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PWM enrichment analysis

Bioconductor version: 2.14

A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.

Author: Robert Stojnic, Diego Diez

Maintainer: Robert Stojnic <robert.stojnic at>

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


biocViews GenomicSequence, SequenceMatching, Software
Version 3.6.1
In Bioconductor since BioC 2.11 (R-2.15)
License LGPL (>= 2)
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, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background
Imports Me
Suggests Me rTRM

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Package Source PWMEnrich_3.6.1.tar.gz
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Mac OS X 10.6 (Snow Leopard) PWMEnrich_3.6.1.tgz
Mac OS X 10.9 (Mavericks) PWMEnrich_3.6.1.tgz
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