rGREAT
GREAT Analysis - Functional Enrichment on Genomic Regions
Bioconductor version: 3.23 · Package version: 2.14.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("rGREAT")Details
| Maintainer | Zuguang Gu <guzuguang@suat-sz.edu.cn> |
| Author | Zuguang Gu [aut, cre] (ORCID: <https://orcid.org/0000-0002-7395-8709>) |
| License | MIT + file LICENSE |
| URL | https://github.com/jokergoo/rGREAT, http://great.stanford.edu/public/html/ |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Coverage, GO, GeneSetEnrichment, GenomeAnnotation, Pathways, Sequencing, Software, WholeGenome |
| Package Short Url | https://bioconductor.org/packages/rGREAT/ |
Citation
From within R, enter citation("rGREAT"):
Zuguang Gu. rGREAT: GREAT Analysis - Functional Enrichment on Genomic Regions. doi:10.18129/B9.bioc.rGREAT, R package version 2.14.0, https://bioconductor.org/packages/rGREAT.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | rGREAT_2.14.0.tar.gz |
| Windows binary (x86_64) | rGREAT_2.14.0.zip |
| macOS binary (arm64) | rGREAT_2.14.0.tgz |
| macOS binary (x86_64) | rGREAT_2.14.0.tgz |
Dependencies
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
LinkingTo: Rcpp
Suggests: testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db
Enhances: BioMartGOGeneSets, UniProtKeywords
Reverse dependencies
Imports Me (1): profileplyr