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MD5sum: fa0b32950575e04fe2132f105f4881ce NeedsCompilation: no Package: AnnotationForge Version: 1.30.1 Depends: R (>= 3.5.0), methods, utils, BiocGenerics (>= 0.15.10), Biobase (>= 1.17.0), AnnotationDbi (>= 1.33.14) Imports: DBI, RSQLite, XML, S4Vectors, RCurl Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, hom.Hs.inp.db, GO.db, BiocStyle, knitr, BiocManager License: Artistic-2.0 MD5sum: 702f203b9e12c0cf24d3e67ab2732a56 NeedsCompilation: no Package: AnnotationFuncs Version: 1.38.0 Depends: R (>= 2.7.0), AnnotationDbi Imports: DBI Suggests: org.Bt.eg.db, GO.db, org.Hs.eg.db, hom.Hs.inp.db License: GPL-2 MD5sum: 46c718f9a686c73c314567e16f9a91d6 NeedsCompilation: no Package: AnnotationHub Version: 2.20.2 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, interactiveDisplayBase, httr, yaml, dplyr Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: 539df1ccd31865a2d5980c9c16e2d99e NeedsCompilation: yes Package: AnnotationHubData Version: 1.18.1 Depends: R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges (>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15) Imports: GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics, jsonlite, BiocManager, biocViews, AnnotationDbi, Biobase, Biostrings, DBI, GenomeInfoDb (>= 1.15.4), OrganismDbi, RSQLite, rBiopaxParser, AnnotationForge, futile.logger (>= 1.3.0), XML, RCurl Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData License: Artistic-2.0 MD5sum: d9ec1f3aafb0d44a337d690777fc6aad NeedsCompilation: no Package: annotationTools Version: 1.62.0 Imports: Biobase, stats 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GenomicAlignments, DESeq, ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2, methods, rtracklayer, ensembldb, VariantAnnotation, dplyr, tidyr, repmis Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi, TBX20BamSubset, Rsamtools, testthat License: LGPL-3 MD5sum: 7804f4889af0124cac19530262866f02 NeedsCompilation: no Package: apComplex Version: 2.54.0 Depends: R (>= 2.10), graph, RBGL Imports: Rgraphviz, stats, org.Sc.sgd.db License: LGPL MD5sum: c03142b230568cf11ae82bd10e005db0 NeedsCompilation: no Package: apeglm Version: 1.10.0 Imports: emdbook, SummarizedExperiment, GenomicRanges, methods, stats, utils, Rcpp LinkingTo: Rcpp, RcppEigen, RcppNumerical Suggests: DESeq2, airway, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 456cc2c7d41ed24a8dccd0b2e95c7fa6 NeedsCompilation: yes Package: appreci8R Version: 1.6.0 Imports: shiny, shinyjs, DT, VariantAnnotation, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens, 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Version: 1.38.0 Depends: sampling, Rsamtools (>= 1.99.0), snow Imports: Biobase, BiocGenerics, Biostrings, DESeq, GenomicRanges, Hmisc, IRanges (>= 2.13.11), R2HTML, RColorBrewer, Rsamtools, ShortRead, XML, biomaRt, edgeR, grDevices, graphics, methods, rJava, stats, svMisc, utils, sendmailR, bitops LinkingTo: Rhtslib (>= 1.15.3) License: Artistic License 2.0 MD5sum: eedec5d41f24e31c289b916c01b41728 NeedsCompilation: yes Package: arrayMvout Version: 1.46.0 Depends: R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy, lumi Imports: simpleaffy, mdqc, affyContam, Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf License: Artistic-2.0 MD5sum: 9e0718d5fcc34765aaa7e8e195036d94 NeedsCompilation: no Package: arrayQuality Version: 1.66.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL MD5sum: 8d6abc85af838ec61dbbec9bbabfd624 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limma, S4Vectors, stats, DRaWR, GenomeInfoDb, Gviz, Matrix, dplyr, fgsea, reshape2, igraph, graphics, e1071, methods, rtracklayer, scales, grid, ggplot2, mGSZ, utils Suggests: knitr License: GPL-3 MD5sum: d36e61e7c13d72756d39b80417c224c2 NeedsCompilation: no Package: ASpli Version: 1.14.0 Depends: methods, grDevices, stats, utils, parallel, edgeR Imports: GenomicRanges, GenomicFeatures, BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, AnnotationDbi, Rsamtools, BiocStyle License: GPL MD5sum: 6fc0263164134256a914726f3bcf1836 NeedsCompilation: no Package: AssessORF Version: 1.6.0 Depends: R (>= 3.5.0), DECIPHER (>= 2.10.0) Imports: Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 2b39e41a73339f7670373bcfe00e7c81 NeedsCompilation: no Package: ASSET Version: 2.6.0 Depends: MASS, msm, rmeta Suggests: RUnit, BiocGenerics License: GPL-2 + file LICENSE MD5sum: 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data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testit, utils LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 6c1c60c8f3e37fa64345556f1a1a731c NeedsCompilation: yes Package: attract Version: 1.40.0 Depends: R (>= 3.4.0), AnnotationDbi Imports: Biobase, limma, cluster, GOstats, graphics, stats, reactome.db, KEGGREST, org.Hs.eg.db, utils, methods Suggests: illuminaHumanv1.db License: LGPL (>= 2.0) MD5sum: 7ee8a0aee2c5332b61cf690758d306a1 NeedsCompilation: no Package: AUCell Version: 1.10.0 Imports: data.table, graphics, grDevices, GSEABase, methods, mixtools, R.utils, shiny, stats, SummarizedExperiment, BiocGenerics, S4Vectors, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, rbokeh, devtools, Rtsne, tsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: 39c9bf9ebb19219fb819867642d7b85f NeedsCompilation: no 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org.Hs.eg.db, WGCNA, methods, GOSemSim, testthat, knitr, rmarkdown, BiocStyle, airway, DESeq2, boot, targetscan.Hs.eg.db, Hmisc, spelling License: MIT + file LICENSE MD5sum: 4a0e124d712e680f626d4d6579980d25 NeedsCompilation: no Package: BiocParallel Version: 1.22.0 Depends: methods Imports: stats, utils, futile.logger, parallel, snow LinkingTo: BH Suggests: BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel, Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit, BiocStyle, knitr, batchtools, data.table License: GPL-2 | GPL-3 MD5sum: bc99f80653597492a63299fd17465431 NeedsCompilation: yes Package: BiocPkgTools Version: 1.6.0 Depends: htmlwidgets Imports: BiocFileCache, BiocManager, biocViews, tibble, methods, rlang, tidyselect, stringr, rvest, rex, dplyr, xml2, rappdirs, readr, httr, htmltools, DT, tools, utils, igraph, tidyr, jsonlite, gh, RBGL, graph, magrittr Suggests: 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omicade4, rmarkdown, testthat License: CeCILL MD5sum: 2d73aecbf88b926e8ba25e651f7f3768 NeedsCompilation: no Package: Biostrings Version: 2.56.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.31.5), S4Vectors (>= 0.25.14), IRanges (>= 2.21.6), XVector (>= 0.27.2) Imports: methods, utils, grDevices, graphics, stats, crayon LinkingTo: S4Vectors, IRanges, XVector Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit Enhances: Rmpi License: Artistic-2.0 MD5sum: 0033c7e0b8cf8762238461be8e532478 NeedsCompilation: yes Package: biosvd Version: 2.23.0 Depends: R (>= 3.1.0) Imports: BiocGenerics, Biobase, methods, grid, graphics, NMF License: Artistic-2.0 MD5sum: ca3d4e4b0c4eb736132812c54e9531cb NeedsCompilation: no Package: BioTIP Version: 1.2.0 Depends: R (>= 3.6) 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matrixStats, rtracklayer, QDNAseq, dmrseq, methods, utils, R.utils, gtools, BiocParallel Suggests: DSS, covr, knitr, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10 License: GPL-3 MD5sum: 4c4a3513036ac9a008187579b407e03f NeedsCompilation: no Package: BiSeq Version: 1.28.0 Depends: R (>= 2.15.2), methods, S4Vectors, IRanges (>= 1.17.24), GenomicRanges, SummarizedExperiment (>= 0.2.0), Formula Imports: methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer, parallel, betareg, lokern, Formula, globaltest License: LGPL-3 MD5sum: b1a4f12d4d33ef04867578d2376a6dc8 NeedsCompilation: no Package: BitSeq Version: 1.32.0 Depends: Rsamtools (>= 1.99.3) Imports: S4Vectors, IRanges LinkingTo: Rhtslib (>= 1.15.5) Suggests: edgeR, DESeq, BiocStyle License: Artistic-2.0 + file LICENSE MD5sum: 3f56149cd98a566ded14f665ccd54eb8 NeedsCompilation: yes Package: blacksheepr Version: 1.2.0 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: 167acdd261452af0e8a1a3635cd86fe5 NeedsCompilation: no Package: blima Version: 1.22.0 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: b350f1df375fb054c82f8666c123b8aa NeedsCompilation: yes Package: BLMA Version: 1.12.0 Depends: ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel, Biobase Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 353a610fc88c4cde077864cea335a85e NeedsCompilation: no Package: bnbc Version: 1.10.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, GenomicRanges Imports: Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, GenomeInfoDb, 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Artistic-2.0 MD5sum: 730408a4ce9f8f30873c09194be68447 NeedsCompilation: no Package: bridge Version: 1.52.0 Depends: R (>= 1.9.0), rama License: GPL (>= 2) MD5sum: 924ee40aa5dd73b38361bbeb78bc17cf NeedsCompilation: yes Package: BridgeDbR Version: 1.22.0 Depends: R (>= 3.3.0), rJava Imports: curl Suggests: BiocStyle, knitr, rmarkdown, testthat License: AGPL-3 MD5sum: 8e210dd7fca27e4ba1d61580db7698b2 NeedsCompilation: no Package: BrowserViz Version: 2.10.0 Depends: R (>= 3.5.0), jsonlite (>= 1.5), httpuv(>= 1.5.0) Imports: methods, BiocGenerics Suggests: RUnit, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 41ccf3da08db935ef3c379dec25a2404 NeedsCompilation: no Package: BSgenome Version: 1.56.