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License: Artistic-2.0 MD5sum: 58af5346b0d77a054e4210a9e28cd9a5 NeedsCompilation: no Package: chimera Version: 1.20.0 Depends: Biobase, GenomicRanges (>= 1.13.3), Rsamtools (>= 1.13.1), GenomicAlignments, methods, AnnotationDbi, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, Homo.sapiens Suggests: BiocParallel, geneplotter Enhances: Rsubread, BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: a2a79808727d93dcdcafaface175fef6 NeedsCompilation: yes Package: chimeraviz Version: 1.4.3 Depends: Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, AnnotationFilter Imports: methods, readr, grid, Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, ArgumentCheck Suggests: 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data.table, dplyr, latticeExtra, Rcpp, RColorBrewer, stringr, scales, flowViz LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib, cytolib(>= 0.99.6) Suggests: testthat, flowWorkspaceData, RSVGTipsDevice, knitr, ggcyto, parallel License: Artistic-2.0 MD5sum: 36e1f4c0d417c3dbe9d287eda15dae3b NeedsCompilation: yes Package: fmcsR Version: 1.20.0 Depends: R (>= 2.10.0), ChemmineR, methods Imports: RUnit, methods, ChemmineR, BiocGenerics, parallel Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap License: Artistic-2.0 MD5sum: 0407c43e357bca8e41497a17b95c6217 NeedsCompilation: yes Package: focalCall Version: 1.12.0 Depends: R(>= 2.10.0), CGHcall Suggests: RUnit, BiocGenerics License: GPL-2 MD5sum: d677a9d65910c16812c9f31a6a32752e NeedsCompilation: no Package: FourCSeq Version: 1.12.0 Depends: R (>= 3.0), GenomicRanges, ggplot2, DESeq2 (>= 1.9.11), splines, methods, LSD Imports: DESeq2, Biobase, Biostrings, GenomicRanges, SummarizedExperiment, Rsamtools, ggbio, reshape2, rtracklayer, fda, 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graphics, grDevices, methods, stats, utils Suggests: CompQuadForm, logistf, survey, SNPRelate, GWASdata, RUnit, knitr License: GPL-3 MD5sum: 4dd7014d3bc4108df6f468c1a103546f NeedsCompilation: no Package: geNetClassifier Version: 1.18.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) MD5sum: 6957f974ac91ad9374c9ee7bd585b7ce NeedsCompilation: no Package: GeneticsDesign Version: 1.46.0 Imports: gmodels, graphics, gtools (>= 2.4.0), mvtnorm, stats License: GPL-2 MD5sum: 650dcb9a1aea3bddf4a80d7f902e3b48 NeedsCompilation: no Package: GeneticsPed Version: 1.40.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: 9562c504fc0c0d45b395d36b111ccd3a NeedsCompilation: yes Package: geneXtendeR Version: 1.4.0 Depends: GO.db, org.Rn.eg.db, rtracklayer, R (>= 3.3.1) Imports: AnnotationDbi, data.table, dplyr, graphics, networkD3, 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.Mmu.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, RColorBrewer, SnowballC, tm, utils, wordcloud Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 3) MD5sum: b9484e6e1af63e5d41dfdd0a13908590 NeedsCompilation: yes Package: GENIE3 Version: 1.0.0 Imports: stats, reshape2 Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods License: GPL (>= 2) MD5sum: 5ddb82b71e0239c2cf52daed37956393 NeedsCompilation: yes Package: genoCN Version: 1.30.0 Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: a061194c8b97b64c01a52e0f127a57c8 NeedsCompilation: yes Package: GenoGAM Version: 1.6.0 Depends: R (>= 3.3), Rsamtools (>= 1.18.2), SummarizedExperiment (>= 1.1.19), GenomicRanges (>= 1.29.14), methods Imports: BiocParallel (>= 1.5.17), 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readr, data.table, GenomicRanges, IRanges Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools License: Artistic-2.0 MD5sum: a8969d8c7befeb4dc4c3ef94f2378ba7 NeedsCompilation: no Package: GenomicFeatures Version: 1.30.3 Depends: BiocGenerics (>= 0.1.0), S4Vectors (>= 0.9.47), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.29.14), AnnotationDbi (>= 1.33.15) Imports: methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RMySQL, RCurl, XVector, Biostrings (>= 2.23.3), rtracklayer (>= 1.29.24), biomaRt (>= 2.17.1), Biobase (>= 2.15.1) Suggests: 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, TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP141.