PWMEnrich

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 gmail.com>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("PWMEnrich")

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

    citation("PWMEnrich")

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