R (>= 2.7.0), methods, AnnotationDbi (>= 1.55.1)
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 (>= 3.5.0), BSgenome (>= 1.60.0),
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 (>= 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 (>= 2.10), IRanges, GenomicRanges, BSgenome (>= 1.25.6)
R (>= 2.10), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges,
BSgenome (>= 1.33.9)
R (>= 2.10), IRanges, GenomeInfoDb, GenomicRanges, BSgenome
(>= 1.25.6)
R (>= 2.7.0), methods, AnnotationDbi (>= 1.18.3)
R (>= 2.10), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges,
BSgenome (>= 1.35.5)
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, IRanges, GenomicRanges, BSgenome
methods, utils, S4Vectors, IRanges, GenomeInfoDb,
GenomicRanges, BSgenome
methods, utils, IRanges, GenomeInfoDb, GenomicRanges, BSgenome
methods, utils, BiocGenerics, S4Vectors, IRanges,
GenomeInfoDb, GenomicRanges, BSgenome
DBI, RSQLite, dplyr, dbplyr, igraph, Rdpack, AnnotationHub
BiocStyle, knitr, AnnotationHub (>= 2.7.13), rmarkdown
BiocStyle, magrittr, dplyr, tibble, knitr, rmarkdown
BiocStyle, knitr, rmarkdown, sessioninfo, AnnotationHub
AnnotationHub, RUnit, BiocGenerics, knitr, curl, httr
BiocStyle, knitr, rmarkdown, testthat, Modstrings,
rtracklayer
dplyr, knitr, BiocStyle, rmarkdown, jsonlite
BiocStyle, knitr, RefManageR, rmarkdown, rCGH, sessioninfo,
AnnotationHub
geneplast, BiocGenerics, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, BiocStyle, sessioninfo, testthat (>=
2.1.0), glue, derfinderPlot, AnnotationHubData, RefManageR,
GenomicRanges, covr
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
Biostrings, BSgenome (>= 1.16.1), BSgenome.Hsapiens.UCSC.hg19
Biostrings, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg19.masked (>= 1.3.19)
BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo
rmarkdown, knitr, pander, testthat, devtools, markdown