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments, ensembldb, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: 6a62c3aed6c3c4b5063ae5114496e137 NeedsCompilation: no Package: GenomicFiles Version: 1.14.0 Depends: R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), GenomicRanges (>= 1.29.6), SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3) Imports: GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25), VariantAnnotation, GenomeInfoDb Suggests: BiocStyle, RUnit, genefilter, deepSNV, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens License: Artistic-2.0 MD5sum: 4496349ca4adc6704faa7defffa73f81 NeedsCompilation: no Package: GenomicInteractions Version: 1.12.0 Depends: R (>= 3.3), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils Suggests: knitr, BiocStyle, testthat License: GPL-3 MD5sum: dfab9b7eb44b6e88d5347759e5cc7d89 NeedsCompilation: no Package: GenomicRanges Version: 1.30.3 Depends: R (>= 2.10), methods, stats4, BiocGenerics (>= 0.21.2), S4Vectors (>= 0.9.47), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.13.1) Imports: utils, stats, XVector LinkingTo: S4Vectors, IRanges Suggests: Biobase, AnnotationDbi (>= 1.21.1), annotate, Biostrings (>= 2.25.3), Rsamtools (>= 1.13.53), SummarizedExperiment (>= 0.1.5), Matrix, GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, BiocStyle, digest, RUnit, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2, KEGG.db, hgu95av2.db, org.Hs.eg.db, org.Mm.eg.db, org.Sc.sgd.db, pasilla, pasillaBamSubset, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, RNAseqData.HNRNPC.bam.chr14, hgu95av2probe License: Artistic-2.0 MD5sum: 0ac346a668aa1aca1c9f3aa3601466e5 NeedsCompilation: yes Package: GenomicScores Version: 1.2.2 Depends: R (>= 3.4), S4Vectors (>= 0.7.21), GenomicRanges, methods, BiocGenerics (>= 0.13.8) Imports: utils, XML, Biobase, IRanges (>= 2.3.23), Biostrings, BSgenome, GenomeInfoDb, AnnotationHub Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5, SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer License: Artistic-2.0 MD5sum: 1a2dfa9706de6202e66f78c7d7f0440c NeedsCompilation: no Package: GenomicTuples Version: 1.12.0 Depends: R (>= 3.3.0), GenomicRanges (>= 1.23.15), GenomeInfoDb (>= 1.7.2), S4Vectors (>= 0.9.38) Imports: methods, BiocGenerics (>= 0.17.0), Rcpp (>= 0.11.2), IRanges (>= 2.5.26), data.table LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 11c04cd66ccdf380c98cc1f2762473ea NeedsCompilation: yes Package: Genominator Version: 1.32.0 Depends: R (>= 2.10), methods, RSQLite, DBI (>= 0.2-5), BiocGenerics (>= 0.1.0), IRanges (>= 2.5.27), GenomeGraphs Imports: graphics, stats, utils Suggests: biomaRt, ShortRead, yeastRNASeq License: Artistic-2.0 MD5sum: 3e652f338f4fad0517d6b653333c82eb NeedsCompilation: no Package: genoset Version: 1.34.0 Depends: R (>= 2.10), BiocGenerics (>= 0.11.3), GenomicRanges (>= 1.17.19), SummarizedExperiment (>= 1.1.6) Imports: S4Vectors (>= 0.13.13), GenomeInfoDb (>= 1.1.3), IRanges (>= 2.5.12), methods, graphics Suggests: RUnit, knitr, BiocStyle, rmarkdown, DNAcopy, stats, BSgenome, Biostrings Enhances: parallel License: Artistic-2.0 MD5sum: 6876c1a52713800a65ee97e0abd9b291 NeedsCompilation: yes Package: genotypeeval Version: 1.10.0 Depends: R (>= 3.3.0), VariantAnnotation Imports: ggplot2, rtracklayer, BiocGenerics, GenomicRanges, GenomeInfoDb, IRanges, methods, BiocParallel, Rtsne, graphics, stats Suggests: rmarkdown, testthat, SNPlocs.Hsapiens.dbSNP141.