PWMEnrich

DOI: 10.18129/B9.bioc.PWMEnrich    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see PWMEnrich.

PWM enrichment analysis

Bioconductor version: 3.8

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 (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("PWMEnrich")

For older versions of R, please refer to the appropriate Bioconductor release.

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	MotifAnnotation, SequenceMatching, Software
Version	4.18.0
In Bioconductor since	BioC 2.11 (R-2.15) (6.5 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, universalmotif
Links To Me
Build Report

Package Archives

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

Source Package	PWMEnrich_4.18.0.tar.gz
Windows Binary	PWMEnrich_4.18.0.zip
Mac OS X 10.11 (El Capitan)	PWMEnrich_4.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PWMEnrich
Source Repository (Developer Access)	git clone [email protected]:packages/PWMEnrich
Package Short Url	http://bioconductor.org/packages/PWMEnrich/
Package Downloads Report	Download Stats