R (>= 2.7.0), methods, AnnotationDbi (>= 1.65.2)
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 (>= 4.3.0), 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 (>= 4.3.0), AnnotationDbi (>= 1.56.2), methods
R (>= 2.7.0), methods, AnnotationDbi (>= 1.18.3)
tools, jsonlite, RCurl, data.table, methods
utils, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb,
BSgenome
ape, treeio, tibble, tidyr, dplyr, readr, purrr, igraph,
geneplast, BiocFileCache
GenomicFeatures, GenomeInfoDb, rtracklayer, bumphunter,
derfinder (>= 1.21.7), AnnotationDbi, IRanges, org.Hs.eg.db,
utils, methods
methods, utils, stats, GenomeInfoDb, AnnotationHub, digest
AnnotationDbi, AnnotationHub, BiocFileCache, DBI, methods,
utils
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
frma, GEOquery, affy, ath1121501.db, BiocStyle, knitr,
rmarkdown
biomaRt, GO.db, GenomeInfoDb, knitr, testthat, GetoptLong, DT
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
annotate, BiocStyle, dplyr, GO.db, KEGGREST, knitr,
rmarkdown, SomaDataIO, testthat (>= 3.0.0), tibble, withr
BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo
rmarkdown, knitr, pander, testthat, devtools, markdown,
ggplot2