DOI: 10.18129/B9.bioc.motifcounter    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see motifcounter.

R package for analysing TFBSs in DNA sequences

Bioconductor version: 3.13

'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.

Author: Wolfgang Kopp [aut, cre]

Maintainer: Wolfgang Kopp <wolfgang.kopp at>

Citation (from within R, enter citation("motifcounter")):


To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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HTML R Script Introduction to the `motifcounter` package
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biocViews MotifAnnotation, SequenceMatching, Software, Transcription
Version 1.16.0
In Bioconductor since BioC 3.5 (R-3.4) (4.5 years)
License GPL-2
Depends R (>= 3.0)
Imports Biostrings, methods
Suggests knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc
Depends On Me
Imports Me
Suggests Me
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