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.23.9), GenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), rtracklayer (>= 1.39.7) Imports: methods, utils, stats, matrixStats, BiocGenerics, S4Vectors, IRanges, XVector, 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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: b9a4043e1105cccfb40a7cf7758ea317 NeedsCompilation: no Package: ChIPexoQual Version: 1.12.0 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) MD5sum: 8698325d1d5da4f36535e74783268c0e NeedsCompilation: no Package: ChIPpeakAnno Version: 3.22.4 Depends: R (>= 3.5), methods, IRanges (>= 2.13.12), Biostrings (>= 2.47.6), GenomicRanges (>= 1.31.8), S4Vectors (>= 0.17.25) Imports: BiocGenerics (>= 0.1.0), GO.db, biomaRt, BSgenome, GenomicFeatures, GenomeInfoDb, grid, matrixStats, AnnotationDbi, limma, multtest, RBGL, graph, BiocManager, stats, regioneR, DBI, ensembldb, Biobase, seqinr, idr, GenomicAlignments, DelayedArray, SummarizedExperiment, rtracklayer, Rsamtools, VennDiagram Suggests: reactome.db, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, gplots, BiocStyle, knitr, rmarkdown, testthat, trackViewer, motifStack, OrganismDbi License: GPL (>= 2) MD5sum: 3a2fdfbb6bd1dc6eb366ed2dc8502c06 NeedsCompilation: no Package: ChIPQC Version: 1.24.1 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: 9c6c3554b283401353f9f31074e6ca93 NeedsCompilation: no Package: ChIPseeker Version: 1.24.0 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: 1eaba253baaa2554d9e1510498b05c35 NeedsCompilation: no Package: chipseq Version: 1.38.0 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: 3462b428aabb183cb28c32e07bd74b93 NeedsCompilation: yes Package: ChIPseqR Version: 1.42.0 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: 9703f0473cdb54ccb894bd0007b00a59 NeedsCompilation: yes Package: ChIPSeqSpike Version: 1.8.0 Depends: R (>= 3.5), rtracklayer (>= 1.37.6) Imports: tools, stringr, Rsamtools, GenomicRanges, IRanges, seqplots, ggplot2, LSD, corrplot, methods, stats, 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Rcpp, grid, plotly, shiny, miniUI, stats, utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment, RColorBrewer, BSgenome LinkingTo: Rcpp, RcppArmadillo Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr License: MIT + file LICENSE MD5sum: bd846f329a018a17fdf1896ab74108e9 NeedsCompilation: yes Package: CHRONOS Version: 1.16.0 Depends: R (>= 3.5) Imports: XML, RCurl, RBGL, parallel, foreach, doParallel, openxlsx, igraph, circlize, graph, stats, utils, grDevices, graphics, methods, biomaRt Suggests: RUnit, BiocGenerics, knitr License: GPL-2 MD5sum: e39b914b82e2d88e09ddb7860ecf925c NeedsCompilation: no Package: cicero Version: 1.6.2 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), 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SingleCellExperiment, SummarizedExperiment, matrixStats, S4Vectors Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle License: MIT + file LICENSE MD5sum: 7ca7074aa7e22b72fe22e3c1da8957d0 NeedsCompilation: no Package: CMA Version: 1.46.0 Depends: R (>= 2.10), methods, stats, Biobase Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm License: GPL (>= 2) MD5sum: a7047a2a1e5463a2c84cf3218c6eabbe NeedsCompilation: no Package: cmapR Version: 1.0.0 Depends: R (>= 3.5) Imports: methods, rhdf5, data.table, prada, SummarizedExperiment, matrixStats Suggests: knitr, testthat, BiocStyle License: file LICENSE MD5sum: df1a5b0352edf25c993e069c41a6452a NeedsCompilation: no Package: cn.farms Version: 1.36.0 Depends: R (>= 3.0), Biobase, methods, ff, oligoClasses, snow Imports: DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, 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1.50.0), GO.db (>= 3.3.0), R.utils (>= 2.3.0), KEGGREST (>= 1.14.0) 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: a156f7c901a3ad397ed57e9b08a84469 NeedsCompilation: yes Package: CNORdt Version: 1.30.0 Depends: R (>= 1.8.0), CellNOptR (>= 0.99), abind License: GPL-2 MD5sum: e0609d8fe78cadd140169ccafeb59665 NeedsCompilation: yes Package: CNORfeeder Version: 1.28.0 Depends: R (>= 3.6.0), CellNOptR (>= 1.4.0), graph Suggests: minet, catnet, Rgraphviz, RUnit, BiocGenerics, igraph Enhances: MEIGOR License: GPL-3 MD5sum: ba1f41baafd633b10d5c0ece75ae755b NeedsCompilation: no Package: CNORfuzzy Version: 1.30.0 Depends: R (>= 2.15.0), CellNOptR (>= 1.4.0), nloptr (>= 0.8.5) Suggests: xtable, Rgraphviz, RUnit, BiocGenerics License: GPL-2 MD5sum: 92a28263b222746cd0b969f2d78e17db NeedsCompilation: yes Package: CNORode Version: 1.30.0 Depends: CellNOptR (>= 1.5.14), genalg Enhances: MEIGOR License: GPL-2 MD5sum: 5cfde7cc719417d7d5ec409ae1ace8d7 NeedsCompilation: yes Package: CNTools Version: 1.44.0 Depends: R (>= 2.10), methods, tools, stats, genefilter License: LGPL MD5sum: a28ac31639fb984b7ac001b20d14f8d0 NeedsCompilation: yes Package: CNVfilteR Version: 1.2.0 Depends: R (>= 3.6) Imports: IRanges, GenomicRanges, SummarizedExperiment, pracma, regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics, utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings, methods Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked License: Artistic-2.0 MD5sum: 065b47d076437330b44acf8c2e67bd16 NeedsCompilation: no Package: cnvGSA Version: 1.32.0 Depends: brglm, doParallel, foreach, GenomicRanges, methods, splitstackshape Suggests: cnvGSAdata, org.Hs.eg.db License: LGPL MD5sum: 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NeedsCompilation: no Package: CNVrd2 Version: 1.26.0 Depends: R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags, ggplot2, gridExtra Imports: DNAcopy, IRanges, Rsamtools Suggests: knitr License: GPL-2 MD5sum: 92418cbe8e54844947e636a9a1822511 NeedsCompilation: no Package: CNVtools Version: 1.81.0 Depends: R (>= 2.10), survival License: GPL-3 MD5sum: d0abd6eee0843406878cf1b69ad9c9f1 NeedsCompilation: yes Package: cobindR Version: 1.25.0 Imports: methods, seqinr, yaml, rtfbs, gplots, mclust, gmp, BiocGenerics (>= 0.13.8), IRanges, Biostrings, BSgenome, biomaRt Suggests: RUnit Enhances: rGADEM, seqLogo, genoPlotR, parallel, VennDiagram, RColorBrewer, vcd, MotifDb, snowfall License: Artistic-2.0 MD5sum: b147659f7662c8e3eac578ecffb0eaa0 NeedsCompilation: no Package: CoCiteStats Version: 1.60.0 Depends: R (>= 2.0), org.Hs.eg.db Imports: AnnotationDbi License: CPL MD5sum: cec060735ad2fe436a9da5faefe6e72f NeedsCompilation: no Package: COCOA Version: 2.2.1 Depends: R (>= 3.5), GenomicRanges Imports: BiocGenerics, S4Vectors, IRanges, data.table, ggplot2, Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid, grDevices, simpleCache, fitdistrplus Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: bde10fc0bfd040114bb161d081752dfd NeedsCompilation: no Package: codelink Version: 1.56.0 Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>= 2.17.8), limma Imports: annotate Suggests: genefilter, parallel, knitr License: GPL-2 MD5sum: 68fd8512aa00df69fd4a034a9d334c30 NeedsCompilation: no Package: CODEX Version: 1.20.0 Depends: R (>= 3.2.3), Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors Suggests: WES.1KG.WUGSC License: GPL-2 MD5sum: 96fa4bfc9abdc7444faa82a9357fd248 NeedsCompilation: no Package: coexnet Version: 1.10.3 Depends: R (>= 3.6) Imports: affy, siggenes, GEOquery, vsn, igraph, acde, Biobase, limma, graphics, stats, utils, STRINGdb, SummarizedExperiment, minet, rmarkdown Suggests: RUnit, BiocGenerics, knitr License: LGPL MD5sum: e90db85a72f7c2d4ff1f6e895823d0e2 NeedsCompilation: no Package: CoGAPS Version: 3.8.0 Depends: R (>= 3.5.0) Imports: BiocParallel, cluster, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5 LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: GPL (== 2) MD5sum: ff9529a4270ad2c709e4f6d9e3205eca NeedsCompilation: yes Package: cogena Version: 1.22.0 Depends: R (>= 3.6), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools Suggests: knitr, rmarkdown (>= 2.1) License: LGPL-3 MD5sum: 225d32c30c43923284282b551e142e1b NeedsCompilation: no Package: coGPS Version: 1.32.0 Depends: R (>= 2.13.0) Imports: graphics, grDevices Suggests: limma License: GPL-2 MD5sum: 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Imports: ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix, BB, reshape2, alabama, cobs, Biobase, vegan, grDevices, graphics, methods, SummarizedExperiment Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: 4371bb698b025749da7361475822a4d0 NeedsCompilation: no Package: coMET Version: 1.20.0 Depends: R (>= 3.6.0), grid, utils, biomaRt, Gviz, psych Imports: colortools, hash,grDevices, gridExtra, rtracklayer, IRanges, S4Vectors, GenomicRanges, stats, corrplot Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 21080e432572670e82a7ca8b13be0704 NeedsCompilation: no Package: compartmap Version: 1.6.0 Depends: R (>= 3.5.0), minfi, Homo.sapiens, mixOmics Imports: SummarizedExperiment, GenomicRanges, gtools, parallel Suggests: covr, testthat, knitr License: GPL-3 + file LICENSE MD5sum: 9d2ac08bb5aadc89d0d63ea9ab1987cf NeedsCompilation: no Package: COMPASS Version: 1.26.0 Depends: R (>= 3.0.3) Imports: methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr, knitr, abind, clue, grDevices, utils, pdist, magrittr, reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown LinkingTo: Rcpp (>= 0.11.0) Suggests: flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData, ggplot2 License: Artistic-2.0 MD5sum: 156415aa43797bd38a94f43e9c1660cb NeedsCompilation: yes Package: compcodeR Version: 1.24.0 Depends: R (>= 3.0.2), sm Imports: tcltk, knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, gdata, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods Suggests: BiocStyle, EBSeq, DESeq, DESeq2 (>= 1.1.31), baySeq (>= 2.2.0), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), rmarkdown Enhances: rpanel, DSS License: GPL (>= 2) MD5sum: d0052c8dbe839caa7859cd3b94ad6821 NeedsCompilation: no Package: compEpiTools Version: 1.22.0 Depends: R (>= 3.1.1), methods, topGO, GenomicRanges Imports: AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel, grDevices, gplots, IRanges, GenomicFeatures, XVector, methylPipe, GO.db, S4Vectors, GenomeInfoDb Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer License: GPL MD5sum: 0c46701a39d79c115ba557854a279d62 NeedsCompilation: no Package: CompGO Version: 1.24.0 Depends: RDAVIDWebService Imports: rtracklayer, Rgraphviz, ggplot2, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, pcaMethods, reshape2, pathview License: GPL-2 MD5sum: 4bdf146db3d65eac67881c8da1ffc81a NeedsCompilation: no Package: ComplexHeatmap Version: 2.4.3 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices Imports: circlize (>= 0.4.5), GetoptLong, colorspace, clue, RColorBrewer, GlobalOptions (>= 0.1.0), parallel, png Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, Cairo, jpeg, tiff, fastcluster, dendextend (>= 1.0.1), grImport, grImport2, glue, GenomicRanges, gridtext License: MIT + file LICENSE MD5sum: 428e05e8f7495f7486c7861e2bea7490 NeedsCompilation: no Package: CONFESS 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Version: 2.0.0 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: b306e7c868be8881027408e8a3964004 NeedsCompilation: no Package: DAPAR Version: 1.20.3 Depends: R (>= 4.0.0), foreach, parallel, doParallel, igraph Imports: MSnbase, 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), highcharter (>= 0.7.0), DAPARdata (>= 1.16.0), siggenes, graph, lme4, readxl, clusterProfiler, dplyr, tidyr,AnnotationDbi, tidyverse, vsn, FactoMineR, factoextra, visNetwork Suggests: BiocGenerics, Biobase, testthat, 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Version: 1.0.0 Depends: R (>= 3.6.0) Imports: CompQuadForm, ggplot2, KernSmooth, matrixStats, methods, parallel, pbapply, stats, statmod Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA, knitr, limma, readxl, rmarkdown, S4Vectors, SummarizedExperiment, testthat, covr License: GPL-2 | file LICENSE MD5sum: d58b78a6d37e369b9008bebefec83255 NeedsCompilation: no Package: debCAM Version: 1.6.0 Depends: R (>= 3.5) Imports: methods, rJava, BiocParallel, stats, Biobase, SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR, pcaPP, apcluster, graphics Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl License: GPL-2 MD5sum: af14878c445dd854189553783860ace2 NeedsCompilation: no Package: debrowser Version: 1.16.3 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 Suggests: testthat, rmarkdown, knitr, R.rsp License: GPL-3 + file LICENSE MD5sum: dea579beffa27455917f6f1038cba567 NeedsCompilation: no Package: DECIPHER Version: 2.16.1 Depends: R (>= 3.3.0), Biostrings (>= 2.35.12), RSQLite (>= 1.1), stats, parallel Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, S4Vectors, IRanges, XVector License: GPL-3 MD5sum: 07533f59c74df8cd4c51eb68b136e72a NeedsCompilation: yes Package: deco Version: 1.4.1 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 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reshape, rlang, scales, stats, stringr, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE MD5sum: d572aa82bcd1167f100c9d0430d80fe0 NeedsCompilation: no Package: DEGseq Version: 1.42.