motifcounter
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see motifcounter.
R package for analysing TFBSs in DNA sequences
Bioconductor version: Release (3.23)
'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")):Wolfgang Kopp. motifcounter: R package for analysing TFBSs in DNA sequences. doi:10.18129/B9.bioc.motifcounter, R package version 1.35.0, https://bioconductor.org/packages/motifcounter.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | 1.35.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | motifcounter_1.35.0.tar.gz |
| Windows Binary (x86_64) | motifcounter_1.35.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| 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 |