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rGADEM

de novo motif discovery


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews ChIPSeq, ChIPchip, Microarray, MotifDiscovery, Sequencing, Software
Version 2.50.0
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
See More
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_2.50.0.tar.gz
Windows Binary rGADEM_2.50.0.zip
macOS Binary (x86_64) rGADEM_2.50.0.tgz
macOS Binary (arm64) rGADEM_2.50.0.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