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: 9d37144a7ff7c0d4b114093cc987367d NeedsCompilation: yes Package: DelayedArray Version: 0.14.1 Depends: R (>= 3.4), methods, stats4, matrixStats, BiocGenerics (>= 0.31.5), S4Vectors (>= 0.25.15), IRanges (>= 2.17.3) Imports: stats, Matrix LinkingTo: S4Vectors Suggests: BiocParallel, HDF5Array, genefilter, SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit License: Artistic-2.0 MD5sum: d2417e300179bc4de74d5ac6728f3f40 NeedsCompilation: yes Package: DelayedDataFrame Version: 1.4.0 Depends: R (>= 3.6), S4Vectors (>= 0.23.19), DelayedArray (>= 0.7.5) Imports: 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grDevices, graphics, Rcpp, stats, utils LinkingTo: Rcpp Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: a89bbbdc969b9e49482e24a63e4aef7b NeedsCompilation: yes Package: flagme Version: 1.44.0 Depends: gcspikelite, xcms, CAMERA Imports: gplots, graphics, MASS, methods, SparseM, stats, utils License: LGPL (>= 2) MD5sum: 7b1a5c6befd53d04ba222dfd6dc6b9fb NeedsCompilation: yes Package: flowAI Version: 1.18.5 Depends: R (>= 3.6) Imports: ggplot2, flowCore, plyr, changepoint, knitr, reshape2, RColorBrewer, scales, methods, graphics, stats, utils, rmarkdown Suggests: testthat, shiny License: GPL (>= 2) MD5sum: 1acb67fa754c0aa8193162b3f51ce27b NeedsCompilation: no Package: flowBeads Version: 1.26.0 Depends: R (>= 2.15.0), methods, Biobase, rrcov, flowCore Imports: flowCore, rrcov, knitr, xtable Suggests: flowViz License: Artistic-2.0 MD5sum: 58f09006eca58ba75e2cf7e5fd459b12 NeedsCompilation: no Package: flowBin Version: 1.24.0 Depends: methods, flowCore, flowFP, R (>= 2.10) Imports: 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flowWorkspace, ncdfFlow(>= 2.19.5), flowViz, fda (>= 2.2.6), Biobase, methods, grDevices, graphics, stats, cluster, utils, KernSmooth, lattice, ks, RColorBrewer, rrcov Suggests: xtable, testthat, openCyto Enhances: RBGL,graph License: Artistic-2.0 MD5sum: 00aefa08cecdd163470184d9ac58961e NeedsCompilation: no Package: flowTime Version: 1.12.0 Depends: R (>= 3.4), flowCore, plyr Imports: utils Suggests: knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, moments, stats License: Artistic-2.0 MD5sum: 6f8695e4f100f70ee3ea94f6d18a93b2 NeedsCompilation: no Package: flowTrans Version: 1.40.0 Depends: R (>= 2.11.0), flowCore, flowViz,flowClust Imports: flowCore, methods, flowViz, stats, flowClust License: Artistic-2.0 MD5sum: ccb0b32e6a0487b63efe02ed9b1af3b4 NeedsCompilation: no Package: flowType Version: 2.25.0 Depends: R (>= 2.10), Rcpp (>= 0.10.4), BH (>= 1.51.0-3) Imports: Biobase, graphics, grDevices, methods, flowCore, flowMeans, sfsmisc, rrcov, flowClust, flowMerge, stats LinkingTo: Rcpp, 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Biobase, BiocGenerics, cytolib (>= 1.99.26), lattice, latticeExtra, XML, ggplot2, graph, graphics, grDevices, methods, stats, stats4, utils, RBGL, tools, Rgraphviz, data.table, dplyr, Rcpp, stringr, scales, matrixStats, RcppParallel, RProtoBufLib, digest, flowCore(>= 1.99.20), ncdfFlow(>= 2.25.4) LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib (>= 2.0.1),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: 09689d5fa26497cafd6fbc698f5c7766 NeedsCompilation: yes Package: fmcsR Version: 1.30.0 Depends: R (>= 2.10.0), ChemmineR, methods Imports: RUnit, methods, ChemmineR, BiocGenerics, parallel Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap License: Artistic-2.0 MD5sum: 4a51421df56aeab205d8df5dddb8a552 NeedsCompilation: yes Package: focalCall Version: 1.21.0 Depends: R(>= 2.10.0), CGHcall Suggests: RUnit, 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BiocGenerics, Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools (>= 1.6.1), rtracklayer (>= 1.14.1), ChIPpeakAnno (>= 2.2.0), VariantAnnotation, plyr, snpStats, ggplot2 (>= 0.9.0), reshape (>= 0.8.4), scales Suggests: org.Hs.eg.db Enhances: parallel License: GPL-3 MD5sum: bf6b7c195212fbb904f1c27ecc7a1c05 NeedsCompilation: no Package: funtooNorm Version: 1.12.0 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: 3b00394242b82d40fca6b3fedb947669 NeedsCompilation: no Package: GA4GHclient Version: 1.12.0 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: 1ff77bfca97e55c6713c146966642a0e NeedsCompilation: no Package: GA4GHshiny Version: 1.10.0 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: 3fe64aff5bb5442fbbe371662d3e9075 NeedsCompilation: no Package: gaga Version: 2.34.0 Depends: R (>= 2.8.0), Biobase, coda, EBarrays, mgcv Enhances: parallel License: GPL (>= 2) MD5sum: 4b7fda570a0df049afdc2c730608b832 NeedsCompilation: yes Package: gage Version: 2.38.3 Depends: R (>= 2.10) Imports: graph, KEGGREST, AnnotationDbi, GO.db Suggests: pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq, DESeq2, edgeR, limma License: GPL (>= 2.0) MD5sum: d389899bad5334840c180319192654ab NeedsCompilation: no Package: gaggle Version: 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splines, grDevices, graphics, stats, methods Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: GPL-3 MD5sum: 81432b05439747e2419965523a535796 NeedsCompilation: no Package: gcatest Version: 1.18.0 Depends: R (>= 3.2) Imports: lfa Suggests: knitr, ggplot2 License: GPL-3 MD5sum: 2515c9770f58dff5658e66d9bc15c57d NeedsCompilation: yes Package: gCMAP Version: 1.32.0 Depends: GSEABase, limma (>= 3.20.0) Imports: Biobase, methods, GSEAlm, Category, Matrix (>= 1.0.9), parallel, annotate, genefilter, AnnotationDbi, DESeq, grDevices, graphics, stats, utils, bigmemory, bigmemoryExtras (>= 1.1.2) Suggests: BiocGenerics, reactome.db, RUnit, GO.db, mgsa License: Artistic-2.0 OS_type: unix MD5sum: 33486f779425d55e9c4bbc40bfd020ef NeedsCompilation: no Package: gCMAPWeb Version: 1.27.0 Depends: Biobase, gCMAP (>= 1.3.0), methods, R (>= 3.4), Rook Imports: brew, BiocGenerics, annotate, AnnotationDbi, graphics, grDevices, GSEABase, hwriter, parallel, stats, utils, yaml Suggests: affy, ArrayExpress, hgfocus.db, hgu133a.db, mgug4104a.db, org.Hs.eg.db, org.Mm.eg.db, RUnit Enhances: bigmemory, bigmemoryExtras License: Artistic-2.0 OS_type: unix MD5sum: 02e1b808bab57f4e6661acd109b49d75 NeedsCompilation: no Package: gCrisprTools Version: 1.16.0 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: b0f6aeb5ca5a62cfa117471ee60bdf6b NeedsCompilation: no Package: gcrma Version: 2.60.0 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: 94613518f1aedc7aad6f5f51d346930b NeedsCompilation: yes Package: GCSConnection Version: 1.0.1 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: bf4e5980cfd3327a2f8eedadf9ad5930 NeedsCompilation: yes Package: GCSscore Version: 1.2.0 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: b361df39700b79be233291f316eb6d84 NeedsCompilation: no Package: GDCRNATools Version: 1.8.0 Depends: R (>= 3.5.0) Imports: shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2, clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival, survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons, BiocParallel Suggests: knitr, testthat License: Artistic-2.0 MD5sum: 337f6f174b8647b66c0933542f49d9b5 NeedsCompilation: no Package: GDSArray Version: 1.8.0 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: 9c1facc3751ab72cf5137a18a7a971af NeedsCompilation: no Package: gdsfmt Version: 1.24.1 Depends: R (>= 2.15.0), methods Suggests: parallel, digest, Matrix, RUnit, knitr, crayon, BiocGenerics License: LGPL-3 MD5sum: e9bf44c094d2a910ea5c4154afd2a605 NeedsCompilation: yes Package: geecc Version: 1.21.0 Depends: R (>= 3.3.0), methods Imports: MASS, hypergea (>= 1.3.0), gplots, Rcpp (>= 0.11.3), graphics, stats, utils LinkingTo: Rcpp Suggests: hgu133plus2.db, GO.db, AnnotationDbi License: GPL (>= 2) MD5sum: dd2541b287cc367bed5a450852430ce4 NeedsCompilation: yes Package: GEM Version: 1.14.0 Depends: R (>= 3.3) Imports: tcltk, ggplot2, methods, stats, grDevices, graphics, utils Suggests: knitr, RUnit, testthat, BiocGenerics License: Artistic-2.0 MD5sum: f97126edfd3e6a8eee102dbc939d23e5 NeedsCompilation: no Package: gemini Version: 1.2.0 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: 54c09533dcf4d7154ab9b35fe6b2e5ea NeedsCompilation: no Package: genArise Version: 1.64.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: 423e78beb0305fa4ab3f9ed516671e5a NeedsCompilation: no Package: genbankr Version: 1.16.0 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: 6675a2989d1f68054844d39bebacdda6 NeedsCompilation: no Package: GeneAccord Version: 1.6.0 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: adfa060d2be0d757358162936cc6edfc NeedsCompilation: no Package: GeneAnswers Version: 2.30.0 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: a959a8d50240ada5abd7ff249ea54f13 NeedsCompilation: no Package: geneAttribution Version: 1.14.0 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: 2b5e4d67b5cf013d69397bd39a20eb0d NeedsCompilation: no Package: GeneBreak Version: 1.18.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: 310edf8c016fb223b5a677dcc82a6a77 NeedsCompilation: no Package: geneClassifiers Version: 1.12.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: 865f5d008e8fa9549ed0c0c2a230fe62 NeedsCompilation: no Package: GeneExpressionSignature Version: 1.34.0 Depends: R (>= 2.13), Biobase, PGSEA Suggests: apcluster,GEOquery License: GPL-2 MD5sum: f53b25a04edc07f7122900e05f9d12c9 NeedsCompilation: no Package: genefilter Version: 1.70.0 Imports: BiocGenerics (>= 0.31.2), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 MD5sum: 249034238590abc6a0801527513f93d4 NeedsCompilation: yes Package: genefu Version: 2.20.0 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: d50ee2d0e14cd3f371e093e9ad600bb3 NeedsCompilation: no Package: GeneGA Version: 1.38.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: 2063f401c60aa54f049a0aa47f4a0e2a NeedsCompilation: no Package: GeneGeneInteR Version: 1.14.0 Depends: R (>= 4.0) Imports: snpStats, mvtnorm, GGtools, Rsamtools, igraph, kernlab, FactoMineR, plspm, IRanges, GenomicRanges, data.table,grDevices, graphics,stats, utils, methods License: GPL (>= 2) MD5sum: 725082a6860d2b4f65fd2624bc52f69a NeedsCompilation: yes Package: GeneMeta Version: 1.60.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: b0ec50d35a91c4a057f4f8aa5fc973cc NeedsCompilation: no Package: GeneNetworkBuilder Version: 1.30.0 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: ef3a06ffee714f556537bbd37771db40 NeedsCompilation: yes Package: GeneOverlap Version: 1.24.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 655e0bdaa34140e2b09bcf660248665c NeedsCompilation: no Package: geneplast Version: 1.14.0 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: d1e90f10ae14b0c0783e4452fabe005d NeedsCompilation: no Package: geneplotter Version: 1.66.0 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: 1a2a8ca3b0f6a101f078992db9dce0ec NeedsCompilation: no Package: geneRecommender Version: 1.60.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: ca7e55724bff844be2b86349dace0c32 NeedsCompilation: no Package: GeneRegionScan Version: 1.44.0 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: b9374aa11a1896c5cdcaf216627fef1f NeedsCompilation: no Package: geneRxCluster Version: 1.24.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: f8c5594cab1c24dccb9ca27cf44ea081 NeedsCompilation: yes Package: GeneSelectMMD Version: 2.32.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: c38eba229d6a8dea637d5dc64636056f NeedsCompilation: yes Package: GENESIS Version: 2.18.0 Imports: Biobase, BiocGenerics, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, dplyr, foreach, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL-3 MD5sum: 75b296154e26297fb1c91c6178b8fc4e NeedsCompilation: yes Package: GeneStructureTools Version: 1.8.0 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: 0afd9401100d2af961ff0e58bbfafc33 NeedsCompilation: no Package: geNetClassifier Version: 1.28.0 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: 88138e629c3e78561e216e0f25fa4897 NeedsCompilation: no Package: GeneticsDesign Version: 1.55.0 Imports: gmodels, graphics, gtools (>= 2.4.0), mvtnorm, stats License: GPL-2 MD5sum: b6fce0923363ab41047f6186cb81df71 NeedsCompilation: no Package: GeneticsPed Version: 1.50.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: f6dee08385a5480eb46e6aba00cc7ff1 NeedsCompilation: yes Package: GeneTonic Version: 1.0.1 Depends: R (>= 4.0.0) Imports: AnnotationDbi, bs4Dash, ComplexHeatmap, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, 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: 5a819586f8d008aef6cb10f3c53269d6 NeedsCompilation: no Package: geneXtendeR Version: 1.14.0 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: 3ad949a0b64edf85836b3874d111a591 NeedsCompilation: yes Package: GENIE3 Version: 1.10.0 Imports: stats, reshape2 Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods License: GPL (>= 2) MD5sum: bfa658f6cf6eb638ece27b899761a647 NeedsCompilation: yes Package: genoCN Version: 1.40.0 Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: a5fefffd65376834c7a2b552b4ae74d1 NeedsCompilation: yes Package: GenoGAM Version: 2.6.0 Depends: R (>= 3.5), SummarizedExperiment (>= 1.1.19), HDF5Array (>= 1.8.0), rhdf5 (>= 2.21.6), S4Vectors (>= 0.23.18), Matrix (>= 1.2-8), data.table (>= 1.9.4) Imports: Rcpp (>= 0.12.14), sparseinv (>= 0.1.1), Rsamtools (>= 1.18.2), GenomicRanges (>= 1.23.16), BiocParallel (>= 1.5.17), DESeq2 (>= 1.11.23), futile.logger (>= 1.4.1), GenomeInfoDb (>= 1.7.6), GenomicAlignments (>= 1.7.17), IRanges (>= 2.5.30), Biostrings (>= 2.39.14), DelayedArray (>= 0.3.19), methods, stats LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, chipseq (>= 1.21.2), LSD (>= 3.0.0), genefilter (>= 1.54.2), ggplot2 (>= 2.1.0), testthat, knitr, rmarkdown License: GPL-2 MD5sum: 380ccac6757c2713f384068220b10c81 NeedsCompilation: yes Package: genomation Version: 1.20.0 Depends: R (>= 3.0.0),grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), RUnit, Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown License: Artistic-2.0 MD5sum: a6b52c5c3ade64fa495b250a78ef8859 NeedsCompilation: yes Package: GenomeInfoDb Version: 1.24.2 Depends: R (>= 3.1), methods, BiocGenerics (>= 0.13.8), S4Vectors (>= 0.25.12), IRanges (>= 2.13.12) Imports: stats, stats4, utils, RCurl, GenomeInfoDbData Suggests: GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 8c2b3a7b7c365e67947f1882023b5d7f NeedsCompilation: no Package: genomeIntervals Version: 1.44.2 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: 41d21ef5a082adf69b8a98b2bee7d195 NeedsCompilation: no Package: genomes Version: 3.18.0 Depends: readr, curl License: GPL-3 MD5sum: f40e6633c40fe8ea433b76ba14f202f7 NeedsCompilation: no Package: GenomicAlignments Version: 1.24.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.25.14), IRanges (>= 2.21.6), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.39.3), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.55.7), Rsamtools (>= 1.31.2) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle License: Artistic-2.0 MD5sum: 5a7b85379d84067cf19c0859b24eeec7 NeedsCompilation: yes Package: GenomicDataCommons Version: 1.12.0 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: 203ac071371c697cd782348b70b15c88 NeedsCompilation: no Package: GenomicFeatures Version: 1.40.1 Depends: BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.29), IRanges (>= 2.13.23), GenomeInfoDb (>= 1.23.10), 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.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, 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: 9f886377d76dcae83712537c4e7e455f NeedsCompilation: no Package: GenomicFiles Version: 1.24.0 Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), GenomicRanges (>= 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stats, utils, plyr, gridExtra, sjstats, parallel, ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack Suggests: readxl, GEOquery, knitr, rmarkdown License: LGPL (>= 3) MD5sum: a349936636c02bf9a4e2fd04891d1683 NeedsCompilation: no Package: GenomicRanges Version: 1.40.0 Depends: R (>= 2.10), methods, stats4, BiocGenerics (>= 0.25.3), S4Vectors (>= 0.25.14), IRanges (>= 2.21.6), GenomeInfoDb (>= 1.15.2) Imports: utils, stats, XVector (>= 0.27.2) 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, 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GPL-2 + file LICENSE MD5sum: 8f842db45f45b2ccd2603b49873784df NeedsCompilation: no Package: gmoviz Version: 1.0.1 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: e49b68733f5ad07af130055a2265bbe5 NeedsCompilation: no Package: GMRP Version: 1.16.0 Depends: R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix, base,GenomicRanges Suggests: BiocStyle, BiocGenerics License: GPL (>= 2) MD5sum: 372366cbd9ad0e7a6fd3f8d8bc480afd NeedsCompilation: no Package: GNET2 Version: 1.4.0 Depends: R (>= 3.3) Imports: ggplot2,xgboost,Rcpp,reshape2,grid,DiagrammeR,methods,stats,matrixStats,graphics,SummarizedExperiment,dplyr,igraph, grDevices LinkingTo: Rcpp Suggests: knitr, rmarkdown License: Apache 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SummarizedExperiment, edgeR, S4Vectors Imports: seqLogo, Biostrings, GenomicFeatures (>= 1.39.4), IRanges, seqinr, graphics, grDevices, stats, utils, grid, methods, DBI, RMySQL, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2 Suggests: clinfun, knitr, BSgenome.Hsapiens.UCSC.hg19 License: GPL-2 MD5sum: 054695dd077a4c66821fff748e2c6520 NeedsCompilation: no Package: InterMineR Version: 1.10.0 Depends: R (>= 3.4.1) Imports: Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, igraph, httr, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, methods Suggests: BiocStyle, Gviz, knitr, rmarkdown, GeneAnswers, GO.db, org.Hs.eg.db License: LGPL MD5sum: 4c904ae700de4ddf19dc1837668206a2 NeedsCompilation: no Package: IntramiRExploreR Version: 1.10.0 Depends: R (>= 3.4) Imports: igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats, utils, grDevices, graphics Suggests: RDAVIDWebService, gProfileR, topGO, KEGGprofile, org.Dm.eg.db, rmarkdown, testthat License: GPL-2 MD5sum: 8d556ba69eed89c7cff6aa40b404cdc1 NeedsCompilation: no Package: inveRsion Version: 1.36.0 Depends: methods, haplo.stats Imports: graphics, methods, utils License: GPL (>= 2) MD5sum: 4b54881d46058a901b7376f805ef7b2f NeedsCompilation: yes Package: IONiseR Version: 2.12.0 Depends: R (>= 3.4) Imports: rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2, methods, BiocGenerics, XVector, tibble, stats, BiocParallel, bit64, stringr, utils Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData License: MIT + file LICENSE MD5sum: 43ec89e694e98c336c721ade70edbb18 NeedsCompilation: no Package: iPAC Version: 1.32.0 Depends: R(>= 2.15),gdata, scatterplot3d, Biostrings, multtest License: GPL-2 MD5sum: 45228075d9b138a35ff4be35c3212f43 NeedsCompilation: no Package: ipdDb Version: 1.6.0 Depends: R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1), AnnotationHub Imports: Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats, assertthat Suggests: knitr, rmarkdown, testthat 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License: Artistic-2.0 MD5sum: 9a50c66e2623a607b0442ea4bc8ce600 NeedsCompilation: yes Package: MethylMix Version: 2.18.0 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: d867c0fd9ab415391403bcd2f0e364e5 NeedsCompilation: no Package: methylMnM Version: 1.26.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: d5e545f467bd0bbb643dda916904bab8 NeedsCompilation: yes Package: methylPipe Version: 1.22.0 Depends: R (>= 3.2.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) MD5sum: e1319a8052755fae4901511b0a3d386c NeedsCompilation: yes 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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: 5e157593c1586698989938117bc764bc NeedsCompilation: no Package: methyvim Version: 1.10.0 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: 3faba7b7e2b243d2095e12ff1a10c48d NeedsCompilation: no Package: MetID Version: 1.6.0 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: 3fc6b8f29749e4e4bd62a1086d9c474f NeedsCompilation: no Package: MetNet Version: 1.6.0 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: 958b80d8d39c6e687c800c3f34440346 NeedsCompilation: no Package: mfa Version: 1.10.0 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 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Version: 1.10.0 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: 1f1df9b06dcd88a3a7624d99091f46f1 NeedsCompilation: no Package: microbiomeDASim Version: 1.2.0 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: f8a4cdac92dc2cf6de1c6cc3055bee43 NeedsCompilation: no Package: MicrobiotaProcess Version: 1.0.5 Depends: R (>= 4.0.0) Imports: ape, plyr, tidyr, ggplot2, phyloseq, magrittr, dplyr, Biostrings, ggrepel, vegan, rentrez, reshape, zoo, ggtree, tidytree, gtools, MASS, methods, randomForest, rlang, tibble, grDevices, stats, utils, coin, ggsignif, scales, Rmisc, DECIPHER, biomformat, yaml, phangorn, patchwork Suggests: DT, 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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: 1f89f0fcdf39f8b0c5bd0ee1645207e8 NeedsCompilation: no Package: MIMOSA Version: 1.26.0 Depends: R (>= 3.0.2), MASS, plyr, reshape, Biobase, ggplot2 Imports: methods, Formula, data.table, pracma, MCMCpack, coda, modeest, testthat, Rcpp, scales, dplyr, tidyr, rlang LinkingTo: Rcpp, RcppArmadillo Suggests: parallel, knitr License: MIT + file LICENSE MD5sum: b9b7940906e3e0d7024596855424fc33 NeedsCompilation: yes Package: MineICA Version: 1.28.0 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: 4d6077af3dbee802a3b0ebb8e88cadca NeedsCompilation: no Package: minet Version: 3.46.0 Imports: infotheo License: Artistic-2.0 MD5sum: 1d363ad19e499adf005f3692658b1803 NeedsCompilation: yes Package: minfi Version: 1.34.0 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 (>= 0.9.8), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 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GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA License: GPL-3 MD5sum: 9ffe7922179498bc955cae4a6e14fd00 NeedsCompilation: no Package: MiRaGE Version: 1.30.0 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: 75d6c45678fef569a2fc6234d13db523 NeedsCompilation: no Package: miRBaseConverter Version: 1.12.