rGREAT
This is the released version of rGREAT; for the devel version, see rGREAT.
All Bioconductor versions of rGREAT
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1
GREAT Analysis - Functional Enrichment on Genomic Regions
Bioconductor version: 3.23 · Package version: 2.14.0
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.
Maintainer: Zuguang Gu <guzuguang at suat-sz.edu.cn>
Citation
From within R, enter citation("rGREAT"):
Zuguang Gu. rGREAT: GREAT Analysis - Functional Enrichment on Genomic Regions. doi:10.18129/B9.bioc.rGREAT, R package version 2.14.0, https://bioconductor.org/packages/rGREAT.
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")
BiocManager::install("rGREAT")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 2.14.0 |
| License | MIT + file LICENSE |
| URL | https://github.com/jokergoo/rGREAT http://great.stanford.edu/public/html/ |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11 years) |
| Downloads rank | 281 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Coverage, GO, GeneSetEnrichment, GenomeAnnotation, Pathways, Sequencing, Software, WholeGenome |
| Package Short Url | https://bioconductor.org/packages/rGREAT/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rGREAT")| The rGREAT package | HTML |
| Reference Manual | |
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | rGREAT_2.14.0.tar.gz |
| Windows binary (x86_64) | rGREAT_2.14.0.zip |
| macOS binary (arm64) | rGREAT_2.14.0.tgz |
| macOS binary (x86_64) | rGREAT_2.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/rGREAT |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rGREAT |
| Package Downloads Report | Download Stats |
Dependencies
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, org.Hs.eg.db, RColorBrewer, S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp
LinkingTo: Rcpp
Suggests: testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db
Enhances: BioMartGOGeneSets, UniProtKeywords
Reverse dependencies
Imports Me (1): profileplyr