompilation: no Package: pdInfoBuilder Version: 1.56.0 Depends: R (>= 3.2.0), methods, Biobase (>= 2.27.3), RSQLite (>= 1.0.0), affxparser (>= 1.39.4), oligo (>= 1.31.5) Imports: Biostrings (>= 2.35.12), BiocGenerics (>= 0.13.11), DBI (>= 0.3.1), IRanges (>= 2.1.43), oligoClasses (>= 1.29.6), S4Vectors (>= 0.5.22) License: Artistic-2.0 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BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr, knitr, rmarkdown, pkgdown License: GPL-3 + file LICENSE MD5sum: 625b2033b41bdd894d2d328697dd8796 NeedsCompilation: no Package: perturbatr Version: 1.12.0 Depends: R (>= 3.5), methods, stats Imports: dplyr, ggplot2, tidyr, assertthat, lme4, splines, igraph, foreach, parallel, doParallel, diffusr, lazyeval, tibble, grid, utils, graphics, scales, magrittr, formula.tools, rlang Suggests: testthat, lintr, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 2300078744d8ac59f122d3e6679dfacc NeedsCompilation: no Package: PFP Version: 1.0.0 Depends: R (>= 4.0) Imports: graph, igraph, KEGGgraph, clusterProfiler, ggplot2, plyr, tidyr, magrittr, stats, methods, utils Suggests: knitr, testthat, rmarkdown, org.Hs.eg.db License: GPL-2 MD5sum: 1b2955d6cb69886a95158764eab245c8 NeedsCompilation: no Package: pgca Version: 1.16.0 Imports: utils, stats Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 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NeedsCompilation: no Package: phemd Version: 1.8.0 Depends: R (>= 3.5), monocle Imports: SingleCellExperiment, RColorBrewer, igraph, transport, pracma, cluster, Rtsne, destiny, Seurat, RANN, ggplot2, maptree, pheatmap, scatterplot3d, VGAM, methods, grDevices, graphics, stats, utils, cowplot, S4Vectors, BiocGenerics, SummarizedExperiment, Biobase, phateR, reticulate Suggests: knitr License: GPL-2 MD5sum: 8541e8adcac2a16878fe7ec766577bec NeedsCompilation: no Package: PhenoGeneRanker Version: 1.0.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 International License MD5sum: 1d63f3040d5f45c806e5a508c67b1ae7 NeedsCompilation: no Package: phenopath Version: 1.16.0 Imports: Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr, tibble, ggplot2, tidyr LinkingTo: Rcpp Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment License: Apache License (== 2.0) MD5sum: 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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: e084d4207b41a2dcb13827f359c0c7b6 NeedsCompilation: no Package: PhyloProfile Version: 1.6.6 Depends: R (>= 4.1.0) Imports: ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, DT, energy, ExperimentHub, ggplot2, gridExtra, pbapply, RColorBrewer, RCurl, shiny, shinyBS, shinyjs, OmaDB, plyr, xml2, zoo Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 818046c5b592fea64a0425ba30c8461f NeedsCompilation: no Package: phyloseq Version: 1.36.0 Depends: R (>= 3.3.0) Imports: ade4 (>= 1.7.4), ape (>= 5.0), Biobase (>= 2.36.2), BiocGenerics (>= 0.22.0), biomformat (>= 1.0.0), Biostrings (>= 2.40.0), cluster (>= 2.0.4), data.table (>= 1.10.4), foreach (>= 1.4.3), ggplot2 (>= 2.1.0), igraph (>= 1.0.1), methods (>= 3.3.0), multtest (>= 2.28.0), plyr (>= 1.8.3), reshape2 (>= 1.4.1), scales 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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: 789531f2ea7d96e9978fc0eac466542b NeedsCompilation: no Package: pickgene Version: 1.64.