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils License: GPL (>= 2) MD5sum: 939b52b1803d348f07ebe9d84a4a8ee2 NeedsCompilation: no Package: miRcomp Version: 1.18.0 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: d168d9fdcb4aadac21a7ed1403847f47 NeedsCompilation: no Package: mirIntegrator Version: 1.18.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: 51a0d19cb8a6d5b53002da2312e068d2 NeedsCompilation: no Package: miRLAB Version: 1.18.0 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: e7e28252d4ed5ce9a2a0d7d177330c67 NeedsCompilation: no Package: miRmine Version: 1.10.0 Depends: R (>= 3.4), SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, DESeq2 License: GPL (>= 3) 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GSEABase, org.Hs.eg.db, MatrixCorrelation, energy Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 03da565f7436553bf26c266915380fb6 NeedsCompilation: yes Package: miRspongeR Version: 1.14.0 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: f34a3a7dd5a42c04cc7050271cbd06ac NeedsCompilation: yes Package: Mirsynergy Version: 1.23.0 Depends: R (>= 3.0.2), igraph, ggplot2 Imports: graphics, grDevices, gridExtra, Matrix, parallel, RColorBrewer, reshape, scales, utils Suggests: glmnet, RUnit, BiocGenerics, knitr License: GPL-2 MD5sum: 7b8ffc3444cbaf80e94df54701cd8381 NeedsCompilation: no Package: missMethyl Version: 1.22.0 Depends: R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Imports: AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData License: GPL-2 MD5sum: 05fad03bc0e55cf107681a890163fb2e NeedsCompilation: no Package: missRows Version: 1.8.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: a3cf5707172d198efa3a77578c684bbe NeedsCompilation: no Package: mitch Version: 1.0.10 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: 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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: 8c3dd5699b990edc89a074ea53e65abc NeedsCompilation: no Package: MLP Version: 1.36.0 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: 22434aeab4013111c71861f0feacbeeb NeedsCompilation: no Package: MLSeq Version: 2.6.0 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: 63c7335444b57cfd031b03f57c09bac7 NeedsCompilation: no Package: MMAPPR2 Version: 1.2.0 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: 824a482a059bf03985059a1d10a7f6b8 NeedsCompilation: no Package: MMDiff2 Version: 1.16.0 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: 0c359e791290e2bf6f2e97f6693b974d NeedsCompilation: no Package: MmPalateMiRNA Version: 1.37.0 Depends: R (>= 2.13.0), methods, Biobase, xtable, limma, statmod, lattice, vsn Imports: limma, lattice, Biobase Suggests: GOstats, graph, Category, org.Mm.eg.db, microRNA, targetscan.Mm.eg.db, RSQLite, DBI, AnnotationDbi, 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WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 3be1417588c3595d9e2ef487f95f37c2 NeedsCompilation: no Package: Modstrings Version: 1.4.1 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: f8dcfc8662962d6ca36a841528767403 NeedsCompilation: no Package: MOFA Version: 1.4.0 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: 9202e66bfeecc3dcd179c64ee767da51 NeedsCompilation: yes Package: mogsa Version: 1.22.1 Depends: R (>= 3.4.0) Imports: methods, graphite, genefilter, 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BiocParallel, qqman, pheatmap, methods, metap, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, BLMA, GenomeInfoDb Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 7ac2e48f77469ce945f3d598daf7f857 NeedsCompilation: no Package: MultiMed Version: 2.10.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE MD5sum: cebd13920bc7b54b787667b035c79ddf NeedsCompilation: no Package: multiMiR Version: 1.10.0 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: 07778d43eda39031d9de416139fc7107 NeedsCompilation: no Package: multiOmicsViz Version: 1.12.0 Depends: R (>= 3.3.2) Imports: methods, parallel, doParallel, foreach, grDevices, graphics, utils, SummarizedExperiment, stats Suggests: BiocGenerics License: LGPL MD5sum: 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Suggests: paxtoolsr, BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, cgdsr License: LGPL-3 + file LICENSE MD5sum: 9c68f2c02ee856cdad65413086382162 NeedsCompilation: no Package: netDx Version: 1.0.4 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 Suggests: curatedTCGAData, TCGAutils, rmarkdown, testthat, knitr License: MIT + file LICENSE MD5sum: 5af4f3e4e581bd442302046a2eb73033 NeedsCompilation: no Package: nethet Version: 1.20.1 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: 4a0c281bcd03a49ea881280657f6f870 NeedsCompilation: yes Package: 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License: MIT + file LICENSE MD5sum: 14292f6a56df252e903a590d438253ad NeedsCompilation: no Package: normalize450K Version: 1.16.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: 31413ee08849a6e4552165c1ddb19c98 NeedsCompilation: no Package: NormalyzerDE Version: 1.6.0 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: 1d2443b58cc04fb0a4abfed28baf61cb NeedsCompilation: no Package: NormqPCR Version: 1.34.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: 08a0f7e3e91b1f5fbea22a0799d725ff NeedsCompilation: no Package: normr Version: 1.14.0 Depends: R (>= 3.3.0) Imports: methods, stats, utils, grDevices, parallel, GenomeInfoDb, GenomicRanges, IRanges, Rcpp (>= 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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: 76a4975d88a8319a7f275fa27692e698 NeedsCompilation: yes Package: oligoClasses Version: 1.50.4 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: 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parallel, grDevices, graphics, stats, utils, methods, BiocGenerics Suggests: knitr, rmarkdown, testthat, devtools, BiocManager License: MIT + file LICENSE MD5sum: 6fba129d8781d0c053c37dceea03d0a6 NeedsCompilation: no Package: OmicsMarkeR Version: 1.19.0 Depends: R (>= 3.2.0) Imports: graphics, stats, utils, plyr (>= 1.8), data.table (>= 1.9.4), caret (>= 6.0-37), DiscriMiner (>= 0.1-29), e1071 (>= 1.6-1), randomForest (>= 4.6-10), gbm (>= 2.1), pamr (>= 1.54.1), glmnet (>= 1.9-5), caTools (>= 1.14), foreach (>= 1.4.1), permute (>= 0.7-0), assertive (>= 0.3-0), assertive.base (>= 0.0-1) Suggests: testthat, BiocStyle, knitr License: GPL-3 MD5sum: e4900ca71d1be679463a2c85a0236fa2 NeedsCompilation: no Package: OMICsPCA Version: 1.6.0 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: 3c535d164b29e1ab8812b2b12b177bb0 NeedsCompilation: no Package: omicsPrint Version: 1.8.0 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: f3ec2b9a0a5622f27546fd3876da56c0 NeedsCompilation: no Package: OmnipathR Version: 1.2.1 Depends: R(>= 3.6.0), igraph, graphics, methods, utils Imports: dplyr, rlang Suggests: tidyr, dnet, gprofiler2, BiocStyle, testthat, knitr, rmarkdown, ggplot2, ggraph License: MIT + file LICENSE MD5sum: 063a3d2d60c8fe0c4642f8ffae3509e0 NeedsCompilation: no Package: Onassis Version: 1.10.0 Depends: R (>= 4.0), rJava, OnassisJavaLibs Imports: GEOmetadb, 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dplyr, smatr, ggplot2, ggrepel LinkingTo: Rcpp Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander License: GPL (>= 3) MD5sum: 9ff9bd4b8b972166c306df81d81b0d19 NeedsCompilation: yes Package: oneSENSE Version: 1.10.0 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: 1dac2e33ee6186e258c7399c85fe540d NeedsCompilation: no Package: onlineFDR Version: 1.6.0 Imports: stats Suggests: knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: dfd1d09eeb0a22b59cac783a6673790b NeedsCompilation: no Package: ontoProc Version: 1.10.1 Depends: R (>= 3.5), ontologyIndex Imports: Biobase, S4Vectors, methods, AnnotationDbi, stats, utils, shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle, SingleCellExperiment, SingleR License: Artistic-2.0 MD5sum: 2502f63a1415fbefaab36dd53b43be74 NeedsCompilation: no Package: openCyto Version: 2.0.0 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: 5d53f0d942d89a06eb21fc7979105745 NeedsCompilation: yes Package: openPrimeR Version: 1.10.4 Depends: R (>= 4.0) 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), 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rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales License: GPL-2 MD5sum: 3964802c93d2f8f8b28226de5525ca8d NeedsCompilation: yes Package: PAA Version: 1.22.0 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: fb439b76f25b79c7bab7873458bcf7dd NeedsCompilation: yes Package: packFinder Version: 1.0.0 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: 9430a6b96196d1d1a9f7bede28377905 NeedsCompilation: no Package: PADOG Version: 1.30.0 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) 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b0e37c8f221c965568648c6c2d5cf591 NeedsCompilation: no Package: ROntoTools Version: 2.16.0 Depends: methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz Suggests: RUnit, BiocGenerics License: CC BY-NC-ND 4.0 + file LICENSE MD5sum: d0381a9cc76c4e18a0e28bd556c5b590 NeedsCompilation: no Package: ropls Version: 1.20.0 Depends: Biobase Imports: graphics, grDevices, methods, MultiDataSet, stats Suggests: BiocGenerics, BiocStyle, knitr, multtest, omicade4, rmarkdown, testthat License: CeCILL MD5sum: b7d01611157b60494e7d49d22d8d9a53 NeedsCompilation: no Package: ROSeq Version: 1.0.0 Depends: R (>= 4.0) Imports: pbmcapply, edgeR, limma Suggests: knitr, rmarkdown, testthat, RUnit, BiocGenerics License: GPL-3 MD5sum: 5604d34d498212a3bcad227c4cfe0f78 NeedsCompilation: no Package: ROTS Version: 1.16.0 Depends: R (>= 3.3) Imports: Rcpp, stats, Biobase, methods LinkingTo: Rcpp Suggests: testthat License: GPL (>= 2) MD5sum: 9adba5452dca491c0ab3c16042944f73 NeedsCompilation: yes Package: RPA Version: 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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 | file LICENSE MD5sum: 9610d218b688348638aac8d4e260f728 NeedsCompilation: yes Package: rsbml Version: 2.46.0 Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils Imports: BiocGenerics, graph, utils License: Artistic-2.0 MD5sum: ead8624d4d5159b1c78d1c64164e9161 NeedsCompilation: yes Package: rScudo Version: 1.4.0 Depends: R (>= 3.6) Imports: methods, stats, igraph, stringr, grDevices, Biobase, S4Vectors, SummarizedExperiment, BiocGenerics