Package: annotation Version: 1.0.0 Depends: R (>= 3.3.0), VariantAnnotation, AnnotationHub, TxDb.Hsapiens.UCSC.hg19.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 License: Artistic-2.0 MD5sum: b598db057b00666d32daca23f939d195 Package: arrays Version: 0.1 Depends: R (>= 3.0.0) Suggests: affy, limma, hgfocuscdf, knitr, rmarkdown License: Artistic-2.0 MD5sum: 3392c71138ef9f37ac28896156aeb46f Package: chipseqDB Version: 0.99.128314 Depends: R (>= 3.4.0) Imports: BiocStyle, knitr, Rsubread, Rsamtools, rtracklayer, csaw, edgeR, statmod, locfit, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, ChIPpeakAnno, Gviz Suggests: knitr, knitcitations License: Artistic-2.0 MD5sum: aeede53d908c3ca5834c20d3dc37f95f Package: cytofWorkflow Version: 1.0.2 Depends: R (>= 3.4.0) Imports: BiocStyle, knitr, readxl, matrixStats, flowCore, ggplot2, reshape2, 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GenomicFeatures, MotifDb, S4Vectors, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, motifStack, org.Sc.sgd.db, seqLogo Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 566766c6b25f40209ded6c37de62a6fd Package: liftOver Version: 0.99.129508 Depends: R (>= 3.4.0) Imports: gwascat, GenomicRanges, rtracklayer, Homo.sapiens, BiocGenerics Suggests: knitr, knitcitations License: Artistic-2.0 MD5sum: 1dabc00a19e34299de81301232d3bd3c Package: methylationArrayAnalysis Version: 0.99.7 Depends: R (>= 3.3.0) Suggests: knitr, rmarkdown, BiocStyle, limma, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, RColorBrewer, missMethyl, matrixStats, minfiData, Gviz, DMRcate, stringr, FlowSorted.Blood.450k License: Artistic-2.0 MD5sum: 15be4a0ade7358a24ec35d7c00c6eeec Package: proteomics Version: 1.0.0 Depends: R (>= 3.3.0), mzR, mzID, MSnID, MSnbase, rpx, MLInterfaces, pRoloc, pRolocdata, MSGFplus, rols, hpar Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 186f12510733bac22a43f149fdfebea2 Package: RNAseq123 Version: 1.0.0 Depends: R (>= 3.3.0), Glimma (>= 1.1.9), limma, edgeR, Mus.musculus Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: 430e86d912f9ff8819486483145907c9 Package: rnaseqGene Version: 1.0.0 Depends: R (>= 3.3.0), BiocStyle, airway, Rsamtools, GenomicFeatures, GenomicAlignments, BiocParallel, magrittr, DESeq2, vsn, dplyr, ggplot2, pheatmap, RColorBrewer, PoiClaClu, ggbeeswarm, genefilter, AnnotationDbi, org.Hs.eg.db, ReportingTools, Gviz, sva, fission, Suggests: knitr, rmarkdown License: Artistic-2.0 MD5sum: ac77d79ff80a42458d455a4175d3a8c1 Package: RnaSeqGeneEdgeRQL Version: 0.99.18 Depends: R (>= 3.3.0), edgeR, gplots, org.Mm.eg.db, GO.db Suggests: knitr, knitcitations License: Artistic-2.0 MD5sum: ca09b0af7cbcb71ee50337dbd671dfb2 Package: sequencing Version: 1.0.0 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 License: Artistic-2.0 MD5sum: 097b17f3842d49405c21d56cfcbc1896 Package: simpleSingleCell Version: 0.99.129200 Depends: R (>= 3.4.0) Imports: BiocStyle, knitr, BiocParallel, Rtsne, mvoutlier, destiny, R.utils, readxl, scater, scran, org.Mm.eg.db, RBGL, gplots, limma, dynamicTreeCut, edgeR, TxDb.Mmusculus.UCSC.mm10.ensGene Suggests: knitr, knitcitations License: Artistic-2.0 MD5sum: 7dee653abbb5f39e3c6f5d9ad8aefe5b Package: TCGAWorkflow Version: 0.99.73 Depends: R (>= 3.3.0) Imports: AnnotationHub, knitr, ELMER, biomaRt, BSgenome.Hsapiens.UCSC.hg19, circlize, c3net, ChIPseeker, ComplexHeatmap, clusterProfiler, downloader (>= 0.4), gaia, GenomicRanges, GenomeInfoDb, ggplot2, ggthemes, graphics, minet, MotIV, motifStack, pathview, pbapply, parallel, rGADEM, RTCGAToolbox, SummarizedExperiment, TCGAbiolinks, TCGAWorkflowData, DT Suggests: roxygen2 (>= 5.0.0) License: Artistic-2.0 MD5sum: 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