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 (>= 3.6.0), BiocStyle, knitr, readxl, CATALYST, diffcyt,
HDCytoData, uwot, cowplot
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, flowWorkspace
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,
enrichplot
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.utils, TeachingDemos, statmod,
BiocWorkflowTools
R (>= 3.5.0), DRIMSeq, DEXSeq, stageR, DESeq2, edgeR, rafalib,
devtools
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, ReportingTools, Gviz, sva, RUVSeq,
fission
R (>= 3.3.0), edgeR, gplots, org.Mm.eg.db, GO.db, BiocStyle
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
dplyr, fastqcr, stringr, tidyr, stats, utils, magrittr,
reticulate
plyranges (>= 1.7.7), dplyr, SummarizedExperiment, readr,
stats, utils
recount, GenomicRanges, limma, edgeR, DESeq2, regionReport,
clusterProfiler, org.Hs.eg.db, gplots, derfinder, GenomicState,
bumphunter, derfinderPlot
utils, methods, knitr, callr, rmarkdown, CodeDepends,
BiocStyle
dcanr, edgeR, ggplot2, gridExtra, GSEABase, mclust,
org.Hs.eg.db, plyr, reshape2, rtracklayer, singscore,
SummarizedExperiment, TCGAbiolinks
AnnotationHub, knitr, ELMER, biomaRt,
BSgenome.Hsapiens.UCSC.hg19, circlize, c3net, ChIPseeker,
ComplexHeatmap, ggpubr, clusterProfiler, downloader (>= 0.4),
gaia, GenomicRanges, GenomeInfoDb, ggplot2, ggthemes, graphics,
minet, motifStack, pathview, pbapply, parallel, rGADEM, pander,
maftools, RTCGAToolbox, SummarizedExperiment, TCGAbiolinks,
TCGAWorkflowData (>= 1.9.0), DT, gt
affy, limma, hgfocuscdf, knitr, rmarkdown, BiocStyle
knitr, kableExtra, 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
chipseqDBData, BiocStyle, BiocFileCache, ChIPpeakAnno, Gviz,
Rsamtools, TxDb.Mmusculus.UCSC.mm10.knownGene, csaw, edgeR,
knitr, org.Mm.eg.db, rtracklayer, rmarkdown
csaw, chipseqDBData, edgeR,
TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, rtracklayer,
Rsamtools, Gviz, knitr, BiocStyle
knitr, rmarkdown, bookdown, rappdirs, BiocFileCache, DESeq2,
limma, ggplot2, tidyr, tximeta (>= 1.4.2), macrophage (>=
1.2.0),
BiocStyle, BiocWorkflowTools, knitr, sessioninfo, rmarkdown
readxl, R.utils, SingleCellExperiment, scater, scran, limma,
BiocFileCache, org.Mm.eg.db
knitr, rmarkdown, BiocStyle, BiocWorkflowTools, spelling