Package: annotation Version: 1.33.0 Depends: R (>= 3.3.0), VariantAnnotation, AnnotationHub, Organism.dplyr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.ensGene, org.Hs.eg.db, org.Mm.eg.db, Homo.sapiens, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome, TxDb.Athaliana.BioMart.plantsmart22 Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 24273a2a3349e82733efc007aa6cbd1a NeedsCompilation: no Package: arrays Version: 1.35.0 Depends: R (>= 3.0.0) Suggests: affy, limma, hgfocuscdf, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 3b6c684dd08357b11507bd647687acf6 NeedsCompilation: no Package: BP4RNAseq Version: 1.19.0 Depends: R (>= 4.0.0) Imports: dplyr, fastqcr, stringr, tidyr, stats, utils, magrittr, reticulate Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: c753ec93ff44954737dc38d2377d3477 NeedsCompilation: no Package: CAGEWorkflow Version: 1.25.0 Depends: R (>= 3.6.0), CAGEfightR, nanotubes Suggests: knitr, magick, rmarkdown, BiocStyle, BiocWorkflowTools, pheatmap, ggseqlogo, viridis, magrittr, ggforce, ggthemes, tidyverse, dplyr, GenomicRanges, SummarizedExperiment, GenomicFeatures, BiocParallel, InteractionSet, Gviz, DESeq2, limma, edgeR, statmod, BiasedUrn, sva, TFBSTools, motifmatchr, pathview, BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, JASPAR2016, png License: GPL-3 MD5sum: ab1b53f473a4b8d5dadadeb266c9df6e NeedsCompilation: no Package: chipseqDB Version: 1.33.0 Suggests: chipseqDBData, BiocStyle, BiocFileCache, ChIPpeakAnno, Gviz, Rsamtools, TxDb.Mmusculus.UCSC.mm10.knownGene, csaw, edgeR, knitr, org.Mm.eg.db, rtracklayer, rmarkdown License: Artistic-2.0 MD5sum: a6f7c60b7ed8108d694e2754c771d0b2 NeedsCompilation: no Package: csawUsersGuide Version: 1.25.0 Suggests: knitr, BiocStyle, BiocManager License: GPL-3 MD5sum: 88bea359d4b096cd24816bdd77077227 NeedsCompilation: no Package: cytofWorkflow Version: 1.33.0 Depends: R (>= 3.6.0), BiocStyle, knitr, readxl, CATALYST, diffcyt, HDCytoData, uwot, cowplot Suggests: knitcitations, markdown, rmarkdown License: Artistic-2.0 MD5sum: 54dac6bb7c8f602a279ed92b5d63269d NeedsCompilation: no Package: EGSEA123 Version: 1.33.0 Depends: R (>= 3.4.0), EGSEA (>= 1.5.2), limma (>= 3.49.2), edgeR, illuminaio Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 757cd362ca64e0c84399c8cdc3c292d9 NeedsCompilation: no Package: ExpHunterSuite Version: 1.17.0 Depends: R (>= 4.1.0) Imports: ReactomePA, limma, edgeR, NOISeq, biomaRt, topGO, diffcoexp, DT, ggplot2, stringr, WGCNA, dplyr, AnnotationDbi, BiocGenerics, enrichplot, rmarkdown, stats, Biobase, DESeq2, ROCR, data.table, knitr, magrittr, SummarizedExperiment, miRBaseVersions.db, grDevices, graphics, utils, BiocParallel, MKinfer, matrixStats, ggupset, rlang, plyr, tidyr, GO.db, Matrix, fastcluster, DOSE, heatmaply, EnhancedVolcano, ggrepel, clusterProfiler, GenomicRanges, GenomicFeatures, tximport, annotatr, ggridges, FactoInvestigate, FactoMineR Suggests: optparse, PerformanceAnalytics, naivebayes, reshape2, org.Hs.eg.db, org.Mm.eg.db, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: