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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PWMEnrich")
In most cases, you don't need to download the package archive at all.
PWMEnrich
|
This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see PWMEnrich.
PWM enrichment analysis
Bioconductor version: 2.12
Asses the enrichment of already known PWMs (from JASPAR and MotifDb) in DNA sequences. The package implements multiple algorithms, including fixed-threshold (Z-score) and threshold-free (Lognormal normalization and Clover) methods. These can be applied to a single sequence (e.g. enhancer of interest) or a group of sequences (e.g. a set of ChIP-chip/seq peaks). The output is a ranked list of PWMs according to their level of enrichment compared to genomic background. Custom sets of PWMs and genomic background are also supported.
Author: Robert Stojnic, with contributions from Diego Diez
Maintainer: Robert Stojnic <robert.stojnic at gmail.com>
Citation (from within R,
enter citation("PWMEnrich")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("PWMEnrich")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PWMEnrich")
| R Script | Overview of the 'PWMEnrich' package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Bioinformatics, GenomicSequence, SequenceMatching, Software |
| Version | 2.2.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (3.5 years) |
| License | GPL-3 |
| Depends | methods, grid, BiocGenerics, Biostrings |
| Imports | seqLogo, gdata, evd |
| LinkingTo | |
| Suggests | MotifDb, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | PWMEnrich.Dmelanogaster.background |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | PWMEnrich_2.2.0.tar.gz |
| Windows Binary | PWMEnrich_2.2.0.zip |
| Mac OS X 10.6 (Snow Leopard) | PWMEnrich_2.2.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/PWMEnrich/tree/release-2.12 |
| Package Short Url | http://bioconductor.org/packages/PWMEnrich/ |
| Package Downloads Report | Download Stats |
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