Suggests: testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret, e1071, parallel, doParallel License: GPL-3 MD5sum: 66708d805aa8301ee9ca060d524aa331 NeedsCompilation: no Package: RSeqAn Version: 1.8.0 Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: ba82c45e6f3b85fe087206fb8320ab47 NeedsCompilation: yes Package: Rsubread Version: 2.2.6 Imports: grDevices, stats, utils, Matrix License: GPL (>= 3) MD5sum: 91858da87d35e6b5fe8cb8238e927769 NeedsCompilation: yes Package: RSVSim Version: 1.28.0 Depends: R (>= 3.0.0), Biostrings, GenomicRanges Imports: methods, IRanges, ShortRead Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer License: LGPL-3 MD5sum: a7e8517029f6f27571167e8368351a9c NeedsCompilation: no Package: rSWeeP Version: 1.0.0 Depends: R (>= 4.0) Imports: pracma, stats Suggests: Biostrings, methods, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: ad04fd103802b80762e28e12bae4094c NeedsCompilation: no Package: rTANDEM Version: 1.27.0 Depends: XML, Rcpp, data.table (>= 1.8.8) Imports: 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RaggedExperiment, RCircos, RCurl, RJSONIO, S4Vectors (>= 0.23.10), stats, stringr, SummarizedExperiment, survival, TCGAutils, XML Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown License: file LICENSE MD5sum: 6b99f86634cd4d5c2c18cec5898e6f1f NeedsCompilation: no Package: RTN Version: 2.12.1 Depends: R (>= 3.5.0), methods, Imports: RedeR, minet, viper, mixtools, snow, stats, limma, data.table, IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr, pheatmap, grDevices, graphics, utils Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 74d15eb450630afd16cb2038699fc45f NeedsCompilation: no Package: RTNduals Version: 1.12.2 Depends: R(>= 3.5), RTN(>= 2.12.1), methods Imports: graphics, grDevices, stats, utils Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: a939535e7ba71c863582974a3c4f32ed NeedsCompilation: no Package: RTNsurvival Version: 1.12.2 Depends: R(>= 3.5), RTN(>= 2.12.1), RTNduals(>= 1.12.1), methods Imports: survival, RColorBrewer, grDevices, graphics, stats, utils, scales, data.table, egg, ggplot2, pheatmap, dunn.test Suggests: Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 31c590754dc267ec4f469344400963ca NeedsCompilation: no Package: RTopper Version: 1.34.0 Depends: R (>= 2.11.0), Biobase Imports: limma, multtest Suggests: limma, org.Hs.eg.db, KEGG.db, GO.db License: GPL (>= 3) MD5sum: 042b7b6bbdde992a384f6c42368ed7f2 NeedsCompilation: no Package: rtracklayer Version: 1.48.0 Depends: R (>= 3.3), methods, GenomicRanges (>= 1.37.2) Imports: XML (>= 1.98-0), BiocGenerics (>= 0.25.1), S4Vectors (>= 0.23.18), IRanges (>= 2.13.13), XVector (>= 0.19.7), GenomeInfoDb (>= 1.15.2), Biostrings (>= 2.47.6), zlibbioc, RCurl (>= 1.4-2), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6), tools LinkingTo: S4Vectors, IRanges, XVector Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit License: Artistic-2.0 + file LICENSE MD5sum: 6ffb9ba086f4cfc95cd1ab58cff4a235 NeedsCompilation: yes Package: Rtreemix Version: 1.50.0 Depends: R (>= 2.5.0) Imports: methods, graph, Biobase, Hmisc Suggests: Rgraphviz License: LGPL MD5sum: ace5dd73216246bc5ffe4a9f154483fe NeedsCompilation: yes Package: rTRM Version: 1.26.0 Depends: R (>= 2.10), igraph (>= 1.0) Imports: AnnotationDbi, DBI, RSQLite Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2 License: GPL-3 MD5sum: 597bda486ae37722a8cfbe9695382bdf NeedsCompilation: no Package: rTRMui Version: 1.26.0 Imports: shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 459e6054005efe492a5679eaab2aa385 NeedsCompilation: no Package: runibic Version: 1.10.0 Depends: R (>= 3.4.0), biclust, 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(>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva Imports: utils, methods, MASS, tools, IRanges Suggests: pd.hg.u95a License: MIT MD5sum: db2d578718261cad74118432db59184d NeedsCompilation: no Package: SCANVIS Version: 1.2.0 Depends: R (>= 3.6) Imports: IRanges,plotrix,RCurl,rtracklayer Suggests: knitr, rmarkdown License: file LICENSE MD5sum: d91b48ff279bdba451ee21e4ebd063ac NeedsCompilation: no Package: scater Version: 1.16.2 Depends: SingleCellExperiment, ggplot2 Imports: BiocGenerics, SummarizedExperiment, Matrix, ggbeeswarm, rlang, grid, DelayedArray, DelayedMatrixStats, methods, S4Vectors, stats, utils, viridis, Rcpp, BiocNeighbors, BiocSingular, BiocParallel LinkingTo: Rcpp, beachmat Suggests: BiocStyle, BiocFileCache, biomaRt, beachmat, cowplot, destiny, knitr, scRNAseq, robustbase, rmarkdown, Rtsne, uwot, NMF, testthat, pheatmap, Biobase, limma, DropletUtils License: GPL-3 MD5sum: 55a506df196075acf640a12c62de2148 NeedsCompilation: yes Package: scBFA Version: 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SingleCellExperiment, scran, scater, data.table, dplyr, ggplot2, randomForest, graphics, methods, stats, DelayedArray Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: afcc9256a6224408acb524e4254827e5 NeedsCompilation: no Package: scDD Version: 1.12.0 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: df7e550089223003962c8af4a4a31b08 NeedsCompilation: yes Package: scde Version: 2.16.0 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: 36a4bfa9630e4326af300741d64d97aa NeedsCompilation: yes Package: scds Version: 1.4.0 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: f1adb44733fc3b3f6712c0ec9a96c947 NeedsCompilation: no Package: scFeatureFilter Version: 1.8.0 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: 2186df09ee66d5c0fc3f85c50ddac819 NeedsCompilation: no Package: scfind Version: 1.9.0 Depends: R(>= 3.4) Imports: SingleCellExperiment, SummarizedExperiment, methods, stats, bit, dplyr, hash, reshape2, Rcpp(>= 0.12.12) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 207cc2bcdfd7ab507faf3ab30dd7a92d NeedsCompilation: yes Package: scGPS Version: 1.2.0 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: 0902393233bc29273fbc9cf4805bf6ba NeedsCompilation: yes Package: schex Version: 1.2.0 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: e99694e5fdfd44ffb1a0788548ed4fb7 NeedsCompilation: no Package: scHOT Version: 1.0.0 Depends: R (>= 4.0) Imports: S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix, SummarizedExperiment, IRanges, methods, stats, BiocParallel, reshape, ggplot2, igraph, grDevices, ggforce, graphics Suggests: knitr, rmarkdown, scater, scattermore, scales, matrixStats, deldir License: GPL-3 MD5sum: ba52789340e08402d3b672bdfb0f962d NeedsCompilation: no Package: ScISI Version: 1.60.0 Depends: R (>= 2.10), GO.db, RpsiXML, annotate, apComplex Imports: AnnotationDbi, GO.db, RpsiXML, annotate, methods, org.Sc.sgd.db, utils Suggests: ppiData, xtable License: LGPL MD5sum: a72a984035ace5ade71cb8c24b8a95a1 NeedsCompilation: no Package: scMAGeCK Version: 1.0.0 Imports: Seurat, stats, utils Suggests: knitr, rmarkdown License: BSD_2_clause MD5sum: 35812c5da07ba2b09e58d764a3f3f512 NeedsCompilation: yes Package: scmap Version: 1.10.0 Depends: R(>= 3.4) Imports: Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 1d535369ceeb63f93339562c468e5b35 NeedsCompilation: yes Package: scMerge Version: 1.4.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, cluster, DelayedArray, DelayedMatrixStats, distr, dplyr, igraph, M3Drop (>= 1.9.4), parallel, pdist, proxy, Rcpp (>= 0.12.18), RcppEigen (>= 0.3.3.4.0), ruv, S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3), SummarizedExperiment LinkingTo: Rcpp (>= 0.12.18), RcppEigen, testthat Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, scater, testthat, badger License: GPL-3 MD5sum: 599273b0f3366b9c1ca540614dc6894f NeedsCompilation: yes Package: scmeth Version: 1.8.0 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: ed0154187e6ed40514c7253ccd58524c NeedsCompilation: no Package: SCnorm Version: 1.10.0 Depends: R (>= 3.4.0), Imports: SingleCellExperiment, SummarizedExperiment, stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, S4Vectors, ggplot2, forcats, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) MD5sum: 0de174f046310f05289809e42dbc33ef NeedsCompilation: no Package: scone Version: 1.12.0 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: 089770a07ddfa9524d6fa67bc343240f NeedsCompilation: no Package: Sconify Version: 1.8.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: df2da2d423d9a9d6a28a39672a459aa4 NeedsCompilation: no Package: SCOPE Version: 1.0.0 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: bc3e7fc400f2f18a954820155ba65ac8 NeedsCompilation: no Package: scoreInvHap Version: 1.10.0 Depends: R (>= 3.4.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: cd4e5b31ae255a1d9aab7808ff4a0429 NeedsCompilation: no Package: scPCA Version: 1.2.0 Depends: R (>= 3.6) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca, cluster, kernlab, origami Suggests: testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, Matrix, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark License: MIT + file LICENSE MD5sum: 19ae8db9a11ea6bbe176ef6a4f9e151f NeedsCompilation: no Package: scPipe Version: 1.10.0 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: 4ed9fbc49ab25b90b773e455edeb8626 NeedsCompilation: yes Package: scran Version: 1.16.0 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, IRanges, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, scater, edgeR, limma, BiocNeighbors, igraph, statmod, DelayedArray, DelayedMatrixStats, BiocSingular, dqrng LinkingTo: Rcpp, beachmat, BH, dqrng Suggests: testthat, BiocStyle, knitr, beachmat, HDF5Array, scRNAseq, dynamicTreeCut, DESeq2, monocle, Biobase, pheatmap License: GPL-3 MD5sum: 2276dee3b19eaf33b6a17712ab0a6555 NeedsCompilation: yes Package: scRecover Version: 1.4.1 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 (>= 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MD5sum: a421cf79cc478985d3d8430b83c34a00 NeedsCompilation: no Package: scsR Version: 1.23.0 Depends: R (>= 2.14.0), STRINGdb, methods, BiocGenerics, Biostrings, IRanges, plyr, tcltk Imports: sqldf, hash, ggplot2, graphics,grDevices, RColorBrewer Suggests: RUnit License: GPL-2 MD5sum: f2c5922c993ddb5775435451204b4415 NeedsCompilation: no Package: scTensor Version: 1.4.3 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, MeSH.Hsa.eg.db, LRBase.Mmu.eg.db, MeSH.Mmu.eg.db, LRBaseDbi, Seurat, Homo.sapiens License: Artistic-2.0 MD5sum: 4a29dde89fbe228fb2dc897b5a859b88 NeedsCompilation: no Package: scTGIF Version: 1.2.2 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: e0462b37da4e5ff9f3c0a6ebc42ba0aa NeedsCompilation: no Package: scTHI Version: 1.0.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown License: GPL-2 MD5sum: cfbddad1ecabb531c9bbc3ae43592dcb NeedsCompilation: no Package: SDAMS Version: 1.8.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: 455406ecd0e79368cc6701a575e6901f NeedsCompilation: no Package: segmentSeq Version: 2.22.0 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: f27df31700eaaaca05ac1699eca76605 NeedsCompilation: no Package: selectKSigs Version: 1.0.0 Depends: R(>= 3.6) Imports: HiLDA, magrittr, gtools, methods, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr License: GPL-3 MD5sum: fd26882e847a36947277c9fa238d35f9 NeedsCompilation: yes Package: SELEX Version: 1.20.