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PscanRBackgrounds

This is the development version of PscanRBackgrounds; to use it, please install the devel version of Bioconductor.

Precomputed Promoter Backgrounds for PscanR


Bioconductor version: Development (3.24)

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.

Author: Federico Zambelli [aut, cre] ORCID iD ORCID: 0000-0003-3487-4331 , Diana Betelli [aut] ORCID iD ORCID: 0009-0007-6207-7715 , Giulio Pavesi [aut] ORCID iD ORCID: 0000-0001-5705-6249 , Italy's National Recovery and Resilience Plan (PNRR) [fnd] (project ELIXIRNextGenIT, R0000010)

Maintainer: Federico Zambelli <federico.zambelli at unimi.it>

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

Federico Zambelli, Diana Betelli, Giulio Pavesi. PscanRBackgrounds: Precomputed Promoter Backgrounds for PscanR. doi:10.18129/B9.bioc.PscanRBackgrounds, R package version 0.99.7, https://bioconductor.org/packages/PscanRBackgrounds.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("PscanRBackgrounds")

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("PscanRBackgrounds")
PscanR Background Resources HTML
Reference ManualPDF
NEWSText
Need some help? Ask on the Bioconductor Support site!

Details

biocViews Arabidopsis_thaliana_Data, Drosophila_melanogaster_Data, ExperimentHub, Genome, Homo_sapiens_Data, Mus_musculus_Data, Saccharomyces_cerevisiae_Data, Software
Version0.99.7
In Bioconductor sinceBioC 3.24 (R-4.6)
License CC BY 4.0
Depends R (>= 4.5.0)
Imports ExperimentHub
System Requirements
URLhttps://github.com/Federico77z/PscanRBackgrounds https://doi.org/10.5281/zenodo.21821764
Bug Reportshttps://github.com/Federico77z/PscanRBackgrounds/issues
See More
Suggests BiocStyle, ExperimentHubData, knitr, rmarkdown, testthat (>= 3.0.0)
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Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repositorygit clone https://git.bioconductor.org/packages/PscanRBackgrounds
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/PscanRBackgrounds
Package Short Url https://bioconductor.org/packages/PscanRBackgrounds/
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