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PWMEnrich

This is the development version of PWMEnrich; for the stable release version, see PWMEnrich.

PWM enrichment analysis

Bioconductor version: Development (3.18)

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: Diego Diez <diego10ruiz at gmail.com>

Citation (from within R, enter citation("PWMEnrich")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews MotifAnnotation, SequenceMatching, Software
Version 4.37.0
In Bioconductor since BioC 2.11 (R-2.15) (11 years)
License LGPL (>= 2)
Depends R (>= 3.5.0), methods, BiocGenerics, Biostrings
Imports grid, seqLogo, gdata, evd, S4Vectors
Linking To
Suggests MotifDb, BSgenome, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr
System Requirements
Enhances
URL
See More
Depends On Me PWMEnrich.Dmelanogaster.background, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background
Imports Me
Suggests Me rTRM
Links To Me
Build Report  

Package Archives

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

Source Package PWMEnrich_4.37.0.tar.gz
Windows Binary PWMEnrich_4.37.0.zip
macOS Binary (x86_64) PWMEnrich_4.37.0.tgz
macOS Binary (arm64) PWMEnrich_4.37.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PWMEnrich
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PWMEnrich
Bioc Package Browser https://code.bioconductor.org/browse/PWMEnrich/
Package Short Url https://bioconductor.org/packages/PWMEnrich/
Package Downloads Report Download Stats