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DESCRIPTION
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DESCRIPTION
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Package: PeakyFinders
Type: Package
Title: Mining, Calling, and Importing Epigenomic Peaks in R
Version: 0.99.4
Authors@R:
c(person(given = "Brian",
family = "Schilder",
role = c("cre"),
email = "[email protected]",
comment = c(ORCID = "0000-0001-5949-2191"))
)
Description:
Contains flexible and user-friendly functions to find, import, and harmonise
epigenomic peaks data from
**GEO**, **ENCODE**, **ROADMAP**, and **AnnotationHub**.
Efficiently imports multiple peak files in one function call
(either genome-wide or specific regions) using parallelisation.
When peaks are not available, automatically calls peaks from
*bedGraph* or *bigWig* files.
URL: https://github.com/neurogenomics/PeakyFinders
BugReports: https://github.com/neurogenomics/PeakyFinders/issues
Encoding: UTF-8
Depends: R (>= 4.1)
biocViews:
Genetics, FunctionalGenomics, SystemsBiology, WholeGenome, DataImport
Imports:
data.table,
utils,
R.utils,
methods,
tools,
stats,
BiocGenerics,
GenomicRanges,
GenomeInfoDb,
rtracklayer,
regioneR,
httr,
parallel,
MACSr,
GEOquery,
AnnotationHub,
stringr,
echoconda
Suggests:
rworkflows,
markdown,
rmarkdown,
magick,
remotes,
knitr,
BiocStyle,
covr,
testthat (>= 3.0.0),
hexSticker,
here,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
BSgenome.Hsapiens.UCSC.hg19.masked,
BSgenome.Hsapiens.UCSC.hg38.masked,
piggyback
Remotes:
github::macs3-project/MACSr,
github::RajLabMSSM/echoconda
RoxygenNote: 7.2.3
VignetteBuilder: knitr
License: GPL-3
Config/testthat/edition: 3
LazyData: true