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
Description: 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.
Version: 1.2.0
biocViews: Bioinformatics, SequenceMatching
Date: 2012-06-22
Depends: methods, Biostrings, grid
Suggests: BSgenome.Dmelanogaster.UCSC.dm3,
        PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel
Collate: 'AllDataClasses.R' 'background.R' 'clover.R' 'diff.R' 'misc.R'
        'parallel.R' 'plot.R' 'PWMBackground-methods.R' 'PWM-methods.R'
        'pwm.R' 'readData.R' 'seqLogoSupp.R' 'similarity.R'
Packaged: 2012-10-02 07:48:00 UTC; biocbuild
Built: R 2.15.1; ; 2012-10-02 13:12:47 UTC; windows
