rGREAT: an R/bioconductor package for functional enrichment on genomic regions

• Published in: Bioinformatics (Oxford, England) Vol. 39; no. 1
• Main Authors: Gu, Zuguang, Hübschmann, Daniel
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2023; Oxford Publishing Limited (England)
• Subjects: Algorithms; Annotations; Applications Note; Availability; Bioinformatics; Enrichment; Gene Ontology; Genome; Genomics; Organisms; Software
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btac745

Abstract Summary GREAT (Genomic Regions Enrichment of Annotations Tool) is a widely used tool for functional enrichment on genomic regions. However, as an online tool, it has limitations of outdated annotation data, small numbers of supported organisms and gene set collections, and not being extensible for users. Here, we developed a new R/Bioconductorpackage named rGREAT which implements the GREAT algorithm locally. rGREAT by default supports more than 600 organisms and a large number of gene set collections, as well as self-provided gene sets and organisms from users. Additionally, it implements a general method for dealing with background regions. Availability and implementation The package rGREAT is freely available from the Bioconductor project: https://bioconductor.org/packages/rGREAT/. The development version is available at https://github.com/jokergoo/rGREAT. Gene Ontology gene sets for more than 600 organisms retrieved from Ensembl BioMart are presented in an R package BioMartGOGeneSets which is available at https://github.com/jokergoo/BioMartGOGeneSets. Supplementary information Supplementary data are available at Bioinformatics online.