c2d3a619100dc7cdd3bdc53cbf72a696 NeedsCompilation: no Package: ExpressionNormalizationWorkflow Version: 1.35.0 Imports: Biobase (>= 2.24.0), limma (>= 3.20.9), lme4 (>= 1.1.7), matrixStats (>= 0.10.3), pvca (>= 1.4.0), snm (>= 1.12.0), sva (>= 3.10.0), vsn (>= 3.32.0) Suggests: knitr, BiocStyle License: GPL (>= 3) MD5sum: 0d204e62ceb4b3b217c26dfb91c8c968 NeedsCompilation: no Package: fluentGenomics Version: 1.21.0 Depends: R (>= 4.0) Imports: plyranges (>= 1.7.7), dplyr, SummarizedExperiment, readr, stats, utils Suggests: knitr, rmarkdown, bookdown, rappdirs, BiocFileCache, DESeq2, limma, ggplot2, tidyr, tximeta (>= 1.4.2), macrophage (>= 1.2.0), License: MIT + file LICENSE MD5sum: 7b022c97b7da1aeb75b0debf3ea26002 NeedsCompilation: no Package: generegulation Version: 1.33.0 Depends: R (>= 3.3.0), BSgenome.Scerevisiae.UCSC.sacCer3, Biostrings, GenomicFeatures, MotifDb, S4Vectors, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, motifStack, org.Sc.sgd.db, seqLogo Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 0232037b414d6a9868cecc0a25ac9363 NeedsCompilation: no Package: highthroughputassays Version: 1.33.0 Depends: R (>= 3.3.0), flowCore, flowStats, flowWorkspace Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 5a23a24f70f3b647e81634b521ffd5fe NeedsCompilation: no Package: liftOver Version: 1.33.0 Depends: R (>= 3.3.0), gwascat, GenomicRanges, rtracklayer, Homo.sapiens, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: bc72b60f4df5fe23391b64cd74b3aaeb NeedsCompilation: no Package: maEndToEnd Version: 2.29.0 Depends: R (>= 3.5.0), Biobase, oligoClasses, ArrayExpress, pd.hugene.1.0.st.v1, hugene10sttranscriptcluster.db, oligo, arrayQualityMetrics, limma, topGO, ReactomePA, clusterProfiler, gplots, ggplot2, geneplotter, pheatmap, RColorBrewer, dplyr, tidyr, stringr, matrixStats, genefilter, openxlsx, Rgraphviz, enrichplot Suggests: BiocStyle, knitr, devtools, rmarkdown License: MIT + file LICENSE MD5sum: 5080060586061fd33aa10fdd20f3248e NeedsCompilation: no Package: methylationArrayAnalysis Version: 1.33.1 Depends: R (>= 3.3.0), knitr, rmarkdown, BiocStyle, limma, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, RColorBrewer, missMethyl, matrixStats, minfiData, Gviz, DMRcate, stringr, FlowSorted.Blood.450k License: Artistic-2.0 MD5sum: f295af5775b4d175b4cf5ff923a652bb NeedsCompilation: no Package: recountWorkflow Version: 1.33.0 Depends: R (>= 3.6.0) Imports: recount, GenomicRanges, limma, edgeR, DESeq2, pheatmap, regionReport, clusterProfiler, org.Hs.eg.db, gplots, derfinder, GenomicState, bumphunter, derfinderPlot Suggests: BiocStyle, BiocWorkflowTools, knitr, magick, sessioninfo, rmarkdown License: Artistic-2.0 MD5sum: 1595bb259a26d3cb55cf1fa7690c34eb NeedsCompilation: no Package: RNAseq123 Version: 1.33.0 Depends: R (>= 3.3.0), Glimma (>= 1.1.9), limma, edgeR, gplots, RColorBrewer, Mus.musculus, R.utils, TeachingDemos, statmod, BiocWorkflowTools Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 