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GREAT Analysis - Functional Enrichment on Genomic Regions

Bioconductor version: Release (3.19)

GREAT (Genomic Regions Enrichment of Annotations Tool) is a type of functional enrichment analysis directly performed on genomic regions. This package implements the GREAT algorithm (the local GREAT analysis), also it supports directly interacting with the GREAT web service (the online GREAT analysis). Both analysis can be viewed by a Shiny application. 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.

Author: Zuguang Gu [aut, cre]

Maintainer: Zuguang Gu < at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

The rGREAT package HTML
Reference Manual PDF


biocViews Coverage, GO, GeneSetEnrichment, GenomeAnnotation, Pathways, Sequencing, Software, WholeGenome
Version 2.6.0
In Bioconductor since BioC 3.1 (R-3.2) (9.5 years)
License MIT + file LICENSE
Depends R (>= 4.0.0), GenomicRanges, IRanges, methods
Imports graphics, rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats, GlobalOptions, shiny, DT, GenomicFeatures, digest, GO.db, progress, circlize, AnnotationDbi, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene,, RColorBrewer, S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp
System Requirements
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Suggests testthat (>= 0.3), knitr, rmarkdown, BiocManager,, msigdbr, KEGGREST, reactome.db
Linking To Rcpp
Enhances BioMartGOGeneSets, UniProtKeywords
Depends On Me
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Package Archives

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

Source Package rGREAT_2.6.0.tar.gz
Windows Binary
macOS Binary (x86_64) rGREAT_2.6.0.tgz
macOS Binary (arm64) rGREAT_2.6.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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