motifcounter - R package for analysing TFBSs in DNA sequences
'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 higher-order background models and accounting
for self-overlapping motif matches when determining motif
enrichment. The background model allows to capture dinucleotide
(or higher-order 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
self-overlapping motif structures as exemplified by repeat-like
or palindromic motifs, and allow to determine the p-value and
fold-enrichment for a set of observed motif matches.