7622d6f77cb355ae229a54c93fb923a8 NeedsCompilation: no Package: rnaseqDTU Version: 1.29.0 Depends: R (>= 3.5.0), DRIMSeq, DEXSeq, stageR, DESeq2, edgeR, rafalib, devtools Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 0ecc32f3bb3c47c325f274302229687b NeedsCompilation: no Package: rnaseqGene Version: 1.33.0 Depends: R (>= 3.3.0), BiocStyle, airway (>= 1.5.3), tximeta, magrittr, DESeq2, apeglm, vsn, dplyr, ggplot2, hexbin, pheatmap, RColorBrewer, PoiClaClu, glmpca, ggbeeswarm, genefilter, AnnotationDbi, org.Hs.eg.db, Gviz, sva, RUVSeq, fission Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: af8599771f250055d46a798c822ad2ce NeedsCompilation: no Package: RnaSeqGeneEdgeRQL Version: 1.33.0 Depends: R (>= 3.3.0), edgeR (>= 4.3.6), gplots, org.Mm.eg.db, GO.db, BiocStyle Suggests: knitr, knitcitations, rmarkdown License: Artistic-2.0 MD5sum: d1fa3a44f61c6d9253a8d39ff3a67f22 NeedsCompilation: no Package: seqpac Version: 1.9.1 Depends: R (>= 4.2.0) Imports: Biostrings (>= 2.46.0), foreach (>= 1.5.1), GenomicRanges (>= 1.30.3), Rbowtie (>= 1.18.0), ShortRead (>= 1.36.1), tibble (>= 3.1.2), BiocParallel (>= 1.12.0), cowplot (>= 0.9.4), data.table (>= 1.14.0), digest (>= 0.6.27), doParallel (>= 1.0.16), dplyr (>= 1.0.6), factoextra (>= 1.0.7), FactoMineR (>= 1.41), ggplot2 (>= 3.3.3), IRanges (>= 2.12.0), parallel (>= 3.4.4), reshape2 (>= 1.4.4), rtracklayer (>= 1.38.3), stringr (>= 1.4.0), stats (>= 3.4.4), methods, S4Vectors Suggests: benchmarkme (>= 0.6.0), DESeq2 (>= 1.18.1), GenomeInfoDb (>= 1.14.0), gginnards (>= 0.0.2), qqman (>= 0.1.8), rmarkdown, BiocStyle, knitr, testthat, UpSetR (>= 1.4.0), venneuler, R.utils, bigreadr, readr, vroom License: GPL-3 MD5sum: 1610b1d27dc2b910263910ae5e90bdbd NeedsCompilation: no Package: sequencing Version: 1.33.0 Depends: R (>= 3.3.0), GenomicRanges, GenomicAlignments, Biostrings, Rsamtools, ShortRead, BiocParallel, rtracklayer, VariantAnnotation, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, RNAseqData.HNRNPC.bam.chr14 Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 17fcd0baa44417d91ed8e7c97df2b666 NeedsCompilation: no Package: simpleSingleCell Version: 1.33.0 Imports: utils, methods, knitr, callr, rmarkdown, CodeDepends, BiocStyle Suggests: readxl, R.utils, SingleCellExperiment, scater, scran, limma, BiocFileCache, org.Mm.eg.db License: Artistic-2.0 MD5sum: 940c12a9d546a2a20eb839a61d6492a4 NeedsCompilation: no Package: spicyWorkflow Version: 1.9.0 Depends: R (>= 4.3.0) Suggests: knitr, rmarkdown, BiocStyle, EBImage, cytomapper, ggplot2, ggpubr, lisaClust, spicyR, ClassifyR, scater, dplyr, simpleSeg, FuseSOM, HDF5Array, parallel, tidySingleCellExperiment, SpatialDatasets, Statial, treekoR License: GPL-3 MD5sum: 22841760cee41e0ce8e539720069c982 NeedsCompilation: no Package: variants Version: 1.33.0 Depends: R (>= 3.3.0), VariantAnnotation, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131 Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 06206ccb638c0f4693814767d07087ea NeedsCompilation: no