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grDevices, stats, tools, graphics Suggests: testthat License: GPL-3 | file LICENSE MD5sum: 2016154d02048efa5c726aa598429e16 Package: ABSSeq Version: 1.44.0 Depends: R (>= 2.10), methods Imports: locfit, limma Suggests: edgeR License: GPL (>= 3) MD5sum: c327ed67b3dc21ba14609c01f37ff5d8 Package: acde Version: 1.20.0 Depends: R(>= 3.3), boot(>= 1.3) Imports: stats, graphics Suggests: BiocGenerics, RUnit License: GPL-3 MD5sum: 19a383ff7a5f22333987a0244bc5a838 Package: ACE Version: 1.8.0 Depends: R (>= 3.4) Imports: Biobase, QDNAseq, ggplot2, grid, stats, utils, methods, grDevices, GenomicRanges Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: efd6f43145a753c15eab0ab8fef2087b Package: aCGH Version: 1.68.0 Depends: R (>= 2.10), cluster, survival, multtest Imports: Biobase, grDevices, graphics, methods, stats, splines, utils License: GPL-2 MD5sum: e6e7649fcf0eb8f33d7a5c798a56fc9c Package: ACME Version: 2.46.0 Depends: R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics Imports: 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Package: AlpsNMR Version: 3.0.6 Depends: R (>= 4.0), dplyr (>= 0.7.5), future (>= 1.10.0), magrittr (>= 1.5) Imports: utils, graphics, stats, grDevices, signal (>= 0.7-6), assertthat (>= 0.2.0), rlang (>= 0.3.0.1), stringr (>= 1.3.1), tibble(>= 1.3.4), tidyr (>= 1.0.0), readxl (>= 1.1.0), plyr (>= 1.8.4), purrr (>= 0.2.5), glue (>= 1.2.0), reshape2 (>= 1.4.3), GGally (>= 1.4.0), mixOmics (>= 6.3.2), matrixStats (>= 0.54.0), writexl (>= 1.0), fs (>= 1.2.6), rmarkdown (>= 1.10), speaq (>= 2.4.0), htmltools (>= 0.3.6), ggrepel (>= 0.8.0), pcaPP (>= 1.9-73), furrr (>= 0.1.0), ggplot2 (>= 3.1.0), baseline (>= 1.2-1), zip (>= 2.0.4), tidyselect (>= 0.2.5), BiocParallel, SummarizedExperiment, S4Vectors Suggests: DT (>= 0.5), testthat (>= 2.0.0), plotly (>= 4.7.1), ChemoSpec, knitr License: file LICENSE MD5sum: db801d5d50e70791215901667a689c71 Package: alsace Version: 1.26.0 Depends: R (>= 2.10), ALS, ptw (>= 1.0.6) Suggests: lattice, knitr License: GPL (>= 2) MD5sum: 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rmarkdown License: GPL (>= 2) MD5sum: 5e86660344cc782d92e5c90098880f89 Package: amplican Version: 1.12.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.22.0), Biostrings (>= 2.44.2), data.table (>= 1.10.4-3) Imports: Rcpp, utils (>= 3.4.1), S4Vectors (>= 0.14.3), ShortRead (>= 1.34.0), IRanges (>= 2.10.2), GenomicRanges (>= 1.28.4), GenomeInfoDb (>= 1.12.2), BiocParallel (>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 2.2.0), ggthemes (>= 3.4.0), waffle (>= 0.7.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), dplyr (>= 0.7.2), rmarkdown (>= 1.6), knitr (>= 1.16), clusterCrit (>= 1.2.7) LinkingTo: Rcpp Suggests: testthat, BiocStyle, GenomicAlignments License: GPL-3 MD5sum: 97b184688d40baed22c842ec7733de1e Package: Anaquin Version: 2.14.0 Depends: R (>= 3.3), ggplot2 (>= 2.2.0) Imports: ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils, plyr, DESeq2 Suggests: RUnit, rmarkdown License: BSD_3_clause + file LICENSE 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MD5sum: dd28a84e17694f9855b0b377c369da2d Package: annotate Version: 1.68.0 Depends: R (>= 2.10), AnnotationDbi (>= 1.27.5), XML Imports: Biobase, DBI, xtable, graphics, utils, stats, methods, BiocGenerics (>= 0.13.8), httr Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, License: Artistic-2.0 MD5sum: 7cf1098034fcd5c68fe6f50482894056 Package: AnnotationDbi Version: 1.52.0 Depends: R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges Imports: DBI, RSQLite, S4Vectors (>= 0.9.25) Suggests: hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 MD5sum: fb1ecd8f86deafc210c4f0557b378acb Package: AnnotationFilter Version: 1.14.0 Depends: R (>= 3.4.0) 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BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3), DESeq2, NanoporeRNASeq, BSgenome, apeglm, utils, DEXSeq Enhances: parallel License: GPL-3 + file LICENSE MD5sum: a0bf692fd6fcd68316670d9535727571 Package: bamsignals Version: 1.22.0 Depends: R (>= 3.2.0) Imports: methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges, GenomicRanges, zlibbioc LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 1a3ea9a1bf5f6cfc7f1384bf2eea8b7a Package: BANDITS Version: 1.6.0 Depends: R (>= 3.6.0) Imports: Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings License: GPL (>= 3) MD5sum: c206ddb12dc2bb711d6b38b4e12d030b Package: banocc Version: 1.14.0 Depends: R (>= 3.5.1), rstan (>= 2.17.4) 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(>= 4.0), SingleCellExperiment Imports: Biobase, BiocGenerics, coda, cowplot, ggExtra, ggplot2, graphics, grDevices, MASS, methods, Rcpp (>= 0.11.3), S4Vectors, scran, stats, stats4, SummarizedExperiment, viridis, utils, Matrix, matrixStats, assertthat, reshape2, BiocParallel, hexbin LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, testthat, magick License: GPL (>= 2) MD5sum: 9c9b570816a764ec47fc688ea03e37db Package: BasicSTARRseq Version: 1.18.0 Depends: GenomicRanges,GenomicAlignments Imports: S4Vectors,methods,IRanges,GenomeInfoDb,stats Suggests: knitr License: LGPL-3 MD5sum: ca9a76358447c1f61ae86bacfdd58f9b Package: basilisk Version: 1.2.1 Imports: utils, methods, parallel, reticulate, filelock, basilisk.utils Suggests: knitr, rmarkdown, BiocStyle, testthat, callr License: GPL-3 MD5sum: 949a0b6f02dc34dd85b9be8c49b69c20 Package: basilisk.utils Version: 1.2.2 Imports: utils, methods, rappdirs, filelock Suggests: knitr, rmarkdown, BiocStyle, testthat, 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4.0.0), SingleCellExperiment Imports: Rcpp (>= 1.0.4.6), stats, purrr, scater, scran, SummarizedExperiment, coda, rhdf5, S4Vectors, Matrix, assertthat, mclust, RCurl, DirichletReg, xgboost, utils, ggplot2, scales, BiocFileCache LinkingTo: Rcpp, RcppArmadillo, RcppDist, RcppProgress Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, dplyr, viridis, patchwork, RColorBrewer, Seurat License: MIT + file LICENSE MD5sum: 54a0ac1a7ecd9a3ce5eb428f5616d123 Package: bayNorm Version: 1.8.0 Depends: R (>= 3.5), Imports: Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix, parallel, MASS, locfit, fitdistrplus, stats, methods, graphics, grDevices, SingleCellExperiment, SummarizedExperiment, BiocParallel, utils LinkingTo: Rcpp, RcppArmadillo,RcppProgress Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat License: GPL (>= 2) MD5sum: 7ff6ed0c7d3dae4f80d78193bf9e6b92 Package: baySeq Version: 2.24.0 Depends: R (>= 2.3.0), methods, GenomicRanges, abind, parallel Imports: edgeR 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rmarkdown, AnnotationHub, httr License: GPL-3 MD5sum: abf8f3c5237046c4f18999a40d89d240 Package: BgeeDB Version: 2.16.0 Depends: R (>= 3.6.0), topGO, tidyr Imports: data.table, curl, RCurl, digest, methods, stats, utils, dplyr, RSQLite, graph, Biobase Suggests: knitr, BiocStyle, testthat, rmarkdown License: GPL-3 + file LICENSE MD5sum: b02116a656616ffb27b41ddc0d497797 Package: BGmix Version: 1.50.0 Depends: R (>= 2.3.1), KernSmooth License: GPL-2 MD5sum: a0513c3e7860fe0ccc5468bb01579426 Package: bgx Version: 1.56.0 Depends: R (>= 2.0.1), Biobase, affy (>= 1.5.0), gcrma (>= 2.4.1) Imports: Rcpp (>= 0.11.0) LinkingTo: Rcpp Suggests: affydata, hgu95av2cdf License: GPL-2 MD5sum: 5c52c178c288642dbce5a7ff4610d061 Package: BHC Version: 1.42.0 License: GPL-3 MD5sum: 45309560a7201173d09e8a4f5fdf5475 Package: BicARE Version: 1.48.0 Depends: R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase License: GPL-2 MD5sum: 37b79c23eabf9c3d8f55131c4929450a Package: BiFET Version: 1.10.0 Imports: stats, 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testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) License: GPL-2 MD5sum: 78ac12bc7561fc132b06d15b94f8f902 Package: BioMM Version: 1.6.0 Depends: R (>= 3.6) Imports: stats, utils, grDevices, lattice, BiocParallel, glmnet, rms, precrec, nsprcomp, ranger, e1071, ggplot2, vioplot, CMplot, imager, topGO, xlsx Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 2af0f0406dff12a82fe8a7ebd79ead39 Package: BioMVCClass Version: 1.58.0 Depends: R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz License: LGPL MD5sum: 85470d4ce4e2af20bcb8165d7c4d2031 Package: biomvRCNS Version: 1.30.0 Depends: IRanges, GenomicRanges, Gviz Imports: methods, mvtnorm Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: b58731bd83c520d823af864da5cd1380 Package: BioNet Version: 1.50.0 Depends: R (>= 2.10.0), graph, RBGL Imports: igraph (>= 1.0.1), AnnotationDbi, Biobase Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML License: GPL (>= 2) MD5sum: 583c6faf484c255392466ca8577e5d8c Package: BioNetStat Version: 1.10.5 Depends: R (>= 3.5), shiny, igraph, shinyBS, pathview, DT Imports: BiocParallel, RJSONIO, whisker, yaml, pheatmap, ggplot2, plyr, utils, stats, RColorBrewer, Hmisc, psych, knitr, rmarkdown, markdown License: GPL (>= 3) MD5sum: 16c728ca730aba0a463f4f4617da72db Package: BioQC Version: 1.18.0 Depends: Biobase Imports: edgeR, Rcpp, methods, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, org.Hs.eg.db, ineq, covr License: GPL (>= 3) MD5sum: 4be1b099a18bffa267bc193243c23224 Package: biosigner Version: 1.18.2 Depends: Biobase, ropls Imports: methods, e1071, MultiDataSet, randomForest Suggests: BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, omicade4, rmarkdown, testthat License: CeCILL MD5sum: 5e76c329fa316614e75351383316bf37 Package: Biostrings 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S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, limma Suggests: testthat, knitr, rmarkdown, BiocStyle, arm, earth, xgboost, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) License: file LICENSE MD5sum: f3f8866309508ac92c16605d5fe701bc Package: biovizBase Version: 1.38.0 Depends: R (>= 3.5.0), methods Imports: grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors (>= 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: c0bbcef56b535dfa8892a566bb1a61f1 Package: BiRewire Version: 3.22.0 Depends: igraph, slam, tsne, Matrix 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2f9c2269349bdded760e9b03d8e4d48b Package: BitSeq Version: 1.34.0 Depends: Rsamtools (>= 1.99.3) Imports: S4Vectors, IRanges LinkingTo: Rhtslib (>= 1.15.5) Suggests: edgeR, DESeq, BiocStyle License: Artistic-2.0 + file LICENSE MD5sum: 3643350ad31c8fec73075c5c926f9281 Package: blacksheepr Version: 1.4.0 Depends: R (>= 3.6) 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: 5ba2f91f8247802a46a0700e973485f9 Package: blima Version: 1.24.0 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: 30f275e23b944307d81c816c5daa08fd Package: BLMA Version: 1.14.0 Depends: ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel, Biobase, metafor, methods Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 24589c08487ed3240d49107245e1899d Package: bluster Version: 1.0.0 Imports: stats, methods, utils, Matrix, Rcpp, igraph, S4Vectors, BiocParallel, BiocNeighbors LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut, scRNAseq, scuttle, scater, scran, pheatmap, viridis License: GPL-3 MD5sum: b274d37560398e46e9a342f94dc9fcd3 Package: bnbc Version: 1.12.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, GenomicRanges Imports: Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, GenomeInfoDb, S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 11c93b37993a2da736f581f7a420567a Package: BPRMeth Version: 1.16.0 Depends: R (>= 3.5.0), GenomicRanges Imports: assertthat, methods, MASS, doParallel, parallel, e1071, earth, foreach, randomForest, stats, IRanges, S4Vectors, data.table, graphics, truncnorm, mvtnorm, Rcpp (>= 0.12.14), matrixcalc, magrittr, kernlab, ggplot2, cowplot, BiocStyle LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown License: GPL-3 | file LICENSE MD5sum: cf953afce3f59db0391b651824e921b9 Package: BRAIN Version: 1.36.0 Depends: R (>= 2.8.1), PolynomF, Biostrings, lattice License: GPL-2 MD5sum: fa8074fae5b46afe5952045498663ca9 Package: brainflowprobes Version: 1.4.1 Depends: R (>= 3.6.0) Imports: Biostrings (>= 2.52.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), bumphunter (>= 1.26.0), cowplot (>= 1.0.0), derfinder (>= 1.18.1), derfinderPlot (>= 1.18.1), GenomicRanges (>= 1.36.0), ggplot2 (>= 3.1.1), RColorBrewer (>= 1.1), utils, grDevices, GenomicState (>= 0.99.7) Suggests: BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo, testthat (>= 2.1.0), covr License: Artistic-2.0 MD5sum: d73bb7a7850a6b79cf264e5f62e7b749 Package: BrainSABER Version: 1.0.0 Depends: R (>= 4.0), biomaRt, SummarizedExperiment Imports: data.table, lsa, methods, S4Vectors, utils, BiocFileCache Suggests: BiocStyle, ComplexHeatmap, fastcluster, heatmaply, knitr, plotly License: Artistic-2.0 MD5sum: ab51072965b1bf5a533d5b2f83a710b7 Package: BrainStars Version: 1.34.0 Depends: RCurl, Biobase, methods Imports: RJSONIO, Biobase License: Artistic-2.0 MD5sum: fe3fc0c6500538077fbe6a2c4f0e223f Package: branchpointer Version: 1.16.0 Depends: caret, R(>= 3.4) Imports: plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt, Biostrings, parallel, utils, stats, BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges, GenomeInfoDb, IRanges, S4Vectors, data.table Suggests: knitr, BiocStyle License: BSD_3_clause + file LICENSE MD5sum: cece90d2525412abe6d236d1c4b103d6 Package: breakpointR Version: 1.8.0 Depends: R (>= 3.5), GenomicRanges, cowplot, breakpointRdata Imports: methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>= 1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2, BiocGenerics, gtools, doParallel, foreach Suggests: knitr, BiocStyle, testthat License: file LICENSE MD5sum: f57dfe445492987834b8c151c37b4870 Package: brendaDb Version: 1.4.0 Imports: dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel, crayon, utils, tidyr, curl, xml2, grDevices, rlang, BiocFileCache, rappdirs LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, devtools License: MIT + file LICENSE MD5sum: bb3cd37bdabdf9368f5aba2ab279e524 Package: BRGenomics Version: 1.2.0 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: bb5bd70f5408514f7d756a8a28a4378b Package: bridge Version: 1.54.0 Depends: R (>= 1.9.0), rama License: GPL (>= 2) MD5sum: dcf17676352e19c8d3b118f081e6c39c Package: BridgeDbR Version: 2.0.2 Depends: R (>= 3.3.0), rJava Imports: curl Suggests: BiocStyle, knitr, rmarkdown, testthat License: AGPL-3 MD5sum: b68e1b0ebff129ca5dc5ecf3624b779c Package: BrowserViz Version: 2.12.0 Depends: R (>= 3.5.0), jsonlite (>= 1.5), httpuv(>= 1.5.0) Imports: methods, BiocGenerics Suggests: RUnit, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 56f3df3a7128b570ad159faf063de212 Package: BSgenome Version: 1.58.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.25.6), GenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), rtracklayer (>= 1.39.7) Imports: methods, utils, stats, matrixStats, BiocGenerics, S4Vectors, IRanges, XVector (>= 0.29.3), GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools, rtracklayer Suggests: BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit License: Artistic-2.0 MD5sum: 41f11018d73e8b53677635e73843807d Package: bsseq Version: 1.26.0 Depends: R (>= 4.0), methods, BiocGenerics, GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5) Imports: IRanges (>= 2.23.9), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors (>= 0.27.12), R.utils (>= 2.0.0), DelayedMatrixStats (>= 1.5.2), permute, limma, DelayedArray (>= 0.15.16), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array (>= 1.15.19), rhdf5 LinkingTo: Rcpp, beachmat Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat (>= 1.5.2), BatchJobs License: Artistic-2.0 MD5sum: 8e3a2b7dde50a814d07ea2595a9edbc4 Package: BubbleTree Version: 2.20.0 Depends: R (>= 3.5), IRanges, GenomicRanges, plyr, dplyr, magrittr Imports: BiocGenerics (>= 0.31.6), BiocStyle, Biobase, ggplot2, WriteXLS, gtools, RColorBrewer, limma, grid, gtable, gridExtra, biovizBase, e1071, methods, grDevices, stats, utils Suggests: knitr, rmarkdown License: LGPL (>= 3) MD5sum: 06a82a61b2630880dae5f8a5f50cf258 Package: BufferedMatrix Version: 1.54.0 Depends: R (>= 2.6.0), methods License: LGPL (>= 2) MD5sum: 199aa1fc17fd120e791f2f32cc5fb780 Package: BufferedMatrixMethods Version: 1.54.0 Depends: R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods LinkingTo: BufferedMatrix Suggests: affyio, affy License: GPL (>= 2) MD5sum: 79b04f73a1d1c7cbfc941955931e2d37 Package: BUMHMM Version: 1.14.0 Depends: R (>= 3.4) Imports: devtools, stringi, gtools, stats, utils, SummarizedExperiment, Biostrings, IRanges Suggests: testthat, knitr, BiocStyle License: GPL-3 MD5sum: def78130a319d1fd97f9d6603aef44e4 Package: bumphunter Version: 1.32.0 Depends: R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), GenomeInfoDb, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats Suggests: testthat, RUnit, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 6c888d56d990a324602e1da35143d86a Package: BUS Version: 1.46.0 Depends: R (>= 2.3.0), minet Imports: stats, infotheo License: GPL-3 MD5sum: 765e5c55d708114e547565d74a14a590 Package: BUScorrect Version: 1.8.0 Depends: R (>= 3.5.0) Imports: gplots, methods, grDevices, stats, SummarizedExperiment Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 407c2994f62f8fce1ed30fbf470f25f3 Package: BUSpaRse Version: 1.4.2 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: 10d23573f85373e1bbfd3a5f7f538f69 Package: CAFE Version: 1.26.0 Depends: R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio Imports: affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 5fb24cebed7cd2eb3042e2a1c43d62e4 Package: CAGEfightR Version: 1.10.0 Depends: R (>= 3.5), GenomicRanges (>= 1.30.1), rtracklayer (>= 1.38.2), SummarizedExperiment (>= 1.8.1) Imports: pryr(>= 0.1.3), assertthat(>= 0.2.0), methods(>= 3.6.3), Matrix(>= 1.2-12), BiocGenerics(>= 0.24.0), S4Vectors(>= 0.16.0), IRanges(>= 2.12.0), GenomeInfoDb(>= 1.14.0), GenomicFeatures(>= 1.29.11), GenomicAlignments(>= 1.22.1), BiocParallel(>= 1.12.0), GenomicFiles(>= 1.14.0), Gviz(>= 1.22.2), InteractionSet(>= 1.9.4), GenomicInteractions(>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-3 + file LICENSE MD5sum: 56eab3d44db0bdcad0f20d92593973e8 Package: CAGEr Version: 1.32.1 Depends: methods, MultiAssayExperiment, R (>= 3.5.0) Imports: beanplot, BiocGenerics, BiocParallel, BSgenome, data.table, DelayedArray, formula.tools, GenomeInfoDb, GenomicAlignments, GenomicRanges (>= 1.37.16), ggplot2 (>= 2.2.0), gtools, IRanges (>= 2.18.0), KernSmooth, memoise, plyr, Rsamtools, reshape, rtracklayer, S4Vectors (>= 0.27.5), som, stringdist, stringi, SummarizedExperiment, utils, vegan, VGAM Suggests: BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: b5d213a40783b33ed9735051b3378690 Package: calm Version: 1.4.0 Imports: mgcv, stats, graphics Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 7cebc2c6837724032412569580c41453 Package: CAMERA Version: 1.46.0 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: 9b1b15c9a438d8e44b99e032cbed58ca Package: canceR Version: 1.24.0 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: be3d451fbdfcae437188fd94f57f9958 Package: cancerclass Version: 1.34.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 MD5sum: 8965a068e29629ea67b7bb947c81ae1e Package: CancerInSilico Version: 2.10.0 Depends: R (>= 3.4), Rcpp Imports: methods, utils, graphics, stats LinkingTo: Rcpp, BH Suggests: testthat, knitr, rmarkdown, BiocStyle, Rtsne, viridis, rgl, gplots License: GPL-2 MD5sum: fd1f5f9f1411aceeedbc679bdd870223 Package: CancerMutationAnalysis Version: 1.32.0 Depends: R (>= 2.10.0), qvalue Imports: AnnotationDbi, limma, methods, stats Suggests: KEGG.db License: GPL (>= 2) + file LICENSE MD5sum: c5ab2700841729b392a7dce8b5fbc86b Package: CancerSubtypes Version: 1.16.0 Depends: R (>= 3.5.0), sigclust, NMF Imports: SNFtool, iCluster, cluster, impute, limma, ConsensusClusterPlus, grDevices, survival Suggests: BiocGenerics, knitr, RTCGA.mRNA License: GPL (>= 2) MD5sum: b4dbe92cb13716e34f958f5ac2aeb8a0 Package: CAnD Version: 1.22.0 Imports: methods, ggplot2, reshape Suggests: RUnit, BiocGenerics, BiocStyle License: Artistic-2.0 MD5sum: ecb2702f45c743ea99a5478f15818040 Package: caOmicsV Version: 1.20.0 Depends: R (>= 3.2), igraph (>= 0.7.1), bc3net (>= 1.0.2) License: GPL (>= 2.0) MD5sum: 1c8c675d921b0c6f9fe2bf744facc135 Package: Cardinal Version: 2.8.0 Depends: BiocGenerics, BiocParallel, EBImage, graphics, methods, S4Vectors (>= 0.27.3), stats, ProtGenerics Imports: Biobase, dplyr, irlba, lattice, Matrix, matter, magrittr, mclust, nlme, parallel, signal, sp, stats4, utils, viridisLite Suggests: BiocStyle, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 8b90b94ba7ac12ad71acf883da76f130 Package: CARNIVAL Version: 1.2.0 Depends: R (>= 4.0) Imports: doParallel, readr, viper, AnnotationDbi, Category, ggplot2, UniProt.ws, lpSolve, igraph Suggests: knitr, readxl, testthat (>= 2.1.0) License: Apache License (== 3.0) | file LICENSE MD5sum: 85923e69112a8b10d57a84590f909e29 Package: casper Version: 2.24.2 Depends: R (>= 3.6.0), Biobase, IRanges, methods, GenomicRanges Imports: BiocGenerics (>= 0.31.6), coda, EBarrays, gaga, gtools, GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors (>= 0.9.25), sqldf, survival, VGAM Enhances: parallel License: GPL (>= 2) MD5sum: 8a3006b513915286a2f17152aaf078db Package: CATALYST Version: 1.14.1 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: 28a172f92a73b72e811e400d335b055e Package: Category Version: 2.56.0 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, KEGG.db, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db License: Artistic-2.0 MD5sum: 53ec73d7d172d84febacca37ceb22fec Package: categoryCompare Version: 1.34.0 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, KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter License: GPL-2 MD5sum: ff30c98215ebf10c5945bad72871c548 Package: CausalR Version: 1.22.0 Depends: R (>= 3.2.0) Imports: igraph Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 8ff26c40546525300e9989a96866e783 Package: cbaf Version: 1.12.1 Depends: R (>= 3.5.0) Imports: BiocFileCache, RColorBrewer, cgdsr, genefilter, gplots, grDevices, stats, utils, xlsx Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 89720418cc76973977f4b2558d88631c Package: cBioPortalData Version: 2.2.11 Depends: R (>= 4.0.0), AnVIL, MultiAssayExperiment Imports: BiocFileCache (>= 1.5.3), digest, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment, RTCGAToolbox (>= 2.19.7), S4Vectors, SummarizedExperiment, stats, tibble, tidyr, TCGAutils (>= 1.9.4), utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: AGPL-3 MD5sum: 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Suggests: knitr, BiocStyle, BiocGenerics, testthat License: MIT + file LICENSE MD5sum: 6c0b254dcdfaaaa87cb74a53cd37a49f Package: celaref Version: 1.8.0 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: b74efc484728db8d0b6c6048e13922b1 Package: celda Version: 1.6.1 Depends: R (>= 3.6) Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, reshape2, MAST, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, stringi, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro, pROC, scater (>= 1.14.4), scran, SingleCellExperiment, dbscan, DelayedArray, Seurat, stringr, Matrix, ComplexHeatmap, multipanelfigure, circlize LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, M3DExampleData, TENxPBMCData License: MIT + file LICENSE MD5sum: 5b51e8bcd54f8da7984cda87a7440e3d Package: CellaRepertorium Version: 1.0.0 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: 6d0ae0ab8126b9146068da7873508c1e Package: cellbaseR Version: 1.14.0 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: 08cddcdce84f26b406ea624c98c1b1ff Package: CellBench Version: 1.6.0 Depends: R (>= 3.6), SingleCellExperiment, magrittr, methods, stats, tibble, utils Imports: 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: 2014b3fa4ad971f9c801f224a81cfa19 Package: cellHTS2 Version: 2.54.0 Depends: R (>= 2.10), RColorBrewer, Biobase, methods, genefilter, splots, vsn, hwriter, locfit, grid Imports: prada, GSEABase, Category, stats4, BiocGenerics Suggests: ggplot2 License: Artistic-2.0 MD5sum: 9bc1136652b448347d439ea8c4751574 Package: cellity Version: 1.18.0 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: a5611d8a1344aa204f2937596456d8f6 Package: CellMapper Version: 1.16.0 Depends: S4Vectors, methods Imports: stats, utils Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub License: Artistic-2.0 MD5sum: 58bef824c1fde665e9d56731cf27af6b Package: CellMixS Version: 1.6.1 Depends: kSamples, R (>= 4.0) Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne License: GPL (>= 2) MD5sum: c2fa38bf5450bbc6fc93fc499b9eeb3f Package: CellNOptR Version: 1.36.0 Depends: R (>= 3.5.0), RBGL, graph, methods, hash, RCurl, Rgraphviz, XML, ggplot2 Imports: igraph, stringi, stringr, Suggests: data.table, dplyr, tidyr, readr, RUnit, BiocGenerics, Enhances: doParallel License: GPL-3 MD5sum: 6c779d8f8cd0bdad2a1da6ff2eacbaef Package: cellscape Version: 1.14.0 Depends: R (>= 3.3) Imports: htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0), plyr (>= 1.8.3), dplyr (>= 0.4.3), gtools (>= 3.5.