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DESCRIPTION
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DESCRIPTION
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Package: JASPAR2024
Type: Package
Title: Data package for JASPAR database (version 2024)
Version: 0.99.6
Authors@R: person(given = "Damir", family = "Baranasic",
role = c("aut", "cre"),
email = "[email protected]",
comment = c(ORCID = "0000-0001-5948-0932"))
Description: JASPAR (https://testjaspar.uio.no/) is a widely-used open-access
database presenting manually curated high-quality and
non-redundant DNA-binding profiles for transcription factors (TFs)
across taxa. In this 10th release and 20th-anniversary update,
the CORE collection has expanded with 329 new profiles. We updated
three existing profiles and provided orthogonal support for
72 profiles from the previous release UNVALIDATED collection.
Altogether, the JASPAR 2024 update provides a 20 percent increase
in CORE profiles from the previous release. A trimming algorithm
enhanced profiles by removing low information content flanking
base pairs, which were likely uninformative (within the capacity
of the PFM models) for TFBS predictions and modelling TF-DNA
interactions. This release includes enhanced metadata, featuring a
refined classification for plant TFs structural DNA-binding
domains. The new JASPAR collections prompt updates to the genomic
tracks of predicted TF-binding sites in 8 organisms, with human
and mouse tracks available as native tracks in the UCSC Genome
browser. All data are available through the JASPAR web interface
and programmatically through its API and the updated Bioconductor
and pyJASPAR packages. Finally, a new TFBS extraction tool
enables users to retrieve predicted JASPAR TFBSs intersecting
their genomic regions of interest.
Depends: R (>= 4.3.0), methods, BiocFileCache, utils
License: GPL-2
URL: https://testjaspar.uio.no//
NeedsCompilation: no
biocViews: AnnotationData, FunctionalAnnotation, AnnotationHub
LazyData: no
RoxygenNote: 7.2.3
Suggests:
knitr,
rmarkdown,
BiocStyle,
RSQLite
VignetteBuilder: knitr
BugReports: https://github.com/da-bar/JASPAR2024