To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("PWMEnrich")

In most cases, you don't need to download the package archive at all.

PWMEnrich

PWM enrichment analysis

Bioconductor version: Release (3.0)

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:

source("http://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")

 

PDF R Script Overview of the 'PWMEnrich' package
PDF   Reference Manual
Text   NEWS

Details

biocViews SequenceMatching, Software
Version 4.2.0
In Bioconductor since BioC 2.11 (R-2.15)
License LGPL (>= 2)
Depends methods, grid, BiocGenerics, Biostrings
Imports seqLogo, gdata, evd
Suggests MotifDb, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background
System Requirements
URL
Depends On Me PWMEnrich.Dmelanogaster.background, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background
Imports Me
Suggests Me rTRM

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source PWMEnrich_4.2.0.tar.gz
Windows Binary PWMEnrich_4.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) PWMEnrich_4.2.0.tgz
Mac OS X 10.9 (Mavericks) PWMEnrich_4.2.0.tgz
Browse/checkout source (username/password: readonly)
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