Package: annotation Version: 1.34.0 Depends: R (>= 3.3.0), GenomeInfoDb, 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: c24c2e4632a025f4cece247818558fda NeedsCompilation: no Package: arrays Version: 1.36.0 Depends: R (>= 3.0.0) Suggests: affy, limma, hgfocuscdf, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 811ae3a6c0217bbc24db169809f834aa NeedsCompilation: no Package: BP4RNAseq Version: 1.20.0 Depends: R (>= 4.0.0) Imports: dplyr, fastqcr, stringr, tidyr, stats, utils, magrittr, reticulate Suggests: knitr, rmarkdown, testthat License: GPL-2 MD5sum: e467f6d60e0830b7cca891afae2a53c0 NeedsCompilation: no Package: CAGEWorkflow Version: 1.26.0 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: ddd23f27e333db1bbc256cb4ea6a636e NeedsCompilation: no Package: chipseqDB Version: 1.34.0 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: da7f5b072be6f3d6f68870580129ad38 NeedsCompilation: no Package: csawUsersGuide Version: 1.26.0 Suggests: knitr, BiocStyle, BiocManager License: GPL-3 MD5sum: af5dff70d802d06ccb41a4134c315c43 NeedsCompilation: no Package: cytofWorkflow Version: 1.34.0 Depends: R (>= 3.6.0), BiocStyle, knitr, readxl, CATALYST, diffcyt, HDCytoData, uwot, cowplot Suggests: knitcitations, markdown, rmarkdown License: Artistic-2.0 MD5sum: 428a63dbc7c5febe5912729024534366 NeedsCompilation: no Package: EGSEA123 Version: 1.34.0 Depends: R (>= 3.4.0), EGSEA (>= 1.5.2), limma (>= 3.49.2), edgeR, illuminaio Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 5740b775ea24def993d098c806e8509e 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: 1.36.0 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: ec018a4169ff31a1bc90da679614e18b NeedsCompilation: no Package: fluentGenomics Version: 1.22.0 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: f9ba1b42b2455f11147d9a00d98f2752 NeedsCompilation: no Package: generegulation Version: 1.34.0 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: 138268273f60e0688572e6cd9880a52d NeedsCompilation: no Package: GeoMxWorkflows Version: 1.16.0 Depends: R (>= 4.0), NanoStringNCTools, GeomxTools Imports: Biobase, S4Vectors, rjson, readxl, EnvStats, dplyr, reshape2, methods, utils, stats, data.table, outliers, BiocGenerics, ggplot2, ggrepel, ggforce, cowplot, scales, umap, Rtsne, pheatmap, BiocStyle, networkD3 Suggests: rmarkdown, knitr License: MIT MD5sum: c1edf6d6f16fadaf216e0e3ab3e5fb2d NeedsCompilation: no Package: highthroughputassays Version: 1.34.0 Depends: R (>= 3.3.0), flowCore, flowStats, flowWorkspace Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 55ac30603302c4dc2c87d509386ee2a5 NeedsCompilation: no Package: liftOver Version: 1.34.0 Depends: R (>= 3.3.0), gwascat, GenomeInfoDb, GenomicRanges, rtracklayer, Homo.sapiens, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 9f01af6c4e5ae295fe227f5350a09fab 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: 1.34.0 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: d4dfd36d7ba33f1de06e4a5e80afebf7 NeedsCompilation: no Package: recountWorkflow Version: 1.34.0 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: b4c68af9273506136a9bd26c27008fe5 NeedsCompilation: no Package: RNAseq123 Version: 1.34.0 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: a7b198f005bf4df07644906ea38710e8 NeedsCompilation: no Package: rnaseqDTU Version: 1.30.0 Depends: R (>= 3.5.0), DRIMSeq, DEXSeq, stageR, DESeq2, edgeR, rafalib, devtools Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: db97c04ab570fd4a00307a37589031b2 NeedsCompilation: no Package: rnaseqGene Version: 1.34.0 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: 5c5567b5d0abc7970d96a07c3e966064 NeedsCompilation: no Package: RnaSeqGeneEdgeRQL Version: 1.34.0 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: c7429c705afdddf1cd289b123c7b8c26 NeedsCompilation: no Package: seqpac Version: 1.10.0 Depends: R (>= 4.5.0) 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, readr 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, vroom License: GPL-3 MD5sum: f806a3c8f8e015771ba606d64108e3b8 NeedsCompilation: no Package: sequencing Version: 1.34.0 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: d209c1ff12f2a4f0b120529fc30dfa86 NeedsCompilation: no Package: simpleSingleCell Version: 1.34.0 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: 7ea0d622c1fd6e64bb5aada2165924e7 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: 1.34.0 Depends: R (>= 3.3.0), GenomeInfoDb, 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: cce7481467a9cdfd707724e112e86b59 NeedsCompilation: no