motifcounter
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see motifcounter.
R package for analysing TFBSs in DNA sequences
Bioconductor version: 3.9
'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 "3.6") 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")| Introduction to the `motifcounter` package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | MotifAnnotation, SequenceMatching, Software, Transcription |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 years) |
| License | GPL-2 |
| Depends | R (>= 3.0) |
| Imports | Biostrings, methods |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | motifcounter_1.8.0.tar.gz |
| Windows Binary | motifcounter_1.8.0.zip |
| Mac OS X 10.11 (El Capitan) | motifcounter_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/motifcounter |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/motifcounter |
| Bioc Package Browser | https://code.bioconductor.org/browse/motifcounter/ |
| Package Short Url | https://bioconductor.org/packages/motifcounter/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |