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JASPAR2024

Data package for JASPAR database (version 2024)


Bioconductor version: Release (3.18)

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.

Author: Damir Baranasic [aut, cre]

Maintainer: Damir Baranasic <damir.baranasic at lms.mrc.ac.uk>

Citation (from within R, enter citation("JASPAR2024")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("JASPAR2024")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("JASPAR2024")
JASPAR2022 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AnnotationData, AnnotationHub, FunctionalAnnotation
Version 0.99.6
License GPL-2
Depends R (>= 4.3.0), methods, BiocFileCache, utils
Imports
System Requirements
URL https://testjaspar.uio.no//
Bug Reports https://github.com/da-bar/JASPAR2024
See More
Suggests knitr, rmarkdown, BiocStyle, RSQLite
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me monaLisa
Links To Me

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package JASPAR2024_0.99.6.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Package Short Url https://bioconductor.org/packages/JASPAR2024/
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