motifmatchr

This is the development version of motifmatchr; for the stable release version, see motifmatchr.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6

Fast Motif Matching in R

Bioconductor version: Development (3.24)

Quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library, which was developed by Pasi Rastas, Janne Korhonen, and Petri Martinmäki.

Author: Alicia Schep [aut, cre], Stanford University [cph]

Maintainer: Alicia Schep <aschep at gmail.com>

Citation (from within R, enter citation("motifmatchr")):

Alicia Schep. motifmatchr: Fast Motif Matching in R. doi:10.18129/B9.bioc.motifmatchr, R package version 1.35.0, https://bioconductor.org/packages/motifmatchr.

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")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("motifmatchr")

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("motifmatchr")

motifmatchr	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	MotifAnnotation, Software
Version	1.35.0
In Bioconductor since	BioC 3.6 (R-3.4) (9 years)
License	GPL-3 + file LICENSE
Depends	R (>= 3.3)
Imports	Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, Seqinfo
System Requirements	C++11
URL

Suggests	testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19
Linking To	Rcpp, RcppArmadillo
Enhances
Depends On Me
Imports Me	ATACseqTFEA, enhancerHomologSearch, epiregulon, esATAC, pageRank
Suggests Me	CAGEWorkflow, chromVAR, GRaNIE, Signac
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	motifmatchr_1.35.0.tar.gz
Windows Binary (x86_64)	motifmatchr_1.35.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	motifmatchr_1.35.0.tgz
macOS Binary (sonoma-arm64)	motifmatchr_1.35.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/motifmatchr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/motifmatchr
Package Short Url	https://bioconductor.org/packages/motifmatchr/
Package Downloads Report	Download Stats