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: 81d6bac84fae39a36fca1c0271950870 NeedsCompilation: no Package: PICS Version: 2.36.0 Depends: R (>= 3.0.0) Imports: utils, stats, graphics, grDevices, methods, IRanges, GenomicRanges, Rsamtools, GenomicAlignments Suggests: rtracklayer, parallel, knitr License: Artistic-2.0 MD5sum: 978b26683e09adce6162abc7dc938f1a NeedsCompilation: yes Package: Pigengene Version: 1.18.10 Depends: R (>= 4.0.3), graph, BiocStyle (>= 2.18.1) 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 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: fbb3979a2ca12bb5c606e76cd9cd1044 NeedsCompilation: no Package: PING Version: 2.36.0 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: 56577c708ad1865f5270a82b3a11dd4c NeedsCompilation: yes Package: pipeComp Version: 1.2.0 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: 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methods, stats, utils, RcppParallel, SPAtest (>= 3.0.0) LinkingTo: Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0) Suggests: parallel, crayon, RUnit, knitr, markdown, rmarkdown, BiocGenerics, SNPRelate License: GPL-3 MD5sum: d27b0b17e0e084f536d1dc1546924d1f NeedsCompilation: yes Package: sampleClassifier Version: 1.16.0 Depends: R (>= 4.0), MGFM, MGFR, annotate Imports: e1071, ggplot2, stats, utils Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db License: Artistic-2.0 MD5sum: 602ce94c491830329450300e397090f6 NeedsCompilation: no Package: SamSPECTRAL Version: 1.46.0 Depends: R (>= 3.3.3) Imports: methods License: GPL (>= 2) MD5sum: fe0a4da1747f344a41cd66de3ed9eaab NeedsCompilation: yes Package: sangeranalyseR Version: 1.2.0 Depends: R (>= 4.0.0), stringr, ape, Biostrings, DECIPHER, parallel, reshape2, phangorn, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown, kableExtra, seqinr, BiocStyle, logger Suggests: knitr, testthat (>= 2.1.0) License: GPL-2 MD5sum: 211e06e9893d60dc7bc1549975938d7d NeedsCompilation: no Package: sangerseqR Version: 1.28.0 Depends: R (>= 3.0.2), Biostrings Imports: methods, shiny Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 MD5sum: 9012cee809f4f5c86766e2aba477be5c NeedsCompilation: no Package: SANTA Version: 2.28.0 Depends: R (>= 4.1), igraph Imports: graphics, Matrix, methods, stats Suggests: RUnit, BiocGenerics, knitr, formatR, org.Sc.sgd.db, BioNet, DLBCL, msm License: GPL (>= 2) MD5sum: ab3171d3a6cd965007b1243ff6b5b63a NeedsCompilation: yes Package: sarks Version: 1.4.0 Depends: R (>= 4.0) Imports: rJava, Biostrings, IRanges, utils, stats, cluster, binom Suggests: RUnit, BiocGenerics, ggplot2 License: BSD_3_clause + file LICENSE MD5sum: 06edd5d7bd169c7134266a62c5f06a70 NeedsCompilation: no Package: satuRn Version: 1.0.0 Depends: R (>= 4.1) Imports: locfdr, SummarizedExperiment, 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R(>= 3.3) Imports: graphics, stats, utils, methods, e1071, parallel, foreach, doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR, robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1), SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, mclust, scater License: GPL-3 MD5sum: 468b95a01770bc43e20cbdd3a34cc52f NeedsCompilation: yes Package: Scale4C Version: 1.14.0 Depends: R (>= 3.4), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: 8a2a06a4a228e6db3a08cff9a703fda2 NeedsCompilation: no Package: ScaledMatrix Version: 1.0.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular License: GPL-3 MD5sum: ebde9157e2153e388c704a3fcf837dd4 NeedsCompilation: no Package: scAlign Version: 1.6.0 Depends: R (>= 3.6), SingleCellExperiment (>= 1.4), Seurat (>= 2.3.4), tensorflow, purrr, 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SCATE Version: 1.2.0 Depends: parallel, preprocessCore, splines, splines2, xgboost, SCATEData, Rtsne, mclust Imports: utils, stats, GenomicAlignments, GenomicRanges Suggests: rmarkdown, ggplot2, knitr License: MIT + file LICENSE MD5sum: d7f1a1de6fd7ed20b04eee2438f298fb NeedsCompilation: no Package: scater Version: 1.20.1 Depends: SingleCellExperiment, scuttle, ggplot2 Imports: stats, utils, methods, grid, gridExtra, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer Suggests: BiocStyle, biomaRt, cowplot, destiny, knitr, scRNAseq, robustbase, rmarkdown, uwot, NMF, testthat, pheatmap, snifter, Biobase License: GPL-3 MD5sum: 0ebf286f6adb03eef17024a4de3af76a NeedsCompilation: no Package: scBFA Version: 1.6.0 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: e6033ef482f6bc377d88ea907a6a6dc3 NeedsCompilation: no Package: SCBN Version: 1.10.0 Depends: R (>= 3.5.0) Imports: stats Suggests: knitr,rmarkdown License: GPL-2 MD5sum: 7c1632832efb8cb66d02267e1b3191d7 NeedsCompilation: no Package: scCB2 Version: 1.2.0 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: 622d6e39e455e2a1d058df2ae078574e NeedsCompilation: yes Package: scClassifR Version: 1.0.0 Depends: R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment Imports: dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, utils Suggests: knitr, scRNAseq, testthat License: MIT + file LICENSE MD5sum: 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SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 8e1c116cdbd89fc9cc26b8c733d70577 NeedsCompilation: yes Package: scMerge Version: 1.8.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), parallel, pdist, proxy, ruv, S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3), SummarizedExperiment Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, scater, testthat, badger License: GPL-3 MD5sum: 8ebd646fddb169fe46d19b178f32f53b NeedsCompilation: no Package: scmeth Version: 1.12.0 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: 8324c4f5e8fea3cfd9500e04572c2a05 NeedsCompilation: no Package: SCnorm Version: 1.14.0 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: defac70a40da768a842e11fe58718322 NeedsCompilation: no Package: scone Version: 1.16.1 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 Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, BatchJobs, splatter, scater, kableExtra, mclust, TENxPBMCData License: Artistic-2.0 MD5sum: 94c09080148101f98b2db581c07957d9 NeedsCompilation: no Package: Sconify Version: 1.12.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: acca6b2284760c68abe5bbe3e9e22cf9 NeedsCompilation: no Package: SCOPE Version: 1.4.0 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: dd464cf8efc725ca60996c1b7551f0c2 NeedsCompilation: no Package: scoreInvHap Version: 1.14.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: 97a4e44f2d9b0fd3621d400bda5d5bc9 NeedsCompilation: no Package: scp Version: 1.2.0 Depends: R (>= 4.0), QFeatures Imports: methods, stats, utils, SingleCellExperiment, SummarizedExperiment, MultiAssayExperiment, MsCoreUtils, matrixStats, S4Vectors, dplyr, magrittr, rlang Suggests: testthat, knitr, BiocStyle, BiocCheck, rmarkdown, patchwork, ggplot2, impute, scater, sva, preprocessCore, vsn, uwot License: Artistic-2.0 MD5sum: ce40d2b7defc237d08a75d7e7440b408 NeedsCompilation: no Package: scPCA Version: 1.6.2 Depends: R (>= 4.0.2) 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: cbb8f818a16a60ed343937b6cc016853 NeedsCompilation: no Package: scPipe Version: 1.14.0 Depends: R (>= 3.4), ggplot2, methods, SingleCellExperiment Imports: Rhtslib, biomaRt, GGally, MASS, mclust, Rcpp (>= 0.11.3), reshape, BiocGenerics, robustbase, scales, utils, stats, S4Vectors, SummarizedExperiment, AnnotationDbi, org.Hs.eg.db, org.Mm.eg.db, stringr, rtracklayer, hash, dplyr, GenomicRanges, magrittr, glue (>= 1.3.0), rlang, scater (>= 1.11.0) LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat Suggests: Rsubread, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 7c177e26437e7a8576024b5227bf90bd NeedsCompilation: yes Package: scran Version: 1.20.1 Depends: SingleCellExperiment, scuttle Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, bluster, metapod, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, monocle, Biobase, pheatmap, scater License: GPL-3 