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 239dec6ce534010d9c0eb80f6f31e5fa Package: CellScore Version: 1.10.0 Depends: R (>= 3.5.0) Imports: Biobase (>= 2.39.1), graphics (>= 3.5.0), grDevices (>= 3.5.0), gplots (>= 3.0.1), lsa (>= 0.73.1), methods (>= 3.5.0), RColorBrewer(>= 1.1-2), squash (>= 1.0.8), stats (>= 3.5.0), utils(>= 3.5.0) Suggests: hgu133plus2CellScore, knitr License: GPL-3 MD5sum: 6e804b3530683a0211e99cf102c9f607 Package: CellTrails Version: 1.8.0 Depends: R (>= 3.5), SingleCellExperiment Imports: BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats, ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv, reshape2, Rtsne, stats, splines, SummarizedExperiment, utils Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown License: Artistic-2.0 MD5sum: 8f2ee4fbac4d246249bd5182e39fc1ef Package: cellTree Version: 1.20.0 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: 5614fde3523160dbd24283d05b0a703a Package: CEMiTool Version: 1.14.1 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: 868d20e93c96f813b82612df45fc0b16 Package: ceRNAnetsim Version: 1.2.1 Depends: R (>= 4.0.0), dplyr, tidygraph Imports: furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, stats Suggests: knitr, png, rmarkdown, testthat, covr License: GPL (>= 3.0) MD5sum: a64fcd13af6ebba2fb2a932b24c0fac8 Package: CeTF Version: 1.2.4 Depends: R (>= 4.0), methods Imports: circlize, ComplexHeatmap, clusterProfiler, DESeq2, GenomicTools, GenomicTools.fileHandler, ggnetwork, GGally, ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3, S4Vectors, stats, SummarizedExperiment, utils, WebGestaltR LinkingTo: Rcpp, RcppArmadillo Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat License: GPL-3 MD5sum: 0c0160fab1df33dfc95b98e0755edf07 Package: CexoR Version: 1.28.0 Depends: R (>= 2.10.0), S4Vectors, IRanges Imports: Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation Suggests: RUnit, BiocGenerics, BiocStyle License: Artistic-2.0 | GPL-2 + file LICENSE MD5sum: 495733f67da617c0865336b214d12531 Package: CFAssay Version: 1.24.0 Depends: R (>= 2.10.0) License: LGPL MD5sum: edb8aa91d651b6b028ecf3965e0b4d9e Package: cfDNAPro Version: 1.0.0 Depends: R (>= 4.0), magrittr (>= 1.5.0), Imports: stats, utils, dplyr (>= 0.8.3), stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1), Rsamtools (>= 2.4.0), rlang (>= 0.4.0) Suggests: scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat License: GPL-3 MD5sum: d4b9db2fc2ca64ddf6bfdc6fe3cc44d3 Package: CGHbase Version: 1.50.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), marray License: GPL MD5sum: 7c7bcff19549f37deb5df221dd64de7c Package: CGHcall Version: 2.52.0 Depends: R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods, Biobase, CGHbase (>= 1.15.1), snowfall MD5sum: 4b7a4c7e87f5f9edd93d873a92bf979f Package: cghMCR Version: 1.48.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL MD5sum: 510576184acd70452d72c558f350b611 Package: CGHnormaliter Version: 1.44.0 Depends: CGHcall (>= 2.17.0), CGHbase (>= 1.15.0) Imports: Biobase, CGHbase, CGHcall, methods, stats, utils License: GPL (>= 3) MD5sum: 095c187945087893301134fec495d996 Package: CGHregions Version: 1.48.0 Depends: R (>= 2.0.0), methods, Biobase, CGHbase MD5sum: 1ac344a7f805a360acf87b8df39bab5a Package: ChAMP Version: 2.20.1 Depends: R (>= 3.3), minfi, ChAMPdata (>= 2.6.0),DMRcate, Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest, DT, RPMM Imports: prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b4.hg19, limma, DNAcopy, preprocessCore,impute, marray, wateRmelon, plyr,goseq,missMethyl,kpmt,ggplot2, GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly (>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat Suggests: knitr,rmarkdown License: GPL-3 MD5sum: 7b6812391faae214f0dbac0c14bba0d5 Package: ChemmineOB Version: 1.28.4 Depends: R (>= 2.15.1), methods Imports: BiocGenerics, zlibbioc, Rcpp (>= 0.11.0) LinkingTo: BH, Rcpp Suggests: ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager Enhances: ChemmineR (>= 2.13.0) License: file LICENSE MD5sum: 424e9b18d0a1b528f81dfc22e98b2071 Package: ChemmineR Version: 3.42.2 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: c960281ae893c4d225ad90b30e2ccb3a Package: CHETAH Version: 1.6.0 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: b7f5661ef71c9c63d3848417c9040b72 Package: ChIC Version: 1.10.0 Depends: spp, R (>= 3.6) Imports: ChIC.data (>= 1.7.1), caTools, methods,GenomicRanges, IRanges, parallel, progress, caret, grDevices, stats, utils, graphics, S4Vectors, BiocGenerics License: GPL-2 MD5sum: c9b1d3c88943d926c7d23a06b9913062 Package: Chicago Version: 1.18.0 Depends: R (>= 3.2), 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: a6c39ab1b6211cab61be204b5376588d Package: chimera Version: 1.32.0 Depends: Biobase, GenomicRanges (>= 1.13.3), Rsamtools (>= 1.13.1), GenomicAlignments, methods, AnnotationDbi, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens Suggests: BiocParallel, geneplotter Enhances: Rsubread, BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: a3f594028ae868b8fa46264c49229b02 Package: chimeraviz Version: 1.16.1 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, ArgumentCheck, gtools, magick Suggests: testthat, roxygen2, devtools, knitr, lintr License: Artistic-2.0 MD5sum: a82b86ae25a335908bd50ea0f101eb27 Package: ChIPanalyser Version: 1.12.0 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: bbb99a037855d86ef9452a26215fa34c Package: ChIPComp Version: 1.20.0 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: 9dab092b453cfb6f8b0ca59b6a912f0f Package: chipenrich Version: 2.14.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, chipenrich.data, GenomeInfoDb, GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra, MASS, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer, S4Vectors (>= 0.23.10), stats, stringr, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat License: GPL-3 MD5sum: 34e54159dd51077dccb53ae9a7870c78 Package: ChIPexoQual Version: 1.14.0 Depends: R (>= 3.4.0), GenomicAlignments (>= 1.0.1) Imports: methods, utils, GenomeInfoDb, stats, BiocParallel, GenomicRanges (>= 1.14.4), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools (>= 1.16.1), IRanges (>= 1.6), S4Vectors (>= 0.8), biovizBase (>= 1.18), broom (>= 0.4), RColorBrewer (>= 1.1), dplyr (>= 0.5), scales (>= 0.4.0), viridis (>= 0.3), hexbin (>= 1.27), rmarkdown Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat License: GPL (>= 2) 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1b11dfe53f697c3954358f3cc932586d Package: ChIPQC Version: 1.26.0 Depends: R (>= 3.0.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19) Imports: BiocGenerics (>= 0.11.3), S4Vectors (>= 0.1.0), IRanges (>= 1.99.17), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), chipseq (>= 1.12.0), gtools, BiocParallel, methods, reshape2, Nozzle.R1, Biobase, grDevices, stats, utils, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Celegans.UCSC.ce6.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene Suggests: BiocStyle License: GPL (>= 3) MD5sum: db9d63600d713797722ead2e60735b7d Package: ChIPseeker Version: 1.26.2 Depends: R (>= 3.5.0) Imports: AnnotationDbi, BiocGenerics, boot, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, graphics, grDevices, gtools, methods, plotrix, dplyr, parallel, magrittr, RColorBrewer, rtracklayer, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils Suggests: clusterProfiler (>= 3.15.4), ggimage, ggplotify, ggupset, ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, tibble License: Artistic-2.0 MD5sum: 415af68738071f3535690cbd754e5096 Package: chipseq Version: 1.40.0 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: fa08e956631d7f0ec82d0e1ee109929b Package: ChIPseqR Version: 1.44.0 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: ce2dbd91b308bc0bbd806d956cd8a750 Package: ChIPSeqSpike Version: 1.9.0 Depends: R (>= 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foreach, doParallel, openxlsx, igraph, circlize, graph, stats, utils, grDevices, graphics, methods, biomaRt, rJava Suggests: RUnit, BiocGenerics, knitr License: GPL-2 MD5sum: ecb277077b97e24f6fd81742bfeb8b9b Package: cicero Version: 1.8.1 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 (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr License: MIT + file LICENSE MD5sum: fb003edabd27f9b91d4212904e4a61f3 Package: CINdex Version: 1.18.0 Depends: R (>= 3.3), GenomicRanges Imports: bitops,gplots,grDevices,som, dplyr,gridExtra,png,stringr,S4Vectors, IRanges, GenomeInfoDb,graphics, stats, utils Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens License: GPL (>= 2) MD5sum: e7dbe4eac44e7c260b00efed477b90f9 Package: circRNAprofiler Version: 1.4.2 Depends: R(>= 4.0.0) Imports: dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2, edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb, universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, Biostrings, gwascat, BSgenome, Suggests: testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager, License: GPL-3 MD5sum: 0ff2c2cc5515baee30892fcc55e15282 Package: cisPath Version: 1.30.0 Depends: R (>= 2.10.0) Imports: methods, utils License: GPL (>= 3) MD5sum: e579b3da430f473911fdeed3ad17eee7 Package: CiteFuse Version: 1.2.1 Depends: R (>= 4.0) Imports: SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>= 1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid, dbscan, propr, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph, scales, scran (>= 1.14.6), graphics, methods, stats, utils, reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5, rlang Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown License: GPL-3 MD5sum: ef018962eab9c42ced4ccfc09e0e158f Package: ClassifyR Version: 2.10.0 Depends: R (>= 3.5.0), methods, S4Vectors (>= 0.18.0), MultiAssayExperiment (>= 1.6.0), BiocParallel Imports: locfit, grid, utils, plyr Suggests: limma, genefilter, edgeR, car, Rmixmod, ggplot2 (>= 3.0.0), gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, 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rvcheck, stats, tidyr, utils Suggests: AnnotationHub, knitr, org.Hs.eg.db, prettydoc, ReactomePA, testthat License: Artistic-2.0 MD5sum: 5580ac9d6cd36b74b0f2f1f7b67a2c12 Package: clusterSeq Version: 1.14.0 Depends: R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats, utils Imports: BiocGenerics Suggests: BiocStyle License: GPL-3 MD5sum: 43ef022eb8f23106446ef9b07e4c287b Package: ClusterSignificance Version: 1.18.0 Depends: R (>= 3.3.0) Imports: methods, pracma, princurve (>= 2.0.5), scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr License: GPL-3 MD5sum: d21b3624561a0b327f356d00d62e0399 Package: clusterStab Version: 1.62.0 Depends: Biobase (>= 1.4.22), R (>= 1.9.0), methods Suggests: fibroEset, genefilter License: Artistic-2.0 MD5sum: b31d3569bc534fee94c5223e074b75ef Package: clustifyr Version: 1.2.0 Depends: R (>= 4.0) Imports: cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, readr, rlang, 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LinkingTo: S4Vectors, IRanges, XVector Suggests: Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3 License: GPL-2 | file LICENSE License_restricts_use: yes MD5sum: 37ace8add702c580473d65511571284b Package: CNORdt Version: 1.32.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 MD5sum: 249189c88ed6f33966d9cbde06267966 Package: CNORfeeder Version: 1.30.0 Depends: R (>= 3.6.0), CellNOptR (>= 1.4.0), graph Suggests: minet, catnet, Rgraphviz, RUnit, BiocGenerics, igraph Enhances: MEIGOR License: GPL-3 MD5sum: 2945c91bb26d200187815ea1c43bc9e9 Package: CNORfuzzy Version: 1.32.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 MD5sum: 0881029eba2f436c555c9b7a5ae5f94c Package: CNORode Version: 1.32.0 Depends: CellNOptR (>= 1.5.14), genalg 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foreach, ggplot2, plyr, GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics, methods, shiny, shinyFiles, shinyjs, grid, openxlsx Suggests: knitr, RUnit License: GPL-3 MD5sum: 9562feabbe33ee653d2f183ad2b79d07 Package: CNVRanger Version: 1.6.1 Depends: GenomicRanges, RaggedExperiment Imports: BiocGenerics, BiocParallel, GDSArray, GenomeInfoDb, IRanges, S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR, gdsfmt, grDevices, lattice, limma, methods, plyr, qqman, rappdirs, reshape2, stats, utils Suggests: AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, curatedTCGAData, ensembldb, grid, knitr, regioneR, rmarkdown License: Artistic-2.0 MD5sum: def154aacfae4c06d2b17a8e14291819 Package: CNVrd2 Version: 1.28.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 MD5sum: 6ab6895b163b6bb3d0e12915036bad9a 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genefilter, DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods Suggests: knitr, testthat License: GPL (>= 2) MD5sum: f6b15995cd0f2effe916ee1838868f7f Package: covEB Version: 1.16.0 Depends: R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats, LaplacesDemon, Matrix Suggests: curatedBladderData License: GPL-3 MD5sum: fda017ce6ecdffc07ccde61add434bd3 Package: CoverageView Version: 1.28.0 Depends: R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer Imports: S4Vectors (>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges, GenomicAlignments, parallel, tools License: Artistic-2.0 MD5sum: d5bbd0f086d18847b2c266be38029deb Package: covRNA Version: 1.16.0 Depends: ade4, Biobase Imports: parallel, genefilter, grDevices, stats, graphics Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: ef7e34ac9a8f80d9a8768c8e49a4e68d Package: cpvSNP Version: 1.22.0 Depends: R (>= 2.10), GenomicFeatures, GSEABase (>= 1.24.0) Imports: methods, corpcor, BiocParallel, ggplot2, plyr Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: d5ccb876c2ba4ec638846c82ecb168c7 Package: cqn Version: 1.36.0 Depends: R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore, splines, quantreg Imports: splines Suggests: scales, edgeR License: Artistic-2.0 MD5sum: 2b680f42ea16536a92ddec49ee5efffb Package: CRImage Version: 1.38.0 Depends: EBImage, DNAcopy, aCGH Imports: MASS, e1071, foreach, sgeostat License: Artistic-2.0 MD5sum: a17b2ae2b04a3108b8d1d19ec3600bb4 Package: CRISPRseek Version: 1.30.1 Depends: R (>= 3.0.1), BiocGenerics, Biostrings Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges, BSgenome, BiocParallel, hash, methods,reticulate,rhdf5 Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL (>= 2) MD5sum: 10d768f323d339392e6992c079d4ff4a Package: crisprseekplus Version: 1.16.0 Depends: R (>= 3.3.0), shiny, shinyjs, CRISPRseek Imports: DT, utils, GUIDEseq, GenomicRanges, GenomicFeatures, BiocManager, BSgenome, AnnotationDbi, hash Suggests: testthat, rmarkdown, knitr, R.rsp License: GPL-3 + file LICENSE MD5sum: 9cc90e23d0b9d21e0ba3578f229018b7 Package: CrispRVariants Version: 1.18.0 Depends: R (>= 3.5), ggplot2 (>= 2.2.0) Imports: AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>= 0.9.38), utils Suggests: BiocStyle, gdata, GenomicFeatures, knitr, rmarkdown, rtracklayer, sangerseqR, testthat, VariantAnnotation License: GPL-2 MD5sum: 9afbb5c8ce08e2c6cb1897074938fc99 Package: crlmm Version: 1.48.0 Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= 1.17.7) Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>= 1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats, VGAM, parallel, graphics, limma, beanplot LinkingTo: preprocessCore (>= 1.17.7) Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats, RUnit License: Artistic-2.0 MD5sum: 06e60691fc9e2aa1298e1ac82ebc130f Package: crossmeta Version: 1.16.1 Depends: R (>= 4.0) Imports: affy (>= 1.52.0), affxparser (>= 1.46.0), AnnotationDbi (>= 1.36.2), Biobase (>= 2.34.0), BiocGenerics (>= 0.20.0), BiocManager (>= 1.30.4), DT (>= 0.2), DBI (>= 1.0.0), data.table (>= 1.10.4), fdrtool (>= 1.2.15), GEOquery (>= 2.40.0), limma (>= 3.30.13), matrixStats (>= 0.51.0), metaMA (>= 3.1.2), miniUI (>= 0.1.1), oligo (>= 1.38.0), reader(>= 1.0.6), RColorBrewer (>= 1.1.2), RCurl (>= 1.95.4.11), RSQLite (>= 2.1.1), randomcoloR (>= 1.1.0.1), stringr (>= 1.2.0), sva (>= 3.22.0), shiny (>= 1.0.0), shinyjs (>= 2.0.0), shinyBS (>= 0.61), shinyWidgets (>= 0.5.3), shinypanel (>= 0.1.0), statmod (>= 1.4.34), XML (>= 3.98.1.17), readxl (>= 1.3.1) Suggests: knitr, rmarkdown, lydata, org.Hs.eg.db, testthat License: MIT + file LICENSE MD5sum: 827242d1afc03ac177ba862d60dcabe0 Package: CSAR Version: 1.42.0 Depends: R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges Imports: stats, utils Suggests: ShortRead, Biostrings License: Artistic-2.0 MD5sum: 32dfe696bd6f55a94d22198bb5f2754d Package: csaw Version: 1.24.3 Depends: GenomicRanges, SummarizedExperiment Imports: Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi, methods, S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, utils LinkingTo: Rhtslib, zlibbioc, Rcpp Suggests: org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager License: GPL-3 MD5sum: c62f78572c7a33eea1fd82839d83682b Package: CSSP Version: 1.28.0 Imports: methods, splines, stats, utils Suggests: testthat License: GPL-2 MD5sum: 621102395857ad3baaa9bc7ffa37cabb Package: CSSQ Version: 1.2.0 Depends: SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, rtracklayer Imports: GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: e434a2ddf33b101ad4700efde0854d4f Package: ctc Version: 1.64.0 Depends: amap License: GPL-2 MD5sum: 7216ade76bc01e7d8d02e0870887ee58 Package: ctgGEM Version: 1.2.0 Depends: monocle, SummarizedExperiment, Imports: Biobase, BiocGenerics, graphics, grDevices, igraph, methods, utils, sincell, TSCAN, destiny, HSMMSingleCell Suggests: BiocStyle, biomaRt, irlba, knitr, VGAM License: GPL (>= 2) MD5sum: fbeea904b5ff526d16576a88992cde3b Package: cTRAP Version: 1.8.0 Depends: R (>= 3.6.0) Imports: biomaRt, binr, cowplot, data.table, dplyr, DT, fgsea, ggplot2, ggrepel, graphics, highcharter, httr, limma, methods, pbapply, R.utils, readxl, reshape2, rhdf5, scales, shiny, stats, tools, utils Suggests: testthat, knitr, covr, rmarkdown, spelling License: MIT + file LICENSE MD5sum: f6140efbf22bc5ef6a9ca48453cfdefd Package: ctsGE Version: 1.16.0 Depends: R (>= 3.2) Imports: ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat License: GPL-2 MD5sum: e120b221f6a06483981d8fbaac2fdf09 Package: cummeRbund Version: 2.32.0 Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz Imports: methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson License: Artistic-2.0 MD5sum: d12bc60c3a22403d675a6c51c8acfc25 Package: customCMPdb Version: 1.0.0 Depends: R (>= 4.0) Imports: AnnotationHub, RSQLite, XML, utils, ChemmineR, methods, stats, rappdirs, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: e6e05f2ed12dfc9aba0522d9dd0c2864 Package: customProDB Version: 1.30.1 Depends: R (>= 3.0.1), IRanges, AnnotationDbi, biomaRt(>= 2.17.1) Imports: S4Vectors (>= 0.9.25), DBI, GenomeInfoDb, GenomicRanges, Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>= 2.26.3), GenomicFeatures (>= 1.32.0), stringr, RCurl, plyr, VariantAnnotation (>= 1.13.44), rtracklayer, RSQLite, AhoCorasickTrie, methods Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: c6290c4529ab8b4ad3fb97358f6e57cc Package: cycle Version: 1.44.0 Depends: R (>= 2.10.0), Mfuzz Imports: Biobase, stats License: GPL-2 MD5sum: a2e3f9d3d8ddb0e80a450bf21f1ba05e Package: cydar Version: 1.14.1 Depends: SingleCellExperiment Imports: viridis, methods, shiny, graphics, stats, grDevices, utils, BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment, flowCore, Biobase, Rcpp, BiocNeighbors LinkingTo: Rcpp Suggests: ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet, BiocStyle, flowStats License: GPL-3 MD5sum: 2a653ca3e78d34afe495e2128ed8a29d Package: CytoDx Version: 1.10.0 Depends: R (>= 3.5) Imports: doParallel, dplyr, glmnet, rpart, rpart.plot, stats, flowCore,grDevices, graphics, utils Suggests: knitr License: GPL-2 MD5sum: bb5de6a9a6d0bc3dd401f83753a1f876 Package: cytofast Version: 1.6.0 Depends: R (>= 3.6.0) Imports: flowCore, ggplot2, ggridges, RColorBrewer, reshape2, stats, grDevices, Rdpack, methods, grid, FlowSOM Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: dde76a000948e8c0d925335648b0de54 Package: cytolib Version: 2.2.1 Depends: R (>= 3.4) Imports: RcppParallel, RProtoBufLib LinkingTo: Rcpp, BH(>= 1.72.0-2), RProtoBufLib(>= 1.99.8),Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1) Suggests: knitr License: file LICENSE License_restricts_use: yes MD5sum: cf44c25af78de81b185d6bf43b3edd69 Package: cytomapper Version: 1.2.1 Depends: R (>= 4.0), EBImage, SingleCellExperiment, methods Imports: S4Vectors, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 660cbd3798af4e90de7805a10ea27495 Package: CytoML Version: 2.2.2 Depends: R (>= 3.5.0) Imports: cytolib(>= 2.1.18), 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 ( >= 1.99.26),Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1), flowWorkspace Suggests: testthat, flowWorkspaceData , knitr, parallel License: file LICENSE License_restricts_use: yes MD5sum: 9c84c799f109e6d38328c90827ef886e Package: CytoTree Version: 1.0.3 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: 96daab7375740049be2f83b6a4016335 Package: dada2 Version: 1.18.0 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-3 MD5sum: a8b24b62a7ddad994c53d3c36230d903 Package: dagLogo Version: 1.28.1 Depends: R (>= 3.0.1), methods, grid Imports: pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils, biomaRt, motifStack Suggests: XML, grImport, grImport2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 8467aed26d97e238692d373a3048bb59 Package: daMA Version: 1.62.0 Imports: MASS, stats License: GPL (>= 2) MD5sum: 84f865753993d2e30909f666518a67c2 Package: DAMEfinder Version: 1.2.0 Depends: R (>= 4.0) Imports: stats, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, readr, SummarizedExperiment, GenomicAlignments, stringr, plyr, VariantAnnotation, parallel, ggplot2, Rsamtools, BiocGenerics, methods, limma, bumphunter, Biostrings, reshape2, cowplot, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 53be53ecb207b92aebf260f658246040 Package: DaMiRseq Version: 2.2.0 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: 56bc7467dc9f24c20bed164f9d5606e2 Package: DAPAR Version: 1.22.9 Depends: R (>= 4.0.3) 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 (>= 0.8), forcats, methods, highcharter, DAPARdata (>= 1.18.0), siggenes, graph, lme4, readxl, 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: f45bd1e89b3e704c4482f2761e37e1b5 Package: DART Version: 1.38.0 Depends: R (>= 2.10.0), igraph (>= 0.6.0) Suggests: breastCancerVDX, breastCancerMAINZ, Biobase License: GPL-2 MD5sum: 1feafa3222ac514028fd6813e53661be Package: dasper Version: 1.0.0 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: 98896bd86e1466536fb802e60f79c49c Package: DBChIP Version: 1.34.0 Depends: R (>= 2.15.0), edgeR, DESeq Suggests: ShortRead, BiocGenerics License: GPL (>= 2) MD5sum: 74d59fa6aad2010c6f62127dd50bccb8 Package: dcanr Version: 1.6.0 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: f3026db4c17cf6b45f5b4e532320f30c Package: dcGSA Version: 1.18.0 Depends: R (>= 3.3), Matrix Imports: BiocParallel Suggests: knitr License: GPL-2 MD5sum: 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SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 MD5sum: 1874e14f8849e3f502bb4ae8e40f9ab8 Package: debrowser Version: 1.18.3 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, BiocStyle, knitr, R.rsp License: GPL-3 + file LICENSE MD5sum: 2100d58c54cbf47885911431ecad0248 Package: DECIPHER Version: 2.18.1 Depends: R (>= 3.5.0), Biostrings (>= 2.35.12), RSQLite (>= 1.1), stats, parallel Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector License: GPL-3 MD5sum: acd8633cce05ac58e9e019d05f16adb8 Package: deco Version: 1.6.0 Depends: R (>= 3.5.0), AnnotationDbi, BiocParallel, SummarizedExperiment, limma Imports: stats, methods, ggplot2, foreign, graphics, BiocStyle, Biobase, cluster, gplots, RColorBrewer, locfit, made4, ade4, sfsmisc, scatterplot3d, gdata, grDevices, utils, reshape2, gridExtra Suggests: knitr, curatedTCGAData, MultiAssayExperiment, Homo.sapiens License: GPL (>= 3) MD5sum: 07c9e73838d391a6b33429a69e46632e Package: DEComplexDisease Version: 1.10.0 Depends: R (>= 3.3.3) Imports: Rcpp (>= 0.12.7), DESeq2, edgeR, SummarizedExperiment, ComplexHeatmap, grid, parallel, BiocParallel, grDevices, graphics, stats, methods, utils LinkingTo: Rcpp Suggests: knitr License: GPL-3 MD5sum: da567eb1a3d35ea61ca3ea8d30857dff Package: decompTumor2Sig Version: 2.6.0 Depends: R(>= 3.6), ggplot2 Imports: methods, Matrix, quadprog(>= 1.5-5), GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table, GenomeInfoDb Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 8b8a0a460356c79cd84a8857ec0db691 Package: DeconRNASeq Version: 1.32.0 Depends: R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid License: GPL-2 MD5sum: dafcd90c481f444afe4cad7e307cc3e7 Package: decontam Version: 1.10.0 Depends: R (>= 3.4.1), methods (>= 3.4.1) Imports: ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats Suggests: BiocStyle, knitr, rmarkdown, phyloseq License: Artistic-2.0 MD5sum: f27d983273b2056e3a78c8a4a24b3ab9 Package: DeepBlueR Version: 1.16.0 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: cfd82198e8e6eb1290881ea7de3425db Package: deepSNV Version: 1.36.0 Depends: R (>= 2.13.0), methods, graphics, parallel, IRanges, GenomicRanges, SummarizedExperiment, Biostrings, VGAM, VariantAnnotation (>= 1.13.44), Imports: Rhtslib LinkingTo: Rhtslib (>= 1.13.1) Suggests: RColorBrewer, knitr, rmarkdown License: GPL-3 MD5sum: 56ccfc39d2fbfa3e520af464a5fdcab5 Package: DEFormats Version: 1.18.0 Imports: checkmate, data.table, DESeq2, edgeR (>= 3.13.4), GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat License: GPL-3 MD5sum: a9ed762c3fc9efb20371458224fc899f Package: DegNorm Version: 1.0.0 Depends: R (>= 4.0.0), methods Imports: Rcpp (>= 1.0.2),GenomicFeatures, parallel, foreach, S4Vectors, doParallel, Rsamtools (>= 1.31.2), GenomicAlignments, heatmaply, data.table, stats, ggplot2, GenomicRanges, IRanges, plyr, plotly, utils,viridis LinkingTo: Rcpp, RcppArmadillo,S4Vectors,IRanges Suggests: knitr,rmarkdown,formatR License: LGPL (>= 3) MD5sum: 59e8a0647233912ccbbc79b62cacdb04 Package: DEGreport Version: 1.26.0 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: 81b7463c7e912fcbd5a6aaf86110c09f Package: DEGseq Version: 1.44.