Package: JASPAR2024
Type: Package
Title: Data package for JASPAR database (version 2024)
Version: 0.99.7
Authors@R: person(given = "Damir", family = "Baranasic", 
                  role = c("aut", "cre"),
                  email = "damir.baranasic@lms.mrc.ac.uk", 
                  comment = c(ORCID = "0000-0001-5948-0932"))
Description: JASPAR (https://jaspar.elixir.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://jaspar.elixir.no/
NeedsCompilation: no
biocViews: AnnotationData, FunctionalAnnotation, AnnotationHub
RoxygenNote: 7.2.3
Suggests: knitr, rmarkdown, BiocStyle, RSQLite
VignetteBuilder: knitr
BugReports: https://github.com/da-bar/JASPAR2024
git_url: https://git.bioconductor.org/packages/JASPAR2024
git_branch: devel
git_last_commit: 3a1e18a
git_last_commit_date: 2024-10-31
Repository: Bioconductor 3.21
Date/Publication: 2024-11-13
Packaged: 2024-11-13 11:32:51 UTC; biocbuild
Author: Damir Baranasic [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-5948-0932>)
Maintainer: Damir Baranasic <damir.baranasic@lms.mrc.ac.uk>
Built: R 4.6.0; ; 2026-04-30 06:35:31 UTC; unix