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: dd0bd3d7f5720167e02d5eaff0bc1807 NeedsCompilation: no Package: SemDist Version: 1.22.0 Depends: R (>= 3.1), AnnotationDbi, GO.db, annotate Suggests: GOSemSim License: GPL (>= 2) MD5sum: f6fa1f5c6b512db2da11f39b096bc459 NeedsCompilation: no Package: semisup Version: 1.12.4 Depends: R (>= 3.0.0) Imports: VGAM Suggests: knitr, testthat, SummarizedExperiment License: GPL-3 MD5sum: 89f72c3678e29e25c31a90739965d23a NeedsCompilation: no Package: 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ggplot2 License: LGPL-3 MD5sum: 97b6a5d80fc0005f0a5ed05985dbdcc3 NeedsCompilation: yes Package: seqCAT Version: 1.10.0 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: 9926f87d17698428c78d0ea79da1aabb NeedsCompilation: no Package: seqCNA Version: 1.34.0 Depends: R (>= 3.0), GLAD (>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot (>= 0.99), methods License: GPL-3 MD5sum: 2d9f8f5ed75edb1c515088063e2cdd28 NeedsCompilation: yes Package: seqcombo Version: 1.10.0 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: a73f243bf7b9649a1ae7e03fa4f34300 NeedsCompilation: no Package: SeqGSEA Version: 1.28.0 Depends: Biobase, doParallel, DESeq Imports: methods, biomaRt Suggests: easyRNASeq, GenomicRanges License: GPL (>= 3) MD5sum: 414109ac1c5c99bd9eda8fa718e98541 NeedsCompilation: no Package: seqLogo Version: 1.54.3 Depends: methods, grid Imports: stats4 License: LGPL (>= 2) MD5sum: d06a56416c5efae9c75a7b3eb4b5d43f NeedsCompilation: no Package: seqPattern Version: 1.20.0 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: ab8ef689eea1d8ad55dd8d12da9bde40 NeedsCompilation: no Package: seqplots Version: 1.26.0 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: 630baf5e7fa44df3d944bcce22d74318 NeedsCompilation: no Package: seqsetvis Version: 1.8.0 Depends: R (>= 3.5), ggplot2 Imports: data.table, eulerr, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, IRanges, limma, methods, parallel, pbapply, png, RColorBrewer, Rsamtools, rtracklayer, S4Vectors, stats Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, cowplot, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: ecb037d91fe9c637b97e5b14d11f869d NeedsCompilation: no Package: SeqSQC Version: 1.10.0 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: c5af7e032fc7134d295903bdf3591dee NeedsCompilation: no Package: seqTools Version: 1.22.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 2c725f07f8729ca44add826914c5b5f1 NeedsCompilation: yes Package: SeqVarTools Version: 1.26.0 Depends: SeqArray Imports: grDevices, graphics, stats, methods, Biobase, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, dplyr, rlang, tidyr Suggests: BiocGenerics, BiocStyle, RUnit, stringr License: GPL-3 MD5sum: fb32ef7d473c327095aa828e9b05dcc8 NeedsCompilation: no Package: sesame Version: 1.6.0 Depends: R (>= 3.6), sesameData, methods Imports: BiocParallel, grDevices, utils, illuminaio, MASS, GenomicRanges, IRanges, grid, preprocessCore, stats, S4Vectors, randomForest, wheatmap, ggplot2, parallel, matrixStats, DNAcopy, HDF5Array, SummarizedExperiment Suggests: scales, knitr, rmarkdown, testthat, minfi, FlowSorted.CordBloodNorway.450k, FlowSorted.Blood.450k, dplyr, tidyr, BiocStyle License: MIT + file LICENSE MD5sum: 46b28aaccd86955287317b1a91cc7b0c NeedsCompilation: no Package: SEtools Version: 1.2.0 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: 220393caf5bd125fec31c2e8e0f3fe1a NeedsCompilation: no Package: sevenbridges Version: 1.18.1 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: a12cabf15fdf00d5e6b48eb15e89f7a0 NeedsCompilation: no Package: sevenC Version: 1.8.0 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: b6f3ff6fa7312dec3163ae2bd47fd16c NeedsCompilation: no Package: SGSeq Version: 1.22.0 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: 7e20936217f32e9f94eec7e17dfe4e57 NeedsCompilation: no Package: SharedObject Version: 1.2.2 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, Rcpp Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 36c8511c49fc34b5c725759dd369a436 NeedsCompilation: yes Package: shinyMethyl Version: 1.24.0 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: 23eb7dab8892282f6c43d1088d82a8bb NeedsCompilation: no Package: shinyTANDEM Version: 1.26.0 Depends: rTANDEM (>= 1.3.5), shiny, mixtools, methods, xtable License: GPL-3 MD5sum: 923c47758ec08a2fdbe134a5039fa88d NeedsCompilation: no Package: ShortRead Version: 1.46.0 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: 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1.35.0 Depends: Biobase, CGHbase, methods, mvtnorm, Imports: corpcor (>= 1.6.2), graphics, igraph, limma, marray, MASS, penalized, quadprog, snowfall, stats Suggests: CGHcall License: GPL (>= 2) MD5sum: 18539933f62a264bdb01aad11844d575 NeedsCompilation: no Package: SigCheck Version: 2.20.0 Depends: R (>= 3.2.0), MLInterfaces, Biobase, e1071, BiocParallel, survival Imports: graphics, stats, utils, methods Suggests: BiocStyle, breastCancerNKI, qusage License: Artistic-2.0 MD5sum: f8cf64f7861240491e06f8bc0e857553 NeedsCompilation: no Package: sigFeature Version: 1.6.0 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: 7ab7ec861bf13d38f431dc68ad358499 NeedsCompilation: no Package: SigFuge Version: 1.26.0 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: 43b3cb72730290f78f178d3886b3ade1 NeedsCompilation: no Package: siggenes Version: 1.62.0 Depends: Biobase, multtest, splines, methods Imports: stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: 0f0afee19215cf5b504de6329b82c173 NeedsCompilation: no Package: sights Version: 1.14.0 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: fc7d1bc7e63eafd25d05ccecf7f5e008 NeedsCompilation: no Package: signatureSearch Version: 1.2.5 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, Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase, DelayedArray LinkingTo: Rcpp Suggests: knitr, testthat, rmarkdown, BiocStyle, org.Hs.eg.db License: Artistic-2.0 MD5sum: 958f2f6ce63fd33c51cf180bb148c8b8 NeedsCompilation: yes Package: signeR Version: 1.14.0 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: ff5fb45f2e939aa9c3387494ec82558c NeedsCompilation: yes Package: signet Version: 1.7.0 Depends: R (>= 3.4.0) Imports: graph, igraph, RBGL, graphics, utils, stats, methods Suggests: graphite, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: c9c427ffb47d29b7388cb4e379644bd7 NeedsCompilation: no Package: sigPathway Version: 1.56.0 Depends: R (>= 2.10) Suggests: hgu133a.db (>= 1.10.0), XML (>= 1.6-3), AnnotationDbi 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mzR, ggplot2, grid, reshape2, grDevices, stats, utils Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: c19af063055b65fc34c211c507b1d689 NeedsCompilation: no Package: SimBindProfiles Version: 1.26.0 Depends: R (>= 2.10), methods, Ringo Imports: limma, mclust, Biobase License: GPL-3 MD5sum: d10d5f15f8f577ee0fb531341a38afb1 NeedsCompilation: no Package: SIMD Version: 1.6.0 Depends: R (>= 3.5.0) Imports: edgeR, statmod, methylMnM, stats, utils Suggests: BiocStyle, knitr,rmarkdown License: GPL-3 MD5sum: d53ad0c1f2bde555ea6da6faf4bc4fad NeedsCompilation: yes Package: SimFFPE Version: 1.0.0 Depends: Biostrings Imports: dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods Suggests: BiocStyle License: LGPL-3 MD5sum: 8d47fd84b75e7cc45dafd190f7e09366 NeedsCompilation: no Package: similaRpeak Version: 1.20.0 Depends: R6 (>= 2.0) Imports: stats Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 8a46d691afd3582bceee416101467d26 NeedsCompilation: no Package: SIMLR Version: 1.14.0 Depends: R (>= 4.0), Imports: parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy, RSpectra LinkingTo: Rcpp Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph License: file LICENSE MD5sum: 5091d85c3c34df812869fd2667d052e5 NeedsCompilation: yes Package: simpleaffy Version: 2.64.0 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: ecfdb652d02addc1215832401becfa15 NeedsCompilation: yes Package: simulatorZ Version: 1.22.0 Depends: R (>= 3.5), Biobase, SummarizedExperiment, survival, CoxBoost, BiocGenerics Imports: graphics, stats, gbm, Hmisc, GenomicRanges, methods Suggests: RUnit, BiocStyle, curatedOvarianData, parathyroidSE, superpc License: Artistic-2.0 MD5sum: befa904865994b49942890fdd5fc0ccb NeedsCompilation: yes Package: sincell Version: 1.20.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: GPL (>= 2) MD5sum: 22c0f6a682cd1faae8eed7e4879a2ba4 NeedsCompilation: yes Package: SingleCellExperiment Version: 1.10.1 Depends: SummarizedExperiment Imports: S4Vectors (>= 0.23.19), methods, BiocGenerics, utils, stats Suggests: testthat, BiocStyle, knitr, rmarkdown, scRNAseq, Rtsne, Matrix License: GPL-3 MD5sum: c640d435f6eccbbe9fb280cc492c7004 NeedsCompilation: no Package: SingleCellSignalR Version: 1.0.0 Depends: R (>= 4.0) Imports: BiocManager, circlize, limma, igraph, gplots, grDevices, edgeR, SIMLR, data.table, pheatmap, stats, Rtsne, graphics, stringr, foreach, multtest, scran, utils, Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 4c3b3e18298c8f3ab7082293e0fa0c7c NeedsCompilation: no Package: singleCellTK Version: 1.8.0 Depends: R (>= 3.5), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase Imports: ape, colourpicker, cluster, ComplexHeatmap, data.table, DESeq2, DT, ggplot2, ggtree, gridExtra, GSVA (>= 1.26.0), GSVAdata, limma, MAST, matrixStats, methods, multtest, plotly, RColorBrewer, Rtsne, S4Vectors, shiny, shinyjs, shinyBS, sva, reshape2, AnnotationDbi, shinyalert, circlize, enrichR, celda, shinycssloaders, shinythemes, umap Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, bladderbatch, rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable, spelling, GSEABase License: MIT + file LICENSE MD5sum: f691bd989342b4d6164b78527dd9f17b NeedsCompilation: no Package: SingleR Version: 1.2.4 Depends: SummarizedExperiment Imports: methods, Matrix, S4Vectors, BiocGenerics, DelayedArray, DelayedMatrixStats, BiocNeighbors, BiocParallel, BiocSingular, stats, utils, Rcpp, ExperimentHub LinkingTo: Rcpp, beachmat Suggests: testthat, knitr, rmarkdown, BiocStyle, beachmat, SingleCellExperiment, scater, scRNAseq, scran, ggplot2, pheatmap, grDevices, gridExtra, viridis, AnnotationHub, AnnotationDbi License: GPL-3 + file LICENSE MD5sum: 5459cb1954301acc0ce52cc5a9818c24 NeedsCompilation: yes Package: singscore Version: 1.8.0 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: 21a680f6898f8be4a3ab694a5972a913 NeedsCompilation: no Package: SISPA Version: 1.18.0 Depends: R (>= 3.2),genefilter,GSVA,changepoint Imports: data.table, plyr, ggplot2 Suggests: knitr License: GPL-2 MD5sum: d9f1dc076660228dc46819ccd58e9d43 NeedsCompilation: no Package: sitePath Version: 1.4.2 Depends: R (>= 3.6.0) Imports: ape, seqinr, Rcpp, methods, graphics, utils, stats LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 