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This is the development version of rGREAT; for the stable release version, see rGREAT.
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.
Maintainer: Zuguang Gu <z.gu at dkfz.de>
Citation (from within R,
enter citation("rGREAT")
):
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.
Reference Manual |
biocViews | Coverage, GO, GeneSetEnrichment, GenomeAnnotation, Pathways, Sequencing, Software, WholeGenome |
Version | 2.1.0 |
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 |
Follow Installation instructions to use this package in your R session.
Source Package | |
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 |
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