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R package for analysing TFBSs in DNA sequences

Bioconductor version: Release (3.19)

'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 "4.4") and enter:

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


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


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to the `motifcounter` package HTML R Script
Reference Manual PDF


biocViews MotifAnnotation, SequenceMatching, Software, Transcription
Version 1.28.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-2
Depends R (>= 3.0)
Imports Biostrings, methods
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Suggests knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc
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Follow Installation instructions to use this package in your R session.

Source Package motifcounter_1.28.0.tar.gz
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macOS Binary (x86_64) motifcounter_1.28.0.tgz
macOS Binary (arm64) motifcounter_1.28.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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