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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 3.2 of Bioconductor; for the stable, up-to-date release version, see PWMEnrich.
PWM enrichment analysis
Bioconductor version: 3.2
A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.
Author: Robert Stojnic, 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")
| Overview of the 'PWMEnrich' package | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | MotifAnnotation, SequenceMatching, Software |
| Version | 4.6.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (3.5 years) |
| License | LGPL (>= 2) |
| Depends | methods, grid, BiocGenerics, Biostrings |
| Imports | seqLogo, gdata, evd |
| LinkingTo | |
| Suggests | MotifDb, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | PWMEnrich.Dmelanogaster.background, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background |
| Imports Me | |
| Suggests Me | rTRM |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | PWMEnrich_4.6.0.tar.gz |
| Windows Binary | PWMEnrich_4.6.0.zip |
| Mac OS X 10.6 (Snow Leopard) | PWMEnrich_4.6.0.tgz |
| Mac OS X 10.9 (Mavericks) | PWMEnrich_4.6.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/PWMEnrich/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/PWMEnrich/ |
| Package Downloads Report | Download Stats |
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