| Title: | Precomputed Promoter Backgrounds for PscanR |
|---|---|
| Description: | Provides ExperimentHub metadata and documentation for the promoter-background score distributions used by PscanR transcription factor binding motif enrichment analyses. Each of the 105 backgrounds is a separate ExperimentHub resource, covering the JASPAR 2020, 2022 and 2024 CORE collections, seven genome assemblies of five organisms, and five promoter windows. The files are hosted on Zenodo, one record per JASPAR release, and archived together in a version-specific Zenodo record. |
| Authors: | Federico Zambelli [aut, cre] (ORCID: <https://orcid.org/0000-0003-3487-4331>), Diana Betelli [aut] (ORCID: <https://orcid.org/0009-0007-6207-7715>), Giulio Pavesi [aut] (ORCID: <https://orcid.org/0000-0001-5705-6249>), Italy's National Recovery and Resilience Plan (PNRR) [fnd] (project ELIXIRNextGenIT, R0000010) |
| Maintainer: | Federico Zambelli <[email protected]> |
| License: | CC BY 4.0 |
| Version: | 0.99.7 |
| Built: | 2026-11-06 21:05:30 UTC |
| Source: | https://github.com/bioc/PscanRBackgrounds |
One ExperimentHub resource per combination of JASPAR CORE release (2020, 2022, 2024), genome assembly (hg38, hs1, mm10, mm39, dm6, sacCer3, TAIR9) and promoter window (200u_50d, 450u_50d, 500u_0d, 950u_50d, 1000u_0d), for 105 resources in total.
Each resource is a tab-separated text file. The first line is the
header [SHORT TFBS MATRIX]; each following line holds a JASPAR
matrix identifier, the number of promoters, the mean score and the score
standard deviation. The resources use the FilePath dispatch class,
so retrieval returns the path to the locally cached file.
For each motif of the JASPAR collection matching the organism's taxonomic group, PscanR scans every unique promoter sequence of the assembly over the given window, keeps the best normalized PWM score per promoter, and records the number of promoters with the mean and standard deviation of those scores. PscanR compares foreground promoters against these statistics.
Resource titles have the form
PscanR_bg_v2_J<release>_<assembly>_<up>u_<down>d_<source>, for
example PscanR_bg_v2_J2020_hg38_200u_50d_UCSC. The installed
extdata/catalog_v2.tsv lists, for every resource, the annotation
source and retrieval date, promoter, motif and annotation hashes, the
PscanR scanner version and commit, and the SHA-256 checksum of the file.
PscanR users normally retrieve a background with PscanR's own retrieval
function, which verifies that checksum.
The backgrounds are distributed under CC BY 4.0. See the installed
DATA_SOURCES.md for upstream attribution.
Generated with the pipeline at
https://github.com/Federico77z/PscanRBackgrounds-pipeline. The
files are hosted on Zenodo, one record per JASPAR release
(doi:10.5281/zenodo.23183695, doi:10.5281/zenodo.23183713,
doi:10.5281/zenodo.23183720), and archived together in
doi:10.5281/zenodo.21821764. See the installed
scripts/make-data.R.
Zambelli F, Pesole G, Pavesi G. (2009). Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. Nucleic Acids Research. doi:10.1093/nar/gkp464.
metadata <- utils::read.csv(system.file( "extdata", "metadata.csv", package = "PscanRBackgrounds" )) head(metadata[c("Title", "Genome", "Species")]) catalog <- utils::read.delim(system.file( "extdata", "catalog_v2.tsv", package = "PscanRBackgrounds" )) table(catalog$assembly, catalog$jaspar_release)metadata <- utils::read.csv(system.file( "extdata", "metadata.csv", package = "PscanRBackgrounds" )) head(metadata[c("Title", "Genome", "Species")]) catalog <- utils::read.delim(system.file( "extdata", "catalog_v2.tsv", package = "PscanRBackgrounds" )) table(catalog$assembly, catalog$jaspar_release)