rGREAT

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see rGREAT.

Client for GREAT Analysis

Bioconductor version: 3.13

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, GO, GeneSetEnrichment, GenomeAnnotation, Pathways, Sequencing, Software, WholeGenome

Version 1.24.0

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/

Suggests testthat (>= 0.3), knitr, circlize (>= 0.4.8), rmarkdown

Linking To

Enhances

Depends On Me

Imports Me 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_1.24.0.tar.gz

Windows Binary rGREAT_1.24.0.zip (32- & 64-bit)

macOS 10.13 (High Sierra) rGREAT_1.24.0.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 3.13 Source Archive