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: db596e218730cdb1df7833a2998a7c99 Package: DelayedArray Version: 0.16.3 Depends: R (>= 3.4), methods, stats4, Matrix, BiocGenerics (>= 0.31.5), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2), IRanges (>= 2.17.3) Imports: stats LinkingTo: S4Vectors Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit License: Artistic-2.0 MD5sum: 5dc980f0310ea27682281599f35ee930 Package: DelayedDataFrame Version: 1.6.0 Depends: R (>= 3.6), S4Vectors (>= 0.23.19), DelayedArray (>= 0.7.5) Imports: methods, stats, BiocGenerics Suggests: testthat, knitr, rmarkdown, SeqArray, GDSArray License: GPL-3 MD5sum: 6176896b97757e0aca8631db297c960e Package: DelayedMatrixStats Version: 1.12.3 Depends: MatrixGenerics, DelayedArray (>= 0.15.3) Imports: methods, matrixStats (>= 0.56.0), sparseMatrixStats, Matrix, S4Vectors (>= 0.17.5), IRanges, HDF5Array (>= 1.17.2), BiocParallel Suggests: testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark, profmem License: MIT + file LICENSE MD5sum: 9c2be74a44638787be02a176f10d6175 Package: deltaCaptureC Version: 1.4.0 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, 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MD5sum: 48ab9473486963073bc46d50a06c4c23 Package: DEqMS Version: 1.8.0 Depends: R(>= 3.5),graphics,stats,ggplot2,limma(>= 3.34) Suggests: BiocStyle,knitr,rmarkdown,plyr,matrixStats,reshape2,farms,utils,ggrepel,ExperimentHub,LSD License: LGPL MD5sum: ba53e089c722922fb78d03dccd47708e Package: derfinder Version: 1.24.2 Depends: R (>= 3.5.0) Imports: BiocGenerics (>= 0.25.1), AnnotationDbi (>= 1.27.9), BiocParallel (>= 1.15.15), bumphunter (>= 1.9.2), derfinderHelper (>= 1.1.0), GenomeInfoDb (>= 1.3.3), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges (>= 1.17.40), Hmisc, IRanges (>= 2.3.23), methods, qvalue (>= 1.99.0), Rsamtools (>= 1.25.0), rtracklayer, S4Vectors (>= 0.23.19), stats, utils Suggests: BiocStyle (>= 2.5.19), sessioninfo, derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat (>= 2.1.0), TxDb.Hsapiens.UCSC.hg19.knownGene, covr License: Artistic-2.0 MD5sum: 781453cd6e58934289be3a664ebdbe6c 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BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), magrittr, rmarkdown, AnnotationHub Enhances: RMariaDB, shiny License: LGPL MD5sum: c9f6da498304ef6e41058da7e2585571 Package: ensemblVEP Version: 1.32.1 Depends: methods, BiocGenerics, GenomicRanges, VariantAnnotation Imports: S4Vectors (>= 0.9.25), Biostrings, SummarizedExperiment, GenomeInfoDb, stats Suggests: RUnit License: Artistic-2.0 MD5sum: aac9a29728303b26c41855be8f5cec15 Package: EpiDISH Version: 2.6.1 Depends: R (>= 4.0) Imports: MASS, e1071, quadprog, parallel, stats, matrixStats, stringr, locfdr, Matrix Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat License: GPL-2 MD5sum: 5c6bd18071761ead0124264c664427d7 Package: epigenomix Version: 1.30.0 Depends: R (>= 3.2.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment Imports: BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray License: LGPL-3 MD5sum: e42568ab3e951f8242b5c26a9600d92a Package: 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rmarkdown, testthat, httptest, AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: 74421c1848389331342831360f6e3d21 Package: epivizr Version: 2.20.0 Depends: R (>= 3.0), methods, Imports: epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4), GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi License: Artistic-2.0 MD5sum: d68549cd8e152a932e56dc40d86474a1 Package: epivizrChart Version: 1.12.0 Depends: R (>= 3.4.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, 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BiocGenerics, GenomicFeatures, S4Vectors Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle License: MIT + file LICENSE MD5sum: de4890c017745a395403e846dd79a56d Package: erccdashboard Version: 1.24.0 Depends: R (>= 3.2), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0) Imports: edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr, qvalue, reshape2, ROCR, scales, stringr License: GPL (>= 2) MD5sum: 9d3d31cd8bf9a4a5c7ff242e1e93cc43 Package: erma Version: 1.6.0 Depends: R (>= 3.1), methods, Homo.sapiens, GenomicFiles (>= 1.5.2) Imports: rtracklayer (>= 1.38.1), S4Vectors (>= 0.23.18), BiocGenerics, GenomicRanges, SummarizedExperiment, ggplot2, GenomeInfoDb, Biobase, shiny, BiocParallel, IRanges, AnnotationDbi Suggests: rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel License: Artistic-2.0 MD5sum: f0e9aefe9886bec746bbbfbf764e02ff Package: ERSSA Version: 1.8.0 Depends: R (>= 4.0.0) Imports: edgeR (>= 3.23.3), DESeq2 (>= 1.21.16), ggplot2 (>= 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GSVA, SingleCellExperiment, limma, ggridges, msigdbr, stats, BiocParallel, Matrix Suggests: Seurat, SeuratObject, knitr, rmarkdown, BiocStyle, testthat, dittoSeq (>= 1.1.2) License: Apache License 2.0 MD5sum: bfbaaa849ad06f58c72db4faacb1fa25 Package: esetVis Version: 1.16.0 Imports: mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils, grDevices, methods Suggests: ggplot2, ggvis, rbokeh, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment License: GPL-3 MD5sum: fb28093c0e2c9386acee67ac21a388f3 Package: eudysbiome Version: 1.20.0 Depends: R (>= 3.1.0) Imports: plyr, Rsamtools, R.utils, Biostrings License: GPL-2 MD5sum: ec85181b8466cb30ba698b882b77976a Package: evaluomeR Version: 1.6.6 Depends: R (>= 3.6), SummarizedExperiment, MultiAssayExperiment, cluster (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14), flexmix (>= 2.3.15) Imports: corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2, ggdendro, plotrix, stats, matrixStats, Rdpack, 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Biobase, graph, methods, stats, utils, corpcor, RUnit, XML, flowCore (>= 1.32.0) Suggests: gatingMLData License: Artistic-2.0 MD5sum: db8afae120e917f5d9b95d1a9a54ee83 Package: flowViz Version: 1.54.0 Depends: R (>= 2.7.0), flowCore(>= 1.41.9), lattice Imports: stats4, Biobase, flowCore, graphics, grDevices, grid, KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer, stats, utils, hexbin,IDPmisc Suggests: colorspace, flowStats, knitr, testthat License: Artistic-2.0 MD5sum: 11fa7a770d2cec71cf4029992d973be7 Package: flowVS Version: 1.22.4 Depends: R (>= 3.2), methods, flowCore, flowViz, flowStats Suggests: knitr, vsn, License: Artistic-2.0 MD5sum: 9fa69b4f6ce179e27d12f4a24cd85643 Package: flowWorkspace Version: 4.2.0 Depends: R (>= 3.5.0) Imports: Biobase, BiocGenerics, cytolib (>= 2.1.20), lattice, latticeExtra, XML, ggplot2, graph, graphics, grDevices, methods, stats, stats4, utils, RBGL, tools, Rgraphviz, data.table, dplyr, Rcpp, scales, matrixStats, RcppParallel, RProtoBufLib, digest, aws.s3, aws.signature, flowCore(>= 2.1.1), ncdfFlow(>= 2.25.4) LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib (>= 2.1.15),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: ceab0b28fd373794e3d61619ae70d8a8 Package: fmcsR Version: 1.32.0 Depends: R (>= 2.10.0), ChemmineR, methods Imports: RUnit, methods, ChemmineR, BiocGenerics, parallel Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap License: Artistic-2.0 MD5sum: 27e63ce22d620ccdbc4013baf6d8e5e1 Package: fmrs Version: 1.0.0 Depends: R (>= 4.0.0) Imports: methods, survival, stats Suggests: BiocGenerics, testthat, knitr, utils License: GPL (>= 3) MD5sum: 0cba76f699277b1fd4483422cb42cfc0 Package: FoldGO Version: 1.8.0 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: ed54d2ca65eedc83cf807259155843f2 Package: FourCSeq Version: 1.24.0 Depends: R (>= 3.0), splines, LSD, DESeq2 (>= 1.9.11), ggplot2 Imports: Biobase, Biostrings, GenomicRanges, SummarizedExperiment, Rsamtools, ggbio, reshape2, rtracklayer, fda, GenomicAlignments, gtools, Matrix, methods Suggests: BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene License: GPL (>= 3) MD5sum: 920822a8a2d53a023e26eb2d9007cd2f Package: FRASER Version: 1.2.1 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: 03c191cfd4bafca1f67e66f079067575 Package: frenchFISH Version: 1.2.0 Imports: utils, MCMCpack, NHPoisson Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 4fa1f6fbae21b8523b2a74c83b42af0a Package: FRGEpistasis Version: 1.26.0 Depends: R (>= 2.15), MASS, fda, methods, stats Imports: utils License: GPL-2 MD5sum: 356ce4c6ce320fbadee6b012cf6f0652 Package: frma Version: 1.42.0 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: 6714a1b7b6b713c204d20121cb051f42 Package: frmaTools Version: 1.42.0 Depends: R (>= 2.10.0), affy Imports: Biobase, DBI, methods, preprocessCore, stats, utils Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData License: GPL (>= 2) MD5sum: 240d7fa20f0ca3a7f9c627f460fd20a9 Package: FScanR Version: 1.0.0 Depends: R (>= 4.0) Imports: stats Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 4183fe19b48e8c34dc2719a6a5ac0dc3 Package: FunChIP Version: 1.16.0 Depends: R (>= 3.2), GenomicRanges Imports: shiny, fda, doParallel, GenomicAlignments, Rcpp, methods, foreach, parallel, GenomeInfoDb, Rsamtools, grDevices, graphics, stats, RColorBrewer LinkingTo: Rcpp License: Artistic-2.0 MD5sum: 8ae78b4a2d198418c4dd7f4dd88a5eaf Package: funtooNorm Version: 1.14.0 Depends: R(>= 3.4) Imports: pls, matrixStats, minfi, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb, grDevices, graphics, stats Suggests: prettydoc, minfiData, knitr, rmarkdown License: GPL-3 MD5sum: 68c317a744f3f4b53722c78e7fa4aa0a Package: GA4GHclient Version: 1.14.0 Depends: S4Vectors Imports: BiocGenerics, Biostrings, dplyr, GenomeInfoDb, GenomicRanges, httr, IRanges, jsonlite, methods, VariantAnnotation Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: fa465a85ba15d77a2ab4d5ead6b0c16a Package: GA4GHshiny Version: 1.12.0 Depends: GA4GHclient Imports: AnnotationDbi, BiocGenerics, dplyr, DT, GenomeInfoDb, openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny, shinyjs, tidyr, shinythemes Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: e0626472222bf6c82408321c940708af Package: gaga Version: 2.36.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: parallel License: GPL (>= 2) MD5sum: 1b7ceaaa9ab68cd497de4bb187c5f901 Package: gage Version: 2.40.2 Depends: R (>= 3.5.0) Imports: graph, KEGGREST, AnnotationDbi, GO.db Suggests: pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma License: GPL (>= 2.0) MD5sum: 4ef469fcafacc92e58be9049aaaa6b82 Package: gaggle Version: 1.58.0 Depends: R (>= 2.3.0), rJava (>= 0.4), graph (>= 1.10.2), RUnit (>= 0.4.17) License: GPL (>= 2) MD5sum: cb6d803d3492d50c56f8beedbfa343bd Package: gaia Version: 2.34.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: abb12f50235db858afd603ee9094dfc3 Package: GAPGOM Version: 1.6.0 Depends: R (>= 4.0) Imports: stats, utils, methods, Matrix, fastmatch, plyr, dplyr, magrittr, data.table, 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: 0be2950aece5bd13ee4a982f248f618d Package: GAprediction Version: 1.16.0 Depends: R (>= 3.3) Imports: glmnet, stats, utils, Matrix Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: a13f3d606a2f6fe029f75be38ff2a190 Package: garfield Version: 1.18.0 Suggests: knitr License: GPL-3 MD5sum: 5b8522666aedac4e28d4f8cc6b2f783f Package: GARS Version: 1.10.0 Depends: R (>= 3.5), ggplot2, cluster Imports: DaMiRseq, MLSeq, stats, methods, SummarizedExperiment Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: bd253656c8de138f4b90cbb730496c2e Package: GateFinder Version: 1.10.0 Imports: splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 4ad7a3721cba0b5c1d59d8bff437d566 Package: gcapc Version: 1.14.0 Depends: R (>= 3.4) Imports: BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings, BSgenome, GenomicRanges, Rsamtools, GenomicAlignments, matrixStats, MASS, splines, grDevices, graphics, stats, methods Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: GPL-3 MD5sum: e88ad1fb6b877700943d748e189dc8f6 Package: gcatest Version: 1.20.0 Depends: R (>= 3.2) Imports: lfa Suggests: knitr, ggplot2 License: GPL-3 MD5sum: 0bfbbd30a13bbccd59d230852f1aedb8 Package: gCrisprTools Version: 1.18.0 Depends: R (>= 3.6) Imports: Biobase, limma, RobustRankAggreg, ggplot2, PANTHER.db, rmarkdown, grDevices, graphics, stats, utils, parallel, SummarizedExperiment Suggests: edgeR, knitr, grid, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 5ab3dd758653de6ef55b7052aa29c42c Package: gcrma Version: 2.62.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector, Biostrings (>= 2.11.32), splines, BiocManager Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe License: LGPL MD5sum: afb63ad1cd35f5ebbfba44eeed22ff97 Package: GCSConnection Version: 1.2.0 Depends: R (>= 4.0.0) Imports: Rcpp (>= 1.0.2), httr, googleAuthR, googleCloudStorageR, methods, jsonlite, utils LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: c6254fc20e84a9954d1301986c08a39c Package: GCSFilesystem Version: 1.0.0 Depends: R (>= 4.0.0) Imports: stats Suggests: testthat, knitr, rmarkdown, BiocStyle, GCSConnection License: GPL (>= 2) MD5sum: 578f6f7464098683231ef7076d564978 Package: GCSscore Version: 1.4.0 Depends: R (>= 3.6) Imports: BiocManager, Biobase, utils, methods, RSQLite, devtools, dplR, stringr, graphics, stats, affxparser, data.table Suggests: siggenes, GEOquery, R.utils License: GPL (>= 3) MD5sum: ca06e84251cfa79847692ddae6c804b9 Package: GDCRNATools Version: 1.10.1 Depends: R (>= 3.5.0) Imports: shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 1cfd2bb9de0797823b08addae69a73c3 Package: GDSArray Version: 1.10.1 Depends: R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>= 0.5.32) Imports: tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray Suggests: testthat, knitr, BiocStyle, BiocManager License: GPL-3 MD5sum: c894ad0f6ba5ffeb750f1a6062df1aff Package: gdsfmt Version: 1.26.1 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, Matrix, RUnit, knitr, crayon, BiocGenerics License: LGPL-3 MD5sum: 9166643e2556aac632d31a75dfcaa3e3 Package: GEM Version: 1.16.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics License: Artistic-2.0 MD5sum: ac95b3df9f342a1851d264f9121d0243 Package: gemini Version: 1.4.0 Depends: R (>= 3.6.0) Imports: dplyr, grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: a898f2f526b1acb10f756c9d1c4c4fdc Package: genArise Version: 1.66.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: 67293c6537ffcc9c9f2d8ce78a4061df Package: genbankr Version: 1.18.0 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: 06789d695a486e8c4258b171b6de395b Package: GeneAccord Version: 1.8.0 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: 8f99639f34651669b99f53a1ca0b5abe Package: GeneAnswers Version: 2.32.0 Depends: R (>= 3.0.0), igraph, RCurl, annotate, Biobase (>= 1.12.0), methods, XML, RSQLite, MASS, Heatplus, RColorBrewer Imports: RBGL, annotate, downloader Suggests: GO.db, KEGG.db, reactome.db, biomaRt, AnnotationDbi, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db, graph License: LGPL (>= 2) MD5sum: db6428f9a0f8a9061d760d79642f44be Package: geneAttribution Version: 1.16.0 Imports: utils, GenomicRanges, org.Hs.eg.db, BiocGenerics, GenomeInfoDb, GenomicFeatures, IRanges, rtracklayer Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 736ddc7672236351c4a9f4f055f300a4 Package: GeneBreak Version: 1.20.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: 13029e12fad57beb8e69be8370c9a5eb Package: geneClassifiers Version: 1.14.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: 46e067107bb382b25dbdf6de881df094 Package: GeneExpressionSignature Version: 1.36.0 Depends: R (>= 2.13), Biobase, PGSEA Suggests: apcluster,GEOquery License: GPL-2 MD5sum: 721ab468422cca08a2e554c91611c375 Package: genefilter Version: 1.72.1 Imports: BiocGenerics (>= 0.31.2), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 MD5sum: 1269f604a1aaad7a281f5b7f4526451d Package: genefu Version: 2.22.1 Depends: survcomp, mclust, limma, biomaRt, iC10, AIMS, R (>= 2.10) Imports: amap, impute Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival License: Artistic-2.0 MD5sum: bafeb4716eeb5c4b6026478d5576fa23 Package: GeneGA Version: 1.40.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: 1e78b8f6cab65bfefe8804165945d3a0 Package: GeneGeneInteR Version: 1.16.0 Depends: R (>= 4.0) Imports: snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods, GGtools License: GPL (>= 2) MD5sum: c2070d83a16791cac86a18043b912242 Package: GeneMeta Version: 1.62.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: 506f19e970f9a51bf175e9facfdeb76a Package: GeneNetworkBuilder Version: 1.32.0 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb, BiocStyle, magick License: GPL (>= 2) MD5sum: 99edf8f93cfe5502381f44c71248133b Package: GeneOverlap Version: 1.26.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 2adc5c9316b50eb01b533aa47024b33a Package: geneplast Version: 1.16.0 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: 87f010f16e6cbd69dfd1bda887163b28 Package: geneplotter Version: 1.68.0 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: 1f5bac4589342723ba0186b095d78c90 Package: geneRecommender Version: 1.62.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: 11020118fd439d067890ea854b92f0be Package: GeneRegionScan Version: 1.46.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) MD5sum: ec6b9fe2e4b3cd49c9b24c85525f516b Package: geneRxCluster Version: 1.26.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 9da1f50268766609e4acc17103260b70 Package: GeneSelectMMD Version: 2.34.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: a3d0cdf805bae9b70e926883ba063c35 Package: GENESIS Version: 2.20.1 Imports: Biobase, BiocGenerics, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, foreach, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 142967e1ce57504e3ede5d0b5cf5d7c2 Package: GeneStructureTools Version: 1.10.0 Imports: Biostrings,GenomicRanges,IRanges,data.table,plyr,stringdist,stringr,S4Vectors,BSgenome.Mmusculus.UCSC.mm10,stats,utils,Gviz,rtracklayer,methods Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 970d22889863d2704fc1fd9ea51cf363 Package: geNetClassifier Version: 1.30.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics, grDevices Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) MD5sum: 0d1c0fcd3b055871d98645f734f87dfb Package: GeneticsPed Version: 1.52.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: 141d6e98cdf83c0764a9df45f0be188e Package: GeneTonic Version: 1.2.0 Depends: R (>= 4.0.0) Imports: AnnotationDbi, bs4Dash, colorspace, ComplexHeatmap, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce, ggplot2, ggrepel, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tools, utils, viridis, visNetwork Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 66d0b8e3fad195187a28d7cd41b15e9d Package: geneXtendeR Version: 1.16.0 Depends: rtracklayer, GO.db, R (>= 3.5.0) Imports: data.table, dplyr, graphics, networkD3, RColorBrewer, SnowballC, tm, utils, wordcloud, AnnotationDbi, BiocStyle, org.Rn.eg.db Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer License: GPL (>= 3) MD5sum: 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BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 2a5195783ece37cf977e00b6fa778a48 Package: genomeIntervals Version: 1.46.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 1.5.8), GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: ba74139b56dd6244be83c07b7bb35eb0 Package: genomes Version: 3.20.0 Depends: readr, curl License: GPL-3 MD5sum: ed6d03cbb65045f32f827bf37785c8f0 Package: GenomicAlignments Version: 1.26.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), 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: b1cd526c6d50134d44adf6722e9ddaa6 Package: GenomicDataCommons Version: 1.14.0 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: 1f2f00e4d2769f14464ac48c3f1e2dc0 Package: GenomicFeatures Version: 1.42.3 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), rtracklayer (>= 1.39.7), 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 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: acbc8dec91f42792b5770fdeee314671 Package: GenomicFiles Version: 1.26.0 Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), MatrixGenerics, GenomicRanges (>= 1.31.16), SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>= 1.17.29), rtracklayer (>= 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License: LGPL (>= 3) MD5sum: 44602f3e28ce6250157f17ea1624c663 Package: GenomicRanges Version: 1.42.0 Depends: R (>= 2.10), methods, stats4, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.15.2) Imports: utils, stats, XVector (>= 0.29.2) LinkingTo: S4Vectors, IRanges Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, BiocStyle License: Artistic-2.0 MD5sum: a344913b52886d0adcbf3da05f729cbd Package: GenomicScores Version: 2.2.0 Depends: R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: stats, utils, XML, Biobase, BiocManager, BiocFileCache, IRanges (>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub, rhdf5, DelayedArray, HDF5Array Suggests: 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, shinythemes, shinyjs, shinycustomloader, data.table, DT License: Artistic-2.0 MD5sum: 03ce474e4be56d6b5e2fdb5c43a9d35a Package: GenomicTuples Version: 1.24.0 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), GenomeInfoDb (>= 1.15.2), S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 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Suggests: testthat, ggplot2, gridExtra, ape, ggrepel, knitr, reshape, xtable License: GPL (>= 2) MD5sum: 6b3f3f01d0c8e51d3265db85b3c8e8e8 Package: GenVisR Version: 1.22.1 Depends: R (>= 3.3.0), methods Imports: AnnotationDbi, biomaRt (>= 2.45.8), BiocGenerics, Biostrings, DBI, FField, GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, viridis, data.table, BSgenome, GenomeInfoDb, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 + file LICENSE MD5sum: d5d6709aff932246be7ac5e6a10f737a Package: GEOmetadb Version: 1.52.0 Depends: GEOquery,RSQLite Suggests: knitr, rmarkdown, dplyr, tm, wordcloud License: Artistic-2.0 MD5sum: 8be7ed7fc0fcbf600d34728029646df6 Package: GEOquery Version: 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ensembldb (>= 1.99.13), AnnotationDbi, AnnotationFilter, rlang Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: a6ef1606802e7332a4cb71a73c6e5108 Package: ggcyto Version: 1.18.0 Depends: methods, ggplot2(>= 3.3.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 3.33.1) Imports: plyr, scales, hexbin, data.table, RColorBrewer, gridExtra, rlang Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr License: Artistic-2.0 MD5sum: 8541de7c634f24d689fba08e12f81d61 Package: GGPA Version: 1.2.0 Depends: R (>= 4.0.0), stats, methods, graphics, GGally, network, sna, scales, matrixStats Imports: Rcpp (>= 0.11.3) LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle License: GPL (>= 2) MD5sum: 7664d1cb49bc29dd638ada1d7f901a46 Package: GGtools Version: 5.25.3 Depends: R (>= 2.14), GGBase (>= 3.19.7), data.table, parallel, Homo.sapiens Imports: methods, utils, stats, BiocGenerics (>= 0.25.1), snpStats, ff, Rsamtools, AnnotationDbi, Biobase, bit, VariantAnnotation, hexbin, rtracklayer, Gviz, stats4, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges (>= 1.29.6), iterators, Biostrings, ROCR, biglm, ggplot2, reshape2 Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37, multtest, aod, rmeta Enhances: MatrixEQTL, foreach, doParallel, gwascat License: Artistic-2.0 MD5sum: 2776a0b801e0af3e9d27de9393f15a6a Package: ggtree Version: 2.4.2 Depends: R (>= 3.5.0) Imports: ape, aplot (>= 0.0.4), dplyr, ggplot2 (>= 3.0.0), grid, magrittr, methods, purrr, rlang, rvcheck, tidyr, tidytree (>= 0.2.6), treeio (>= 1.8.0), utils, scales Suggests: emojifont, ggimage, ggplotify, grDevices, knitr, prettydoc, rmarkdown, stats, testthat, tibble License: Artistic-2.0 MD5sum: 7298fe5847fc6b9382473bd34f561950 Package: ggtreeExtra Version: 1.0.4 Imports: ggplot2, utils, rlang, ggnewscale, stats Suggests: ggtree, treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown License: GPL-3 MD5sum: de0b95e293bb842a8bc3d0355bfdec5d Package: GIGSEA Version: 1.8.0 Depends: R (>= 3.5), Matrix, MASS, locfdr, stats, utils Suggests: knitr, rmarkdown License: LGPL-3 MD5sum: 151aec841d52476c122c53d93089d918 Package: girafe Version: 1.42.0 Depends: R (>= 2.10.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.25), Rsamtools (>= 1.31.2), intervals (>= 0.13.1), ShortRead (>= 1.37.1), genomeIntervals (>= 1.25.1), grid Imports: methods, Biobase, Biostrings (>= 2.47.6), graphics, grDevices, stats, utils, IRanges (>= 2.13.12) Suggests: MASS, org.Mm.eg.db, RColorBrewer Enhances: genomeIntervals License: Artistic-2.0 MD5sum: 725fb39f72ed2be66623752fde22c63d Package: GISPA Version: 1.14.0 Depends: R (>= 3.5) Imports: Biobase, changepoint, data.table, genefilter, graphics, GSEABase, HH, lattice, latticeExtra, plyr, scatterplot3d, stats Suggests: knitr License: GPL-2 MD5sum: 26b1d132fe1e31358ba5037857a8b1cc Package: GLAD Version: 2.54.0 Depends: R (>= 2.10) Imports: aws License: GPL-2 MD5sum: 2aa7d4b9239d193cd0f51fad36337fa2 Package: GladiaTOX Version: 1.6.1 Depends: R (>= 3.6.0), data.table (>= 1.9.4) Imports: DBI, RMySQL, RSQLite, numDeriv, RColorBrewer, parallel, stats, methods, graphics, grDevices, xtable, tools, brew, stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML Suggests: roxygen2, knitr, rmarkdown, testthat, BiocStyle License: GPL-2 MD5sum: 2520d6e25072af26562174980b210748 Package: Glimma Version: 2.0.0 Depends: R (>= 4.0.0) Imports: htmlwidgets, edgeR, DESeq2, limma, SummarizedExperiment, stats, jsonlite, methods, S4Vectors Suggests: testthat, knitr, rmarkdown, BiocStyle, IRanges, GenomicRanges, pryr License: GPL-3 MD5sum: 3d698c0a025b9d929b2c744f0651946b Package: glmGamPoi Version: 1.2.0 Imports: Rcpp, DelayedMatrixStats, matrixStats, DelayedArray, HDF5Array, SummarizedExperiment, methods, stats, utils, splines LinkingTo: Rcpp, RcppArmadillo, beachmat Suggests: testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat, MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown, BiocStyle, TENxPBMCData, scran License: GPL-3 MD5sum: b91ec9b3125906c34a305b8098a9e492 Package: glmSparseNet Version: 1.8.1 Depends: R (>= 3.5), Matrix, MultiAssayExperiment, glmnet Imports: SummarizedExperiment, STRINGdb, biomaRt, futile.logger, sparsebn, sparsebnUtils, forcats, dplyr, readr, ggplot2, survminer, reshape2, stats, stringr, rlang, parallel, methods, loose.rock (>= 1.0.12) Suggests: testthat, knitr, rmarkdown, survival, survcomp, pROC, VennDiagram, BiocStyle, curatedTCGAData, TCGAutils License: GPL (>= 3) MD5sum: b6fd4bda502c9c6c98fb5267286da660 Package: GlobalAncova Version: 4.8.0 Depends: methods, corpcor, globaltest Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM Suggests: GO.db, KEGG.db, golubEsets, hu6800.db, vsn, Rgraphviz License: GPL (>= 2) MD5sum: 710a4dd49df92e59c3a7fb72b4fd6e61 Package: globalSeq Version: 1.18.0 Depends: R (>= 3.0.0) Suggests: knitr, testthat, SummarizedExperiment, S4Vectors License: GPL-3 MD5sum: 2ac54bd76228c8b53ac5f75d60fc63dc Package: globaltest Version: 5.44.0 Depends: methods, survival Imports: Biobase, AnnotationDbi, annotate, graphics Suggests: vsn, golubEsets, KEGGREST, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart, mstate License: GPL (>= 2) MD5sum: 136f383f8161c0aef1b9ddb9a1a78502 Package: gmapR Version: 1.32.0 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Rsamtools (>= 1.31.2) Imports: S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>= 0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3), Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase, BSgenome, GenomicAlignments (>= 1.15.6), BiocParallel Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines License: Artistic-2.0 MD5sum: 21ea55947b74ec733eb02b8e6a97d347 Package: GmicR Version: 1.4.0 Imports: AnnotationDbi, ape, bnlearn, Category, DT, doParallel, foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db, org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics, reshape2, stats, utils Suggests: knitr, rmarkdown, testthat License: GPL-2 + file LICENSE MD5sum: 2e293aeb10327c11e79c258c163b9cd6 Package: gmoviz Version: 1.2.0 Depends: circlize, GenomicRanges, graphics, R (>= 4.0) Imports: grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics, Biostrings, GenomeInfoDb, methods, GenomicAlignments, GenomicFeatures, IRanges, rtracklayer, pracma, colorspace, S4Vectors Suggests: testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle, BiocManager License: GPL-3 MD5sum: 06f474bfb5f773e450f96d49f54f523f Package: GMRP Version: 1.18.