rGREAT

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see rGREAT.

Client for GREAT Analysis


Bioconductor version: 3.10

This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user's input and automatically retrieving results from GREAT web server.

Author: Zuguang Gu

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

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

Installation

To install this package, start R (version "3.6") 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")
Analyze with GREAT HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Coverage, GO, GeneSetEnrichment, GenomeAnnotation, Pathways, Sequencing, Software, WholeGenome
Version 1.18.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License MIT + file LICENSE
Depends R (>= 3.1.2), GenomicRanges, IRanges, methods
Imports rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats
System Requirements
URL https://github.com/jokergoo/rGREAT http://great.stanford.edu/public/html/
See More
Suggests testthat (>= 0.3), knitr, circlize (>= 0.4.8), rmarkdown
Linking To
Enhances
Depends On Me
Imports Me profileplyr
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package rGREAT_1.18.0.tar.gz
Windows Binary rGREAT_1.18.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) rGREAT_1.18.0.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 3.10 Source Archive