rGADEM

DOI: 10.18129/B9.bioc.rGADEM    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see rGADEM.

de novo motif discovery

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	The rGADEM users guide
PDF		Reference Manual

Details

biocViews	ChIPSeq, ChIPchip, Microarray, MotifDiscovery, Sequencing, Software
Version	2.44.1
In Bioconductor since	BioC 2.6 (R-2.11) (12.5 years)
License	Artistic-2.0
Depends	R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo
Imports	Biostrings, GenomicRanges, methods, graphics, seqLogo
LinkingTo
Suggests	BSgenome.Hsapiens.UCSC.hg19, rtracklayer
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	TCGAWorkflow
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	rGADEM_2.44.1.tar.gz
Windows Binary	rGADEM_2.44.1.zip (64-bit only)
macOS Binary (x86_64)	rGADEM_2.44.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/rGADEM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/rGADEM
Package Short Url	https://bioconductor.org/packages/rGADEM/
Package Downloads Report	Download Stats