MD5sum: 435a34857a13ee9a6594cfe2efca28bf NeedsCompilation: yes Package: scRecover Version: 1.8.0 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), Rmagic (>= 1.3.0), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL MD5sum: 6dbad72419123ad24c2ed6379233aa95 NeedsCompilation: no Package: scRepertoire Version: 1.2.0 Depends: ggplot2, R (>= 4.0) Imports: Biostrings, dplyr, reshape2, ggalluvial, stringr, vegan, powerTCR, SummarizedExperiment, plyr, parallel, doParallel, methods, utils, rlang Suggests: knitr, rmarkdown, BiocStyle, scater, circlize, scales, Seurat License: Apache License 2.0 MD5sum: c2880c8369e012b0bd134117efc77a3b NeedsCompilation: no Package: scruff Version: 1.10.0 Depends: R (>= 3.5.0) Imports: data.table, GenomicAlignments, GenomicFeatures, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: b7b5876be10e87f597631689e20bda8a NeedsCompilation: no Package: scry Version: 1.4.0 Depends: R (>= 4.0), stats, methods Imports: DelayedArray, glmpca (>= 0.2.0), HDF5Array, Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, knitr, rmarkdown, TENxPBMCData, testthat License: Artistic-2.0 MD5sum: c7661bbefcc9573eef5286b01f462da9 NeedsCompilation: no Package: scTensor Version: 2.2.0 Depends: R (>= 3.5.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor, rTensor, abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi, grDevices, graphics, stats, utils, outliers, Category, meshr, GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2 Suggests: testthat, LRBase.Hsa.eg.db, LRBase.Mmu.eg.db, LRBaseDbi, Seurat, scTGIF, Homo.sapiens License: Artistic-2.0 MD5sum: 65c04027bab742332c076821697b6039 NeedsCompilation: no Package: scTGIF Version: 1.6.0 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: 695dcf8f94dd67eab96dc0dcdce679b6 NeedsCompilation: no Package: scTHI Version: 1.4.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown License: GPL-2 MD5sum: e70e426c5e6a1602bef23ee7a214e484 NeedsCompilation: no Package: scuttle Version: 1.2.1 Depends: SingleCellExperiment Imports: methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors, BiocParallel, GenomicRanges, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat LinkingTo: Rcpp, beachmat Suggests: BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran License: GPL-3 MD5sum: b0271029c4db5f943c0832a78b9536bd NeedsCompilation: yes Package: SDAMS Version: 1.12.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: efda431db8c119d83464084835525b8d NeedsCompilation: no Package: sechm Version: 1.0.0 Depends: R (>= 4.1) Imports: S4Vectors, SummarizedExperiment, seriation, ComplexHeatmap, circlize, methods, randomcoloR, stats, grid, grDevices Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: bf04e5d9c73bc928a529cde0bd769b4c NeedsCompilation: no Package: segmentSeq Version: 2.26.0 Depends: R (>= 3.0.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils, abind Suggests: BiocStyle, BiocGenerics License: GPL-3 MD5sum: f51561954ad849fee2835cebd23e81e5 NeedsCompilation: no Package: selectKSigs Version: 1.4.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: fba91fbf9649aa4accf23487d9c8facb NeedsCompilation: yes Package: SELEX Version: 1.24.0 Depends: rJava (>= 0.5-0), 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Depends: R (>= 3.5.0), gdsfmt (>= 1.23.5) 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: 442b2eea24758d0c388293e7c1f4aef6 NeedsCompilation: yes Package: seqbias Version: 1.40.0 Depends: R (>= 3.0.2), GenomicRanges (>= 0.1.0), Biostrings (>= 2.15.0), methods LinkingTo: Rhtslib (>= 1.15.3) Suggests: Rsamtools, ggplot2 License: LGPL-3 MD5sum: ef4494289d1301883e1c57eec705cc86 NeedsCompilation: yes Package: seqCAT Version: 1.14.1 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: ed8a64f4a0f611321e3dd1ccef035ea7 