PWMEnrich
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see PWMEnrich.
PWM enrichment analysis
Bioconductor version: 3.9
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("PWMEnrich")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| Overview of the 'PWMEnrich' package | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | MotifAnnotation, SequenceMatching, Software |
| Version | 4.20.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (11.5 years) |
| License | LGPL (>= 2) |
| Depends | methods, grid, BiocGenerics, Biostrings |
| Imports | seqLogo, gdata, evd |
| System Requirements | |
| URL |
See More
| Suggests | MotifDb, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | PWMEnrich.Dmelanogaster.background, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background |
| Imports Me | |
| Suggests Me | rTRM |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PWMEnrich_4.20.0.tar.gz |
| Windows Binary | PWMEnrich_4.20.0.zip |
| Mac OS X 10.11 (El Capitan) | PWMEnrich_4.20.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |