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motifcounter
This is the released version of motifcounter; for the devel version, see motifcounter.
R package for analysing TFBSs in DNA sequences
Bioconductor version: Release (3.22)
'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 mdc-berlin.de>
citation("motifcounter")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("motifcounter")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("motifcounter")
Details
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Follow Installation instructions to use this package in your R session.