rGREAT

GREAT Analysis - Functional Enrichment on Genomic Regions

Bioconductor version: Release (3.17)

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 "4.3") 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")

1. Analyze with online GREAT	HTML	R Script
2. Analyze with local GREAT	HTML	R Script
3. Work with other organisms	HTML	R Script
4. Work with other geneset databases	HTML	R Script
5. Other documents	HTML
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Details

biocViews	Coverage, GO, GeneSetEnrichment, GenomeAnnotation, Pathways, Sequencing, Software, WholeGenome
Version	2.2.0
In Bioconductor since	BioC 3.1 (R-3.2) (8.5 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, org.Hs.eg.db, RColorBrewer, S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp
Linking To	Rcpp
Suggests	testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db
System Requirements
Enhances	BioMartGOGeneSets, UniProtKeywords
URL	https://github.com/jokergoo/rGREAT http://great.stanford.edu/public/html/

Depends On Me
Imports Me	ATACCoGAPS, profileplyr
Suggests Me	TADCompare
Links To Me
Build Report

Package Archives

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

Source Package	rGREAT_2.2.0.tar.gz
Windows Binary	rGREAT_2.2.0.zip
macOS Binary (x86_64)	rGREAT_2.2.0.tgz
macOS Binary (arm64)	rGREAT_2.2.0.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