motifcounter

DOI: 10.18129/B9.bioc.motifcounter    

R package for analysing TFBSs in DNA sequences

Bioconductor version: Release (3.15)

'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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	MotifAnnotation, SequenceMatching, Software, Transcription
Version	1.20.0
In Bioconductor since	BioC 3.5 (R-3.4) (5.5 years)
License	GPL-2
Depends	R (>= 3.0)
Imports	Biostrings, methods
LinkingTo
Suggests	knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	motifcounter_1.20.0.tar.gz
Windows Binary
macOS Binary (x86_64)	motifcounter_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/motifcounter
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/motifcounter
Package Short Url	https://bioconductor.org/packages/motifcounter/
Package Downloads Report	Download Stats