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 (>= 3.3.0), BiocStyle, ChIPpeakAnno, Gviz, Rsamtools,
Rsubread, TxDb.Mmusculus.UCSC.mm10.knownGene, csaw, edgeR,
knitr, locfit, org.Mm.eg.db, rtracklayer, statmod
R (>= 3.4.0), EGSEA (>= 1.5.2), limma, edgeR, illuminaio
R (>= 3.3.0), GGdata, GGtools, GenomeInfoDb, S4Vectors,
SNPlocs.Hsapiens.dbSNP144.GRCh37, bibtex, biglm, data.table,
doParallel, foreach, knitcitations, lumi, lumiHumanAll.db,
parallel, rmeta, scatterplot3d, snpStats, grid, yri1kgv
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), flowCore, flowStats, flowViz
R (>= 3.3.0), gwascat, GenomicRanges, rtracklayer,
Homo.sapiens, BiocGenerics
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
R (>= 3.3.0), knitr, rmarkdown, BiocStyle, limma, minfi,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylation450kmanifest, RColorBrewer, missMethyl,
matrixStats, minfiData, Gviz, DMRcate, stringr,
FlowSorted.Blood.450k
R (>= 3.3.0), mzR, mzID, MSnID, MSnbase, rpx, MLInterfaces,
pRoloc, pRolocdata, MSGFplus, rols, hpar
R (>= 3.3.0), Glimma (>= 1.1.9), limma, edgeR, gplots,
RColorBrewer, Mus.musculus
R (>= 3.5.0), DRIMSeq, DEXSeq, stageR, DESeq2, edgeR, rafalib,
devtools
R (>= 3.3.0), BiocStyle, airway, Rsamtools, GenomicFeatures,
GenomicAlignments, BiocParallel, magrittr, DESeq2, apeglm, vsn,
dplyr, ggplot2, pheatmap, RColorBrewer, PoiClaClu, ggbeeswarm,
genefilter, AnnotationDbi, org.Hs.eg.db, ReportingTools, Gviz,
sva, RUVSeq, fission
R (>= 3.3.0), edgeR, gplots, org.Mm.eg.db, GO.db
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), BiocStyle, knitr, BiocParallel, Rtsne,
mvoutlier, destiny, readxl, gdata, SingleCellExperiment,
scater, org.Mm.eg.db, scran, limma, pheatmap, dynamicTreeCut,
cluster, edgeR, TxDb.Mmusculus.UCSC.mm10.ensGene, scRNAseq,
DropletUtils, BiocFileCache, BiocNeighbors, TENxBrainData
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
affy, limma, hgfocuscdf, knitr, rmarkdown, BiocStyle
BiocStyle (>= 2.5.19), BiocWorkflowTools, knitr, sessioninfo,
rmarkdown, knitcitations