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
R (>= 3.4.0), EGSEA (>= 1.5.2), limma, edgeR, illuminaio
R (>= 3.3.0), BSgenome.Scerevisiae.UCSC.sacCer3, Biostrings,
GenomicFeatures, MotifDb, S4Vectors,
TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, motifStack,
org.Sc.sgd.db, seqLogo
R (>= 3.3.0), Glimma (>= 1.1.9), limma, edgeR, Mus.musculus
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,
R (>= 3.3.0), GenomicRanges, GenomicAlignments, Biostrings,
Rsamtools, ShortRead, BiocParallel, rtracklayer,
VariantAnnotation, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19,
RNAseqData.HNRNPC.bam.chr14
R (>= 3.3.0), VariantAnnotation, cgdv17, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
PolyPhen.Hsapiens.dbSNP131
BiocStyle, knitr, readxl, matrixStats, flowCore, ggplot2,
ggridges, reshape2, dplyr, limma, ggrepel, RColorBrewer,
pheatmap, ComplexHeatmap, FlowSOM, ConsensusClusterPlus, Rtsne,
cowplot, lme4, multcomp
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
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
BiocStyle (>= 2.5.19), BiocWorkflowTools, knitr, devtools,
rmarkdown, knitcitations