Abstract Summary GREAT 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 However, as an online tool, it has limitations of outdated annotation data, small numbers of supported organisms and gene set collections, and not being extensible for users.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/Bioconductor package named rGREAT which implements the GREAT algorithm locally. rGREAT by default supports more than 500 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 556 organisms are freely available at https://jokergoo.github.io/rGREAT_genesets/ . Contact z.gu@dkfz.de or d.huebschmann@dkfz.de Supplementary information Supplementary data are available at Bioinformatics online.

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