rGADEM

DOI: 10.18129/B9.bioc.rGADEM    

de novo motif discovery

Bioconductor version: Release (3.6)

rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software.

Author: Arnaud Droit, Raphael Gottardo, Gordon Robertson and Leiping Li

Maintainer: Arnaud Droit <arnaud.droit at crchuq.ulaval.ca>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("rGADEM")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("rGADEM")

 

PDF	R Script	The rGADEM users guide
PDF		Reference Manual

Details

biocViews	ChIPSeq, ChIPchip, Microarray, MotifDiscovery, Sequencing, Software
Version	2.26.0
In Bioconductor since	BioC 2.6 (R-2.11) (8 years)
License	Artistic-2.0
Depends	R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo
Imports	Biostrings, IRanges, methods, graphics, seqLogo
LinkingTo
Suggests	BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	MotIV
Suggests Me
Build Report

Package Archives

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

Source Package	rGADEM_2.26.0.tar.gz
Windows Binary	rGADEM_2.26.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	rGADEM_2.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rGADEM
Package Short Url	http://bioconductor.org/packages/rGADEM/
Package Downloads Report	Download Stats