36939b07b0eeb87183b93beb51c2eaf0 NeedsCompilation: yes Package: sizepower Version: 1.58.0 Depends: stats License: LGPL MD5sum: 791e61800e9c63539366da03856e0f19 NeedsCompilation: no Package: skewr Version: 1.20.0 Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports: minfi, S4Vectors (>= 0.19.1), RColorBrewer Suggests: GEOquery, knitr, minfiData License: GPL-2 MD5sum: ad6a666be12d721aa4eda4feb5ff8bf8 NeedsCompilation: no Package: slalom Version: 1.10.0 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: aef1b2a8c5bf0e945188202651717118 NeedsCompilation: yes Package: SLGI Version: 1.48.0 Depends: R (>= 2.10), ScISI, 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DESeq2, DEXSeq (>= 1.9.7), testthat, knitr License: MIT + file LICENSE MD5sum: 2e7d4b1f1e26dee40ca99cbf535c81ab NeedsCompilation: no Package: SummarizedBenchmark Version: 2.6.0 Depends: R (>= 3.6), tidyr, SummarizedExperiment, S4Vectors, BiocGenerics, methods, UpSetR, rlang, stringr, utils, BiocParallel, ggplot2, mclust, dplyr, digest, sessioninfo, crayon, tibble Suggests: iCOBRA, BiocStyle, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt License: GPL (>= 3) MD5sum: 42006fde814e1e74dbd441bf6fceac7f NeedsCompilation: no Package: SummarizedExperiment Version: 1.18.2 Depends: R (>= 3.2), methods, GenomicRanges (>= 1.33.6), Biobase, DelayedArray (>= 0.3.20) Imports: utils, stats, tools, Matrix, BiocGenerics (>= 0.15.3), S4Vectors (>= 0.25.14), IRanges (>= 2.21.6), GenomeInfoDb (>= 1.13.1) Suggests: annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, jsonlite, rhdf5, HDF5Array (>= 1.7.5), airway, RUnit, testthat License: Artistic-2.0 MD5sum: aa68ba5e3ef706d9d3d42627c25a313a NeedsCompilation: no Package: supraHex Version: 1.26.0 Depends: R (>= 3.6), hexbin Imports: ape, MASS, grDevices, graphics, stats, utils, methods License: GPL-2 MD5sum: fd34d1a55b5c73e2b97753af2a3d14b2 NeedsCompilation: no Package: survcomp Version: 1.38.0 Depends: survival, prodlim, R (>= 3.4) Imports: ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid, rmeta, stats, graphics Suggests: Hmisc, CPE, clinfun, xtable, Biobase, BiocManager License: Artistic-2.0 MD5sum: c6f9bba863f94b5bf4697be498a9a2d7 NeedsCompilation: yes Package: survtype Version: 1.4.0 Depends: SummarizedExperiment, pheatmap, survival, survminer, clustvarsel, stats, utils Suggests: maftools, scales, knitr License: Artistic-2.0 MD5sum: a3c3c820929bd87c162b1c6504f216b0 NeedsCompilation: no Package: Sushi Version: 1.26.0 Depends: R (>= 2.10), zoo,biomaRt Imports: graphics, grDevices License: GPL (>= 2) MD5sum: f0b79e9f73991b74e1676f83d8bc3583 NeedsCompilation: no Package: sva Version: 3.36.0 Depends: R (>= 3.2), mgcv, genefilter, BiocParallel Imports: matrixStats, stats, graphics, utils, limma, edgeR Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat License: Artistic-2.0 MD5sum: beed83482d56f66bb0ff5fc649aebdde NeedsCompilation: yes Package: SVAPLSseq Version: 1.13.0 Depends: R (>= 3.4) Imports: methods, stats, SummarizedExperiment, edgeR, ggplot2, limma, lmtest, parallel, pls Suggests: BiocStyle License: GPL-3 MD5sum: 412e5e470d947e132f4c3805cf7a4962 NeedsCompilation: no Package: SWATH2stats Version: 1.18.0 Depends: R(>= 2.10.0) Imports: data.table, reshape2, grid, ggplot2, stats, grDevices, graphics, utils, biomaRt Suggests: testthat, knitr Enhances: imsbInfer, MSstats, PECA, aLFQ License: GPL-3 MD5sum: baf52c78d3906f161fa6bea93d6a589e NeedsCompilation: no Package: SwathXtend Version: 2.10.0 Depends: e1071, openxlsx, VennDiagram, 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NeedsCompilation: no Package: synapter Version: 2.12.0 Depends: R (>= 3.1.0), methods, MSnbase (>= 2.1.2) Imports: RColorBrewer, lattice, qvalue, multtest, utils, tools, Biobase, knitr, Biostrings, cleaver (>= 1.3.3), readr (>= 0.2), rmarkdown (>= 1.0) Suggests: synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle License: GPL-2 MD5sum: f310da8fb65349eb633ff28ee7c29e24 NeedsCompilation: no Package: synergyfinder Version: 2.2.4 Depends: R (>= 3.6.0), methods Imports: drc (>= 2.5-12), reshape2 (>= 1.4.1), ggplot2 (>= 2.1.0), grid (>= 3.2.4), lattice (>= 0.20-33), nleqslv(>= 3.0), stats (>= 3.3.0), graphics (>= 3.3.0), grDevices (>= 3.3.0) Suggests: knitr, rmarkdown License: Mozilla Public License 2.0 MD5sum: e98b501b24e9605663c029a8927d64a8 NeedsCompilation: yes Package: SynExtend Version: 1.0.0 Depends: R (>= 4.0.0), DECIPHER (>= 2.14.0), igraph (>= 1.2.4.1) Imports: methods, Biostrings, S4Vectors, IRanges, utils, stats Suggests: knitr License: GPL-3 MD5sum: 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systemPipeRdata, GenomicAlignments License: Artistic-2.0 MD5sum: 0bac5856f33a958c6cbd7cc108e3636a NeedsCompilation: no Package: TAPseq Version: 1.0.0 Depends: R (>= 4.0) Imports: methods, GenomicAlignments, GenomicRanges, IRanges, BiocGenerics, S4Vectors (>= 0.20.1), GenomeInfoDb, BSgenome, GenomicFeatures, Biostrings, dplyr, tidyr, BiocParallel Suggests: testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer License: MIT + file LICENSE MD5sum: e64119377f29ad3f30eb90ef5a35b762 NeedsCompilation: no Package: target Version: 1.2.0 Depends: R (>= 3.6) Imports: BiocGenerics, GenomicRanges, IRanges, matrixStats, methods, stats, graphics, shiny Suggests: testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS, covr License: GPL-3 MD5sum: 7b34f439975505990d5bf31c6c79430c NeedsCompilation: no Package: TargetScore Version: 1.26.0 Depends: pracma, Matrix Suggests: TargetScoreData, gplots, Biobase, GEOquery License: GPL-2 MD5sum: 5fbdcd54ef0f86f85c34fa41a38106ef NeedsCompilation: no Package: TargetSearch Version: 1.44.0 Depends: ncdf4 Imports: graphics, grDevices, methods, stats, utils, stringr, assertthat Suggests: TargetSearchData, BiocStyle, knitr License: GPL (>= 2) MD5sum: 7d7322ff252b7ef72cb4fd1bd9f621fe NeedsCompilation: yes Package: TarSeqQC Version: 1.18.0 Depends: R (>= 3.5.1), methods, GenomicRanges, Rsamtools (>= 1.9.2), ggplot2, plyr, openxlsx Imports: grDevices, stats, utils, S4Vectors, IRanges, BiocGenerics, reshape2, GenomeInfoDb, BiocParallel, Biostrings, cowplot, graphics, GenomicAlignments, Hmisc Suggests: BiocManager, RUnit License: GPL (>= 2) MD5sum: 06790ae362e37ef1e902fcdafcaa1d43 NeedsCompilation: no Package: TBSignatureProfiler Version: 1.0.0 Depends: R (>= 4.0.0) Imports: ASSIGN (>= 1.23.1), GSVA, SummarizedExperiment, S4Vectors, methods, BiocParallel, ComplexHeatmap, RColorBrewer, ggplot2, reshape2, circlize, glmnet, ROCit, bioDist, readr, boot, DESeq2, caret, ggfortify, e1071, DT, edgeR, singscore, gdata, shiny Suggests: testthat, spelling, lintr, covr, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 5410faf747b1543bbcb6c6b34267f972 NeedsCompilation: no Package: TCC Version: 1.28.0 Depends: R (>= 3.0), methods, DESeq, DESeq2, edgeR, baySeq, ROC Suggests: RUnit, BiocGenerics Enhances: snow License: GPL-2 MD5sum: 6e95f5a29d69af1e902688d66cf0829b NeedsCompilation: no Package: TCGAbiolinks Version: 2.16.4 Depends: R (>= 3.5) Imports: downloader (>= 0.4), grDevices, dplyr, graphics, tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite (>= 1.0.0), plyr, knitr, methods, biomaRt, ggplot2, stringr (>= 1.0.0), IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils, SummarizedExperiment (>= 1.4.0), 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, TCGAbiolinksGUI.data, supraHex, limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra, survival, doParallel, parallel, ggrepel (>= 0.6.3), scales, grid License: GPL (>= 3) MD5sum: ca43fe0a4a890143138a32fd3ab26dd4 NeedsCompilation: no Package: TCGAbiolinksGUI Version: 1.14.0 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: 620b4af9c1d127bdbe10935305784627 NeedsCompilation: no Package: TCGAutils Version: 1.8.1 Depends: R (>= 3.6.0) 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, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: cc524270ecc1fffab344286604bb5a3d NeedsCompilation: no Package: TCseq Version: 1.12.1 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: 2ef3178776a7e2252ba5250d26bc321d NeedsCompilation: no Package: TDARACNE Version: 1.38.0 Depends: 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License: Artistic-2.0 MD5sum: b3bafaf0dfaa39ccae7e5d1e9de47fa0 NeedsCompilation: no Package: TFBSTools Version: 1.26.0 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: 5fffe1125bb06fb6d15d11033135ac2f NeedsCompilation: yes Package: TFEA.ChIP Version: 1.8.0 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: c53216799d1d05097fce69464ba97d87 NeedsCompilation: no Package: TFHAZ Version: 1.10.0 Depends: R(>= 3.4) Imports: GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 630005595ba56d381e0cb3e79a8e0948 NeedsCompilation: no Package: TFutils Version: 1.8.0 Depends: R (>= 3.5.0) Imports: methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase 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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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: 146ee04925b55980105929dbb9e8ee38 NeedsCompilation: no Package: UNDO Version: 1.30.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: acf79f08a4dc24de93fb03c456d79333 NeedsCompilation: no Package: unifiedWMWqPCR Version: 1.24.0 Depends: methods Imports: BiocGenerics, stats, graphics, HTqPCR License: GPL (>= 2) MD5sum: 32cbd3b1c9de8bd8d99e060712a9bfc4 NeedsCompilation: no Package: UniProt.ws Version: 2.28.0 Depends: methods, utils, RSQLite, RCurl, BiocGenerics 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Version: 1.14.0 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: bf6a26190e9fd0940d1e28f687eb07c4 NeedsCompilation: no Package: VanillaICE Version: 1.50.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: 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: 3df28f1dfb9a560593d4a248fbfa294d NeedsCompilation: yes Package: variancePartition Version: 1.18.3 Depends: R (>= 3.6.0), ggplot2, limma, foreach, scales, Biobase, methods Imports: MASS, pbkrtest (>= 0.4-4), lmerTest, iterators, splines, colorRamps, BiocParallel, gplots, progress, reshape2, lme4 (>= 1.1-10), doParallel, grDevices, graphics, utils, stats Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr License: GPL (>= 2) MD5sum: aa3b8c6197e306e8eead624d998f8098 NeedsCompilation: no Package: VariantAnnotation Version: 1.34.0 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.15.3), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.37.4), SummarizedExperiment (>= 1.9.9), Rsamtools (>= 1.99.0) Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.17.24), IRanges (>= 2.13.13), XVector (>= 0.19.7), Biostrings (>= 2.47.6), 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: 0edaa9df55e47902086ce11af641fc29 NeedsCompilation: yes Package: VariantExperiment Version: 1.2.0 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: afeb132b931bb4a551214ffc5971c108 NeedsCompilation: no Package: VariantFiltering Version: 1.24.0 Depends: R (>= 3.0.0), 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), 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