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("rGREAT")):
Installation
To install this package, start R (version "4.2") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Coverage, GO, GeneSetEnrichment, GenomeAnnotation, Pathways, Sequencing, Software, WholeGenome |
| Version | 2.0.2 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 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 |
| System Requirements | |
| URL | https://github.com/jokergoo/rGREAT http://great.stanford.edu/public/html/ |
See More
| Suggests | testthat (>= 0.3), knitr, rmarkdown, BiocManager, org.Mm.eg.db, msigdbr, KEGGREST, reactome.db |
| Linking To | Rcpp |
| Enhances | BioMartGOGeneSets, UniProtKeywords |
| Depends On Me | |
| Imports Me | ATACCoGAPS, profileplyr |
| Suggests Me | TADCompare |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| 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 |
| 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 |
| Old Source Packages for BioC 3.16 | Source Archive |