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene License: file LICENSE MD5sum: 3919fd303d82b9de9aa7771724e59db7 NeedsCompilation: no Package: genphen Version: 1.6.0 Depends: R(>= 3.3), randomForest, e1071, ggplot2, effsize, Biostrings, rjags License: GPL (>= 2) MD5sum: d925273a0f8e9eff40c32c77d8060ae4 NeedsCompilation: no Package: GenRank Version: 1.6.0 Depends: R (>= 3.2.3) Imports: matrixStats, reshape2, survcomp Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 42fbb7f1456220484f157b933e42132a NeedsCompilation: no Package: GenVisR Version: 1.8.1 Depends: R (>= 3.3.0) Imports: AnnotationDbi, biomaRt, BiocGenerics, Biostrings, DBI, FField, GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), grid, gridExtra, gtable, gtools, IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, stats, utils, viridis Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown License: GPL-3 + file LICENSE MD5sum: acddce32511268198fb32d4214292274 NeedsCompilation: no Package: GEOmetadb Version: 1.40.0 Depends: GEOquery,RSQLite Suggests: knitr, rmarkdown, dplyr, tm, wordcloud License: Artistic-2.0 MD5sum: a6aa842323d85602ec49afee4047db6f NeedsCompilation: no Package: GEOquery Version: 2.46.15 Depends: methods, Biobase Imports: httr, readr, xml2, dplyr, tidyr, magrittr, limma Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr License: GPL-2 MD5sum: 3907def1fa695612a976ac6a893f9d3f NeedsCompilation: no Package: GEOsearch Version: 1.1.4 Depends: R(>= 3.2) Imports: RCurl, org.Hs.eg.db, org.Mm.eg.db Suggests: knitr, shiny, DT, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db, org.Mmu.eg.db, org.Pf.plasmo.db, org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db License: GPL (>= 2) MD5sum: c4a68a28c75119994551c714ec6ace83 NeedsCompilation: no Package: GEOsubmission Version: 1.30.0 Imports: affy, Biobase, utils License: GPL (>= 2) MD5sum: d3cc015eb807c52bce9a1a3ffdab53b7 NeedsCompilation: no Package: gespeR Version: 1.10.1 Depends: methods, graphics, ggplot2, R(>= 2.10) Imports: Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel, parallel, foreach, reshape2, dplyr Suggests: knitr License: GPL-3 MD5sum: d71ed15ec3ed6901dd8a1f45f5d6e9f3 NeedsCompilation: no Package: GEWIST Version: 1.22.0 Depends: R (>= 2.10), car License: GPL-2 MD5sum: 4d76d2304eb2666b258d9fd76ae00074 NeedsCompilation: no Package: GGBase Version: 3.40.0 Depends: R (>= 2.14), methods, snpStats Imports: limma, genefilter, Biobase, BiocGenerics, S4Vectors, IRanges, Matrix, AnnotationDbi, digest, GenomicRanges, SummarizedExperiment Suggests: GGtools, illuminaHumanv1.db License: Artistic-2.0 MD5sum: 7d446b3ee10a5ec721a2c0795e8be1a4 NeedsCompilation: no Package: ggbio Version: 1.26.1 Depends: methods, BiocGenerics, ggplot2 (>= 1.0.0) Imports: grid, grDevices, graphics, stats, utils, gridExtra, scales, reshape2, gtable, Hmisc, biovizBase (>= 1.23.3), Biobase, S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.29.14), SummarizedExperiment, Biostrings, Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer (>= 1.25.16), GenomicFeatures (>= 1.29.11), OrganismDbi, GGally, ensembldb (>= 1.99.13), AnnotationDbi, AnnotationFilter Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex License: Artistic-2.0 MD5sum: 29e166261c64a469e56bb5241989c4a8 NeedsCompilation: no Package: ggcyto Version: 1.6.2 Depends: methods, ggplot2(>= 2.0.0), flowCore(>= 1.41.5), ncdfFlow(>= 2.17.1), flowWorkspace(>= 3.17.24) Imports: plyr, scales, data.table, RColorBrewer, gridExtra Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggjoy License: Artistic-2.0 MD5sum: 3b9ad32b9577f0a91e1500a85b1ca340 NeedsCompilation: no Package: GGtools Version: 5.14.0 Depends: R (>= 2.14), GGBase (>= 3.19.7), data.table, parallel, Homo.sapiens Imports: methods, utils, stats, BiocGenerics, snpStats, ff, Rsamtools, AnnotationDbi, Biobase, bit, VariantAnnotation, hexbin, rtracklayer, Gviz, stats4, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges (>= 