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motifmatchr

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

Fast Motif Matching in R


Bioconductor version: Development (3.20)

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")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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

Details

biocViews MotifAnnotation, Software
Version 1.27.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3 + file LICENSE
Depends R (>= 3.3)
Imports Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, GenomeInfoDb
System Requirements C++11
URL
See More
Suggests testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19
Linking To Rcpp, RcppArmadillo
Enhances
Depends On Me
Imports Me ATACCoGAPS, ATACseqTFEA, enhancerHomologSearch, epiregulon, esATAC, pageRank, spatzie
Suggests Me chromVAR, GRaNIE, MethReg, CAGEWorkflow, MOCHA, Signac
Links To Me
Build Report Build Report

Package Archives

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

Source Package motifmatchr_1.27.0.tar.gz
Windows Binary motifmatchr_1.27.0.zip (64-bit only)
macOS Binary (x86_64) motifmatchr_1.27.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/motifmatchr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/motifmatchr
Bioc Package Browser https://code.bioconductor.org/browse/motifmatchr/
Package Short Url https://bioconductor.org/packages/motifmatchr/
Package Downloads Report Download Stats