NeedsCompilation: no Package: seqCNA Version: 1.38.0 Depends: R (>= 3.0), GLAD (>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot (>= 0.99), methods License: GPL-3 MD5sum: dca2bdb34175f6a6714568930f55c109 NeedsCompilation: yes Package: seqcombo Version: 1.14.1 Depends: R (>= 3.4.0) Imports: Biostrings, cowplot, dplyr, ggplot2, grid, igraph, magrittr, methods, utils, yulab.utils Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble License: Artistic-2.0 MD5sum: 41787b7e2ad5a2fdbf3d5907b03c8e11 NeedsCompilation: no Package: SeqGate Version: 1.2.0 Depends: S4Vectors, SummarizedExperiment, GenomicRanges Imports: stats, methods, BiocManager Suggests: testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown License: GPL (>= 2.0) MD5sum: fb84b76f0ebe5901e63169ea98d88299 NeedsCompilation: no Package: SeqGSEA Version: 1.32.0 Depends: Biobase, doParallel, DESeq2 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covr, cowplot, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 21f0219336bb7f1aa4895d0e600e2998 NeedsCompilation: no Package: SeqSQC Version: 1.14.0 Depends: R (>= 3.4), ExperimentHub (>= 1.3.7), SNPRelate (>= 1.10.2) Imports: e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges, methods, rbokeh, RColorBrewer, reshape2, rmarkdown, S4Vectors, stats, utils Suggests: BiocStyle, knitr, testthat License: GPL-3 MD5sum: df93718f9a6f180e3d6a331897ebb905 NeedsCompilation: no Package: seqTools Version: 1.26.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 9e5ca21ca6164308d9057fd6763423d5 NeedsCompilation: yes Package: SeqVarTools Version: 1.30.0 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: 167a615f78e4bba965f975c1b9e4fa4e NeedsCompilation: no Package: sesame Version: 1.10.5 Depends: R (>= 4.1), sesameData, methods Imports: BiocParallel, grDevices, utils, stringr, tibble, illuminaio, MASS, GenomicRanges, IRanges, grid, preprocessCore, S4Vectors, randomForest, wheatmap, ggplot2, KernSmooth, graphics, parallel, matrixStats, DNAcopy, stats, SummarizedExperiment Suggests: scales, knitr, rmarkdown, testthat, dplyr, tidyr, BiocStyle, IlluminaHumanMethylation450kmanifest, minfi, FlowSorted.CordBloodNorway.450k, FlowSorted.Blood.450k, HDF5Array License: MIT + file LICENSE MD5sum: b5868347f3d4c1cc447538a0d05b417b NeedsCompilation: no Package: SEtools Version: 1.6.0 Depends: R (>= 4.0) Imports: S4Vectors, SummarizedExperiment, data.table, seriation, ComplexHeatmap, circlize, methods, BiocParallel, randomcoloR, edgeR, openxlsx, sva, stats, DESeq2, Matrix, grid Suggests: BiocStyle, knitr, rmarkdown, ggplot2, pheatmap License: GPL MD5sum: 83a46f296d560d66298c6e161e719b08 NeedsCompilation: no Package: sevenbridges Version: 1.22.0 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: f3dafe195ba0481c624f78c1ec3e126f NeedsCompilation: no Package: sevenC Version: 1.12.0 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: 56aad61b2fe15a4e2d50663d6e4e0faf NeedsCompilation: no Package: SGSeq Version: 1.26.0 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 (>= 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prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle License: GPL-3 MD5sum: 7a85ad9f5437edf8513e5487ba514612 NeedsCompilation: no Package: siggenes Version: 1.66.