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 | R Script | |
Reference Manual |
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 |
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_2.52.0.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 |