1.29.6), iterators, Biostrings, ROCR, biglm, ggplot2, reshape2 Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37, multtest, aod, rmeta Enhances: MatrixEQTL, foreach, doParallel, gwascat License: Artistic-2.0 MD5sum: e20180c38e2f4af7073e7e70c593f59f NeedsCompilation: no Package: ggtree Version: 1.10.5 Depends: R (>= 3.3.2), ggplot2 (>= 2.2.0), treeio Imports: ape, grDevices, grid, magrittr, methods, rvcheck, scales, tidyr, utils Suggests: 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utils Suggests: BiocStyle, RProtoBuf, httpuv, knitr, rmarkdown, testthat, ggbio, ggplot2, BSgenome.Hsapiens.UCSC.hg19, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Apache License (== 2.0) | file LICENSE MD5sum: 725c6e578581c4c3ce5f7d75e7d16365 NeedsCompilation: yes Package: GOpro Version: 1.4.2 Depends: R (>= 3.4) Imports: AnnotationDbi, dendextend, doParallel, foreach, parallel, org.Hs.eg.db, GO.db, Rcpp, stats, graphics, MultiAssayExperiment, IRanges, S4Vectors LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat License: GPL-3 MD5sum: f22bc36e7604ab90ad8bae74d120e2b4 NeedsCompilation: yes Package: goProfiles Version: 1.40.0 Depends: Biobase, AnnotationDbi, GO.db Suggests: org.Hs.eg.db License: GPL-2 MD5sum: bfc052aa17d9413b9ede7f9a664abc96 NeedsCompilation: no Package: GOSemSim Version: 2.4.1 Depends: R (>= 3.3.2) Imports: AnnotationDbi, GO.db, methods, utils LinkingTo: Rcpp Suggests: AnnotationHub, BiocInstaller, clusterProfiler, DOSE, 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BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva License: GPL-3 + file LICENCE MD5sum: 272cb444367e5ac7d949ba5743023e38 NeedsCompilation: yes Package: Harshlight Version: 1.50.0 Depends: R (>= 2.10) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) MD5sum: a2d3538c86f90797be5c51b0684d38a6 NeedsCompilation: yes Package: HCsnip Version: 1.17.0 Depends: R(>= 2.10.0), survival, coin, fpc, clusterRepro, impute, randomForestSRC, sm, sigaR, Biobase License: GPL (>= 2) MD5sum: c66519e9e516c08c1736325703b1e64f NeedsCompilation: no Package: HDF5Array Version: 1.6.0 Depends: R (>= 3.4), methods, DelayedArray (>= 0.3.18), rhdf5 Imports: utils, tools, BiocGenerics, S4Vectors, IRanges Suggests: h5vcData, SummarizedExperiment (>= 1.5.6), GenomicRanges, BiocStyle License: Artistic-2.0 MD5sum: 38953abecbf950006d1fd53c419fb81f NeedsCompilation: no Package: HDTD Version: 1.12.0 Depends: R (>= 3.4) Imports: stats 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statmod License: GPL-3 MD5sum: d6bdf93749583ce23d57fa03bfc55dba NeedsCompilation: yes Package: methylPipe Version: 1.12.0 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: 13866482efbc45ea7e02e9f5efcac7c4 NeedsCompilation: yes Package: MethylSeekR Version: 1.18.0 Depends: rtracklayer (>= 1.16.3), parallel (>= 2.15.1), mhsmm (>= 0.4.4) Imports: IRanges (>= 1.16.3), BSgenome (>= 1.26.1), GenomicRanges (>= 1.10.5), geneplotter (>= 1.34.0), graphics (>= 2.15.2), grDevices (>= 2.15.2), parallel (>= 2.15.2), stats (>= 2.15.2), utils (>= 2.15.2) Suggests: BSgenome.Hsapiens.UCSC.hg18 License: GPL (>= 2) MD5sum: 35cab7e74d0d68eb3e5ea06e4d65d537 NeedsCompilation: no Package: methylumi Version: 2.24.1 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, methyAnalysis, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 MD5sum: b54a5892bb74b505310dc9a3cf593eb6 NeedsCompilation: no Package: methyvim Version: 1.0.0 Depends: R (>= 3.4.0) Imports: stats, cluster, methods, ggplot2, gridExtra, superheat, wesanderson, magrittr, dplyr, gtools, tmle, future, doFuture, BiocParallel, BiocGenerics, 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: d4c7e6437bf051a9029cb9e5431cbe37 NeedsCompilation: no Package: mfa Version: 1.0.0 Depends: R (>= 3.4.0) Imports: methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack, MCMCglmm, coda, magrittr, tibble, Biobase LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: fe473558b1c60e09af27a775c8aeb724 NeedsCompilation: yes Package: Mfuzz Version: 2.38.0 Depends: R (>= 2.5.0), Biobase (>= 2.5.5), e1071 Imports: tcltk, tkWidgets Suggests: marray License: GPL-2 MD5sum: afb0c8076785c3ad4cebb9d385e1a950 NeedsCompilation: no Package: MGFM Version: 1.12.0 Depends: AnnotationDbi,annotate Suggests: hgu133a.db License: GPL-3 MD5sum: 46878c93c7d3588ef395abc0aa11ed6f NeedsCompilation: no Package: MGFR Version: 1.4.0 Depends: R (>= 3.3) Imports: biomaRt, annotate License: GPL-3 MD5sum: 6903615c7a5737817485955f92aec9eb NeedsCompilation: no Package: mgsa Version: 1.26.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: 7e8b3fb659ddd4e506b6badd951b94d4 NeedsCompilation: yes Package: MiChip Version: 1.32.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: 5d0c84248cf1cc20915939e677651692 NeedsCompilation: no Package: microbiome Version: 1.0.2 Depends: R (>= 3.4.0), phyloseq, ggplot2 Imports: dplyr, reshape2, stats, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitcitations, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE MD5sum: b13a220249750e8e9d941b6331a90e18 NeedsCompilation: no Package: microRNA Version: 1.36.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: 7f7931bfd50369298d31e1c37a44d6e8 NeedsCompilation: yes Package: MIGSA Version: 1.2.0 Depends: R (>= 3.4), methods, BiocGenerics Imports: AnnotationDbi, Biobase, BiocParallel, data.table, edgeR, futile.logger, ggdendro, ggplot2, GO.db, GOstats, graph, graphics, grDevices, grid, GSEABase, limma, matrixStats, mGSZ, org.Hs.eg.db, RBGL, reshape2, Rgraphviz, RJSONIO, stats, utils, vegan Suggests: breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, pbcmc, MIGSAdata License: GPL (>= 2) MD5sum: 6349ac72b124a653de8a5a5e8aeb1fca NeedsCompilation: no Package: mimager Version: 1.2.0 Depends: Biobase Imports: BiocGenerics, S4Vectors, preprocessCore, grDevices, methods, grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 License: MIT + file LICENSE MD5sum: a103cda215ffa145c620e5220fdc6417 NeedsCompilation: no Package: MIMOSA Version: 1.16.1 Depends: R (>= 3.0.2), MASS, plyr, reshape, Biobase, ggplot2 Imports: methods, Formula, data.table, pracma, MCMCpack, coda, modeest, testthat, Rcpp, scales, LinkingTo: Rcpp, RcppArmadillo Suggests: parallel, knitr License: Artistic-2.0 MD5sum: 58f4ec773a4383a131de1027877c4e08 NeedsCompilation: yes Package: MineICA Version: 1.18.0 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 Enhances: doMC License: GPL-2 MD5sum: 2bec2d68ca750fc8406270648057bd18 NeedsCompilation: no Package: minet Version: 3.36.0 Imports: infotheo License: file LICENSE MD5sum: f44d51df2dd765a35a64e0d30724e028 NeedsCompilation: yes Package: minfi Version: 1.24.0 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, matrixStats (>= 0.50.0), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: cf2840b3b2f03814f4848e760caf1517 NeedsCompilation: no Package: MinimumDistance Version: 1.22.0 Depends: R (>= 3.3), VanillaICE (>= 1.31.3) Imports: methods, BiocGenerics, Biobase, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 0.2.0), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, SNPchip, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: 7f2a50d5a1537aeca7575f144756e0d7 NeedsCompilation: no Package: MiPP Version: 1.50.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: 40aac88eb8a8d880518e29b626e7f2bb NeedsCompilation: no Package: MIRA Version: 1.0.1 Depends: R (>= 3.4) Imports: BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table, ggplot2, Biobase, stats, bsseq, methods Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown Enhances: simpleCache License: GPL-3 MD5sum: fc8d3c3ac0f8f7483bf5cce0a1557caf NeedsCompilation: no Package: MiRaGE Version: 1.20.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: BiocGenerics, S4Vectors, AnnotationDbi 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: 7eeda5b4993eeb4ad0f62e77e7d839d4 NeedsCompilation: no Package: miRBaseConverter Version: 1.0.4 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils License: GPL (>= 2) MD5sum: 4807bf73e82b07fec2262a942cdf0d9b NeedsCompilation: no Package: miRcomp Version: 1.8.0 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: 6b486255764d9e783e3f1b22026bda4a NeedsCompilation: no Package: mirIntegrator Version: 1.8.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: ca9d1ec739cff43b8c9b9ce6ef520736 NeedsCompilation: no Package: miRLAB Version: 1.8.0 Imports: RCurl, httr, stringr, Hmisc, energy, entropy, Roleswitch, gplots, glmnet, impute, limma, pcalg Suggests: knitr, RUnit, BiocGenerics, AnnotationDbi, org.Hs.eg.db, GOstats, Category License: GPL (>= 2) MD5sum: 3dd0b3177211ba14efe3186686c84eb8 NeedsCompilation: no Package: miRmine Version: 1.0.0 Depends: R (>= 3.4), SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, DESeq2 License: GPL (>= 3) MD5sum: 74c7e54c8be1e4ac9d54d4ee873dbc13 NeedsCompilation: no Package: miRNAmeConverter Version: 1.6.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: a46df72abadfb24d017f38129b845392 NeedsCompilation: no Package: miRNApath Version: 1.38.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: 2cefba91d236c2f9c9bcc26627e5cc28 NeedsCompilation: no Package: miRNAtap Version: 1.12.0 Depends: R (>= 3.3.0), AnnotationDbi Imports: DBI, RSQLite, stringr, sqldf, plyr, methods Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat License: GPL-2 MD5sum: 61a7a803d1d9fe51216cc1f667704946 NeedsCompilation: no Package: miRsponge Version: 1.2.0 Depends: R (>= 3.4.1) Imports: corpcor, parallel, igraph, ProNet, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, varhandle, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, org.Hs.eg.db License: GPL-3 MD5sum: 3e86ba80194b5402b487406cf89ab910 NeedsCompilation: no Package: Mirsynergy Version: 1.14.1 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: 0ba4c0859fb87cd454bd2faf7bb11ff7 NeedsCompilation: no Package: missMethyl Version: 1.12.0 Depends: R (>= 2.3.0) Imports: limma, minfi, methylumi, IlluminaHumanMethylation450kmanifest, statmod, ruv, stringr, IlluminaHumanMethylation450kanno.ilmn12.hg19, org.Hs.eg.db, AnnotationDbi, BiasedUrn, GO.db, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 Suggests: minfiData, BiocStyle, knitr, rmarkdown, edgeR, tweeDEseqCountData License: GPL-2 MD5sum: dfb67af6998825615d9d9aff3bab6cb8 NeedsCompilation: no Package: mitoODE Version: 1.16.0 Depends: R (>= 2.14.0), minpack.lm, MASS, parallel, mitoODEdata, KernSmooth License: LGPL MD5sum: dd9fb2b49bfc3266a5afa9cc50aa53f9 NeedsCompilation: yes Package: MLInterfaces Version: 1.58.1 Depends: R (>= 2.9), methods, BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, rda, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4 Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, rgl, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party Enhances: parallel License: LGPL MD5sum: d455ceaaa669bc8e87f62c190adb427d NeedsCompilation: no Package: MLP Version: 1.26.0 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: bec96cb5ea57de17832e63ba4d8b4a6b NeedsCompilation: no Package: MLSeq Version: 1.18.0 Depends: R (>= 3.0.0), caret, DESeq2, Biobase, limma, randomForest, edgeR Imports: methods Suggests: knitr, e1071, kernlab, earth, ellipse, fastICA, gam, ipred, klaR, MASS, mda, mgcv, mlbench, nnet, party, pls, pROC, proxy, RANN, spls, affy License: GPL (>= 2) MD5sum: e6b781624d69ca7d1a1f556004af550c NeedsCompilation: no Package: MMDiff2 Version: 1.6.0 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: 3311d0b0fa785b2f0bf338a3dcbd7e77 NeedsCompilation: no Package: MmPalateMiRNA Version: 1.28.0 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, clValid, class, cluster, multtest, RColorBrewer, latticeExtra License: GPL-3 MD5sum: df07f9a99e1bb17a55a9321f5a3a9279 NeedsCompilation: no Package: MODA Version: 1.4.