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: 2b7ffc929994423c2d5a12f44f1c6575 NeedsCompilation: no Package: sights Version: 1.18.0 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: e083c06de9dbd3bf9fc9cee06bf5492a NeedsCompilation: no Package: signatureSearch Version: 1.6.3 Depends: R(>= 3.6.0), Rcpp, SummarizedExperiment 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 LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, org.Hs.eg.db, signatureSearchData, DT License: Artistic-2.0 MD5sum: 53ab9b18308a9bcc86e6b838dc4f3d04 NeedsCompilation: yes Package: signeR Version: 1.18.1 Depends: VariantAnnotation, NMF Imports: BiocGenerics, Biostrings, class, graphics, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: 7284cac3e0cdb1e94e55f6f7f39ced5a NeedsCompilation: yes Package: sigPathway Version: 1.60.0 Depends: R (>= 2.10) Suggests: hgu133a.db (>= 1.10.0), XML (>= 1.6-3), AnnotationDbi (>= 1.3.12) License: GPL-2 MD5sum: 44f6036756791646d6149bc56f8b2bc7 NeedsCompilation: yes Package: SigsPack Version: 1.6.0 Depends: R (>= 3.6) Imports: quadprog (>= 1.5-5), methods, 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NeedsCompilation: yes Package: singscore Version: 1.12.0 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: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 44aa4b9d0f5a7b9dc97e0998816e1225 NeedsCompilation: no Package: SISPA Version: 1.22.0 Depends: R (>= 3.5),genefilter,GSVA,changepoint Imports: data.table, plyr, ggplot2 Suggests: knitr License: GPL-2 MD5sum: ee1eabc775184418f1a14960602c3fbb NeedsCompilation: no Package: sitadela Version: 1.0.1 Depends: R (>= 4.1.0) Imports: Biobase, BiocGenerics, biomaRt, Biostrings, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, methods, parallel, Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, utils Suggests: BSgenome, knitr, RMySQL, RUnit License: Artistic-2.0 MD5sum: 0bf90d38f37d397a68a067543fb5eea5 NeedsCompilation: no Package: sitePath 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glmpca, pheatmap, plotly, tibble, magrittr, DT, stats Suggests: systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocGenerics, Biostrings, methods License: Artistic-2.0 MD5sum: b00418e13af36f1a213bb106f3517b3a NeedsCompilation: no Package: TADCompare Version: 1.2.0 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, rGREAT, SpectralTAD License: MIT + file LICENSE MD5sum: 6eea1a0b87f8e11c91f5d710b4b695db NeedsCompilation: no Package: TAPseq Version: 1.4.0 Depends: R (>= 4.0) Imports: methods, GenomicAlignments, GenomicRanges, IRanges, BiocGenerics, S4Vectors (>= 0.20.1), GenomeInfoDb, BSgenome, GenomicFeatures, Biostrings, dplyr, tidyr, BiocParallel Suggests: testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer License: MIT + file LICENSE MD5sum: d3c4e3365fc09cd2efff7d0711f8936c NeedsCompilation: no Package: target Version: 1.6.0 Depends: R (>= 3.6) Imports: BiocGenerics, GenomicRanges, IRanges, matrixStats, methods, stats, graphics, shiny Suggests: testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS, covr License: GPL-3 MD5sum: b93ef0fde65cc44770eb0016ab3a7f41 NeedsCompilation: no Package: TargetScore Version: 1.30.0 Depends: pracma, Matrix Suggests: TargetScoreData, gplots, Biobase, GEOquery License: GPL-2 MD5sum: 2c092377935b1f27a2f9153333134d0f NeedsCompilation: no Package: TargetSearch Version: 1.48.0 Imports: graphics, grDevices, methods, ncdf4, stats, utils, assertthat Suggests: TargetSearchData, BiocStyle, knitr, tinytest License: GPL (>= 2) MD5sum: 42d1737a68bb27604fe4cb62c7497437 NeedsCompilation: yes Package: TarSeqQC Version: 1.22.0 Depends: R (>= 3.5.1), methods, GenomicRanges, Rsamtools (>= 1.9.2), ggplot2, plyr, openxlsx Imports: grDevices, stats, utils, S4Vectors, IRanges, BiocGenerics, reshape2, 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S4Vectors (>= 0.19.23), SummarizedExperiment (>= 1.11.6) Imports: dynamicTreeCut, dplyr, edgeR, DESeq2, ggplot2 (>= 3.0.0), graphics, Hmisc, limma, methods, magrittr, proxy, stats, tibble, tidyr, vegan, viridis, utils Suggests: Biobase, BiocFileCache (>= 1.5.8), circlize, ComplexHeatmap, GO.db, grDevices, grid, knitr, org.Mm.eg.db, org.Hs.eg.db, MASS, RColorBrewer, rmarkdown, UpSetR, License: MIT + file LICENSE MD5sum: 82e3d869096ef9190c95d3c1f3d2f88e NeedsCompilation: no Package: TimiRGeN Version: 1.2.0 Depends: R (>= 4.0), Mfuzz, MultiAssayExperiment Imports: biomaRt, clusterProfiler, dplyr (>= 0.8.4), FreqProf, gtools (>= 3.8.1), gplots, ggdendro, gghighlight, ggplot2, graphics, grDevices, igraph (>= 1.2.4.2), RCy3, readxl, reshape2, rWikiPathways, scales, stats, tidyr (>= 1.0.2), stringr (>= 1.4.0) Suggests: BiocManager, kableExtra, knitr (>= 1.27), org.Hs.eg.db, org.Mm.eg.db, testthat, rmarkdown License: GPL-3 MD5sum: 7f73b29b0e774d0d5aaf19088098e0c2 NeedsCompilation: no Package: TIN Version: 1.24.0 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: b26da7a2e19f76170c54670dfcdaaa20 NeedsCompilation: no Package: TissueEnrich Version: 1.12.0 Depends: R (>= 3.5), ensurer (>= 1.1.0), 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: fc3b1232ef676afdda4032e536df55cb NeedsCompilation: no Package: TitanCNA Version: 1.30.0 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: f9526f1532050191e426c3b5c39acc0b NeedsCompilation: yes Package: tkWidgets Version: 1.70.0 Depends: R (>= 2.0.0), methods, widgetTools (>= 1.1.7), DynDoc (>= 1.3.0), tools Suggests: Biobase, hgu95av2 License: Artistic-2.0 MD5sum: 5ab5977b3f50ec45eb240e0418d7d7e6 NeedsCompilation: no Package: tLOH Version: 1.0.0 Depends: R (>= 4.0) Imports: scales, stats, utils, ggplot2, data.table, purrr, dplyr, VariantAnnotation, GenomicRanges, MatrixGenerics Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: a009b2743ab766cf5311c42c664da9f5 NeedsCompilation: no Package: TMixClust Version: 1.14.0 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: 2fb70166b3e562c0c510446af2de6df5 NeedsCompilation: no Package: TNBC.CMS Version: 1.8.0 Depends: R (>= 3.6.0), e1071, quadprog, SummarizedExperiment Imports: GSVA (>= 1.26.0), pheatmap, grDevices, RColorBrewer, pracma, GGally, R.utils, forestplot, ggplot2, ggpubr, survival, grid, stats, methods Suggests: knitr 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Enhances: parallel License: GPL-3 MD5sum: dac5083f3e8ff783fe5a715bd339e8c8 NeedsCompilation: yes Package: tomoda Version: 1.2.0 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: 62633ef79b9d862a7c8fe9c6331df92a NeedsCompilation: no Package: topconfects Version: 1.8.0 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: 89f17c16a64ea94156d8c9c3f617f7aa NeedsCompilation: no Package: topdownr Version: 1.14.0 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 (>= 1.2.10), MSnbase 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License: MIT + file LICENSE MD5sum: 2ee0635486ebd97c3aa9ed9feaf8f061 NeedsCompilation: no Package: TPP Version: 3.20.1 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: c61595234dedf38e60f3157d44beb040 NeedsCompilation: no Package: TPP2D Version: 1.8.0 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 License: GPL-3 MD5sum: 11ee1dbc8413fb3d1a7d28702922fe97 NeedsCompilation: no Package: tracktables Version: 1.26.0 Depends: R (>= 3.0.0) Imports: IRanges, GenomicRanges, XVector, Rsamtools, XML, 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matrixStats Suggests: knitr, rmarkdown, testthat, covr, clusterExperiment License: MIT + file LICENSE MD5sum: 5c4f6d2c6e9afef1f0ba6ef0bf6f06da NeedsCompilation: no Package: TrajectoryGeometry Version: 1.0.0 Depends: R (>= 4.1) Imports: pracma, rgl, ggplot2, stats, methods Suggests: dplyr, knitr, RColorBrewer, rmarkdown License: MIT + file LICENSE MD5sum: 43de8e9adabe30b16f29817945d43c7d NeedsCompilation: no Package: TrajectoryUtils Version: 1.0.0 Depends: SingleCellExperiment Imports: methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment Suggests: BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 05051a749946bb402c031371597c6bb7 NeedsCompilation: no Package: transcriptogramer Version: 1.14.0 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, 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gplots, gtools, pvclust, R.utils, dqrng, SummarizedExperiment, BiocParallel, matrixStats Suggests: knitr, rmarkdown, BiocGenerics, RUnit, BiocStyle License: MIT + file LICENSE MD5sum: c8060582c661d72d946b975abb477132 NeedsCompilation: no Package: traseR Version: 1.22.