PWMEnrich

DOI: 10.18129/B9.bioc.PWMEnrich    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

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

PWM enrichment analysis

Bioconductor version: Development (3.12)

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 "4.0") and enter:

if (!requireNamespace("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

PDF   Reference Manual

Details

biocViews MotifAnnotation, SequenceMatching, Software
Version 4.25.1
In Bioconductor since BioC 2.11 (R-2.15) (8 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
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/PWMEnrich
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PWMEnrich
Package Short Url https://bioconductor.org/packages/PWMEnrich/
Package Downloads Report Download Stats

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