motifcounter

DOI: 10.18129/B9.bioc.motifcounter    

R package for analysing TFBSs in DNA sequences

Bioconductor version: Release (3.8)

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("motifcounter", version = "3.8")

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 1.6.0
In Bioconductor since BioC 3.5 (R-3.4) (1.5 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 universalmotif
Links To Me
Build Report  

Package Archives

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

Source Package motifcounter_1.6.0.tar.gz
Windows Binary motifcounter_1.6.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) motifcounter_1.6.0.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 http://bioconductor.org/packages/motifcounter/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: