Package: PWMEnrich
Imports: seqLogo, gdata, evd
Maintainer: Robert Stojnic <robert.stojnic@gmail.com>
License: GPL-3
Title: PWM enrichment analysis
Type: Package
LazyLoad: yes
Author: Robert Stojnic, with contributions from Diego Diez
Description: 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.
Version: 2.2.0
biocViews: Bioinformatics, SequenceMatching, GenomicSequence, Software
Date: 2013-03-08
Depends: methods, grid, BiocGenerics, Biostrings,
Suggests: MotifDb, BSgenome.Dmelanogaster.UCSC.dm3,
        PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel
Collate: 'AllDataClasses.R' 'AllGenerics.R' 'background.R' 'clover.R'
        'diff.R' 'misc.R' 'MotifEnrichmentResults-methods.R'
        'options.R' 'plot.R' 'PWMBackground-methods.R' 'PWM-methods.R'
        'pwm.R' 'readData.R' 'seqLogoSupp.R' 'similarity.R'
Packaged: 2013-04-04 11:11:38 UTC; biocbuild
Built: R 3.0.0; ; 2013-04-04 17:07:22 UTC; windows
