motifcounter
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/motifcounter/ |
| Package Short Url | https://bioconductor.org/packages/motifcounter/ |
| Package Downloads Report | Download Stats |