To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("rGADEM")
In most cases, you don't need to download the package archive at all.
rGADEM
de novo motif discovery
Bioconductor version: 3.0
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 and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("rGADEM")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rGADEM")
| R Script | The rGADEM users guide | |
| Reference Manual |
Details
| biocViews | ChIPSeq, ChIPchip, Microarray, MotifDiscovery, Sequencing, Software |
| Version | 2.14.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) |
| License | Artistic-2.0 |
| Depends | R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo |
| Imports | Biostrings, IRanges, methods, graphics, seqLogo |
| LinkingTo | |
| Suggests | BSgenome.Hsapiens.UCSC.hg19 |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | MotIV |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | rGADEM_2.14.0.tar.gz |
| Windows Binary | rGADEM_2.14.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | rGADEM_2.14.0.tgz |
| Mac OS X 10.9 (Mavericks) | rGADEM_2.14.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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