Package: annotation
Version: 1.0.11
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
License: Artistic-2.0

Package: cytofWorkflow
Version: 1.0.4
Depends: R (>= 3.4.0)
Imports: BiocStyle, knitr, readxl, matrixStats, flowCore, ggplot2,
        ggridges, reshape2, dplyr, limma, ggrepel, RColorBrewer,
        pheatmap, ComplexHeatmap, FlowSOM, ConsensusClusterPlus, Rtsne,
        cowplot, lme4, multcomp
Suggests: knitcitations
License: Artistic-2.0

Package: EGSEA123
Version: 0.99.19
Depends: R (>= 3.4.0), EGSEA (>= 1.5.2), limma, edgeR, illuminaio
Suggests: knitr, rmarkdown
License: Artistic-2.0

Package: generegulation
Version: 1.0.4
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
License: Artistic-2.0

Package: recountWorkflow
Version: 0.99.38
Depends: R (>= 3.4.0)
Imports: recount (>= 1.2.3), GenomicRanges, limma, edgeR, DESeq2,
        regionReport (>= 1.11.2), clusterProfiler (>= 3.5.5),
        org.Hs.eg.db (>= 3.4.1), gplots, derfinder, rtracklayer (>=
        1.36.4), GenomicFeatures, bumphunter (>= 1.17.2), derfinderPlot
Suggests: BiocStyle (>= 2.5.19), BiocWorkflowTools, knitr, devtools,
        rmarkdown, knitcitations
License: Artistic-2.0

Package: RNAseq123
Version: 1.0.2
Depends: R (>= 3.3.0), Glimma (>= 1.1.9), limma, edgeR, Mus.musculus
Suggests: knitr, rmarkdown
License: Artistic-2.0

Package: rnaseqGene
Version: 1.0.2
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

Package: sequencing
Version: 1.0.4
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

Package: TCGAWorkflow
Version: 0.99.84
Depends: R (>= 3.4.0)
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,
        pander, maftools, RTCGAToolbox, SummarizedExperiment,
        TCGAbiolinks, TCGAWorkflowData, DT
License: Artistic-2.0

Package: variants
Version: 1.0.2
Depends: R (>= 3.3.0), VariantAnnotation, cgdv17, org.Hs.eg.db,
        TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
        PolyPhen.Hsapiens.dbSNP131
Suggests: knitr, rmarkdown
License: Artistic-2.0