Registration Open for Bioc2024
Early registration discount pricing ends May 31!

rGREAT

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 <z.gu at dkfz.de>

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

Installation

To install this package, start R (version "4.4") 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.

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 PDF
NEWS Text
LICENSE Text

Details

biocViews Coverage, GO, GeneSetEnrichment, GenomeAnnotation, Pathways, Sequencing, Software, WholeGenome
Version 2.6.0
In Bioconductor since BioC 3.1 (R-3.2) (9 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, org.Hs.eg.db, RColorBrewer, S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp
System Requirements
URL https://github.com/jokergoo/rGREAT http://great.stanford.edu/public/html/
See More
Suggests testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db
Linking To Rcpp
Enhances BioMartGOGeneSets, UniProtKeywords
Depends On Me
Imports Me ATACCoGAPS
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package rGREAT_2.6.0.tar.gz
Windows Binary rGREAT_2.6.0.zip
macOS Binary (x86_64) rGREAT_2.6.0.tgz
macOS Binary (arm64) rGREAT_2.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/rGREAT
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rGREAT
Bioc Package Browser https://code.bioconductor.org/browse/rGREAT/
Package Short Url https://bioconductor.org/packages/rGREAT/
Package Downloads Report Download Stats