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Bioconductor - rGREAT (development version)

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 (3.22)

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] ORCID: 0000-0002-7395-8709

Maintainer: Zuguang Gu <z.gu at dkfz.de>

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

To install this package, start R (version "4.5") 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")
Details biocViews Coverage, GO, GeneSetEnrichment, GenomeAnnotation, Pathways, Sequencing, Software, WholeGenome Version 2.11.0 In Bioconductor since BioC 3.1 (R-3.2) (10 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 Package Archives

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

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