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

PWMEnrich

PWM enrichment analysis

Bioconductor version: 2.13

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>

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	Bioinformatics, GenomicSequence, SequenceMatching, Software
Version	2.6.2
In Bioconductor since	BioC 2.11 (R-2.15)
License	GPL-3
Depends	methods, grid, BiocGenerics, Biostrings
Imports	seqLogo, gdata, evd
Suggests	MotifDb, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel
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_2.6.2.tar.gz
Windows Binary	PWMEnrich_2.6.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	PWMEnrich_2.6.2.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats