rGADEM
de novo motif discovery
Bioconductor version: 2.9
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>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("rGADEM")
To cite this package in a publication, start R and enter:
citation("rGADEM")
Documentation
| R Script | The rGADEM users guide | |
| Reference Manual |
Details
| biocViews | Microarray, ChIPchip, Sequencing, ChIPSeq, GenomicSequence |
| Depends | R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo |
| Imports | Biostrings, IRanges, methods, graphics, seqLogo |
| Suggests | BSgenome.Hsapiens.UCSC.hg18 |
| System Requirements | |
| License | Artistic-2.0 |
| URL | |
| Depends On Me | |
| Imports Me | MotIV |
| Suggests Me | |
| Version | 2.2.0 |
| Since | Bioconductor 2.6 (R-2.11) |
Package Downloads
| Package Source | rGADEM_2.2.0.tar.gz |
| Windows Binary | rGADEM_2.2.0.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) binary | rGADEM_2.2.0.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Annotation
- Variants
- Flow Cytometry and other assays
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