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: c171e704602658918932ec4b66e0b60f Package: GNET2 Version: 1.6.0 Depends: R (>= 3.6) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment,dplyr,igraph, grDevices, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache License 2.0 MD5sum: a1d742921a338d6defd0952fa9ea8c36 Package: GOexpress Version: 1.24.0 Depends: R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0) Imports: biomaRt (>= 2.18.0), stringr (>= 0.6.2), ggplot2 (>= 0.9.0), RColorBrewer (>= 1.0), gplots (>= 2.13.0), randomForest (>= 4.6), RCurl (>= 1.95) Suggests: BiocStyle License: GPL (>= 3) MD5sum: cd424ef4746a83e6e89a8df4a13e2ba1 Package: GOfuncR Version: 1.10.0 Depends: R (>= 3.4), vioplot (>= 0.2), Imports: Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0), GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils, grDevices, graphics, stats, LinkingTo: Rcpp Suggests: Homo.sapiens, BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 5cdffdb5d06152f9cd46246051295d2d Package: GOpro Version: 1.16.0 Depends: R (>= 3.4) Imports: AnnotationDbi, dendextend, doParallel, foreach, parallel, org.Hs.eg.db, GO.db, Rcpp, stats, graphics, MultiAssayExperiment, IRanges, S4Vectors LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat License: GPL-3 MD5sum: f541f1661efb008064b0ece3e563ba9c Package: goProfiles Version: 1.52.0 Depends: Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr Suggests: org.Hs.eg.db License: GPL-2 MD5sum: ed0f53de20d3cc68b6fca9cfee692342 Package: GOSemSim Version: 2.16.1 Depends: R (>= 3.5.0) Imports: AnnotationDbi, GO.db, methods, utils LinkingTo: Rcpp Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, testthat License: Artistic-2.0 MD5sum: 27d226451915992a1d5bf98eddb41d81 Package: goseq Version: 1.42.0 Depends: R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2) Imports: mgcv, graphics, stats, utils, AnnotationDbi, GO.db,BiocGenerics Suggests: edgeR, org.Hs.eg.db, rtracklayer License: LGPL (>= 2) MD5sum: 26b563e51dd4780d75f62dd8a0167ce0 Package: GOSim Version: 1.28.0 Depends: GO.db, annotate Imports: org.Hs.eg.db, AnnotationDbi, topGO, cluster, flexmix, RBGL, graph, Matrix, corpcor, Rcpp LinkingTo: Rcpp Enhances: igraph License: GPL (>= 2) MD5sum: 7f2b28851e0de08ad7c1b0d61aeb77f9 Package: goSTAG Version: 1.14.2 Depends: R (>= 3.4) Imports: AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 1015f4f320a004d1a30482400d34f816 Package: GOstats Version: 2.56.0 Depends: R (>= 2.10), Biobase (>= 1.15.29), Category (>= 2.43.2), graph Imports: methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>= 1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 06397a1e673313af669741e3c08a17ce Package: GOsummaries Version: 2.26.0 Depends: R (>= 2.15), Rcpp Imports: plyr, grid, gProfileR, reshape2, limma, ggplot2, gtable LinkingTo: Rcpp Suggests: vegan License: GPL (>= 2) MD5sum: c94240cd6a0d617ec95147c032978fa9 Package: GOTHiC Version: 1.26.0 Depends: R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome, data.table Imports: BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools, ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils, stats, GenomeInfoDb Suggests: HiCDataLymphoblast Enhances: parallel License: GPL-3 MD5sum: 7e87096f1a761b54d6da1773e9a51391 Package: goTools Version: 1.64.0 Depends: GO.db Imports: AnnotationDbi, GO.db, graphics, grDevices Suggests: hgu133a.db License: GPL-2 MD5sum: 5f9f8a15f1bb71a7ff1fc06672bb9eeb Package: GPA Version: 1.2.0 Depends: R (>= 4.0.0), methods, graphics, Rcpp Imports: parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS, stats, utils, grDevices LinkingTo: Rcpp Suggests: gpaExample License: GPL (>= 2) MD5sum: e1e83655b21e4cd9b8bb01e3b3fc8e4f Package: gpart Version: 1.8.0 Depends: R (>= 3.5.0), grid, Homo.sapiens, TxDb.Hsapiens.UCSC.hg38.knownGene, Imports: igraph, biomaRt, Rcpp, data.table, OrganismDbi, AnnotationDbi, grDevices, stats, utils, GenomicRanges, IRanges LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE MD5sum: 180f6b5a8b66e54a1b64342968ad289c Package: gpls Version: 1.62.0 Imports: stats Suggests: MASS License: Artistic-2.0 MD5sum: 8e7a02108dba153b50b125d20dec22c8 Package: gprege Version: 1.34.0 Depends: R (>= 2.10), gptk Suggests: spam License: AGPL-3 MD5sum: f07f131f3bc04aa40fbdbee752962207 Package: gpuMagic Version: 1.6.0 Depends: R (>= 3.6.0), methods, utils Imports: Deriv, DescTools, digest, pryr, stringr, BiocGenerics LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: deab421a57b3443fea9b8c56aaffe712 Package: gQTLBase Version: 1.21.1 Imports: GenomicRanges, methods, BatchJobs, BBmisc, S4Vectors, BiocGenerics, foreach, doParallel, bit, ff, rtracklayer, ffbase, GenomicFiles, SummarizedExperiment Suggests: geuvStore2, knitr, rmarkdown, BiocStyle, RUnit, Homo.sapiens, IRanges, erma, GenomeInfoDb, gwascat, geuvPack License: Artistic-2.0 MD5sum: 560eae15f846f67bd83892a15dfd4d87 Package: gQTLstats Version: 1.21.3 Depends: R (>= 3.5.0), Homo.sapiens Imports: methods, snpStats, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicFiles, GenomicRanges, SummarizedExperiment, VariantAnnotation, Biobase, BatchJobs, gQTLBase, limma, mgcv, dplyr, AnnotationDbi, GenomicFeatures, ggplot2, reshape2, doParallel, foreach, ffbase, BBmisc, beeswarm, HardyWeinberg, graphics, stats, utils, shiny, plotly, erma, ggbeeswarm Suggests: geuvPack, geuvStore2, Rsamtools, knitr, rmarkdown, ggbio, BiocStyle, RUnit, multtest, gwascat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, ldblock License: Artistic-2.0 MD5sum: 9d62cab4d6f76c12eab168c1c04c68cb Package: gramm4R Version: 1.4.0 Depends: R (>= 3.6.0) Imports: basicTrendline,investr,minerva,psych,grDevices, graphics, stats,DelayedArray,SummarizedExperiment,DMwR,phyloseq Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 93f708f37991ae589a773c68daa12d1c Package: graper Version: 1.6.0 Depends: R (>= 3.6) Imports: Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: f71935eeffbfccb41f98394072c77906 Package: graph Version: 1.68.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.11) Imports: stats, stats4, utils Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster Enhances: Rgraphviz License: Artistic-2.0 MD5sum: aca3a048950d9437d89486b7ca82406d Package: GraphAlignment Version: 1.54.0 License: file LICENSE License_restricts_use: yes MD5sum: 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(>= 2) MD5sum: b0adff5438a9e47ef207b66fe4304b01 Package: GreyListChIP Version: 1.22.0 Depends: R (>= 4.0), methods, GenomicRanges Imports: GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS, parallel, GenomeInfoDb, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, RUnit Enhances: BSgenome.Hsapiens.UCSC.hg19 License: Artistic-2.0 MD5sum: 9b0185c16ba4659867d2f70a57e3d6fa Package: GRmetrics Version: 1.16.0 Depends: R (>= 4.0), SummarizedExperiment Imports: drc, plotly, ggplot2, S4Vectors, stats Suggests: knitr, rmarkdown, BiocStyle, tinytex License: GPL-3 MD5sum: de17360ff6d5a8e31a81fef43aead1c5 Package: groHMM Version: 1.24.0 Depends: R (>= 3.0.2), MASS, parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), rtracklayer (>= 1.39.7) Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 532a59b180bf4d4d390523be5465035c Package: GRridge Version: 1.14.0 Depends: R (>= 3.2), penalized, Iso, survival, methods, graph,stats,glmnet,mvtnorm Suggests: testthat License: GPL-3 MD5sum: 994eb35535031f3907b344d3b7d0acc7 Package: GSALightning Version: 1.18.0 Depends: R (>= 3.3.0) Imports: Matrix, data.table, stats Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: dc0cd22951017368beee1aba66ba90c9 Package: GSAR Version: 1.24.0 Depends: R (>= 3.0.1), igraph (>= 0.7.1) Imports: stats, graphics Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle License: GPL (>= 2) MD5sum: bfdf229d7cf20355f5879e9f92f82f5b Package: GSCA Version: 2.20.0 Depends: shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5, R(>= 2.10.0) Imports: graphics Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr License: GPL (>= 2) MD5sum: 9ebf6dc3dc322bdb57424db1a8d457fb Package: gscreend Version: 1.4.0 Depends: R (>= 3.6) Imports: SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics Suggests: knitr, testthat License: GPL-3 MD5sum: 8085052dabab56c4d9198ddb374cc055 Package: GSEABase Version: 1.52.1 Depends: R (>= 2.6.0), BiocGenerics (>= 0.13.8), Biobase (>= 2.17.8), annotate (>= 1.45.3), methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr License: Artistic-2.0 MD5sum: d4ce3be86c78c5147ef2dd37abfa172d Package: GSEABenchmarkeR Version: 1.10.1 Depends: Biobase, SummarizedExperiment Imports: AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 2435320f4ed814041d1a9c1c3aec3967 Package: GSEAlm Version: 1.50.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: e5a33a52e1f1e273dd572254c1ceaee5 Package: GSEAmining Version: 1.0.0 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: 799887caf95c912d491fd51a2a184358 Package: gsean Version: 1.10.1 Depends: R (>= 3.5), fgsea, PPInfer Suggests: SummarizedExperiment, knitr, plotly, RANKS, WGCNA, rmarkdown License: Artistic-2.0 MD5sum: d1cb8908c13076fa16ba305cdbc20b74 Package: GSgalgoR Version: 1.0.0 Imports: cluster, doParallel, foreach, matchingR, nsga2R, survival, proxy, stats, methods, Suggests: knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp, Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP, iC10TrainingData, pamr, testthat License: MIT + file LICENSE MD5sum: 30557f18871e1ea0d46b4e69b1d5fe78 Package: GSReg Version: 1.24.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi Suggests: GenomicRanges, GSBenchMark License: GPL-2 MD5sum: 438d6836c4bdbcd745ea9457883a0d3c Package: GSRI Version: 2.38.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 MD5sum: c02f32e919916078883b9080a1944d0f Package: GSVA Version: 1.38.2 Depends: R (>= 3.5.0) Imports: methods, stats, utils, graphics, BiocGenerics, S4Vectors, IRanges, Biobase, SummarizedExperiment, GSEABase, parallel, BiocParallel Suggests: RUnit, limma, RColorBrewer, genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table, plotly License: GPL (>= 2) MD5sum: 147a35c7486a8ebb747c950197247c14 Package: gtrellis Version: 1.22.0 Depends: R (>= 3.1.2), grid, IRanges, GenomicRanges Imports: circlize (>= 0.4.8), GetoptLong, grDevices, utils Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff License: MIT + file LICENSE MD5sum: 0aa748a7379ff37658b9f586eff23958 Package: GUIDEseq Version: 1.20.0 Depends: R (>= 3.2.0), GenomicRanges, BiocGenerics Imports: BiocParallel, Biostrings, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma,dplyr Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: GPL (>= 2) MD5sum: c2a58676bf9c56a91a2b2b890223165b Package: Guitar Version: 2.6.0 Depends: GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges, magrittr, ggplot2, methods, stats,utils ,knitr,dplyr License: GPL-2 MD5sum: 9d4f94c379ed4e38cc350d49d0536d9d Package: Gviz Version: 1.34.1 Depends: R (>= 4.0), methods, S4Vectors (>= 0.9.25), IRanges (>= 1.99.18), GenomicRanges (>= 1.17.20), grid Imports: XVector (>= 0.5.7), 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Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle License: Artistic-2.0 MD5sum: db88f447609422778fb8672f59b8e9be Package: ISAnalytics Version: 1.0.11 Depends: R (>= 4.0), magrittr Imports: utils, reactable, htmltools, dplyr, readr, tidyr, purrr, rlang, forcats, tibble, BiocParallel, stringr, fs, zip, lubridate, lifecycle, ggplot2, ggrepel, stats, upsetjs, psych, grDevices, data.table, readxl, tools Suggests: testthat, covr, knitr, BiocStyle, knitcitations, sessioninfo, rmarkdown, roxygen2, vegan, withr License: CC BY 4.0 MD5sum: 6268c6a69b1f669ad7922fa0a48faaa1 Package: iSEE Version: 2.2.4 Depends: SummarizedExperiment, SingleCellExperiment Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, ComplexHeatmap, circlize, grid Suggests: testthat, BiocStyle, knitr, 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regioneR, GenomicRanges, methods Imports: regioneR, GenomicRanges, IRanges, Rsamtools, stats, graphics, memoise, rtracklayer, GenomeInfoDb, S4Vectors, biovizBase, digest, bezier, GenomicFeatures, bamsignals, AnnotationDbi, grDevices, VariantAnnotation Suggests: BiocStyle, knitr, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db, pasillaBamSubset License: Artistic-2.0 MD5sum: 886a30786720e388f80ac05e61a37f5b Package: KCsmart Version: 2.48.0 Depends: siggenes, multtest, KernSmooth Imports: methods, BiocGenerics Enhances: Biobase, CGHbase License: GPL-3 MD5sum: a7b372497bc2533d5cdd00e141387cb3 Package: kebabs Version: 1.24.0 Depends: R (>= 3.2.0), Biostrings (>= 2.35.5), kernlab Imports: methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.7.3), S4Vectors (>= 0.27.3), e1071, LiblineaR, graphics, grDevices, utils, apcluster LinkingTo: IRanges, XVector, Biostrings, Rcpp, S4Vectors Suggests: SparseM, Biobase, BiocGenerics, knitr License: GPL (>= 2.1) MD5sum: 3d4a85a4330dbfc34f57f7e74e39c002 Package: KEGGgraph Version: 1.50.0 Depends: R (>= 2.10.0) Imports: methods, XML (>= 2.3-0), graph, utils, RCurl Suggests: Rgraphviz, RBGL, testthat, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA License: GPL (>= 2) MD5sum: be94499e40ae52d009b0d9a6b3313d7a Package: KEGGlincs Version: 1.16.0 Depends: R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db (>= 3.3.0) Imports: AnnotationDbi,KEGGgraph,igraph,plyr,gtools,httr,RJSONIO,KEGGREST, methods,graphics,stats,utils, XML, grDevices Suggests: BiocManager (>= 1.20.3), knitr, graph License: GPL-3 MD5sum: 76c160f8030f088882b0f73f33ee0378 Package: keggorthology Version: 2.42.0 Depends: R (>= 2.5.0),stats,graph,hgu95av2.db Imports: AnnotationDbi,graph,DBI, graph, grDevices, methods, stats, tools, utils Suggests: RBGL,ALL License: Artistic-2.0 MD5sum: 7caa1f53ca4381f09940343521ed4215 Package: KEGGprofile 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Enhances: parallel License: GPL-3 MD5sum: 8f5eede78ecc8ac2f5fd3b1092233a55 Package: levi Version: 1.8.0 Imports: DT(>= 0.4), RColorBrewer(>= 1.1-2), colorspace(>= 1.3-2), dplyr(>= 0.7.4), ggplot2(>= 2.2.1), httr(>= 1.3.1), igraph(>= 1.2.1), reshape2(>= 1.4.3), shiny(>= 1.0.5), shinydashboard(>= 0.7.0), shinyjs(>= 1.0), xml2(>= 1.2.0), knitr, Rcpp (>= 0.12.18), grid, grDevices, stats, utils, testthat, methods LinkingTo: Rcpp License: GPL (>= 2) MD5sum: 19a6d97b85c22b53a6d685451c26addd Package: lfa Version: 1.20.0 Depends: R (>= 3.2) Imports: corpcor Suggests: knitr, ggplot2 License: GPL-3 MD5sum: 3b37844fff984fc56e5688c3ab92f8fd Package: limma Version: 3.46.0 Depends: R (>= 3.6.0) Imports: grDevices, graphics, stats, utils, methods Suggests: affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn License: GPL (>= 2) MD5sum: 59c3521c30dc67773621ed7ed0e410e6 Package: limmaGUI Version: 1.66.0 Imports: methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot, xtable, utils License: GPL (>= 2) MD5sum: 505fcfa28eb05eb1d238f720fab019eb Package: LineagePulse Version: 1.10.0 Imports: BiocParallel, circlize, compiler, ComplexHeatmap, ggplot2, gplots, grDevices, grid, knitr, Matrix, methods, RColorBrewer, SingleCellExperiment, splines, stats, SummarizedExperiment, utils License: Artistic-2.0 MD5sum: a7a5c5695e4cf619d619ac3d6366b781 Package: LinkHD Version: 1.4.0 Depends: R(>= 3.6.0), methods, ggplot2, stats Imports: scales, cluster, graphics, ggpubr, gridExtra, vegan, rio, MultiAssayExperiment, emmeans, reshape2, data.table Suggests: MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 97660f5223f2d410a3c203f4079fe9e2 Package: Linnorm Version: 2.14.0 Depends: R(>= 3.4) Imports: Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan, mclust, apcluster, ggplot2, ellipse, limma, utils, statmod, MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo, stats, amap, Rtsne, gmodels LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, knitr, rmarkdown, gplots, RColorBrewer, moments, testthat License: MIT + file LICENSE MD5sum: 78aed31b83ce95d72dcb53afc28d63f4 Package: lionessR Version: 1.4.0 Depends: R (>= 3.6.0) Imports: stats, SummarizedExperiment, S4Vectors Suggests: knitr, rmarkdown, igraph, reshape2, limma, License: MIT + file LICENSE MD5sum: 36d5af6857973b76d7ca1f3b75197ae5 Package: lipidr Version: 2.4.0 Depends: R (>= 3.6.0), SummarizedExperiment Imports: methods, stats, utils, data.table, S4Vectors, rlang, dplyr, tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD, magrittr Suggests: knitr, rmarkdown, BiocStyle, ggrepel, plotly, iheatmapr, spelling, testthat License: MIT + file LICENSE MD5sum: 6a3ffba92be42ed1311fd298b432491f Package: LiquidAssociation Version: 1.44.0 Depends: geepack, methods, yeastCC, org.Sc.sgd.db Imports: Biobase, graphics, grDevices, methods, stats License: GPL (>= 3) MD5sum: 7537555dedc933846a54b788dee82006 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graphics, stats, stats4, methods Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer License: LGPL (>= 2) MD5sum: 74caab87956e043257253a9bfaa43cd4 Package: LymphoSeq Version: 1.18.0 Depends: R (>= 3.3), LymphoSeqDB Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq, RColorBrewer, circlize, grid, utils, stats, ggtree, msa, Biostrings, phangorn, stringdist, UpSetR Suggests: knitr, pheatmap, wordcloud, rmarkdown License: Artistic-2.0 MD5sum: c2b05a5ff9076aad2e96d0a5ba0e96b2 Package: M3C Version: 1.12.0 Depends: R (>= 3.5.0) Imports: ggplot2, Matrix, doSNOW, cluster, parallel, foreach, doParallel, matrixcalc, Rtsne, corpcor, umap Suggests: knitr, rmarkdown License: AGPL-3 MD5sum: 4dc7ad42886e2c2e25acfbfdc1073b98 Package: M3Drop Version: 1.16.0 Depends: R (>= 3.4), numDeriv Imports: RColorBrewer, gplots, bbmle, statmod, grDevices, graphics, stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods Suggests: ROCR, knitr, M3DExampleData, scater, SingleCellExperiment, monocle, Seurat, Biobase License: GPL (>= 2) MD5sum: a4bffd11c67b7e1a48ecfd5769c57c71 Package: maanova Version: 1.60.0 Depends: R (>= 2.10) Imports: Biobase, graphics, grDevices, methods, stats, utils Suggests: qvalue, snow Enhances: Rmpi License: GPL (>= 2) MD5sum: 86649c953c57d886f2affedfcb6e7acb Package: Maaslin2 Version: 1.4.0 Depends: R (>= 3.6) Imports: robustbase, biglm, pcaPP, edgeR, metagenomeSeq, lpsymphony, pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap, logging, data.table, lmerTest, hash, optparse, MuMIn, grDevices, stats, utils, glmmTMB, MASS, cplm, pscl Suggests: knitr, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 1edbbde6071c6b19f7c92f1cee7f571b Package: macat Version: 1.64.0 Depends: Biobase, annotate Suggests: hgu95av2.db, stjudem License: Artistic-2.0 MD5sum: 70520780eeaaa9c65eade30eada4a077 Package: maCorrPlot Version: 1.60.0 Depends: lattice Imports: graphics, grDevices, lattice, stats 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BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW License: Artistic-2.0 MD5sum: 49a4f2785ba0e1000cdabe81eb157c1d Package: metahdep Version: 1.48.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 MD5sum: 835637e1fcf760271f180b97afc25bc7 Package: metaMS Version: 1.26.0 Depends: R (>= 4.0), methods, CAMERA, xcms (>= 1.35) Imports: Matrix, tools, robustbase, BiocGenerics, graphics, stats, utils Suggests: metaMSdata, RUnit License: GPL (>= 2) MD5sum: f5b448284745cfb61c713c1acda108cd Package: MetaNeighbor Version: 1.10.0 Depends: R(>= 3.5) Imports: grDevices, graphics, methods, stats (>= 3.4), utils (>= 3.4), Matrix (>= 1.2), matrixStats (>= 0.54), beanplot (>= 1.2), gplots (>= 3.0.1), RColorBrewer (>= 1.1.2), SummarizedExperiment (>= 1.12), SingleCellExperiment, igraph, dplyr, tidyr, tibble, ggplot2 Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2), UpSetR License: MIT + file LICENSE MD5sum: 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methods, NBPSeq, pander, parallel, qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite, rtracklayer, S4Vectors, stats, stringr, SummarizedExperiment, survcomp, utils, VennDiagram, vsn, yaml, zoo Suggests: BiocManager, BSgenome, knitr, RMySQL, RUnit Enhances: TCC License: GPL (>= 3) MD5sum: 11e06b7087f6b7c7d4fac79e4ae1cb07 Package: metavizr Version: 1.14.0 Depends: R (>= 3.4), metagenomeSeq (>= 1.17.1), methods, data.table, Biobase, digest Imports: epivizr, epivizrData, epivizrServer, epivizrStandalone, vegan, GenomeInfoDb, phyloseq, httr Suggests: knitr, BiocStyle, matrixStats, msd16s (>= 0.109.1), etec16s, testthat, gss, curatedMetagenomicData License: MIT + file LICENSE MD5sum: 04e96932e689db216f9f408badbf669a Package: MetaVolcanoR Version: 1.4.0 Depends: R (>= 3.6.0) Imports: methods, data.table, dplyr, tidyr, plotly, ggplot2, cowplot, parallel, metafor, metap, rlang, topconfects, grDevices, graphics, stats, htmlwidgets Suggests: knitr, testthat License: GPL-3 MD5sum: 09fa61d736ae05088a5a5d302661c5f4 Package: MetCirc Version: 1.20.0 Depends: R (>= 3.5), amap (>= 0.8), circlize (>= 0.3.9), scales (>= 0.3.0), shiny (>= 1.0.0), MSnbase (>= 2.15.3), Imports: ggplot2 (>= 3.2.1), S4Vectors (>= 0.22.0) Suggests: BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr (>= 1.11), methods (>= 3.5), stats (>= 3.5), testthat (>= 2.2.1) License: GPL (>= 3) MD5sum: 750116bd77d4f323e3737a12e134916c Package: MethCP Version: 1.4.0 Depends: R (>= 3.6.0) Imports: methods, utils, stats, S4Vectors, bsseq, DSS, methylKit, DNAcopy, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel Suggests: testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: d38810c289b50cf8a1c865fa9aa5099b Package: methimpute Version: 1.12.0 Depends: R (>= 3.4.0), GenomicRanges, ggplot2 Imports: Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats, GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm, data.table LinkingTo: Rcpp Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: 4c37ff015540852ec15e786bb70b6e25 Package: methInheritSim Version: 1.12.0 Depends: R (>= 3.4) Imports: methylKit, GenomicRanges, GenomeInfoDb, parallel, BiocGenerics, S4Vectors, methods, stats, IRanges, msm Suggests: BiocStyle, knitr, rmarkdown, RUnit, methylInheritance License: Artistic-2.0 MD5sum: 463c55d7cb93f711b6951b7123b06b9a Package: MethPed Version: 1.18.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 MD5sum: 28f9dc742fad7c339c8db918670115aa Package: MethReg Version: 1.0.0 Depends: R (>= 4.0) Imports: dplyr, plyr, GenomicRanges, SummarizedExperiment, DelayedArray, ggplot2, ggpubr, tibble, tidyr, S4Vectors, sesameData, stringr, readr, methods, stats, Matrix, MASS, rlang, pscl, IRanges, sfsmisc, progress 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 License: GPL-3 MD5sum: 3332ab6b60328bd2452188552df4d47c Package: methrix Version: 1.4.07 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: 18e1eb55a810f9989cb9ebfd8b15c1fb Package: MethTargetedNGS Version: 1.22.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings License: Artistic-2.0 MD5sum: 15b7f807074ccb0d6615634fe5dd7379 Package: methyAnalysis Version: 1.32.0 Depends: R (>= 2.10), grid, BiocGenerics, IRanges, GenomeInfoDb (>= 1.22.0), GenomicRanges, Biobase (>= 2.34.0), org.Hs.eg.db Imports: grDevices, stats, utils, lumi, methylumi, Gviz, genoset, SummarizedExperiment, IRanges, GenomicRanges, VariantAnnotation, rtracklayer, bigmemoryExtras,GenomicFeatures, annotate, Biobase (>= 2.5.5), AnnotationDbi, genefilter, biomaRt, methods, parallel Suggests: FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: b7da819d6eff2f0d9f8664bd2fa9de71 Package: MethylAid Version: 1.24.0 Depends: R (>= 3.4) Imports: Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase, grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0), methods, RColorBrewer, shiny, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit License: GPL (>= 2) MD5sum: 04821860f4ac514940dc2d7ad6f46928 Package: methylCC Version: 1.4.0 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: f53585650d81dec741f993468ab74e16 Package: methylGSA Version: 1.8.0 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: f1a07e2c065849fed596bcda2bcde093 Package: methylInheritance Version: 1.14.0 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: ddcd187d5f328b7d069a6dd8dacbf72f Package: methylKit Version: 1.16.1 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: 27fcc258a75f0fc403f48c3009701b34 Package: MethylMix Version: 2.20.0 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: 61cdd1f20904e58639c394b837de829f Package: methylMnM Version: 1.28.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: f17bfa9d535e4e18539b80455d64a2a6 Package: methylPipe Version: 1.24.0 Depends: R (>= 3.2.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 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MD5sum: e009cdf37adc7e249ec0bbccfa302823 Package: methylumi Version: 2.36.0 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: 92aaf13ebb478149251a4c87f50a3cd6 Package: methyvim Version: 1.11.0 Depends: R (>= 3.4.0) Imports: stats, cluster, methods, ggplot2, ggsci, gridExtra, superheat, dplyr, gtools, tmle (>= 1.4.0.1), future, doFuture, S4Vectors, BiocGenerics, BiocParallel, SummarizedExperiment, GenomeInfoDb, bumphunter, IRanges, limma, minfi Suggests: testthat, knitr, rmarkdown, BiocStyle, SuperLearner, earth, nnet, gam, arm, snow, parallel, BatchJobs, minfiData, methyvimData License: file LICENSE MD5sum: 47b1b4a7199d86fdbe91873e21499a92 Package: MetID Version: 1.8.0 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: 4aeabf2eb0e9a8c2d8460a03d952ce1e Package: MetNet Version: 1.8.0 Depends: R (>= 3.6) Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), GENIE3 (>= 1.7.0), methods (>= 3.5), mpmi (>= 0.42), parmigene (>= 1.0.2), ppcor (>= 1.1), sna (>= 2.4), stabs (>= 0.6), stats (>= 3.6) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 2.0-18), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1) License: GPL (>= 3) MD5sum: a0fb4fa88535dbc371a6a239dbbdbaae Package: mfa Version: 1.12.0 Depends: R (>= 3.4.0) Imports: methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack, MCMCglmm, coda, magrittr, tibble, Biobase LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: 1fb52e48d98e49a2d50f212732ab2395 Package: Mfuzz Version: 2.50.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 MD5sum: b6c322651a009a90cc455f409fd6113d Package: MGFM Version: 1.24.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 MD5sum: 7dabba39454062efc3cf3c84c44fada0 Package: MGFR Version: 1.16.0 Depends: R (>= 3.5) Imports: biomaRt, annotate License: GPL-3 MD5sum: 57b414f92b20f1d81e4fb02d22ac843f Package: mgsa Version: 1.38.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: 01e804d23839250d6017ae73999da0fa Package: MiChip Version: 1.44.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: fd592a62668bbbb51a348a837297ed36 Package: microbiome Version: 1.12.0 Depends: R (>= 3.6.0), phyloseq, ggplot2 Imports: dplyr, reshape2, Rtsne, scales, stats, tibble, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitcitations, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE MD5sum: f91009dafcf14b03f5751c34af51ac21 Package: microbiomeDASim Version: 1.4.0 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: 26f6e50234cb9178a210010e9f5c4420 Package: microbiomeExplorer Version: 1.0.1 Depends: shiny, magrittr, metagenomeSeq, Biobase Imports: shinyjs, shinydashboard, shinycssloaders, shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer, dplyr, tidyr, 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: 4a2a695455650d9585da1a23753029a3 Package: MicrobiotaProcess Version: 1.2.2 Depends: R (>= 4.0.0) Imports: ape, plyr, tidyr, ggplot2, phyloseq, magrittr, dplyr, Biostrings, ggrepel, vegan, reshape, zoo, ggtree, tidytree, gtools, MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, Rmisc, patchwork, ggstar Suggests: DT, rmarkdown, prettydoc, treeio, tidyverse, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, biomformat, scales, yaml License: GPL (>= 3.0) MD5sum: 7e2d6006494f69a31a60893e3518963a Package: microRNA Version: 1.48.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: 3fbf382156b7bcd85cb4c32c6dda59bf Package: MIGSA Version: 1.14.1 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: fb33dc45ca66b093994675ef5cc7a4a6 Package: mimager Version: 1.14.0 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: 4622bd8fc46455933444da8c524c85de Package: MIMOSA Version: 1.28.1 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: 465c203977b365ddf1063881a25d0237 Package: MineICA Version: 1.30.0 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply Enhances: doMC License: GPL-2 MD5sum: e5ec3e2cf298cb0358f7b1e6e69e4be1 Package: minet Version: 3.48.0 Imports: infotheo License: Artistic-2.0 MD5sum: 4762edc2a3f7e48477660018b635085b Package: minfi Version: 1.36.0 Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges, SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>= 1.1.9) Imports: S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray (>= 0.15.16), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools License: Artistic-2.0 MD5sum: 6e1eaff6de54a3a74fef8bd8d0f44b3c Package: MinimumDistance Version: 1.34.0 Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1) Imports: methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: 320b18d419551f042ac0454a72d06f01 Package: MiPP Version: 1.62.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: 69801498609a0c3dbe129ab9a264bd98 Package: MIRA Version: 1.12.0 Depends: R (>= 3.5) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 72837806c6acbdc4026e784470641442 Package: MiRaGE Version: 1.32.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: BiocGenerics, S4Vectors, AnnotationDbi, BiocManager Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL MD5sum: ac05f451a3ee38a6f893159b17b26651 Package: miRBaseConverter Version: 1.14.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils License: GPL (>= 2) MD5sum: ab6c0b6c6219e34ff3099b4475da473b Package: miRcomp Version: 1.20.0 Depends: R (>= 3.2), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: 90a1ec98f7f3030087f5f7dc3013db5b Package: mirIntegrator Version: 1.20.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: 4e0eec034b06e81666c8accbf02c8e75 Package: miRLAB Version: 1.20.0 Imports: methods, stats, utils, RCurl, httr, stringr, Hmisc, energy, entropy, Roleswitch, gplots, glmnet, impute, limma, pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc, heatmap.plus, InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit License: GPL (>= 2) MD5sum: 82617c903711ff466a3d5ae98a224d99 Package: miRmine Version: 1.12.0 Depends: R (>= 3.4), SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, DESeq2 License: GPL (>= 3) MD5sum: bd2d26a33de941e6dca2a1491372d94b Package: miRNAmeConverter Version: 1.18.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: e8c4d009465cf2664476d7d32f58498d Package: miRNApath Version: 1.50.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: 649692ee0ce41d37e24deb34ccb6bc69 Package: miRNAtap Version: 1.24.0 Depends: R (>= 3.3.0), AnnotationDbi Imports: DBI, RSQLite, stringr, sqldf, plyr, methods Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat License: GPL-2 MD5sum: 50915fe09b6ec5e5bfa21daa72338efd Package: miRSM Version: 1.8.4 Depends: R (>= 3.5.0) Imports: WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL, NMF, biclust, iBBiG, fabia, BicARE, isa2, s4vd, BiBitR, rqubic, Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero, ppclust, miRspongeR, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, MatrixCorrelation, energy Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: d7c4294241f86ce1d27ceba2d71885f5 Package: miRspongeR Version: 1.16.2 Depends: R (>= 3.5.0) Imports: corpcor, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, varhandle, linkcomm, utils, Rcpp, org.Hs.eg.db Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 77223e5827c02d214c7e3e287b9083f1 Package: missMethyl Version: 1.24.0 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 MD5sum: 47a20b24717bc25198ab6143ca8cb1aa Package: missRows Version: 1.10.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: d7182dd0450ca94130950813bae50a6d Package: mitch Version: 1.2.2 Depends: R (>= 4.0) Imports: stats, grDevices, graphics, utils, MASS, plyr, reshape2, parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r Suggests: stringi, testthat (>= 2.1.0) License: CC BY-SA 4.0 + file LICENSE MD5sum: e3c0860521f3e9b4f2c224416b9939f5 Package: mixOmics Version: 6.14.1 Depends: R (>= 3.5.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, ggrepel, BiocParallel, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, rgl License: GPL (>= 2) MD5sum: d86797922288e56619594146bb127dd3 Package: MLInterfaces Version: 1.70.0 Depends: R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4, tools, grDevices, graphics, stats Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, testthat Enhances: parallel, rda License: LGPL MD5sum: a0cd926372c1467b134f99039608fd3c Package: MLP Version: 1.38.0 Depends: AnnotationDbi, affy, plotrix, gplots, gmodels, gdata, gtools Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, KEGG.db, annotate, Rgraphviz, GOstats, limma, mouse4302.db, reactome.db License: GPL-3 MD5sum: 537ed703b65385b43e1788129a82a840 Package: MLSeq Version: 2.8.0 Depends: caret, ggplot2 Imports: methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, testthat, BiocStyle, VennDiagram, pamr License: GPL (>= 2) MD5sum: 6685b4c256d97365dc55f5ba637d62a7 Package: MMAPPR2 Version: 1.4.0 Depends: R (>= 3.6.0) Imports: ensemblVEP (>= 1.20.0), gmapR, Rsamtools, VariantAnnotation, BiocParallel, Biobase, BiocGenerics, dplyr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, 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: 4b3522aec90e7a8c608053c2367c0de5 Package: MMDiff2 Version: 1.18.0 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: 872d620ca902106d6372899ccbe1765a Package: MMUPHin Version: 1.3.0 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: fc6dcc98ad3353f24cce231317095cf9 Package: mnem Version: 1.6.5 Depends: R (>= 3.6) Imports: cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071 LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM License: GPL-3 MD5sum: b8b49da7e44fd6cf634f24964ff85a6a Package: MODA Version: 1.16.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 3464b760103c6d1e831fab485b2294b6 Package: Modstrings Version: 1.6.0 Depends: R (>= 3.6), Biostrings (>= 2.51.5) Imports: methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices Suggests: BiocStyle, knitr, rmarkdown, testthat, usethis License: Artistic-2.0 MD5sum: fd1577c7f93178d17828dfb2069fe529 Package: MOFA Version: 1.6.2 Depends: R (>= 3.5) Imports: rhdf5, dplyr, reshape2, pheatmap, corrplot, ggplot2, ggbeeswarm, methods, scales, GGally, RColorBrewer, cowplot, ggrepel, MultiAssayExperiment, Biobase, doParallel, foreach, reticulate, grDevices, stats, utils Suggests: knitr, MOFAdata License: LGPL-3 | file LICENSE MD5sum: bd930be79f6327d63f3750f0384643c9 Package: MOFA2 Version: 1.0.1 Depends: R (>= 4.0) Imports: rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods, GGally, RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array, grDevices, stats, magrittr, forcats, utils, corrplot, DelayedArray, Rtsne, uwot, basilisk Suggests: knitr, testthat, Seurat, ggpubr, foreach, psych, MultiAssayExperiment, SummarizedExperiment, SingleCellExperiment, ggrastr License: GPL (>= 2) MD5sum: 8667e6aede94f7e1bf6e54842daf50f0 Package: MOGAMUN Version: 1.0.1 Imports: stats, utils, RCy3, stringr, graphics, grDevices, RUnit, BiocParallel, igraph Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: b621d3939ae7324c229e1e72e9c6f82e Package: mogsa Version: 1.24.0 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: 30ec8440322505ea17d2dcd50a855c5b Package: MOMA Version: 1.2.0 Depends: R (>= 4.0) Imports: circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics, grid, grDevices, magrittr, methods, MKmisc, MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr, reshape2, rlang, stats, stringr, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, viper License: GPL-3 MD5sum: 0fcd469f156521983c278612130b0b6e Package: monocle Version: 2.18.0 Depends: R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-6), DDRTree (>= 0.1.4), Imports: parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, densityClust (>= 0.3), Rtsne, MASS, reshape2, limma, tibble, dplyr, qlcMatrix, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0) LinkingTo: Rcpp Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat License: Artistic-2.0 MD5sum: 0897316d2b4185ab96552c3a66a4f453 Package: MoonlightR Version: 1.16.0 Depends: R (>= 3.5), doParallel, foreach Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png License: GPL (>= 3) MD5sum: ed6df22149623b7738f6cf4662080e8d Package: mosaics Version: 2.28.0 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: 3aa70414ec75f988b052dd79e0343239 Package: MOSim Version: 1.4.0 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: a808232d968f330c60a7a604aae749c8 Package: motifbreakR Version: 2.4.0 Depends: R (>= 3.5.0), grid, MotifDb Imports: methods, compiler, grDevices, grImport, stringr, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP142.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle License: GPL-2 MD5sum: 21517a0cf4c47f8e72a2fc061c6deb88 Package: motifcounter Version: 1.14.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: 6bc5424e0b98d982479579fb504d6bf7 Package: MotifDb Version: 1.32.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes MD5sum: e5c812909e5e2f3661f5e3f3bd92bdd1 Package: motifmatchr Version: 1.12.0 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, GenomeInfoDb LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 + file LICENSE MD5sum: 18e123559ce9644b08e22de5a3eb26a4 Package: motifStack Version: 1.34.0 Depends: R (>= 2.15.1), methods, grid Imports: ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets, stats, stats4, utils, XML Suggests: grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr License: GPL (>= 2) MD5sum: 80be3a5e784bc1e0249efbea894c3914 Package: MouseFM Version: 1.0.0 Depends: R (>= 4.0.0) Imports: httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales, gtools, tidyr, data.table, jsonlite, rlist, GenomeInfoDb, methods, biomaRt, stats, IRanges Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: e1ac639f127bcf5b8106b7a25ffe1545 Package: MPFE Version: 1.26.0 License: GPL (>= 3) MD5sum: 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License: Artistic-2.0 MD5sum: 4154698268c34b3dd14dd060968bcfe4 Package: MSEADbi Version: 1.0.0 Depends: R (>= 4.0) Imports: methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase Suggests: RUnit, BiocGenerics, BiocStyle, knitr, testthat (>= 2.1.0) License: Artistic-2.0 MD5sum: 37a43a917134db2a94c907b22471b142 Package: msgbsR Version: 1.14.0 Depends: R (>= 3.4), GenomicRanges, methods Imports: BSgenome, easyRNASeq, edgeR, GenomicAlignments, GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges, parallel, plyr, Rsamtools, R.utils, stats, SummarizedExperiment, S4Vectors, utils Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-2 MD5sum: cf387395aaecf22a81ae8f3426cd9983 Package: MSGFgui Version: 1.24.0 Depends: mzR, xlsx Imports: shiny, mzID (>= 1.2), MSGFplus, shinyFiles (>= 0.4.0), tools Suggests: knitr, testthat License: GPL (>= 2) MD5sum: a9139ca4a59c7074783d77c939d5de24 Package: MSGFplus Version: 1.24.0 Depends: methods Imports: mzID, ProtGenerics Suggests: knitr, testthat License: GPL (>= 2) MD5sum: 992f64ab2a03c54c93bd151c3ee57184 Package: msImpute Version: 1.0.0 Depends: R (>= 4.0) Imports: softImpute, methods, stats, graphics, pdist, reticulate, scran, data.table, FNN, matrixStats, rdetools, limma, mvtnorm Suggests: BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD License: GPL (>= 2) MD5sum: d76e5f437475adee992597a5188256df Package: msmsEDA Version: 1.28.0 Depends: R (>= 3.0.1), MSnbase Imports: MASS, gplots, RColorBrewer License: GPL-2 MD5sum: 054b49536b037e135af8690a3b0834b4 Package: msmsTests Version: 1.28.0 Depends: R (>= 3.0.1), MSnbase, msmsEDA Imports: edgeR, qvalue License: GPL-2 MD5sum: 7c059722afac79195489ee9c0252800f Package: MSnbase Version: 2.16.1 Depends: R (>= 3.5), methods, BiocGenerics (>= 0.7.1), Biobase (>= 2.15.2), mzR (>= 2.19.6), S4Vectors, ProtGenerics (>= 1.19.3) Imports: BiocParallel, IRanges (>= 2.13.28), plyr, preprocessCore, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID (>= 1.5.2), digest, lattice, ggplot2, XML, scales, MASS, Rcpp LinkingTo: Rcpp Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr, SummarizedExperiment License: Artistic-2.0 MD5sum: 5bd5fe173b36f4d108e0bec67192402b Package: MSnID Version: 1.24.0 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: af0f0b680b98ffbfcc239ce2290995b2 Package: MSPrep Version: 1.0.0 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 Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 1.0.2) License: GPL-3 MD5sum: 960718cc0c9ac2258882390c3cfe085c Package: msPurity Version: 1.16.2 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: dce746ab2d9f0b19931cb37db977177b Package: MSstats Version: 3.22.1 Depends: R (>= 3.6) Imports: lme4, marray, limma, gplots, ggplot2, methods, grid, ggrepel, preprocessCore, reshape2, survival, statmod, minpack.lm, utils, grDevices, graphics, stats, doSNOW, snow, foreach, data.table, MASS, dplyr, tidyr, broom, purrr, stringr, Suggests: BiocStyle, knitr, rmarkdown, MSstatsBioData License: Artistic-2.0 MD5sum: 491e6a686d3f5df9b4e184f7194394f5 Package: MSstatsConvert Version: 1.0.0 Depends: R (>= 4.0) Imports: data.table, log4r, methods, checkmate, utils Suggests: tinytest, covr, knitr, rmarkdown License: Artistic-2.0 MD5sum: c9643b5133664102cbb06938b7218f0f Package: MSstatsPTM Version: 1.0.0 Depends: R (>= 4.0) Imports: broom, dplyr, rlang, stats, tibble, tidyr, tidyselect, Biostrings Suggests: knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle License: Artistic-2.0 MD5sum: ac086583f0b7a02da2fb9f532b22dbba Package: MSstatsQC Version: 2.8.0 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: 6bf030dd26ece309a5782084f47e1000 Package: MSstatsQCgui Version: 1.10.0 Imports: shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid Suggests: knitr License: Artistic License 2.0 MD5sum: 83ce43a415b6795072cfed829f2838b2 Package: MSstatsSampleSize Version: 1.4.0 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: fc57b68ce3ddc583689829110387633a Package: MSstatsTMT Version: 1.8.2 Depends: R (>= 4.0) Imports: limma, lme4, lmerTest, dplyr, tidyr, statmod, methods, reshape2, data.table, matrixStats, stats, utils, ggplot2, grDevices, graphics, MSstats Suggests: BiocStyle, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 58f07a6cd9b2be0c6e0dd6ac7cb63e3b Package: MSstatsTMTPTM Version: 1.0.2 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: 7862f9e5610ec820e543b970a0e3a70a Package: Mulcom Version: 1.40.0 Depends: R (>= 2.10), Biobase Imports: graphics, grDevices, stats, methods, fields License: GPL-2 MD5sum: 41d7e7c5e215b8ee1b5efc5bcc3d3938 Package: MultiAssayExperiment Version: 1.16.0 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, testthat, knitr, rmarkdown, R.rsp, HDF5Array, RaggedExperiment, UpSetR, survival, survminer License: Artistic-2.0 MD5sum: 2d22c454e16544dd23ac357061782c38 Package: MultiBaC Version: 1.0.0 Imports: Matrix, ggplot2, MultiAssayExperiment, ropls, graphics, methods Suggests: knitr, rmarkdown, BiocStyle, devtools License: GPL-3 MD5sum: 558170fb405a4421213755a686609cde Package: multiClust Version: 1.20.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) MD5sum: f2914b98932e0f934c9f408a4891ef11 Package: multicrispr Version: 1.0.0 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: c4f1e674c2e7d934ff11190bd0be2aaf Package: MultiDataSet Version: 1.18.2 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: 2ea83bcd81728d76cc67444227b00667 Package: multiGSEA Version: 1.0.2 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: c6ed7c1d840e6ec8f6219f73aa919332 Package: multiHiCcompare Version: 1.8.0 Depends: R (>= 4.0.0) Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, metap, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, BLMA, GenomeInfoDb Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 3e277d8beeb464367b064ae02003b7c4 Package: MultiMed Version: 2.12.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE MD5sum: 01d2cb16af1ef1082b40f5805097e10f Package: multiMiR Version: 1.12.0 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: e16bcf89f0bdaaa5dd17362200b4868b Package: multiOmicsViz Version: 1.14.0 Depends: R (>= 3.3.2) Imports: methods, parallel, doParallel, foreach, grDevices, graphics, utils, SummarizedExperiment, stats Suggests: BiocGenerics License: LGPL MD5sum: 0fa64bc213d07599b444526af29df12a Package: multiscan Version: 1.50.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) MD5sum: 5c98f2122e8ffcdaa8889068966d26a2 Package: multtest Version: 2.46.0 Depends: R (>= 2.10), methods, BiocGenerics, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL MD5sum: a554c023050ff022287c1c5213e93e59 Package: muscat Version: 1.4.0 Depends: R (>= 4.0) Imports: BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, S4Vectors, scales, scater, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition, viridis Suggests: BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr, phylogram, RColorBrewer, reshape2, rmarkdown, testthat, UpSetR License: GPL (>= 2) MD5sum: 7d09fa6cce8f3a5c3a51f79f3ffc405e Package: muscle Version: 3.32.0 Depends: Biostrings License: Unlimited MD5sum: 9dbeaeaeea0689b67b6f65d8135584bb Package: musicatk Version: 1.0.0 Depends: R (>= 4.0.0), NMF Imports: SummarizedExperiment, VariantAnnotation, cowplot, Biostrings, base, methods, magrittr, tibble, tidyr, gtools, gridExtra, maftools, MCMCprecision, 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 Suggests: testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr License: LGPL-3 MD5sum: 5d094dac3478c6d2e68230c51364ee0d Package: MutationalPatterns Version: 3.0.1 Depends: R (>= 4.0.0), 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 (>= 2.1.0), pracma (>= 1.8.8), IRanges (>= 2.6.0), GenomeInfoDb (>= 1.12.0), Biostrings (>= 2.40.0), ggdendro (>= 0.1-20), cowplot (>= 0.9.2), ggalluvial (>= 0.12.2) Suggests: BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), ccfindR (>= 1.6.0), GenomicFeatures, AnnotationDbi, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 95859590e5012ddf8c6289349ba53218 Package: MVCClass Version: 1.64.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: 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MD5sum: 3a73aac0017d69983fc41a342f78fde9 Package: mzR Version: 2.24.1 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 (>= 2.5.19), knitr, XML License: Artistic-2.0 MD5sum: 97048617e69e37a7dea6010ce0c4e873 Package: NADfinder Version: 1.14.0 Depends: R (>= 3.4), BiocGenerics, IRanges, GenomicRanges, S4Vectors, SummarizedExperiment Imports: graphics, methods, baseline, signal, GenomicAlignments, GenomeInfoDb, rtracklayer, limma, trackViewer, stats, utils, Rsamtools, metap, EmpiricalBrownsMethod,ATACseqQC, corrplot, csaw Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager License: GPL (>= 2) MD5sum: 4f42dbcf13acd316d470f429adb4b326 Package: NanoMethViz Version: 1.0.0 Depends: R (>= 4.0.0), methods, ggplot2 Imports: S4Vectors, SummarizedExperiment, bsseq, forcats, assertthat, AnnotationDbi, Rcpp, dplyr, data.table, e1071, fs, GenomicRanges, ggthemes, glue, patchwork, purrr, readr, rlang, RSQLite, Rsamtools, scales, stats, stringr, tibble, tidyr, utils, zlibbioc LinkingTo: Rcpp Suggests: DSS, Mus.musculus, Homo.sapiens, knitr, rmarkdown License: Apache License (>= 2.0) MD5sum: 9d94ecc5bb35518827ae2c8990b942ee Package: NanoStringDiff Version: 1.20.0 Depends: Biobase Imports: matrixStats, methods, Rcpp LinkingTo: Rcpp Suggests: testthat, BiocStyle License: GPL MD5sum: 3c2811f032020d2b2787005503056142 Package: NanoStringQCPro Version: 1.22.0 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: roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: c86802997052c8c09a6fec42d8b44b9c Package: nanotatoR Version: 1.6.0 Depends: R (>= 3.6) Imports: hash(>= 2.2.6), openxlsx(>= 4.0.17), rentrez(>= 1.1.0), stats, grDevices, graphics, stringr, knitr, testthat, utils, AnnotationDbi, httr, org.Hs.eg.db, rtracklayer Suggests: rmarkdown, yaml License: file LICENSE MD5sum: 2c136774734ae520571bf18897c6b3ac Package: NBAMSeq Version: 1.6.1 Depends: R (>= 3.6), SummarizedExperiment, S4Vectors Imports: DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods, stats, Suggests: knitr, rmarkdown, testthat, ggplot2 License: GPL-2 MD5sum: 645cb4c36300690a188ff818dc8b5aec Package: NBSplice Version: 1.8.0 Depends: R (>= 3.5), methods Imports: edgeR, stats, MASS, car, mppa, BiocParallel, ggplot2, reshape2 Suggests: knitr, RUnit, BiocGenerics, BiocStyle License: GPL (>= 2) MD5sum: 99999e6fd18d7e929d78b5cc9308f0b7 Package: ncdfFlow Version: 2.36.0 Depends: R (>= 2.14.0), flowCore(>= 1.51.7), RcppArmadillo, methods, BH Imports: Biobase,BiocGenerics,flowCore,zlibbioc LinkingTo: Rcpp,RcppArmadillo,BH, Rhdf5lib Suggests: testthat,parallel,flowStats,knitr License: Artistic-2.0 MD5sum: 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ggplot2, gplots, BiocGenerics, rlang Suggests: knitr License: Artistic-2.0 MD5sum: 7f936708452d02bb2c4d3789c434a3ce Package: Nebulosa Version: 1.0.2 Depends: R (>= 4.0), ggplot2, patchwork Imports: Seurat, SingleCellExperiment, SummarizedExperiment, SeuratObject, ks, Matrix, stats, methods Suggests: testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache License: GPL-3 MD5sum: 506cfa56ac8128d5d53cecffe4af7d7c Package: NeighborNet Version: 1.8.0 Depends: methods Imports: graph, stats License: CC BY-NC-ND 4.0 MD5sum: 1de9ccb27d6573991dad3a4eeb2dbf77 Package: netbiov Version: 1.24.0 Depends: R (>= 3.1.0), igraph (>= 0.7.1) Suggests: BiocStyle,RUnit,BiocGenerics,Matrix License: GPL (>= 2) MD5sum: b104f72dcc1af3b9c1b53820834fd993 Package: netboost Version: 1.6.0 Depends: R (>= 3.6.0) Imports: Rcpp, RcppParallel, parallel, grDevices, graphics, stats, utils, dynamicTreeCut, WGCNA, impute, colorspace, methods, R.utils LinkingTo: Rcpp, RcppParallel Suggests: knitr License: GPL-3 OS_type: unix MD5sum: e7e72cb125667e851409488becefb177 Package: netboxr Version: 1.2.0 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: 701a8b16f972e0ad6cc571f4cff80e58 Package: netDx Version: 1.2.2 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 License: MIT + file LICENSE MD5sum: b564fbf2ae2682a6e8c13e77079483c9 Package: nethet Version: 1.22.0 Imports: glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network, ggplot2, grDevices, graphics, stats, utils Suggests: knitr, xtable, BiocStyle, testthat License: GPL-2 MD5sum: 776b141b19ba3272b9552fef5da0788d Package: NetPathMiner Version: 1.26.