rGADEM
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see rGADEM.
de novo motif discovery
Bioconductor version: 3.10
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("rGADEM")):
Installation
To install this package, start R (version "3.6") 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 | 2.34.1 |
| 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 | MotIV, 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_2.34.1.tar.gz |
| Windows Binary | rGADEM_2.34.1.zip |
| Mac OS X 10.11 (El Capitan) | rGADEM_2.34.1.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 3.10 | Source Archive |