To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("PWMEnrich")
In most cases, you don't need to download the package archive at all.
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This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see PWMEnrich.
Bioconductor version: 2.11
Asses the enrichment of already known PWMs (e.g. from JASPAR) in DNA sequences. Motif hits in a sequence or DNA region are considered together and P-values derived for their joint pattern. The package implements multiple algorithms, including fixed-threshold (Z-score) and threshold-free (Lognormal normalization and Clover) methods. The main goal is to identify a set of transcription factors that most likely bind to a single sequence, group of sequences, or show significantly different binding affinity between two sets of sequences.
Author: Robert Stojnic
Maintainer: Robert Stojnic <robert.stojnic at gmail.com>
Citation (from within R,
enter citation("PWMEnrich")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("PWMEnrich")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PWMEnrich")
R Script | Overview of the 'PWMEnrich' package | |
Reference Manual | ||
Text | NEWS |
biocViews | Bioinformatics, SequenceMatching, Software |
Version | 1.2.0 |
In Bioconductor since | BioC 2.11 (R-2.15) (3.5 years) |
License | GPL-3 |
Depends | methods, Biostrings, grid |
Imports | seqLogo, gdata, evd |
LinkingTo | |
Suggests | BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | PWMEnrich.Dmelanogaster.background |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | PWMEnrich_1.2.0.tar.gz |
Windows Binary | PWMEnrich_1.2.0.zip |
Mac OS X 10.6 (Snow Leopard) | |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/PWMEnrich/tree/release-2.11 |
Package Short Url | http://bioconductor.org/packages/PWMEnrich/ |
Package Downloads Report | Download Stats |
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