'motifcounter' provides motif matching, motif counting and motif enrichment functionality based on position frequency matrices. The main features of the packages include the utilization of higherorder background models and accounting for selfoverlapping motif matches when determining motif enrichment. The background model allows to capture dinucleotide (or higherorder nucleotide) composition adequately which may reduced model biases and misleading results compared to using simple GC background models. When conducting a motif enrichment analysis based on the motif match count, the package relies on a compound Poisson distribution or alternatively a combinatorial model. These distribution account for selfoverlapping motif structures as exemplified by repeatlike or palindromic motifs, and allow to determine the pvalue and foldenrichment for a set of observed motif matches.
Package details 


Author  Wolfgang Kopp [aut, cre] 
Bioconductor views  MotifAnnotation SequenceMatching Software Transcription 
Maintainer  Wolfgang Kopp <wolfgang.kopp@mdcberlin.de> 
License  GPL2 
Version  1.14.0 
Package repository  View on Bioconductor 
Installation 
Install the latest version of this package by entering the following in R:

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