R (>= 2.7.0), methods, AnnotationDbi (>= 1.59.1)
R (>= 3.5.0), BSgenome (>= 1.62.0),
BSgenome.Btaurus.UCSC.bosTau9
R (>= 3.5.0), BSgenome (>= 1.54.0),
BSgenome.Hsapiens.UCSC.hg19
R (>= 4.2.0), GenomeInfoDb (>= 1.34.9), BSgenome (>= 1.66.2),
BSgenome.Hsapiens.UCSC.hg38
R (>= 3.5.0), BSgenome (>= 1.60.0),
BSgenome.Mmusculus.UCSC.mm10
R (>= 2.7.0), methods, AnnotationDbi (>= 1.9.7)
R (>= 3.5), Biobase, GenomicRanges, GenomeInfoDbData,
AnnotationHub (>= 2.13.8),
R (>= 2.10), GenomicFeatures (>= 1.7.22),
TxDb.Hsapiens.UCSC.hg18.knownGene, org.Hs.eg.db
R (>= 2.10), GenomicFeatures (>= 1.7.22),
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
R (>= 1.6), AnnotationDbi (>= 1.17.11), methods, OrganismDbi
(>= 1.11.39), GenomicFeatures, GO.db, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene
R (>= 4.1.0), methods, BiocFileCache, utils
R (>= 2.7.0), methods, AnnotationDbi (>= 1.22.5)
R (>= 1.6), AnnotationDbi (>= 1.17.11), methods, OrganismDbi
(>= 1.11.39), GenomicFeatures, GO.db, org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm10.knownGene
R (>= 2.7.0), methods, AnnotationHub (>= 1.46.0),
AnnotationDbi, BiocStyle
R (>= 1.6), AnnotationDbi (>= 1.17.11), methods, OrganismDbi
(>= 1.11.39), GenomicFeatures, GO.db, org.Rn.eg.db,
TxDb.Rnorvegicus.UCSC.rn5.refGene
R (>= 2.7.0), methods, AnnotationDbi (>= 1.33.0)
VariantAnnotation (>= 1.9.15), RSQLite (>= 0.11.0)
R (>= 2.7.0), methods, AnnotationDbi (>= 1.18.3)
tools, jsonlite, RCurl, data.table, methods
utils, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb,
BSgenome
GenomicFeatures, GenomeInfoDb, rtracklayer, bumphunter,
derfinder (>= 1.21.7), AnnotationDbi, IRanges, org.Hs.eg.db,
utils, methods
methods, utils, stats, GenomeInfoDb, AnnotationHub, digest
utils, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb,
BSgenome, rhdf5, HDF5Array
AnnotationDbi, DBI, RSQLite, methods, gtools
methods, utils, BiocGenerics, S4Vectors, IRanges,
GenomeInfoDb, GenomicRanges, BSgenome
DBI, RSQLite, dplyr, dbplyr, igraph, Rdpack, AnnotationHub,
utils
BiocStyle, knitr, AnnotationHub (>= 2.7.13), rmarkdown
BiocStyle, magrittr, dplyr, tibble, knitr, rmarkdown
BiocStyle, rmarkdown, knitr, AnnotationHub, GenomicRanges,
plyranges, sessioninfo
AnnotationHub, RUnit, BiocGenerics, knitr, curl, httr
BiocStyle, knitr, rmarkdown, testthat, Modstrings,
rtracklayer
dplyr, knitr, BiocStyle, rmarkdown, jsonlite
BiocStyle, knitr, RefManageR, rmarkdown, ggridges, httr,
readr, pheatmap, rtracklayer, AnnotationHub
geneplast, BiocGenerics, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, BiocStyle, sessioninfo, testthat (>=
2.1.0), glue, derfinderPlot, AnnotationHubData, RefManageR,
GenomicRanges, covr
knitr, rmarkdown, BiocStyle, TFBSTools (>= 1.31.2)
magrittr, graphite, dplyr, tidyr, tibble, rappdirs, XML,
readxl, stringr, utils, knitr, sets, R.utils, readr,
conflicted, rmarkdown
pd.hg.u95av2, pd.huex.1.0.st.v2, pd.mapping50k.xba240,
pd.hg18.60mer.expr, pd.2006.07.18.hg18.refseq.promoter,
pd.hugene.1.0.st.v1
testthat (>= 3.0.0), AnnotationHub, utils, knitr, rmarkdown
DBI, RUnit, clusterProfiler, knitr, rmarkdown
BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo
rmarkdown, knitr, pander, testthat, devtools, markdown