DOI: 10.18129/B9.bioc.rGREAT  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see rGREAT.

GREAT Analysis - Functional Enrichment on Genomic Regions

Bioconductor version: 3.16

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")):


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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


biocViews Coverage, GO, GeneSetEnrichment, GenomeAnnotation, Pathways, Sequencing, Software, WholeGenome
Version 2.0.2
In Bioconductor since BioC 3.1 (R-3.2) (8 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
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  

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Source Package rGREAT_2.0.2.tar.gz
Windows Binary rGREAT_2.0.2.zip (64-bit only)
macOS Binary (x86_64) rGREAT_2.0.2.tgz
macOS Binary (arm64) rGREAT_2.0.2.tgz
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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/
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