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
System Requirements
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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