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 40de3dd44f367aeacca8657b32ef375d Package: netprioR Version: 1.16.0 Depends: methods, graphics, R(>= 3.3) Imports: stats, Matrix, dplyr, doParallel, foreach, parallel, sparseMVN, ggplot2, gridExtra, pROC Suggests: knitr, BiocStyle, pander License: GPL-3 MD5sum: 37e9da2abe80bfe5afaad27a7f93847f Package: netresponse Version: 1.50.0 Depends: R (>= 2.15.1), Rgraphviz, methods, minet, mclust, reshape2 Imports: dmt, ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer Suggests: knitr License: GPL (>= 2) MD5sum: abed3bd157b3fb09609ddfdd4e42b561 Package: NetSAM Version: 1.30.0 Depends: R (>= 2.15.1), methods, igraph (>= 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irlba, Matrix, DelayedArray, BiocSingular, stats Suggests: testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr License: GPL-3 MD5sum: eae344e69b763cecf9b01035fbbaef5e Package: ngsReports Version: 1.6.1 Depends: R (>= 4.0.0), BiocGenerics, ggplot2, tibble (>= 1.3.1) Imports: Biostrings, checkmate, dplyr (>= 1.0.0), DT, FactoMineR, forcats, ggdendro, grDevices, grid, lifecycle, lubridate, methods, pander, parallel, plotly, readr, reshape2, rmarkdown, Rsamtools, scales, ShortRead, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils, viridisLite, zoo Suggests: BiocStyle, Cairo, knitr, testthat, truncnorm License: file LICENSE MD5sum: 110e3cea6f3d60b74c8295424e884102 Package: nnNorm Version: 2.54.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: 8c8d21f025d28fd70f44e6f1d806a6f6 Package: NOISeq Version: 2.34.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 MD5sum: e7bf360e36521d509155f4bce4aa3283 Package: nondetects Version: 2.20.0 Depends: R (>= 3.2), Biobase (>= 2.22.0) Imports: limma, mvtnorm, utils, methods, arm, HTqPCR (>= 1.16.0) Suggests: knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics (>= 0.8.0) License: GPL-3 MD5sum: ca3a365682ad59b4bc4083637690e82b Package: NoRCE Version: 1.2.0 Depends: 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: cc2fcfd63a41d463041d6fd2a6e0d6ff Package: normalize450K Version: 1.18.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 7b568599865b67fbd1bbe8d338a60840 Package: NormalyzerDE Version: 1.8.0 Depends: R (>= 3.6) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, Biobase, RcmdrMisc, raster, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 MD5sum: 2a53a9e6fcd9867326ca9cbc62fae3f0 Package: NormqPCR Version: 1.36.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: 2cc6d71e424b4dd1d522d67ab1a3cfbb Package: normr Version: 1.16.0 Depends: R (>= 3.3.0) Imports: methods, stats, utils, grDevices, parallel, GenomeInfoDb, GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2), bamsignals (>= 1.4), rtracklayer (>= 1.32) LinkingTo: Rcpp Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown Enhances: BiocParallel License: GPL-2 MD5sum: 52ce62ce422282cc1c6dadc668ddc235 Package: NPARC Version: 1.2.0 Depends: R (>= 4.0.0) Imports: dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr, stats, methods Suggests: testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2, BiocStyle License: GPL-3 MD5sum: fa0bea163c27dd37a881da884cfceed7 Package: npGSEA Version: 1.26.0 Depends: GSEABase (>= 1.24.0) Imports: Biobase, methods, BiocGenerics, graphics, stats Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle License: Artistic-2.0 MD5sum: 15a232656bf923fef48d25a984c8b892 Package: NTW Version: 1.40.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 MD5sum: 0dabe41a9c7bb10ff4640c8234af0672 Package: nucleoSim Version: 1.18.0 Imports: stats, IRanges, S4Vectors, graphics, methods Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: a9be4ad736679e06444ad0b18c83e16a Package: nucleR Version: 2.22.0 Depends: methods Imports: Biobase, BiocGenerics, Biostrings, GenomeInfoDb, GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr, ggplot2, magrittr, parallel, stats, utils, grDevices Suggests: Starr, BiocStyle, knitr, rmarkdown, testthat License: LGPL (>= 3) MD5sum: 3e39c141690d66401497e01299cd246f Package: nuCpos Version: 1.8.0 Depends: R (>= 3.6) Imports: graphics, methods Suggests: NuPoP, Biostrings, testthat License: file LICENSE MD5sum: 630d199a1fe34fe7a67d7753d8121afe Package: NuPoP Version: 1.40.0 Depends: R (>= 2.10) License: GPL-2 MD5sum: 1a626ef2fd33e4f9106a2b5b080a4470 Package: occugene Version: 1.50.0 Depends: R (>= 2.0.0) License: GPL (>= 2) MD5sum: 6186d73837dd2ac1698f6cbc8b09813d Package: OCplus Version: 1.64.0 Depends: R (>= 2.1.0) Imports: multtest (>= 1.7.3), graphics, grDevices, stats, akima License: LGPL MD5sum: f2e86fad521ea3124e4e9b26ab6b7f9f Package: odseq Version: 1.18.0 Depends: R (>= 3.2.3) Imports: msa (>= 1.2.1), kebabs (>= 1.4.1), mclust (>= 5.1) Suggests: knitr(>= 1.11) License: MIT + file LICENSE MD5sum: dbcf9d0dc1483f565f8d802996f108f2 Package: oligo Version: 1.54.1 Depends: R (>= 3.2.0), BiocGenerics (>= 0.13.11), oligoClasses (>= 1.29.6), Biobase (>= 2.27.3), Biostrings (>= 2.35.12) Imports: affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, zlibbioc LinkingTo: preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl Enhances: doMC, doMPI License: LGPL (>= 2) MD5sum: 497d1f9a829cebb06a01c80be7f7c3ca Package: oligoClasses Version: 1.52.0 Depends: R (>= 2.14) Imports: BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods, graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>= 1.23.2), foreach, BiocManager, utils, S4Vectors (>= 0.9.25), RSQLite, DBI, ff Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, VanillaICE, crlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) MD5sum: 56012baac5554526392d409494ed5a46 Package: OLIN Version: 1.68.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 MD5sum: ea49b7e82fa50847af3d9ca6c00c6f4d Package: OLINgui Version: 1.64.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, 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methods, rexposome, limma, sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet, SmartSVA, isva, parallel, SummarizedExperiment, stringr Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata License: MIT + file LICENSE MD5sum: b35d199a80fa03a2b646f4f1a4196f32 Package: OmicsLonDA Version: 1.6.0 Depends: R(>= 3.6) Imports: SummarizedExperiment, gss, plyr, zoo, pracma, ggplot2, BiocParallel, parallel, grDevices, graphics, stats, utils, methods, BiocGenerics Suggests: knitr, rmarkdown, testthat, devtools, BiocManager License: MIT + file LICENSE MD5sum: 98805580fca6bd0aeafa9bc37e61e6dc Package: OMICsPCA Version: 1.8.0 Depends: R (>= 3.5.0), OMICsPCAdata Imports: HelloRanges, fpc, stats, MultiAssayExperiment, pdftools, methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown, kableExtra, rtracklayer, IRanges, GenomeInfoDb, reshape2, ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR, PerformanceAnalytics, tidyr, data.table, cluster, magick Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: f94fa1ab06add3861c1f2c5de28500a6 Package: omicsPrint Version: 1.10.0 Depends: R (>= 3.5), MASS Imports: methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 2) MD5sum: ba8a7d31c5414963a56fdbe752fa70ef Package: Omixer Version: 1.0.4 Depends: R (>= 3.0.0) Imports: dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr, tidyselect, grid, stats, stringr Suggests: knitr, rmarkdown, BiocStyle, magick, testthat License: MIT + file LICENSE MD5sum: 14b455dab97940458f7371cdba30580c Package: OmnipathR Version: 2.0.0 Depends: R(>= 4.0), igraph, graphics, methods, utils, jsonlite Imports: dplyr, stats, rlang, tidyr Suggests: dnet, gprofiler2, BiocStyle, testthat, knitr, rmarkdown, ggplot2, ggraph License: MIT + file LICENSE MD5sum: 2ddec9f2ce03798a3addc935b97fd9ac Package: Onassis Version: 1.12.0 Depends: R (>= 4.0), rJava, OnassisJavaLibs Imports: GEOmetadb, RSQLite, data.table, methods, tools, utils, AnnotationDbi, RCurl, stats, DT, data.table, knitr, Rtsne, dendextend, clusteval, ggplot2, ggfortify Suggests: BiocStyle, rmarkdown, htmltools, org.Hs.eg.db, gplots, GenomicRanges, kableExtra License: GPL-2 MD5sum: 135294af0a7073b35c30a41a059d7942 Package: oncomix Version: 1.12.0 Depends: R (>= 3.4.0) Imports: ggplot2, ggrepel, RColorBrewer, mclust, stats, SummarizedExperiment Suggests: knitr, rmarkdown, testthat, RMySQL License: GPL-3 MD5sum: 599c604d19ed0f072e27bb1725b90f6e Package: OncoScore Version: 1.18.0 Depends: R (>= 4.0.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: ce980c5b599767a6bcfab38f7e485967 Package: OncoSimulR Version: 2.20.0 Depends: R (>= 3.3.0) Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel LinkingTo: Rcpp Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander License: GPL (>= 3) MD5sum: b240261cc11ccc4e6cc537dc38c1bd14 Package: oneSENSE Version: 1.12.0 Depends: R (>= 3.4), webshot, shiny, shinyFiles, scatterplot3d Imports: Rtsne, plotly, gplots, grDevices, graphics, stats, utils, methods, flowCore Suggests: knitr, rmarkdown License: GPL (>= 3) MD5sum: aaccc98a54e2cd4d27e5667501f591f2 Package: onlineFDR Version: 1.8.0 Imports: stats Suggests: knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: 393d98ecb18606dc43c5b91bd7abf001 Package: ontoProc Version: 1.12.0 Depends: R (>= 3.5), ontologyIndex 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 License: Artistic-2.0 MD5sum: 01bfc77f17f6626e2bbf09c56224a78c Package: openCyto Version: 2.2.0 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: cf8adab51d92e3a1eeffd8a5a52d98c8 Package: openPrimeR Version: 1.12.1 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 (>= 2.4.8), GenomicRanges (>= 1.22.4), ggplot2 (>= 2.1.0), plyr (>= 1.8.4), dplyr (>= 0.5.0), stringdist (>= 0.9.4.1), stringr (>= 1.0.0), RColorBrewer (>= 1.1-2), DECIPHER (>= 1.16.1), lpSolveAPI (>= 5.5.2.0-17), digest (>= 0.6.9), Hmisc (>= 3.17-4), ape (>= 3.5), BiocGenerics (>= 0.16.1), S4Vectors 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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: cb388555453d702c15da5b56905e9fba Package: OrderedList Version: 1.62.0 Depends: R (>= 3.6.1), Biobase, twilight Imports: methods License: GPL (>= 2) MD5sum: 76f415252576c88d42f9fbc624fb0838 Package: ORFik Version: 1.10.13 Depends: R (>= 3.6.0), IRanges (>= 2.17.1), GenomicRanges (>= 1.35.1), GenomicAlignments (>= 1.19.0) Imports: S4Vectors (>= 0.21.3), GenomeInfoDb (>= 1.15.5), GenomicFeatures (>= 1.31.10), AnnotationDbi (>= 1.45.0), rtracklayer (>= 1.43.0), Rcpp (>= 1.0.0), data.table (>= 1.11.8), Biostrings (>= 2.51.1), biomartr, BiocGenerics (>= 0.29.1), BiocParallel (>= 1.19.0), BSgenome, DESeq2 (>= 1.24.0), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), cowplot (>= 1.0.0), GGally (>= 1.4.0), methods (>= 3.6.0), R.utils, RCurl, Rsamtools (>= 1.35.0), utils, stats, SummarizedExperiment (>= 1.14.0), fst (>= 0.9.2), xml2 (>= 1.2.0), tools LinkingTo: Rcpp Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: ad8dab4f0aafd26220c7c47bbf8dcec4 Package: Organism.dplyr Version: 1.18.0 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: c6953cce9d5ce0b9e63d329895ec9609 Package: OrganismDbi Version: 1.32.0 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: fef02f905982902d7ea5ed8d92cb5593 Package: OSAT Version: 1.38.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 MD5sum: 5e4267eb42b55cecf482f5ad03497ce1 Package: Oscope Version: 1.20.0 Depends: EBSeq, cluster, testthat, BiocParallel Suggests: BiocStyle License: Artistic-2.0 MD5sum: 7270336dbfe67534548ef12d97a6bc18 Package: OTUbase Version: 1.40.0 Depends: R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>= 1.23.15), Biobase, vegan Imports: Biostrings License: Artistic-2.0 MD5sum: 89550dceff54d96a87d3abdfcc1b4242 Package: OutlierD Version: 1.53.0 Depends: R (>= 2.3.0), Biobase, quantreg License: GPL (>= 2) MD5sum: 1119050adbafaf69a6ae1a94eec14ef1 Package: OUTRIDER Version: 1.8.0 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: 27e8597e531eed8c3e220c53fca02bd4 Package: OVESEG Version: 1.6.0 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: 5a4198682aa00aa2a4083d16e4318dca Package: PAA Version: 1.24.0 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: 6b1e6996bb4eb3b162d6c3988a40d65e Package: packFinder Version: 1.2.0 Depends: R (>= 4.0.0) Imports: Biostrings, GenomicRanges, kmer, ape, methods, IRanges, S4Vectors Suggests: biomartr, knitr, rmarkdown, testthat, dendextend, biocViews, BiocCheck, BiocStyle License: GPL-2 MD5sum: 8d6f24db7d264bcf26632a0669034b71 Package: padma Version: 1.0.0 Depends: R (>= 4.0.0), SummarizedExperiment, S4Vectors Imports: FactoMineR, MultiAssayExperiment, methods, graphics, stats, utils Suggests: testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA, ggplot2, ggrepel, car, cowplot License: GPL (>= 3) MD5sum: f8d9f210a815d5f80ed480b44af93c73 Package: PADOG Version: 1.32.0 Depends: R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase Imports: limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db, hgu133a.db, KEGGREST, nlme Suggests: doParallel, parallel License: GPL (>= 2) MD5sum: 51894c4dc83e492de35f2b63c76912e4 Package: pageRank Version: 1.0.0 Depends: R (>= 4.0) Imports: GenomicRanges, igraph, motifmatchr, stats, utils, grDevices, graphics Suggests: bcellViper, BSgenome.Hsapiens.UCSC.hg19, JASPAR2018, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, TFBSTools, GenomicFeatures, annotate License: GPL-2 MD5sum: d635c4378fe4be01ddf8f74f3efde6db Package: PAIRADISE Version: 1.6.0 Depends: R (>= 3.6), nloptr Imports: SummarizedExperiment, S4Vectors, stats, methods, abind, BiocParallel Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: ee0ea267088b5728fb211309028cbcda Package: paircompviz Version: 1.28.0 Depends: R (>= 2.10), Rgraphviz Imports: Rgraphviz Suggests: multcomp, reshape, rpart, plyr, xtable License: GPL (>= 3.0) MD5sum: c23065fb1cfd80ceb6949614719ec4ce Package: pandaR Version: 1.22.0 Depends: R (>= 3.0.0), methods, Biobase, BiocGenerics, Imports: matrixStats, igraph, ggplot2, grid, reshape, plyr, RUnit, hexbin Suggests: knitr License: GPL-2 MD5sum: 84435fd5ccc306fdb37feae7813f798b Package: panelcn.mops Version: 1.12.0 Depends: R (>= 3.4), cn.mops, methods, utils, stats, graphics Imports: GenomicRanges, Rsamtools, IRanges, S4Vectors, GenomeInfoDb, grDevices Suggests: knitr, rmarkdown, RUnit, BiocGenerics License: LGPL (>= 2.0) MD5sum: 344c6dcad79402835fc19acc9dff7c8e Package: panp Version: 1.60.0 Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5) Imports: Biobase, methods, stats, utils Suggests: gcrma License: GPL (>= 2) MD5sum: c18a035f24af60e410ef2b589ba6396c Package: PANR Version: 1.36.0 Depends: R (>= 2.14), igraph Imports: graphics, grDevices, MASS, methods, pvclust, stats, utils, RedeR Suggests: snow License: Artistic-2.0 MD5sum: b934ad447d49170400e0c9a785c0a0cc Package: PanVizGenerator Version: 1.18.0 Depends: methods Imports: shiny, tools, jsonlite, pcaMethods, FindMyFriends, igraph, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, digest License: GPL (>= 2) MD5sum: 69725518ed89b454911cf29faf7d7287 Package: parglms Version: 1.22.0 Depends: methods Imports: BiocGenerics, BatchJobs, foreach, doParallel Suggests: RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges, gwascat, BiocStyle License: Artistic-2.0 MD5sum: df6a4bc17e3e1348f99159c6a3e451a2 Package: parody Version: 1.48.0 Depends: R (>= 3.5.0), tools, utils Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: 790dddbacaa8c245cf3f5a810058c8db Package: PAST Version: 1.6.0 Depends: R (>= 4.0) Imports: stats, utils, dplyr, rlang, iterators, parallel, foreach, doParallel, qvalue, rtracklayer, ggplot2, GenomicRanges, S4Vectors Suggests: knitr, rmarkdown License: GPL (>= 3) + file LICENSE MD5sum: 7cabe2251a42c8b5b5899fc06ebdba22 Package: Path2PPI Version: 1.20.0 Depends: R (>= 3.2.1), igraph (>= 1.0.1), methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle License: GPL (>= 2) MD5sum: c8b7901acff980bb9811b599e10edaa0 Package: pathifier Version: 1.28.0 Imports: R.oo, princurve (>= 2.0.4) License: Artistic-1.0 MD5sum: f0ffc0fea64340067726423a119e7a3c Package: PathNet 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1.30.1 Depends: R (>= 2.10) Imports: KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi, org.Hs.eg.db, KEGGREST, methods, utils Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics License: GPL (>= 3.0) MD5sum: 6754cb4033d9bfa281c4f0f755874985 Package: pathwayPCA Version: 1.6.3 Depends: R (>= 3.1) Imports: lars, methods, parallel, stats, survival, utils Suggests: airway, circlize, grDevices, knitr, RCurl, reshape2, rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse License: GPL-3 MD5sum: dc13da7e19c00d673b1d829778affbf8 Package: pcaExplorer Version: 2.16.0 Imports: DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, genefilter, ggplot2 (>= 2.0.0), heatmaply, plotly, scales, NMF, plyr, topGO, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, ggrepel, DT, shinyAce, threejs, biomaRt, pheatmap, knitr, rmarkdown, base64enc, tidyr, grDevices, methods Suggests: testthat, BiocStyle, airway, org.Hs.eg.db, htmltools License: MIT + file 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multtest, hu6800.db, KEGG.db, mvtnorm License: GPL (>= 2) MD5sum: 251b4554cdd3181ea22d10d61cea0ce8 Package: PCpheno Version: 1.52.0 Depends: R (>= 2.10), Category, ScISI (>= 1.3.0), SLGI, ppiStats, ppiData, annotate (>= 1.17.4) Imports: AnnotationDbi, Biobase, Category, GO.db, graph, graphics, GSEABase, KEGG.db, methods, ScISI, stats, stats4 Suggests: KEGG.db, GO.db, org.Sc.sgd.db License: Artistic-2.0 MD5sum: 4018da09e2c0dc6ac818230fa7f700af Package: pcxn Version: 2.12.0 Depends: R (>= 3.4), pcxnData Imports: methods, grDevices, utils, pheatmap Suggests: igraph, annotate, org.Hs.eg.db License: MIT + file LICENSE MD5sum: bdcc438900ebe427a4e0441de66e8ca9 Package: pdInfoBuilder Version: 1.54.0 Depends: R (>= 3.2.0), methods, Biobase (>= 2.27.3), RSQLite (>= 1.0.0), affxparser (>= 1.39.4), oligo (>= 1.31.5) Imports: Biostrings (>= 2.35.12), BiocGenerics (>= 0.13.11), DBI (>= 0.3.1), IRanges (>= 2.1.43), oligoClasses (>= 1.29.6), S4Vectors (>= 0.5.22) License: Artistic-2.0 MD5sum: 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Biobase, S4Vectors, SummarizedExperiment, BiocParallel, ggplot2, magicaxis, RColorBrewer, parallel, caTools, methods, downloader, stats, utils, graphics, grDevices, reshape2, jsonlite, data.table Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, BiocGenerics License: Artistic-2.0 MD5sum: c6688e1c5328ae5fccf2c7a202eb04f0 Package: phemd Version: 1.6.0 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: 172ac858be0d78175179ae6ee381fcc3 Package: phenopath Version: 1.14.0 Imports: Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr, tibble, ggplot2, tidyr LinkingTo: Rcpp Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment License: Apache 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RCircos, purrr, readr, tibble Suggests: foreach, doParallel, BiocStyle, knitr, rmarkdown, png, GGally, gridExtra, ggforce, fgsea, RColorBrewer, ggpubr, rtracklayer License: GPL-3 MD5sum: 2005c9fbece64f3ea6ea30779a655ef4 Package: piano Version: 2.6.0 Depends: R (>= 3.5) Imports: BiocGenerics, Biobase, gplots, igraph, relations, marray, fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard, visNetwork, scales, grDevices, graphics, stats, utils, methods Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 62c0d09cdd1ccab2a055a87061071a19 Package: pickgene Version: 1.62.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: 8f4ac6b2c485c79dff8089f074d8e32e Package: PICS Version: 2.34.0 Depends: R (>= 3.0.0) Imports: utils, stats, graphics, grDevices, methods, IRanges, GenomicRanges, Rsamtools, GenomicAlignments Suggests: rtracklayer, parallel, knitr 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limma, CoGAPS, NMF, ROCR, ggalluvial, RColorBrewer, dplyr, reshape2, viridis, scales, ggplot2 Suggests: BiocStyle, gridExtra, grid, testthat, devtools, knitr, rmarkdown, ComplexHeatmap License: GPL (== 2) MD5sum: 209c81c491b328eaef00922d0f566086 Package: pRoloc Version: 1.30.0 Depends: R (>= 2.15), MSnbase (>= 1.19.20), MLInterfaces (>= 1.67.10), methods, Rcpp (>= 0.10.3), BiocParallel Imports: stats4, Biobase, mclust (>= 4.3), caret, e1071, sampling, class, kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS, knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools, plyr, ggplot2, biomaRt, utils, grDevices, graphics LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, synapter, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.15.3), dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape License: GPL-2 MD5sum: 92a6aebad9f73ef9a48614928b0a19b8 Package: 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matrixStats, graphics Suggests: BiocStyle, knitr, rmarkdown License: MIT MD5sum: 34db250d1f638ccdbca5ec711711eb15 Package: ProtGenerics Version: 1.22.0 Depends: methods License: Artistic-2.0 MD5sum: b4542390a4af07e5fd1770fcf026ea66 Package: PSEA Version: 1.24.0 Imports: Biobase, MASS Suggests: BiocStyle License: Artistic-2.0 MD5sum: 7ce4a0ff4f61fee96549b5592d03872b Package: psichomics Version: 1.16.0 Depends: R (>= 4.0), shiny (>= 1.5.0), shinyBS Imports: AnnotationDbi, AnnotationHub, BiocFileCache, cluster, colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR, fastICA, fastmatch, ggplot2, ggrepel, graphics, grDevices, highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma, pairsD3, plyr, Rcpp (>= 0.12.14), recount, Rfast, R.utils, reshape2, shinyjs, stringr, stats, SummarizedExperiment, survival, tools, utils, XML, xtable, methods, org.Hs.eg.db LinkingTo: Rcpp Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi, spelling License: MIT + file LICENSE MD5sum: 77505df30ddedfb960c1c24164c03023 Package: PSICQUIC Version: 1.28.0 Depends: R (>= 3.2.0), methods, IRanges, biomaRt (>= 2.34.1), BiocGenerics, httr, plyr Imports: RCurl Suggests: org.Hs.eg.db License: Apache License 2.0 MD5sum: 275f866993cc226ece92cdc21e06b644 Package: psygenet2r Version: 1.22.5 Depends: R (>= 3.4) Imports: stringr, RCurl, igraph, ggplot2, reshape2, grid, parallel, biomaRt, BgeeDB, topGO, Biobase, labeling, GO.db Suggests: testthat, knitr License: MIT + file LICENSE MD5sum: d45803087012def4cfc54945fdf42902 Package: PubScore Version: 1.2.0 Depends: R (>= 4.0.0) Imports: ggplot2, igraph, ggrepel,rentrez, progress, graphics, dplyr, utils, methods, intergraph, network, sna Suggests: FCBF, plotly, SummarizedExperiment, SingleCellExperiment, knitr, rmarkdown, testthat (>= 2.1.0), BiocManager, biomaRt License: MIT + file LICENSE MD5sum: 47653196dac33ac9c168846283e6f9b5 Package: pulsedSilac Version: 1.4.0 Depends: R (>= 3.6.0) Imports: robustbase, methods, R.utils, taRifx, S4Vectors, SummarizedExperiment, ggplot2, ggridges, stats, utils, UpSetR, cowplot, grid, MuMIn Suggests: testthat (>= 2.1.0), knitr, rmarkdown, gridExtra License: GPL-3 MD5sum: 1ac0382307d346d9a15263cfc75ca4bb Package: puma Version: 3.32.0 Depends: R (>= 3.2.0), oligo (>= 1.32.0),graphics,grDevices, methods, stats, utils, mclust, oligoClasses Imports: Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses Suggests: pumadata, affydata, snow, limma, ROCR,annotate License: LGPL MD5sum: 857bd79abab43b3adb587c8218e31f18 Package: PureCN Version: 1.20.0 Depends: R (>= 3.5.0), DNAcopy, VariantAnnotation (>= 1.14.1) Imports: GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer, S4Vectors, data.table, grDevices, graphics, stats, utils, SummarizedExperiment, GenomeInfoDb, GenomicFeatures, Rsamtools, Biostrings, BiocGenerics, rtracklayer, ggplot2, gridExtra, futile.logger, VGAM, tools, methods, rhdf5, Matrix Suggests: BiocParallel, BiocStyle, PSCBS, TxDb.Hsapiens.UCSC.hg19.knownGene, copynumber, covr, knitr, optparse, org.Hs.eg.db, jsonlite, rmarkdown, testthat Enhances: genomicsdb License: Artistic-2.0 MD5sum: bf63a64e632a8fc2e482bfbacdaf9dbd Package: pvac Version: 1.38.