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 15ae21c96a25dc7d8a6676fb42c7ba82 NeedsCompilation: no Package: mogsa Version: 1.12.2 Depends: R (>= 3.2.0) Imports: methods, graphite, genefilter, BiocGenerics, gplots, GSEABase, Biobase, parallel, corpcor, svd, cluster Suggests: BiocStyle, knitr License: GPL-2 MD5sum: eb31620532f403fe1f50fea5fa590392 NeedsCompilation: no Package: monocle Version: 2.6.4 Depends: R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-1), DDRTree (>= 0.1.4), Imports: parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, densityClust (>= 0.3), Rtsne, MASS, reshape2, limma, tibble, dplyr, qlcMatrix, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0) LinkingTo: Rcpp Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat License: Artistic-2.0 MD5sum: 2d70340bc56008b7e2a648e317a2b8fe NeedsCompilation: yes Package: MoonlightR Version: 1.4.0 Depends: R (>= 3.3), doParallel, foreach Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png License: GPL (>= 3) MD5sum: c5f1f729cd70727732bcadcd1d31fbcc NeedsCompilation: no Package: MoPS Version: 1.12.0 Imports: Biobase License: GPL-3 MD5sum: 18b9444a6662c0c72b203cdd8fac39c1 NeedsCompilation: no Package: mosaics Version: 2.16.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: 433e23b9f3bf9e0ce5e684c8271e01a2 NeedsCompilation: yes Package: motifbreakR Version: 1.8.0 Depends: R (>= 3.2), grid, MotifDb Imports: methods, compiler, grDevices, grImport, stringr, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP142.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle License: GPL-2 MD5sum: 0cca8c925e7a84a8344ac81afa420782 NeedsCompilation: no Package: motifcounter Version: 1.2.1 Depends: R(>= 3.0) Imports: Biostrings, methods 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BSgenome, XVector, BSgenome.Hsapiens.UCSC.hg19 Imports: Biostrings,IRanges,seqLogo,parallel,methods,grid,graphics,XVector License: Artistic-2.0 MD5sum: c9f0273c7bd6d5e8f64597b8373c87c4 NeedsCompilation: no Package: motifStack Version: 1.22.4 Depends: R (>= 2.15.1), methods, grImport, grid, MotIV, ade4, Biostrings Imports: XML, scales, htmlwidgets,grDevices, stats, utils Suggests: RUnit, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr License: GPL (>= 2) MD5sum: df4b1cb077b678de9473aac0c69aa6a5 NeedsCompilation: no Package: MotIV Version: 1.34.0 Depends: R (>= 2.10), BiocGenerics (>= 0.1.0) Imports: graphics, grid, methods, S4Vectors, IRanges (>= 1.13.5), Biostrings (>= 1.24.0), lattice, rGADEM, utils Suggests: rtracklayer License: GPL-2 MD5sum: 8390be8ae7a5b395be282a7f42ddb46f NeedsCompilation: yes Package: MPFE Version: 1.14.0 License: GPL (>= 3) MD5sum: 29e2e9a02bc093f0763d7eac9a19a627 NeedsCompilation: no Package: mpra Version: 1.0.0 Depends: R (>= 3.4.0), methods, 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BiocGenerics, rtracklayer, ggplot2, futile.logger, VGAM, edgeR, tools, limma Suggests: PSCBS, RUnit, BiocStyle, knitr, optparse, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: Artistic-2.0 MD5sum: a06af3d04517932dd2de0145d048ff5b NeedsCompilation: no Package: pvac Version: 1.26.0 Depends: R (>= 2.8.0) Imports: affy (>= 1.20.0), stats, Biobase Suggests: pbapply, affydata, ALLMLL, genefilter License: LGPL (>= 2.0) MD5sum: 8f956855fcdfa2a0ec5e293798062b66 NeedsCompilation: no Package: pvca Version: 1.18.0 Depends: R (>= 2.15.1) Imports: Matrix, Biobase, vsn, stats, lme4 Suggests: golubEsets License: LGPL (>= 2.0) MD5sum: 04f49618687f013a78ac5391197d05cf NeedsCompilation: no Package: Pviz Version: 1.12.0 Depends: R(>= 3.0.0), Gviz(>= 1.7.10) Imports: biovizBase, Biostrings, GenomicRanges, IRanges, data.table, methods Suggests: knitr, pepDat License: Artistic-2.0 MD5sum: b082ff8af175a0492196a2b44b5e03e4 NeedsCompilation: no Package: PWMEnrich Version: 4.14.0 Depends: methods, 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BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP144.GRCh37, BSgenome.Ecoli.NCBI.20080805 License: LGPL-3 MD5sum: 9186180575aacce213feb52899045cfc NeedsCompilation: yes Package: randPack Version: 1.24.0 Depends: methods Imports: Biobase License: Artistic-2.0 MD5sum: 3273a14b241e86254a4efd376f338229 NeedsCompilation: no Package: RankProd Version: 3.4.0 Depends: R (>= 3.2.1), stats, methods, Rmpfr, gmp Imports: graphics License: file LICENSE License_restricts_use: yes MD5sum: 8cac5eddc447420db1ea10ad686cf29b NeedsCompilation: no Package: RareVariantVis Version: 2.6.0 Depends: BiocGenerics, VariantAnnotation, googleVis, GenomicFeatures Imports: S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools, BSgenome, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, SummarizedExperiment, GenomicScores Suggests: knitr License: Artistic-2.0 MD5sum: 939d168705d8871b4c1f33610b5911fa NeedsCompilation: no Package: Rariant Version: 1.14.0 Depends: R (>= 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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: 8fd4c7c75f4b6c31cd4c0dd042d68c5d NeedsCompilation: yes Package: SCnorm Version: 1.0.0 Depends: R (>= 3.4.0), Imports: stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, SummarizedExperiment, S4Vectors, ggplot2, forcats Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) MD5sum: 2e5f18c825b66ef83c6754f879f52215 NeedsCompilation: no Package: scone Version: 1.2.0 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 License: Artistic-2.0 MD5sum: da37b1e1b875a39e8cbe1a9ef51891c1 NeedsCompilation: no Package: scoreInvHap Version: 1.0.0 Depends: R (>= 3.4.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: 3393b9e9af1135546f27279d310893ee NeedsCompilation: no Package: scPipe Version: 1.0.6 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 LinkingTo: Rcpp, Rhtslib, zlibbioc Suggests: knitr, rmarkdown, testthat License: GPL (>= 2) MD5sum: 97d6e5a490cb997d8665a86d7fc25c9c NeedsCompilation: yes Package: scran Version: 1.6.9 Depends: R (>= 3.4), BiocParallel, SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp (>= 0.12.14), stats, methods, utils, graphics, grDevices, Matrix, scater, edgeR, limma, dynamicTreeCut, FNN, igraph, shiny, zoo, statmod, ggplot2, DT, viridis LinkingTo: beachmat, Rcpp, Rhdf5lib Suggests: testthat, BiocStyle, knitr, beachmat, HDF5Array, limSolve, org.Mm.eg.db, DESeq2, monocle, Rtsne, pracma, Biobase, irlba, aroma.light License: GPL-3 MD5sum: a1c0834781684e627d08bcdbbc97a299 NeedsCompilation: yes Package: scsR Version: 1.14.0 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: 9b6d384bb5e0f877c0e9e06a6970e69d NeedsCompilation: no Package: segmentSeq Version: 2.12.0 Depends: R (>= 3.0.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel, GenomicRanges, ShortRead, stats Imports: Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils, abind 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S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat License: MIT + file LICENCE MD5sum: 59c4144df457856ed5a424d1cba75ecd NeedsCompilation: no Package: seqCNA Version: 1.24.0 Depends: R (>= 3.0), GLAD (>= 2.14), doSNOW (>= 1.0.5), adehabitatLT (>= 0.3.4), seqCNA.annot (>= 0.99), methods License: GPL-3 MD5sum: 8f8505afadcdcd47c8c52d6827ad700f NeedsCompilation: yes Package: seqcombo Version: 1.0.0 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: 27a1293f00971b6f951193299edc94dd NeedsCompilation: no Package: SeqGSEA Version: 1.18.0 Depends: Biobase, doParallel, DESeq Imports: methods, biomaRt Suggests: easyRNASeq, GenomicRanges License: GPL (>= 3) MD5sum: 269c2910076886b5e6cf51ad4e224bcc NeedsCompilation: no Package: seqLogo Version: 1.44.0 Depends: methods, grid 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