PWM enrichment analysis

Bioconductor version: Release (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>

To install this package, start R and enter:


To cite this package in a publication, start R and enter:



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


biocViews Bioinformatics, SequenceMatching, Software
Version 1.2.0
In Bioconductor since BioC 2.11 (R-2.15)
License GPL-3
Depends methods, Biostrings, grid
Imports seqLogo, gdata, evd
Suggests BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel
System Requirements
Depends On Me PWMEnrich.Dmelanogaster.background
Imports Me
Suggests Me

Package Downloads

Package Source PWMEnrich_1.2.0.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) PWMEnrich_1.2.0.tgz
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