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) MD5sum: cb19809a8fd02255c322c8646a95be64 Package: pvca Version: 1.30.0 Depends: R (>= 2.15.1) Imports: Matrix, Biobase, vsn, stats, lme4 Suggests: golubEsets License: LGPL (>= 2.0) MD5sum: d4163275c393d550b421059ab2528c60 Package: Pviz Version: 1.24.0 Depends: R(>= 3.0.0), Gviz(>= 1.7.10) Imports: biovizBase, Biostrings, GenomicRanges, IRanges, data.table, methods Suggests: knitr, pepDat License: Artistic-2.0 MD5sum: 1e386736f5143351a1088f0a636fc657 Package: PWMEnrich Version: 4.26.0 Depends: R (>= 3.5.0), methods, grid, BiocGenerics, Biostrings Imports: seqLogo, gdata, evd, S4Vectors Suggests: MotifDb, BSgenome, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr License: LGPL (>= 2) MD5sum: 6bdf786cb9ae746e00cc6e10e8da766e Package: pwOmics Version: 1.22.0 Depends: R (>= 3.2) Imports: data.table, rBiopaxParser, igraph, STRINGdb, graphics, gplots, Biobase, BiocGenerics, AnnotationDbi, biomaRt, AnnotationHub, GenomicRanges, graph, grDevices, stats, utils Suggests: ebdbNet, longitudinal, Mfuzz License: GPL (>= 2) MD5sum: 52deda4b9242c28f82ed3e3adccc81f9 Package: pwrEWAS Version: 1.4.0 Depends: shinyBS, foreach Imports: doParallel, abind, truncnorm, CpGassoc, shiny, ggplot2, parallel, shinyWidgets, BiocManager, doSNOW, limma, genefilter, stats, grDevices, methods, utils, graphics, pwrEWAS.data Suggests: knitr, RUnit, BiocGenerics, rmarkdown License: Artistic-2.0 MD5sum: 04d8c83939ec59005ea1286af4f669d7 Package: qckitfastq Version: 1.6.0 Imports: magrittr, ggplot2, dplyr, seqTools, zlibbioc, data.table, reshape2, grDevices, graphics, stats, utils, Rcpp, rlang, RSeqAn LinkingTo: Rcpp, RSeqAn Suggests: knitr, rmarkdown, kableExtra, testthat License: Artistic-2.0 MD5sum: 3e08b28ad06543da93926e73dc38e4c1 Package: qcmetrics Version: 1.28.0 Depends: R (>= 3.3) Imports: Biobase, methods, knitr, tools, Nozzle.R1, xtable, pander, S4Vectors Suggests: affy, MSnbase, ggplot2, lattice, yaqcaffy, MAQCsubsetAFX, RforProteomics, AnnotationDbi, mzR, hgu133plus2cdf, BiocStyle License: GPL-2 MD5sum: 04cd81d2e11bb2dd6b8a72e16943bd68 Package: QDNAseq Version: 1.26.0 Depends: R (>= 3.1.0) Imports: graphics, methods, stats, utils, Biobase (>= 2.18.0), CGHbase (>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0), GenomicRanges (>= 1.20), IRanges (>= 2.2), matrixStats (>= 0.54.0), R.utils (>= 2.9.0), Rsamtools (>= 1.20), future (>= 1.14.0), future.apply (>= 1.3.0) Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>= 0.6.20), GenomeInfoDb (>= 1.6.0), R.cache (>= 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mvtnorm, qtl, Rgraphviz Suggests: RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats License: GPL (>= 2) MD5sum: 130990f6515f2d39939ce53d576aee22 Package: qPLEXanalyzer Version: 1.8.2 Depends: R (>= 4.0), Biobase, MSnbase Imports: assertthat, BiocGenerics, Biostrings, dplyr (>= 1.0.0), ggdendro, ggplot2, graphics, grDevices, IRanges, limma, magrittr, preprocessCore, purrr, RColorBrewer, readr, rlang, scales, stats, stringr, tibble, tidyr, tidyselect, utils Suggests: gridExtra, knitr, qPLEXdata, testthat, UniProt.ws, vdiffr License: GPL-2 MD5sum: cd84bed829c0fa8593017e5b10a60844 Package: qrqc Version: 1.44.0 Depends: reshape, ggplot2, Biostrings, biovizBase, brew, xtable, testthat Imports: reshape, ggplot2, Biostrings, biovizBase, graphics, methods, plyr, stats LinkingTo: Rhtslib (>= 1.15.3) License: GPL (>= 2) MD5sum: e2d0abe13c83488f8a74676ffbc98d6a Package: qsea Version: 1.16.0 Depends: R (>= 3.5) Imports: Biostrings, graphics, gtools, methods, stats, utils, HMMcopy, rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges, limma, GenomeInfoDb, BiocGenerics, grDevices, zoo, BiocParallel, KernSmooth, MASS Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager License: GPL (>= 2) MD5sum: 12d3a7245845913cfc0f815f27314470 Package: qsmooth Version: 1.6.0 Depends: R (>= 4.0) Imports: SummarizedExperiment, utils, sva, stats, methods, graphics Suggests: bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat License: CC BY 4.0 MD5sum: ff3462df48792fb58a923def8e43936c Package: QSutils Version: 1.8.0 Depends: R (>= 3.5), Biostrings, BiocGenerics,methods Imports: ape, stats, psych Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: file LICENSE MD5sum: e2e39af256f2f893bbfff5f1e26f288b Package: Qtlizer Version: 1.4.0 Depends: R (>= 3.6.0) Imports: httr, curl, GenomicRanges, stringi Suggests: BiocStyle, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 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testthat License: GPL-2 Archs: x64 MD5sum: 98bcd0b9890ec4c2c7a44ffe74df5cdf Package: QuaternaryProd Version: 1.24.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.3), dplyr, yaml (>= 2.1.18) LinkingTo: Rcpp Suggests: knitr License: GPL (>= 3) MD5sum: efd8648a9e4864a6c5d6a85fc296b6af Package: QUBIC Version: 1.18.0 Depends: R (>= 3.1), biclust Imports: Rcpp (>= 0.11.0), methods, Matrix LinkingTo: Rcpp, RcppArmadillo Suggests: QUBICdata, qgraph, fields, knitr, rmarkdown Enhances: RColorBrewer License: CC BY-NC-ND 4.0 + file LICENSE MD5sum: 5c9f89cc1714f352f8ebc74af539c188 Package: qusage Version: 2.24.0 Depends: R (>= 2.10), limma (>= 3.14), methods Imports: utils, Biobase, nlme, emmeans, fftw License: GPL (>= 2) MD5sum: c1f59a0f8317136a13e8c2a6e0925959 Package: qvalue Version: 2.22.0 Depends: R(>= 2.10) Imports: splines, ggplot2, grid, reshape2 Suggests: knitr License: LGPL MD5sum: 27945d2115853963fbe9420e6bef353a Package: R3CPET Version: 1.22.0 Depends: R (>= 3.2), Rcpp (>= 0.10.4), methods Imports: methods, parallel, ggplot2, pheatmap, clValid, igraph, data.table, reshape2, Hmisc, RCurl, BiocGenerics, S4Vectors, IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8), ggbio LinkingTo: Rcpp Suggests: BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny, ChIPpeakAnno License: GPL (>= 2) MD5sum: b4d2644df7e312e44923ae776a55de81 Package: r3Cseq Version: 1.36.0 Depends: GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue Imports: methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf, RColorBrewer Suggests: BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Rnorvegicus.UCSC.rn5.masked License: GPL-3 MD5sum: bc2edbd6eae0c08271247255d4a5d1cd Package: R453Plus1Toolbox Version: 1.40.0 Depends: R (>= 2.12.0), methods, VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6), Biobase Imports: utils, grDevices, graphics, stats, tools, xtable, R2HTML, TeachingDemos, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector, GenomicRanges (>= 1.31.8), SummarizedExperiment, biomaRt, BSgenome (>= 1.47.3), Rsamtools, ShortRead (>= 1.37.1) Suggests: rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2 License: LGPL-3 MD5sum: 5de770566e5900a7abf9ae6d88a5fb50 Package: R4RNA Version: 1.18.0 Depends: R (>= 3.2.0), Biostrings (>= 2.38.0) License: GPL-3 MD5sum: 1361ecde604d7a885d845850404dd22b Package: RadioGx Version: 1.0.0 Depends: R (>= 4.0), CoreGx Imports: SummarizedExperiment, S4Vectors, Biobase, parallel, BiocParallel, RColorBrewer, caTools, magicaxis, methods, reshape2, scales, grDevices, graphics, stats, utils, assertthat, matrixStats, downloader Suggests: rmarkdown, BiocStyle, knitr, pander License: GPL-3 MD5sum: 0110cc666794a79fc93abcbd13069fe5 Package: RaggedExperiment Version: 1.14.2 Depends: R (>= 3.6.0), GenomicRanges (>= 1.37.17) Imports: BiocGenerics, 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Package: rCGH Version: 1.20.0 Depends: R (>= 3.4),methods,stats,utils,graphics Imports: plyr,DNAcopy,lattice,ggplot2,grid,shiny (>= 0.11.1), limma,affy,mclust,TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db,GenomicFeatures,GenomeInfoDb,GenomicRanges,AnnotationDbi, parallel,IRanges,grDevices,aCGH Suggests: BiocStyle, knitr, BiocGenerics, RUnit License: Artistic-2.0 MD5sum: 590742d99c0120b0d85d80be6c74212c Package: RchyOptimyx Version: 2.30.0 Depends: R (>= 2.10) Imports: Rgraphviz, sfsmisc, graphics, methods, graph, grDevices, flowType (>= 2.0.0) Suggests: flowCore License: Artistic-2.0 MD5sum: 941cf14eb4894fdd4b2375b66e5b864e Package: RcisTarget Version: 1.10.0 Depends: R (>= 3.4) Imports: AUCell (>= 1.1.6), BiocGenerics, data.table, feather, graphics, GSEABase, methods, R.utils, stats, SummarizedExperiment, utils Suggests: Biobase, BiocStyle, BiocParallel, doParallel, DT, tibble, foreach, igraph, knitr, 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rmarkdown, testthat, RNAmodR.Data License: Artistic-2.0 MD5sum: 644177505ef29e406f2b9fda53845674 Package: RNAmodR.AlkAnilineSeq Version: 1.4.0 Depends: R (>= 3.6), RNAmodR Imports: methods, S4Vectors, IRanges, BiocGenerics, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, Biostrings, RNAmodR.Data License: Artistic-2.0 MD5sum: 3ad66f6397f3a048d14031f155982581 Package: RNAmodR.ML Version: 1.4.0 Depends: R (>= 3.6), RNAmodR Imports: methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, stats, ranger Suggests: BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data, RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer, keras License: Artistic-2.0 MD5sum: a5156ed3ac12aa405f27a76f5d1e561d Package: RNAmodR.RiboMethSeq Version: 1.4.0 Depends: R (>= 3.6), RNAmodR Imports: methods, S4Vectors, BiocGenerics, IRanges, GenomicRanges, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat, rtracklayer, RNAmodR.Data License: Artistic-2.0 MD5sum: 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(>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25), GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr Imports: IRanges Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RefFreeEWAS, RnBeads.hg19, RnBeads.mm9, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, GLAD, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR License: GPL-3 MD5sum: cb93866f2a502c48a178db51cd33d972 Package: Rnits Version: 1.24.0 Depends: R (>= 3.6.0), Biobase, ggplot2, limma, methods Imports: affy, boot, impute, splines, graphics, qvalue, reshape2 Suggests: BiocStyle, knitr, GEOquery, stringr License: GPL-3 MD5sum: 886c435a96aaeb8e9a659bd40517810d Package: roar Version: 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DT, plotly, heatmaply, magrittr, utils, clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pf.plasmo.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db License: GPL-3 MD5sum: 1aed46ab7f911e71bae755decf9e0629 Package: Rsamtools Version: 2.6.0 Depends: methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8), Biostrings (>= 2.47.6) Imports: utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops, BiocParallel, stats LinkingTo: Rhtslib (>= 1.17.7), S4Vectors, IRanges, XVector, Biostrings Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle License: Artistic-2.0 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ShortRead Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer License: LGPL-3 MD5sum: 37614899d63848bda15836a2cccd5de5 Package: rSWeeP Version: 1.2.0 Depends: R (>= 4.0) Imports: pracma, stats Suggests: Biostrings, methods, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: d88a9361d1fdc0b9edd4f91eff66789a Package: RTCA Version: 1.42.0 Depends: methods,stats,graphics,Biobase,RColorBrewer, gtools Suggests: xtable License: LGPL-3 MD5sum: a215afb5694656ae86f66a3f8743ce20 Package: RTCGA Version: 1.20.0 Depends: R (>= 3.3.0) Imports: XML, assertthat, stringi, rvest, data.table, xml2, dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr, scales Suggests: devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, RTCGA.PANCAN12, magrittr, tidyr License: GPL-2 MD5sum: 37ede9f43d2c6f12463c6d30b01ff7fa Package: 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cc8cda135cd348169c41795265dca395 Package: rTRMui Version: 1.28.0 Imports: shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 0ac243ad9dd2b59eea5fcc4259b49af4 Package: RUVcorr Version: 1.22.0 Imports: corrplot, MASS, stats, lattice, grDevices, gridExtra, snowfall, psych, BiocParallel, grid, bladderbatch, reshape2, graphics Suggests: knitr, hgu133a2.db License: GPL-2 MD5sum: 001c2820b055a8bc50cb050992a84d1c Package: RUVnormalize Version: 1.24.0 Depends: R (>= 2.10.0) Imports: RUVnormalizeData, Biobase Enhances: spams License: GPL-3 MD5sum: b24e583c68fd40a907131ca45a99238e Package: RUVSeq Version: 1.24.0 Depends: Biobase, EDASeq (>= 1.99.1), edgeR Imports: methods, MASS Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 License: Artistic-2.0 MD5sum: eedfd5767f360226e7fe81c5ee92654f Package: RVS Version: 1.12.0 Depends: R (>= 3.5.0) Imports: GENLIB, gRain, snpStats, kinship2, methods, stats, utils Suggests: knitr, testthat, rmarkdown, BiocStyle, 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sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db License: Artistic-2.0 MD5sum: 85a12ac98c2716496a9353002b6c308f Package: SamSPECTRAL Version: 1.44.0 Depends: R (>= 3.3.3) Imports: methods License: GPL (>= 2) MD5sum: f864b8544853289c59931f894d007810 Package: sangeranalyseR Version: 1.0.0 Depends: R (>= 3.6.0), 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: 247a9910faf9f52395fecf9095b44cc3 Package: sangerseqR Version: 1.26.0 Depends: R (>= 3.0.2), Biostrings Imports: methods, shiny Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 MD5sum: 3fe0930bcf5456b537a872e0a9a843ca Package: sarks Version: 1.2.0 Depends: R (>= 4.0) Imports: rJava, Biostrings, IRanges, utils, stats, cluster, binom 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Depends: R (>= 4.0) Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, SingleCellExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost, stats, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, bluster License: GPL-3 MD5sum: 0cdccd2ef3f99447444fb2caf8274a10 Package: scDD Version: 1.14.0 Depends: R (>= 3.4) Imports: fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm, SingleCellExperiment, SummarizedExperiment, grDevices, graphics, stats, S4Vectors, scran Suggests: BiocStyle, knitr, gridExtra License: GPL-2 MD5sum: 8f4d3bcd68b769f5be89eb8c7799e74d Package: scde Version: 2.18.0 Depends: R (>= 3.0.0), flexmix Imports: Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook, rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods, nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown License: GPL-2 MD5sum: 3deb6b4e700674d5ad960293f8c32956 Package: scds Version: 1.6.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot License: MIT + file LICENSE MD5sum: 71e737d35dcc4226c5e013ceb2adb963 Package: SCFA Version: 1.0.0 Depends: R (>= 4.0) Imports: matrixStats, keras, tensorflow, BiocParallel, igraph, Matrix, cluster, clusterCrit, psych, glmnet, RhpcBLASctl, stats, utils, methods, survival Suggests: knitr License: LGPL MD5sum: 840193433a948f778abd163a6cb00da8 Package: scFeatureFilter Version: 1.10.0 Depends: R (>= 3.6) Imports: dplyr (>= 0.7.3), ggplot2 (>= 2.1.0), magrittr (>= 1.5), rlang (>= 0.1.2), tibble (>= 1.3.4), stats, methods Suggests: testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot License: MIT + file LICENSE MD5sum: 73fb0e0a347de5a928b3cc5182fa567a Package: scGPS Version: 1.4.0 Depends: R (>= 3.6), SummarizedExperiment, dynamicTreeCut, SingleCellExperiment Imports: glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1), fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel, grDevices, graphics, stats, utils, DESeq, locfit LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE License: GPL-3 MD5sum: 7c6c0137b89e6b41d52ce3442c631a07 Package: schex Version: 1.4.0 Depends: SingleCellExperiment (>= 1.7.4), Seurat, ggplot2 (>= 3.2.1), shiny Imports: hexbin, stats, methods, cluster, dplyr, entropy, ggforce, scales, grid, concaveman Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran License: GPL-3 MD5sum: c13c562b1ed0873e72a2f447c5a3a5a3 Package: scHOT Version: 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LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown License: GPL-3 MD5sum: ea1963151dc22976d0a13c4b51fb9886 Package: scMerge Version: 1.6.0 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: 4d7fb99d30c0111cf0b07e3c193c728d Package: scmeth Version: 1.10.0 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: 61fc85c27132632eb17b3cbce1ef365f Package: SCnorm Version: 1.12.1 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: 16fdd3a5ce823fc7d2a3fbfd6ce2f079 Package: scone Version: 1.14.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, BatchJobs License: Artistic-2.0 MD5sum: 751a8e6abeba99d22e110d82d024dfbc Package: Sconify Version: 1.10.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 1e32f9a472af7b95424f0345b8291751 Package: SCOPE Version: 1.2.0 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: 69be6a66703dd3924c0d6aa80456fe1f Package: scoreInvHap Version: 1.12.1 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: 035e1436cc7f6893e3b854b445c65661 Package: scp Version: 1.0.0 Depends: R (>= 4.0), QFeatures Imports: methods, stats, utils, SingleCellExperiment, SummarizedExperiment, MultiAssayExperiment, S4Vectors, dplyr, magrittr, rlang Suggests: testthat, knitr, BiocStyle, rmarkdown, patchwork, ggplot2, matrixStats, impute, scater, sva, uwot License: Artistic-2.0 MD5sum: 3683843b8df60c9158afd5a908605728 Package: scPCA Version: 1.4.0 Depends: R (>= 3.6) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca, cluster, kernlab, origami, RSpectra, coop, Matrix, DelayedArray Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark License: MIT + file LICENSE MD5sum: 66a83b83f664082f5d473cf2dc0d72de Package: scPipe Version: 1.12.0 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: b10ae8e1846151b893c3cf49a4c5977c Package: scran Version: 1.18.7 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, scuttle, edgeR, limma, BiocNeighbors, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, bluster, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq, dynamicTreeCut, DESeq2, monocle, Biobase, pheatmap, scater License: GPL-3 MD5sum: 060b38213dad91f8104c22f62294526f Package: scRecover Version: 1.6.0 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: e778c2b450b52b3a41bcde138f84543c Package: scRepertoire Version: 1.0.0 Depends: dplyr, ggalluvial, ggplot2, reshape2, R (>= 4.0) Imports: Biostrings, RColorBrewer, colorRamps, ggdendro, ggfittext, stringr, vegan, powerTCR, SummarizedExperiment, SingleCellExperiment, Seurat Suggests: knitr, rmarkdown, BiocStyle, scater, circlize, scales License: Apache License 2.0 MD5sum: c5c5045d314e2e187699a14b2c8a8b35 Package: scruff Version: 1.8.3 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: c040c2ab666fc21013328a9a07dfa7dd Package: scry Version: 1.2.0 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: 84b768fcce936a63c55ebc46017534cb Package: scTensor Version: 2.0.0 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: 477460fc731703156e11cf86cfd04f6e Package: scTGIF Version: 1.4.0 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: 6309fb87c4b1c99c428ef58b4f35f0cd Package: scTHI Version: 1.2.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown License: GPL-2 MD5sum: 29abc8fc96d93ec9bced92ca38f9606b Package: scuttle Version: 1.0.4 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 License: GPL-3 MD5sum: cd88a2eb0a07af2980a1a574de12c3ea Package: SDAMS Version: 1.10.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: 121ea3315f950ce8d8486cff92b6a488 Package: segmentSeq Version: 2.24.0 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: 9d7bd8737deb4a42b1bf5979a7069f96 Package: selectKSigs Version: 1.2.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: 3092456c633f84b8cf502badea4eb8e7 Package: SELEX Version: 1.22.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: f9a11d5e37a04795688b95e0a1c92618 Package: SemDist Version: 1.24.0 Depends: R (>= 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VariantAnnotation License: GPL-3 MD5sum: 37f56dc52254baac4346a1dda4c9221a Package: seqbias Version: 1.38.0 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: 27725424ccd7431a7d5761967cbbeeac Package: seqCAT Version: 1.12.0 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE MD5sum: 4dcd7c0792cc6cbc30b5d381618da5cc Package: seqCNA Version: 1.36.0 Depends: R (>= 3.0), GLAD (>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot (>= 0.99), methods License: GPL-3 MD5sum: 0f0f9231e3539cf80ddbdeef85126ad2 Package: seqcombo Version: 1.12.0 Depends: R (>= 3.4.0) Imports: Biostrings, cowplot, dplyr, ggplot2, grid, igraph, magrittr, methods, rvcheck, utils Suggests: emojifont, knitr, prettydoc, tibble License: Artistic-2.0 MD5sum: bfe92e8266f16508390a85e2279226f9 Package: SeqGate Version: 1.0.1 Depends: S4Vectors, SummarizedExperiment, GenomicRanges Imports: stats, methods, BiocManager Suggests: testthat, edgeR, BiocStyle, knitr, rmarkdown License: GPL (>= 2.0) MD5sum: bd4b25412d0d05669310323418ddc1d6 Package: SeqGSEA Version: 1.30.0 Depends: Biobase, doParallel, DESeq Imports: methods, biomaRt Suggests: easyRNASeq, GenomicRanges License: GPL (>= 3) MD5sum: 6cedd03e9bc1aebf7b4042f7742031e6 Package: seqLogo Version: 1.56.0 Depends: methods, grid Imports: stats4, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: LGPL (>= 2) MD5sum: fe5cb9c4282a4e76dfa2c22383d48687 Package: seqPattern Version: 1.22.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 MD5sum: 4e8b3df8960bd64926a0095af0d1112a Package: seqplots Version: 1.27.0 Depends: R (>= 3.2.0) Imports: methods, IRanges, BSgenome, digest, rtracklayer, GenomicRanges, Biostrings, shiny (>= 0.13.0), DBI, RSQLite, plotrix, fields, grid, kohonen, parallel, GenomeInfoDb, class, S4Vectors, ggplot2, reshape2, gridExtra, jsonlite, DT (>= 0.1.0), RColorBrewer, Rsamtools, GenomicAlignments, BiocManager Suggests: testthat, BiocStyle, knitr, rmarkdown, covr License: GPL-3 MD5sum: ae6d1e2ac84f9ab792aa219fbfdffb97 Package: seqsetvis Version: 1.10.0 Depends: R (>= 3.6), ggplot2 Imports: data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, IRanges, limma, methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, stats Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, cowplot, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 269ce814f8af53fe558c75bca40a4c05 Package: SeqSQC Version: 1.12.0 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: 88d0508f27c6b7129d5b320832607bdd Package: seqTools Version: 1.24.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 6718f5b4e2ea60dc05e9458c37dacd7d Package: SeqVarTools Version: 1.28.1 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: d8ba29821f146eea225982aff7d7b95c Package: sesame Version: 1.8.12 Depends: R (>= 4.0), sesameData, methods Imports: BiocParallel, grDevices, utils, stringr, tibble, illuminaio, MASS, GenomicRanges, IRanges, grid, preprocessCore, S4Vectors, randomForest, wheatmap, ggplot2, 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: 9387f675a30acead09b6b8ccacb79e2c Package: SEtools Version: 1.4.0 Depends: R (>= 4.0) Imports: S4Vectors, SummarizedExperiment, data.table, pheatmap, seriation, ComplexHeatmap, circlize, methods, BiocParallel, randomcoloR, edgeR, openxlsx Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL MD5sum: 254d45b97d664b6bd82dedf9ae2b9a56 Package: sevenbridges Version: 1.20.1 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: c372eb414bc4e8f60cfd1dcf8e6bb37f Package: sevenC Version: 1.10.0 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: fa64fce639af7cb170e96c64bd2c48f8 Package: SGSeq Version: 1.24.0 Depends: R (>= 4.0), IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), Rsamtools (>= 1.31.2), SummarizedExperiment, methods Imports: AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>= 2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>= 1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19), grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7), stats Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown License: Artistic-2.0 MD5sum: 9c6e716dc24f1012705841f3200c065a Package: SharedObject Version: 1.4.0 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, Rcpp Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: f6061380dc189309f93fec4200e664dc Package: shinyMethyl Version: 1.26.0 Depends: methods, BiocGenerics (>= 0.3.2), shiny (>= 0.13.2), minfi (>= 1.18.2), IlluminaHumanMethylation450kmanifest, matrixStats, R (>= 3.0.0) Imports: RColorBrewer Suggests: shinyMethylData, minfiData, BiocStyle, RUnit, digest, knitr License: Artistic-2.0 MD5sum: 556ea616d0ced277c3e3359949c6ebbc Package: ShortRead Version: 1.48.0 Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), hwriter, methods, zlibbioc, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi License: Artistic-2.0 MD5sum: f2426872677ee403c9b99f0199a434b5 Package: SIAMCAT Version: 1.10.0 Depends: R (>= 3.6.0), mlr, phyloseq Imports: beanplot, glmnet, graphics, grDevices, grid, gridBase, gridExtra, LiblineaR, matrixStats, methods, ParamHelpers, pROC, PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo, progress, corrplot Suggests: BiocStyle, optparse, testthat, knitr, rmarkdown License: GPL-3 MD5sum: a5d84a960c232b34f3b3c1c66c07fa3e Package: SICtools Version: 1.20.0 Depends: R (>= 3.0.0), methods, Rsamtools (>= 1.18.1), doParallel (>= 1.0.8), Biostrings (>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges (>= 1.22.4), IRanges (>= 2.4.8) Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 587b1ea151033ec957dbdf4f48039e6f Package: SigCheck Version: 2.22.0 Depends: R (>= 3.2.0), MLInterfaces, Biobase, e1071, BiocParallel, survival Imports: graphics, stats, utils, methods Suggests: BiocStyle, breastCancerNKI, qusage License: Artistic-2.0 MD5sum: 5d6e9100cc1c4eb992a065d710905a87 Package: sigFeature Version: 1.8.0 Depends: R (>= 3.5.0) Imports: biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer, Matrix, SparseM, graphics, stats, utils, SummarizedExperiment, BiocParallel, methods Suggests: RUnit, BiocGenerics, knitr License: GPL MD5sum: b47111ab7f1efcc458b4b3d4b7fae885 Package: SigFuge Version: 1.28.0 Depends: R (>= 3.1.1), GenomicRanges Imports: ggplot2, matlab, reshape, sigclust Suggests: org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle License: GPL-3 MD5sum: cd500c573c7a02d54fcaee71ad3c15a4 Package: siggenes Version: 1.64.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: 953c65dfe3540c0a6b1b00bd7073a316 Package: sights Version: 1.16.0 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: d26d16a54afe66c082c19ed6bd9cae08 Package: signatureSearch Version: 1.4.6 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 LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, org.Hs.eg.db License: Artistic-2.0 MD5sum: ef776371db8bfccab694e274d0e0f41a Package: signeR Version: 1.16.0 Depends: VariantAnnotation, NMF Imports: BiocGenerics, Biostrings, class, graphics, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMR LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: 8b0e52a471bbfbcd59d342259ad335c3 Package: sigPathway Version: 1.58.0 Depends: R (>= 2.10) Suggests: hgu133a.db (>= 1.10.0), XML (>= 1.6-3), AnnotationDbi (>= 1.3.12) License: GPL-2 MD5sum: f645cd59f34347464d1d0f35b6c324b6 Package: SigsPack Version: 1.4.0 Depends: R (>= 3.6) Imports: quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0), VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb, GenomicRanges, rtracklayer, SummarizedExperiment, graphics, stats, utils Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 84f9971fd525d12397d8640b13ce617d Package: sigsquared Version: 1.22.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: d828817ab0efe76bc166c768b507cffe Package: SIM Version: 1.60.0 Depends: R (>= 3.5), quantreg Imports: graphics, stats, globaltest, quantsmooth Suggests: biomaRt, RColorBrewer License: GPL (>= 2) MD5sum: cf8b3a433ca400f2a22b8c68af1c14a7 Package: SIMAT Version: 1.22.0 Depends: R (>= 3.5.0), Rcpp (>= 0.11.3) Imports: mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: ccf061ad7660cb0c2650310d4d732e03 Package: SimBindProfiles Version: 1.28.0 Depends: R (>= 2.10), methods, Ringo Imports: limma, mclust, Biobase License: GPL-3 MD5sum: 476e316a6dc3d66abe91e6546cc67ebc Package: SIMD Version: 1.8.0 Depends: R (>= 3.5.0) Imports: edgeR, statmod, methylMnM, stats, utils Suggests: BiocStyle, knitr,rmarkdown License: GPL-3 MD5sum: addf72145861807a20ec909e922eec70 Package: SimFFPE Version: 1.2.0 Depends: Biostrings Imports: dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods Suggests: BiocStyle License: LGPL-3 MD5sum: 3f406ec4e2f15e8a413b0cff5513a751 Package: similaRpeak Version: 1.22.0 Depends: R6 (>= 2.0) Imports: stats Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 9e25d9e83cf69305bf74235189fe0f0f Package: SIMLR Version: 1.16.0 Depends: R (>= 4.0.0), Imports: parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra LinkingTo: Rcpp Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph License: file LICENSE MD5sum: ed2cd492d51adf8a4706a8df5d9ba3fc Package: simpleaffy Version: 2.66.0 Depends: R (>= 2.0.0), methods, utils, grDevices, graphics, stats, BiocGenerics (>= 0.1.12), Biobase, affy (>= 1.33.6), genefilter, gcrma Imports: methods, utils, grDevices, graphics, stats, BiocGenerics, Biobase, affy, genefilter, gcrma License: GPL (>= 2) MD5sum: 7191c41cc6a7aa765049d131d1311adf Package: simplifyEnrichment Version: 1.0.0 Depends: R (>= 3.6.0), BiocGenerics, grid Imports: GOSemSim, ComplexHeatmap (>= 2.5.4), circlize, GetoptLong, digest, tm, GO.db, org.Hs.eg.db, AnnotationDbi, slam, methods, clue, grDevices, graphics, stats, utils, proxyC, Matrix, cluster (>= 1.14.2) Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, clusterProfiler, msigdbr, DOSE, DO.db, reactome.db, flexclust, BiocManager License: MIT + file LICENSE MD5sum: 9e251b5f4e5a4c38b49a46b35ba787aa Package: simulatorZ Version: 1.24.0 Depends: R (>= 3.5), Biobase, SummarizedExperiment, survival, CoxBoost, BiocGenerics Imports: graphics, stats, gbm, Hmisc, GenomicRanges, methods Suggests: RUnit, BiocStyle, curatedOvarianData, parathyroidSE License: Artistic-2.0 MD5sum: 3baffd5da68f074865ab55f8d8a86eda Package: sincell Version: 1.22.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: 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BiocStyle, BiocGenerics, SingleCellExperiment, scuttle, scater, scran, scRNAseq, ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex License: GPL-3 + file LICENSE MD5sum: e1e581e28b6ac8e52b8560395c57e718 Package: singscore Version: 1.10.0 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: cdfc98ce4a04e6c5a7d0f22b1f3f2016 Package: SISPA Version: 1.20.0 Depends: R (>= 3.5),genefilter,GSVA,changepoint Imports: data.table, plyr, ggplot2 Suggests: knitr License: GPL-2 MD5sum: f1c6f75a5b97a8ddc281057ca511cad0 Package: sitePath Version: 1.6.6 Depends: R (>= 4.0.0) Imports: RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree, graphics, grDevices, gridExtra, methods, parallel, seqinr, stats, tidytree, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: e6aaf22d12f057c8157df500bde50cec Package: sizepower Version: 1.60.0 Depends: stats License: LGPL MD5sum: 7f2d402eeafb8954b857a635a69d896e Package: skewr Version: 1.22.0 Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports: minfi, S4Vectors (>= 0.19.1), RColorBrewer Suggests: GEOquery, knitr, minfiData License: GPL-2 MD5sum: 2fa4986eba0c1847c17e218dcf3a023b Package: slalom Version: 1.12.0 Depends: R (>= 3.4) Imports: Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase, methods, rsvd, SingleCellExperiment, SummarizedExperiment, stats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: knitr, rhdf5, scater, testthat License: GPL-2 MD5sum: aa87e8d8335175808cd6a31f39fe8cb4 Package: SLGI Version: 1.50.0 Depends: R (>= 2.10), ScISI, lattice Imports: AnnotationDbi, Biobase, GO.db, ScISI, graphics, lattice, methods, stats, BiocGenerics Suggests: GO.db, org.Sc.sgd.db License: 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testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva License: MIT + file LICENSE MD5sum: 987e133f0301b6b5148467261ec9749b Package: SpacePAC Version: 1.28.0 Depends: R(>= 2.15),iPAC Suggests: RUnit, BiocGenerics, rgl License: GPL-2 MD5sum: 4f300acae6323a5bdf111b533869d6b7 Package: Spaniel Version: 1.4.0 Depends: R (>= 3.6), Seurat, SingleCellExperiment, SummarizedExperiment, dplyr Imports: methods, ggplot2, scater (>= 1.13.27), shiny, jpeg, magrittr, utils, S4Vectors Suggests: knitr, rmarkdown, testthat, devtools License: MIT + file LICENSE MD5sum: 00581fb2e35203b3634d94a8d1ada91e Package: sparseDOSSA Version: 1.14.0 Imports: stats, utils, optparse, MASS, tmvtnorm (>= 1.4.10), MCMCpack Suggests: knitr, BiocStyle, BiocGenerics, rmarkdown License: MIT + file LICENSE MD5sum: 7afcbd8dc20be8e04b16c55486ea245b Package: sparseMatrixStats Version: 1.2.1 Depends: MatrixGenerics Imports: Rcpp, Matrix, matrixStats, methods LinkingTo: 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spatialHeatmap Version: 1.0.0 Imports: av, DESeq2, edgeR, WGCNA, flashClust, htmlwidgets, genefilter, ggplot2, ggdendro, grImport, grid, gridExtra, gplots, igraph, rsvg, shiny, dynamicTreeCut, grDevices, graphics, ggplotify, plotly, rols, stats, SummarizedExperiment, shinydashboard, utils, visNetwork, methods, xml2, yaml Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, data.table, ExpressionAtlas, DT, reshape2, Biobase, GEOquery, shinyWidgets License: Artistic-2.0 MD5sum: fd576c02a86f8b824ff6f37a7c35339a Package: specL Version: 1.24.0 Depends: R (>= 3.6), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.5), RSQLite (>= 1.1), seqinr (>= 3.3) Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) License: GPL-3 MD5sum: 8a2312407a6a45a7c4434f2d08ae2446 Package: SpeCond Version: 1.44.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) MD5sum: 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TCGAbiolinksGUI.data, readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1) Suggests: jpeg, png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame, pathview, clusterProfiler, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph, supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid License: GPL (>= 3) MD5sum: bb8695d9137d166837624c6f9c216bb2 Package: TCGAbiolinksGUI Version: 1.16.0 Depends: R (>= 3.3.1), shinydashboard (>= 0.5.3), TCGAbiolinksGUI.data Imports: shiny (>= 0.14.1), downloader (>= 0.4), grid, DT, plotly, readr, maftools, stringr (>= 1.1.0), SummarizedExperiment, ggrepel, data.table, caret, shinyFiles (>= 0.6.2), ggplot2 (>= 2.1.0), pathview, ELMER (>= 2.0.0), clusterProfiler, parallel, TCGAbiolinks (>= 2.5.5), shinyjs (>= 0.7), colourpicker, sesame, shinyBS (>= 0.61) Suggests: testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2, BiocStyle, animation, pander License: GPL (>= 3) MD5sum: 10249190443d28085cd12a51d289f22a Package: TCGAutils Version: 1.10.1 Depends: R (>= 4.0.0) Imports: AnnotationDbi, BiocGenerics, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment (>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2 Suggests: BiocFileCache, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: df4f3d3c06adffa9c0a82936435daed5 Package: TCseq Version: 1.14.0 Depends: R (>= 3.4) Imports: edgeR, BiocGenerics, reshape2, GenomicRanges, IRanges, SummarizedExperiment, GenomicAlignments, Rsamtools, e1071, cluster, ggplot2, grid, grDevices, stats, utils, methods, locfit Suggests: testthat License: GPL (>= 2) MD5sum: 7a0bcda5b9a0005afe62dfd9749e932d Package: TDARACNE Version: 1.40.0 Depends: GenKern, Rgraphviz, Biobase License: GPL-2 MD5sum: eb6511fd4b0fdea650e2cbfae46ab3ac Package: tenXplore Version: 1.12.0 Depends: R (>= 3.4), shiny, restfulSE (>= 0.99.12) Imports: methods, ontoProc (>= 0.99.7), SummarizedExperiment, AnnotationDbi, matrixStats, org.Mm.eg.db, stats, utils Suggests: org.Hs.eg.db, testthat, knitr License: Artistic-2.0 MD5sum: 48ad26b6098a7cc961b3c6f7ab667b00 Package: TEQC Version: 4.12.0 Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5), Rsamtools, hwriter Imports: Biobase (>= 2.15.1) License: GPL (>= 2) MD5sum: a3ab6589bd2182550f7e0fffee143270 Package: ternarynet Version: 1.34.0 Depends: R (>= 2.10.0), methods Imports: utils, igraph License: GPL (>= 2) MD5sum: a5f78b7b2713cfc63e5fcb569254c136 Package: TFARM Version: 1.12.0 Depends: R (>= 3.4) Imports: arules, fields, GenomicRanges, graphics, stringr, methods, stats, gplots Suggests: BiocStyle, knitr, plyr License: Artistic-2.0 MD5sum: 77f98d607a5bf472d1c0a65e6f845755 Package: TFBSTools Version: 1.28.0 Depends: R (>= 3.2.2) Imports: Biobase(>= 2.28), Biostrings(>= 2.36.4), BiocGenerics(>= 0.14.0), BiocParallel(>= 1.2.21), BSgenome(>= 1.36.3), caTools(>= 1.17.1), CNEr(>= 1.4.0), DirichletMultinomial(>= 1.10.0), GenomeInfoDb(>= 1.6.1), GenomicRanges(>= 1.20.6), gtools(>= 3.5.0), grid, IRanges(>= 2.2.7), methods, DBI (>= 0.6), RSQLite(>= 1.0.0), rtracklayer(>= 1.28.10), seqLogo(>= 1.34.0), S4Vectors(>= 0.9.25), TFMPvalue(>= 0.0.5), XML(>= 3.98-1.3), XVector(>= 0.8.0), parallel Suggests: BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr(>= 1.11), testthat, JASPAR2016(>= 1.0.0), JASPAR2018(>= 1.0.0) License: GPL-2 MD5sum: e302aac1259b59d6514456511b1decd0 Package: TFEA.ChIP Version: 1.10.0 Depends: R (>= 3.3) Imports: GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices, dplyr, stats, utils, R.utils, methods, org.Hs.eg.db Suggests: knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, GSEABase, DESeq2, BiocGenerics, ggrepel, rcompanion, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 224b80fdd62d47944ca4040ae9b7dfb8 Package: TFHAZ Version: 1.12.0 Depends: R(>= 3.4) Imports: GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 619e1049dd867a4a912828fc8aa3bdef Package: TFutils Version: 1.10.1 Depends: R (>= 3.5.0) Imports: methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase, rjson, BiocFileCache, DT, httr, readxl Suggests: knitr, data.table, testthat, AnnotationDbi, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, Rsamtools, S4Vectors, org.Hs.eg.db, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR, ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer License: Artistic-2.0 MD5sum: 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GGally, Matrix, uwot, celldex, dittoSeq License: GPL-3 MD5sum: 3df2c6af3eb9dc33d2f9b836ff639ad5 Package: tidySummarizedExperiment Version: 1.0.0 Depends: R (>= 4.0.0), SummarizedExperiment Imports: tibble (>= 3.0.4), dplyr, magrittr, tidyr, ggplot2, rlang, purrr, lifecycle, methods, plotly, utils, S4Vectors, tidyselect, ellipsis, pillar, stringr, cli, fansi Suggests: BiocStyle, testthat, knitr, markdown License: GPL-3 MD5sum: 8c4283900f092acc5ef0eb3f568e166e Package: tigre Version: 1.44.0 Depends: R (>= 2.11.0), BiocGenerics, Biobase Imports: methods, AnnotationDbi, gplots, graphics, grDevices, stats, utils, annotate, DBI, RSQLite Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager License: AGPL-3 MD5sum: c66e41f85c15f91314608993bff5ac4c Package: TileDBArray Version: 1.0.0 Depends: DelayedArray (>= 0.15.16) Imports: methods, Rcpp, tiledb, S4Vectors LinkingTo: Rcpp Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat License: MIT + file LICENSE MD5sum: 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GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, plotrix, Rgraphviz, InteractionSet, graph, utils Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools License: GPL (>= 2) MD5sum: e23f39fb82111b27afe9706942d9af83 Package: tradeSeq Version: 1.4.0 Depends: R (>= 3.6) Imports: mgcv, edgeR, SingleCellExperiment, SummarizedExperiment, slingshot, magrittr, RColorBrewer, BiocParallel, Biobase, pbapply, ggplot2, princurve, methods, monocle, igraph, S4Vectors, tibble, Matrix, viridis, matrixStats Suggests: knitr, rmarkdown, testthat, covr, clusterExperiment License: MIT + file LICENSE MD5sum: 2b416c12be68f5fbd209517e2d1f1a37 Package: transcriptogramer Version: 1.12.0 Depends: R (>= 3.4), methods Imports: biomaRt, data.table, doSNOW, foreach, ggplot2, graphics, grDevices, igraph, limma, parallel, progress, RedeR, snow, stats, tidyr, topGO Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: dae2338b899c5b985bd6f7262ce2d801 Package: transcriptR Version: 1.18.0 Depends: methods, R (>= 3.3) Imports: BiocGenerics, caret, chipseq, e1071, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2, Rsamtools, rtracklayer, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat License: GPL-3 MD5sum: 8ecf4bf8383dc016e6368704a3589452 Package: transite Version: 1.8.0 Depends: R (>= 3.5) Imports: BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0), ggseqlogo (>= 0.1), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils LinkingTo: Rcpp (>= 1.0.4.8) Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: b1cc250d7c72b588e5943414d168b1fe Package: tRanslatome Version: 1.28.0 Depends: R (>= 2.15.0), methods, limma, sigPathway, anota, DESeq, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 MD5sum: 319be30d9d72a09a1dd6b5f583cfcd02 Package: transomics2cytoscape Version: 1.0.0 Imports: RCy3, KEGGREST, dplyr Suggests: testthat, roxygen2, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 8afd17391628f014e69507afd2d3f951 Package: TransView Version: 1.34.0 Depends: methods, GenomicRanges Imports: BiocGenerics, S4Vectors (>= 0.9.25), IRanges, zlibbioc, gplots LinkingTo: Rhtslib (>= 1.15.3) Suggests: RUnit, pasillaBamSubset, BiocManager License: GPL-3 MD5sum: 6454da2774dda1fc101c6ee50e8d61ad Package: traseR Version: 1.20.0 Depends: R (>= 3.2.0),GenomicRanges,IRanges,BSgenome.Hsapiens.UCSC.hg19 Suggests: BiocStyle,RUnit, BiocGenerics License: GPL MD5sum: b4837437164bebe2a42d812451669f30 Package: TreeAndLeaf Version: 1.2.0 Depends: R (>= 4.0) Imports: RedeR, igraph, ape, methods Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, RColorBrewer, geneplast License: Artistic-2.0 MD5sum: 3f288553e1688989186667f132908b12 Package: treeio Version: 1.14.4 Depends: R (>= 3.6.0) Imports: ape, dplyr, jsonlite, magrittr, methods, rlang, tibble, tidytree (>= 0.3.0), utils Suggests: Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown, phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml License: Artistic-2.0 MD5sum: 3d8af78b55f4c3b2c19ab937ec8f22da Package: TreeSummarizedExperiment Version: 1.6.2 Depends: R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18) Imports: methods, BiocGenerics, utils, ape, rlang, dplyr, SummarizedExperiment Suggests: ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 72782f9ba4ce938dd754f309f5892a5c Package: trena Version: 1.12.1 Depends: R (>= 3.5.0), utils, glmnet (>= 2.0.3), MotifDb (>= 1.19.17) Imports: RSQLite, RMySQL, lassopv, randomForest, vbsr, xgboost, BiocParallel, RPostgreSQL, methods, DBI, BSgenome, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, SNPlocs.Hsapiens.dbSNP150.GRCh38, org.Hs.eg.db, Biostrings, GenomicRanges, biomaRt, AnnotationDbi Suggests: RUnit, plyr, knitr, BiocGenerics, rmarkdown, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Athaliana.TAIR.TAIR9 License: GPL-3 MD5sum: 2da42ffeda4aa2460d1df44b6ae705c2 Package: Trendy Version: 1.12.0 Depends: R (>= 3.4) Imports: stats, utils, graphics, grDevices, segmented, gplots, parallel, magrittr, BiocParallel, DT, S4Vectors, SummarizedExperiment, methods, shiny, shinyFiles Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL-3 MD5sum: 2bcd34751fbe270b0f6db092eef99e55 Package: trigger Version: 1.36.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 MD5sum: ed5c48d7b2ae9b682323e01fae531177 Package: trio Version: 3.28.0 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1) Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 MD5sum: 22e4f9b013d00e63fa40d574107da9ba Package: triplex Version: 1.30.0 Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27), XVector (>= 0.11.6), Biostrings (>= 2.39.10) Imports: methods, grid, GenomicRanges LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer License: BSD_2_clause + file LICENSE MD5sum: 4d92e597e0bd2133457c3b277cc9d3a9 Package: tRNA Version: 1.8.0 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE MD5sum: af4b79d46e188b75431e443cb8d26061 Package: tRNAdbImport Version: 1.8.0 Depends: R (>= 3.5), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, BiocGenerics, stringr, xml2, S4Vectors, methods, httr, IRanges, utils Suggests: knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE MD5sum: b4a3d0576d21f5cbed67399dab680296 Package: tRNAscanImport Version: 1.10.0 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, stringr, BiocGenerics, Biostrings, Structstrings, S4Vectors, IRanges, XVector, GenomeInfoDb, rtracklayer, BSgenome, Rsamtools Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 + file LICENSE MD5sum: fb4d6d99eff8141d1c5d3ca05238dc7d Package: TRONCO Version: 2.22.0 Depends: R (>= 4.0.0), Imports: bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, cgdsr, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways License: GPL-3 MD5sum: dd1adf9e79e53b8e14c41f427d8a4482 Package: TSCAN Version: 1.28.0 Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, SingleCellExperiment, DelayedArray, S4Vectors Suggests: knitr, testthat, beachmat, scuttle, scran, BiocParallel, BiocNeighbors, batchelor License: GPL (>= 2) MD5sum: 7b19c443c416fb1759993009797d9bc2 Package: tscR Version: 1.2.0 Depends: R (>= 4.0), dplyr Imports: gridExtra, methods, dtw, class, kmlShape, graphics, cluster, RColorBrewer, grDevices, knitr, rmarkdown, prettydoc, grid, ggplot2, latex2exp, stats, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors Suggests: testthat License: GPL (>= 2) MD5sum: c2e6f3c3605d6cbd4643287125c596ce Package: tspair Version: 1.48.0 Depends: R (>= 2.10), Biobase (>= 2.4.0) License: GPL-2 MD5sum: 317b25ddd4cb2e8b4c32871afcefc2a1 Package: TSRchitect Version: 1.16.0 Depends: R (>= 3.5) Imports: AnnotationHub, BiocGenerics, BiocParallel, dplyr, GenomicAlignments, GenomeInfoDb, GenomicRanges, gtools, IRanges, methods, readxl, Rsamtools (>= 1.14.3), rtracklayer, S4Vectors, SummarizedExperiment, tools, utils Suggests: ENCODExplorer, ggplot2, knitr, rmarkdown License: GPL-3 MD5sum: 029a21141ce798ff93af73a27a96b04c Package: TTMap Version: 1.12.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 MD5sum: 3b475927f4d7282fb820fc2a9ae0bdc8 Package: TurboNorm Version: 1.38.0 Depends: R (>= 2.12.0), convert, limma (>= 1.7.0), marray Imports: stats, grDevices, affy, lattice Suggests: BiocStyle, affydata License: LGPL MD5sum: c0e94e335f4e9be70784ceed02c83330 Package: TVTB Version: 1.16.0 Depends: R (>= 3.4), methods, utils, stats Imports: AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel, Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges, GGally, ggplot2, Gviz, limma, IRanges (>= 2.21.6), reshape2, Rsamtools, S4Vectors (>= 0.25.14), SummarizedExperiment, VariantAnnotation (>= 1.19.9) Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander License: Artistic-2.0 MD5sum: 9772e86236a93c846eaefb8bbdfcd433 Package: tweeDEseq Version: 1.36.0 Depends: R (>= 2.12.0) Imports: MASS, limma, edgeR, parallel, cqn Suggests: tweeDEseqCountData, xtable License: GPL (>= 2) MD5sum: fca293142eff38a8f972274522176369 Package: twilight Version: 1.66.0 Depends: R (>= 2.10), splines (>= 2.2.0), stats (>= 2.2.0), Biobase(>= 1.12.0) Imports: Biobase, graphics, grDevices, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) MD5sum: b3e25ff6f72945b8ec47007db8da3119 Package: twoddpcr Version: 1.14.0 Depends: R (>= 3.4) Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 74ee3a329737e99d53cbf08cafa4359c Package: tximeta Version: 1.8.5 Imports: SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges, GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb, rappdirs, utils, methods, Matrix Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, edgeR, limma, devtools License: GPL-2 MD5sum: 35a431f7cd0fcc2343349e05f6cdb0be Package: tximport Version: 1.18.0 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, csaw, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, fishpond License: GPL (>= 2) MD5sum: 10eda51551a318fa1b9b5540f4103971 Package: TxRegInfra Version: 1.10.0 Depends: R (>= 3.5), RaggedExperiment (>= 1.3.11), mongolite Imports: methods, rjson, GenomicRanges, IRanges, BiocParallel, GenomeInfoDb, S4Vectors, SummarizedExperiment, utils Suggests: knitr, GenomicFiles, EnsDb.Hsapiens.v75, testthat, shiny, biovizBase (>= 1.27.2), Gviz, AnnotationFilter, ensembldb, ontoProc, rjson, graph, TFutils (>= 1.5.4) License: Artistic-2.0 MD5sum: 4897bce04a93b03629b29d718faebf87 Package: TypeInfo Version: 1.56.0 Depends: methods Suggests: Biobase License: BSD MD5sum: 14447c9996f7761f2f09e6af92966114 Package: Ularcirc Version: 1.8.0 Depends: R (>= 3.4.0) Imports: AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments, Organism.dplyr, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, Sushi, yaml Suggests: BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: 84097a65a01177f59e5f89fbd96db8be Package: UMI4Cats Version: 1.0.1 Depends: R (>= 4.0.0), SummarizedExperiment Imports: magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, magrittr, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats, org.Hs.eg.db, annotate, TxDb.Hsapiens.UCSC.hg19.knownGene, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda Suggests: knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat License: Artistic-2.0 MD5sum: 7e89aae79a56bd129c1b7520c83a1413 Package: uncoverappLib Version: 1.0.0 Imports: markdown, shiny, shinyjs, shinyBS, shinyWidgets,shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx, condformat, stringr, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache,rappdirs, TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, BSgenome.Hsapiens.UCSC.hg19, processx, Rsamtools, GenomicRanges Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: c3327e78e8fb96fb29bd4a32fc9f1b68 Package: UNDO Version: 1.32.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 1b4a06c1115c9224dfae85cf4bf80e7c Package: unifiedWMWqPCR Version: 1.26.0 Depends: methods Imports: BiocGenerics, stats, graphics, HTqPCR License: GPL (>= 2) MD5sum: 32379c509dd3c38cdeed561439bcb93b Package: UniProt.ws Version: 2.30.0 Depends: methods, utils, RSQLite, RCurl, BiocGenerics (>= 0.13.8) Imports: AnnotationDbi, BiocFileCache, rappdirs Suggests: RUnit, BiocStyle, knitr License: Artistic License 2.0 MD5sum: 963f796085d08bf374a9c0f44e2b2eb5 Package: Uniquorn Version: 2.10.0 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 MD5sum: d1510839cfa863125749f8a2b3e3e357 Package: universalmotif Version: 1.8.5 Depends: R (>= 3.5.0) Imports: methods, stats, utils, MASS, ggplot2, ggseqlogo, yaml, IRanges, Rcpp, Rdpack (>= 0.7), Biostrings, BiocGenerics, S4Vectors, rlang, grid LinkingTo: Rcpp, RcppThread Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, Logolas, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx Enhances: MotIV, PWMEnrich, rGADEM, motifRG License: GPL-3 MD5sum: 92e70c99e46a29f45a55b44b37f546f3 Package: uSORT Version: 1.16.0 Depends: R (>= 3.3.0), tcltk Imports: igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 MD5sum: 7da4a65346732a1c2c98ede34e854547 Package: VanillaICE Version: 1.52.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, human610quadv1bCrlmm, ArrayTV Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 MD5sum: de3406f99265297ff78abda2236fec1a Package: variancePartition Version: 1.20.0 Depends: R (>= 3.6.0), ggplot2, limma, BiocParallel, scales, Biobase, methods Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, iterators, splines, foreach, doParallel, colorRamps, gplots, progress, reshape2, 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: d6841d26610274d6322daedfbdabc2b2 Package: VariantAnnotation Version: 1.36.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.15.3), 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, snpStats, ggplot2, BiocStyle License: Artistic-2.0 MD5sum: b63befe5786082a61684c24b9ce7f55e Package: VariantExperiment Version: 1.4.2 Depends: R (>= 3.6.0), S4Vectors (>= 0.21.24), SummarizedExperiment (>= 1.13.0), GenomicRanges, GDSArray (>= 1.3.0), DelayedDataFrame (>= 1.0.0) Imports: tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray, SeqVarTools, DelayedArray, Biostrings, IRanges Suggests: testthat, knitr License: GPL-3 MD5sum: 824f4b512bf51b001ae754fdfe3e37b7 Package: VariantFiltering Version: 1.26.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.25.1), VariantAnnotation (>= 1.13.29) Imports: utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Biostrings (>= 2.33.11), GenomeInfoDb (>= 1.3.6), GenomicRanges (>= 1.19.13), SummarizedExperiment, GenomicFeatures, Rsamtools (>= 1.17.8), BSgenome, GenomicScores (>= 1.0.0), Gviz, shiny, shinythemes, shinyjs, DT, shinyTree LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 License: Artistic-2.0 MD5sum: 89fbb267c5deed747d7bde912adb7be7 Package: VariantTools Version: 1.32.0 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: 26c58ea4c4e9307fb3874282ad57d66e Package: vasp Version: 1.2.4 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, Sushi, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) MD5sum: b70cd3ec7349e0f7dd4a454441db9fa8 Package: VaSP Version: 1.2.5 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, Sushi, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) MD5sum: db9d6477e4398d560b3a784150b5eae5 Package: vbmp Version: 1.58.0 Depends: R (>= 2.10) Suggests: Biobase (>= 2.5.5), statmod License: GPL (>= 2) MD5sum: e0e4bae760435fa51f26968f956f0657 Package: VCFArray Version: 1.6.0 Depends: R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28) Imports: tools, GenomicRanges, VariantAnnotation (>= 1.29.3), GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown License: GPL-3 MD5sum: 803a060ada91dc633c875cb7f542ad19 Package: VegaMC Version: 3.28.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods, genoset License: GPL-2 MD5sum: 3f3fc22650528174419e214f8cd78c87 Package: velociraptor Version: 1.0.0 Depends: SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors, DelayedArray, basilisk, zellkonverter, scuttle, SingleCellExperiment, BiocParallel, BiocSingular Suggests: BiocStyle, testthat, knitr, rmarkdown, scran, scater, scRNAseq, ggplot2, Rtsne License: MIT + file LICENSE MD5sum: 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Package: ViSEAGO Version: 1.4.0 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: 439892521e1fc7d35fc991ed3db9b46e Package: VplotR Version: 1.0.0 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown License: GPL-3 MD5sum: f8ae74c0bebd2bc2140ca568879a548e Package: vsn Version: 3.58.0 Depends: R (>= 3.4.0), Biobase Imports: methods, affy, limma, lattice, ggplot2 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