rGREAT

DOI: 10.18129/B9.bioc.rGREAT    

This is the development version of rGREAT; for the stable release version, see rGREAT.

GREAT Analysis - Functional Enrichment on Genomic Regions

Bioconductor version: Development (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>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

HTML	R Script	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		5. Other documents
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Coverage, GO, GeneSetEnrichment, GenomeAnnotation, Pathways, Sequencing, Software, WholeGenome
Version	2.1.2
In Bioconductor since	BioC 3.1 (R-3.2) (7.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6.0), 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
SystemRequirements
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_2.1.2.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/rGREAT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rGREAT
Package Short Url	https://bioconductor.org/packages/rGREAT/
Package Downloads Report	Download Stats