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL MD5sum: ae7785ca8c1a23fccead6d36b4f6667a NeedsCompilation: no Package: Travel Version: 1.0.0 Imports: Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, inline, parallel License: GPL-3 MD5sum: d276ed97abdb123ab96ad68b6b24f38b NeedsCompilation: yes Package: TreeAndLeaf Version: 1.4.2 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: cab5c0568fd07935a2d8eb5d56d057f6 NeedsCompilation: no Package: treeio Version: 1.16.2 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dplyr License: MIT + file LICENSE MD5sum: 89027c5c318d990998c8165991a0d810 NeedsCompilation: no Package: UNDO Version: 1.34.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 226ed69e2f5c2a19c49fb6dd399faf35 NeedsCompilation: no Package: unifiedWMWqPCR Version: 1.28.0 Depends: methods Imports: BiocGenerics, stats, graphics, HTqPCR License: GPL (>= 2) MD5sum: 2632782871c32d444a83a72a0752f507 NeedsCompilation: no Package: UniProt.ws Version: 2.32.0 Depends: methods, utils, RSQLite, RCurl, BiocGenerics (>= 0.13.8) Imports: AnnotationDbi, BiocFileCache, rappdirs Suggests: RUnit, BiocStyle, knitr License: Artistic License 2.0 MD5sum: 6ce699dc31ac30b0d9ab75a99080f72b NeedsCompilation: no Package: Uniquorn Version: 2.12.0 Depends: R (>= 3.5) Imports: stringr, R.utils, WriteXLS, stats, doParallel, foreach, GenomicRanges, IRanges, VariantAnnotation Suggests: testthat, knitr, rmarkdown, BiocGenerics, RUnit License: Artistic-2.0 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lme4 (>= 1.1-10), grDevices, graphics, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr License: GPL (>= 2) MD5sum: bad1236e782a3f1b02d7741284c8b1f3 NeedsCompilation: no Package: VariantAnnotation Version: 1.38.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5), Rsamtools (>= 1.99.0) 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 Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, 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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: e73b363d0af57ee2b1a8ecbabf548a58 NeedsCompilation: yes Package: VariantTools Version: 1.34.0 Depends: 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) License: Artistic-2.0 MD5sum: 300357f19936789ef0d3d87ffb500ecc NeedsCompilation: no Package: VaSP Version: 1.4.0 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, Sushi, 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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: 45d17204b63aafcaccd58a8c9dbfb762 NeedsCompilation: no Package: VennDetail Version: 1.8.0 Imports: utils, grDevices, stats, methods, dplyr, purrr, tibble, magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 694403802e46de7374d64ad1c4e0c6ae NeedsCompilation: no Package: VERSO Version: 1.2.0 Depends: R (>= 4.0.0) Imports: ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 6edd27553671e141b7ff4be10e4f0a26 NeedsCompilation: no Package: vidger Version: 1.12.0 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: b8fa2bed3631388b6f1edd42f7d3492d NeedsCompilation: no Package: viper Version: 1.26.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: 7349a637881d471c2d4dd0990454900b NeedsCompilation: no Package: ViSEAGO Version: 1.6.0 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 License: GPL-3 MD5sum: 36d95fdbf0d74fedd51734da1867eb57 NeedsCompilation: no Package: vissE Version: 1.0.0 Depends: R (>= 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