rGADEM

de novo motif discovery


Bioconductor version: Release (3.19)

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 "4.4") 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 2.52.0
In Bioconductor since BioC 2.6 (R-2.11) (14.5 years)
License Artistic-2.0
Depends R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo
Imports Biostrings, GenomicRanges, methods, graphics, seqLogo
System Requirements
URL
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Suggests BSgenome.Hsapiens.UCSC.hg19, rtracklayer
Linking To
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Depends On Me
Imports Me TCGAWorkflow
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Package Archives

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

Source Package rGADEM_2.52.0.tar.gz
Windows Binary rGADEM_2.52.0.zip
macOS Binary (x86_64) rGADEM_2.52.0.tgz
macOS Binary (arm64) rGADEM_2.52.0.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