rGADEM
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.22 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see rGADEM.
de novo motif discovery
Bioconductor version: Development (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("rGADEM")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | ChIPSeq, ChIPchip, Microarray, MotifDiscovery, Sequencing, Software |
| Version | 2.57.1 |
| In Bioconductor since | BioC 2.6 (R-2.11) (15.5 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | rGADEM_2.57.1.zip |
| macOS Binary (x86_64) | rGADEM_2.57.1.tgz |
| macOS Binary (arm64) | rGADEM_2.57.1.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 |