JASPAR

Bioconductor

Package: JASPAR
Type: Package
Title: Data package for JASPAR databases
Version: 0.99.1
Authors@R: person(given = "Damir", family = "Baranasic", 
        role = c("aut", "cre"),
        email = "[email protected]", 
        comment = c(ORCID = "0000-0001-5948-0932"))
Description: JASPAR (https://jaspar.elixir.no/) is an open-access database that
   has provided high-quality, manually curated, and non-redundant DNA
   binding profiles for transcription factors (TFs) as position 
   frequency matrices (PFMs) for over 20 years. For this 11th release
   of the database, we expanded our CORE and UNVALIDATED collections 
   with new PFMs and updated existing profiles. Specifically, we 
   added 306 and 433 new binding profiles to the CORE (a 12% 
   increase) and UNVALIDATED (a 60% increase) collections, 
   respectively, and updated 13 profiles from the CORE collection.
   With the new collections of PFMs, we updated the TF binding site 
   predictions in eight species and provided the corresponding 
   genomic tracks. Moreover, we updated the profile clusters and 
   familial TF binding sites accordingly. This release introduces a 
   regulatory sequence simulation tool, inMOTIFin, enabling users to 
   simulate regulatory sequences using JASPAR PFMs. To enrich the 
   annotations linked to the TFs, JASPAR now provides scientific 
   literature-based human TF target information derived from a large 
   language model. Notably, this release features the addition of a 
   new collection of deep learning BPnet models, providing a paradigm
   shift in modeling and characterizing TF-DNA interactions, driven 
   by advances in artificial intelligence. JASPAR 2026 provides 1304 
   BPNet models trained on Homo sapiens ENCODE ChIP-seq datasets from
   264 TFs. Interpretation of the BPnet revealed critical binding 
   profiles that were curated and matched to JASPAR CORE PFMs for an 
   easy overview of the binding patterns. Profiles from BPnet models 
   associated with the same TF were clustered to provide a 
   non-redundant summary of the binding properties of the TF, 
   resulting in 266 primary motifs in the new Deep Learning 
   collection. The 2026 release of JASPAR now offers the classical 
   manually curated collections of TF binding profiles and 
   state-of-the-art deep learning models. These collections lay a 
   foundation for future endeavors in genomic research, serving the
   scientific community in uncovering the mechanisms of gene 
   regulation.
Depends: R (>= 4.5.0), methods, BiocFileCache, utils
License: GPL-2
URL: https://jaspar.elixir.no/
NeedsCompilation: no
biocViews: AnnotationData, FunctionalAnnotation, AnnotationHub
LazyData: no
RoxygenNote: 7.3.3
Suggests:
    knitr,
    rmarkdown,
    BiocStyle,
    RSQLite,
    TFBSTools
VignetteBuilder: knitr
BugReports: https://github.com/da-bar/JASPAR