rGADEM

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

de novo motif discovery

Bioconductor version: 3.13

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 (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("rGADEM")

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("rGADEM")

The rGADEM users guide PDF R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ChIPSeq, ChIPchip, Microarray, MotifDiscovery, Sequencing, Software

Version 2.40.0

In Bioconductor since BioC 2.6 (R-2.11) (14 years)

License Artistic-2.0

Depends R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo

Imports Biostrings, GenomicRanges, methods, graphics, seqLogo

System Requirements

URL

Suggests BSgenome.Hsapiens.UCSC.hg19, rtracklayer

Linking To

Enhances

Depends On Me

Imports Me TCGAWorkflow

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package rGADEM_2.40.0.tar.gz

Windows Binary rGADEM_2.40.0.zip

macOS 10.13 (High Sierra) rGADEM_2.40.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/rGADEM

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rGADEM

Bioc Package Browser https://code.bioconductor.org/browse/rGADEM/

Package Short Url https://bioconductor.org/packages/rGADEM/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.13 Source Archive