PWM enrichment analysis

Bioconductor version: Release (2.12)

Asses the enrichment of already known PWMs (from JASPAR and MotifDb) in DNA sequences. The package implements multiple algorithms, including fixed-threshold (Z-score) and threshold-free (Lognormal normalization and Clover) methods. These can be applied to a single sequence (e.g. enhancer of interest) or a group of sequences (e.g. a set of ChIP-chip/seq peaks). The output is a ranked list of PWMs according to their level of enrichment compared to genomic background. Custom sets of PWMs and genomic background are also supported.

Author: Robert Stojnic, with contributions from Diego Diez

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, GenomicSequence, SequenceMatching, Software
Version 2.2.0
In Bioconductor since BioC 2.11 (R-2.16)
License GPL-3
Depends methods, grid, BiocGenerics, Biostrings
Imports seqLogo, gdata, evd
Suggests MotifDb, 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_2.2.0.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) PWMEnrich_2.2.0.tgz
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center