To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("rGADEM")

In most cases, you don't need to download the package archive at all.

rGADEM

de novo motif discovery

Bioconductor version: Release (3.0)

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>

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

Installation

To install this package, start R and enter:

source("http://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 2.14.0
In Bioconductor since BioC 2.6 (R-2.11)
License Artistic-2.0
Depends R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo
Imports Biostrings, IRanges, methods, graphics, seqLogo
Suggests BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
URL
Depends On Me
Imports Me MotIV
Suggests Me

Package Archives

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

Package Source rGADEM_2.14.0.tar.gz
Windows Binary rGADEM_2.14.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) rGADEM_2.14.0.tgz
Mac OS X 10.9 (Mavericks) rGADEM_2.14.0.tgz
Browse/checkout source (username/password: readonly)
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