motifmatchr

DOI: 10.18129/B9.bioc.motifmatchr  

Fast Motif Matching in R

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	motifmatchr
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	MotifAnnotation, Software
Version	1.20.0
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 3.3)
Imports	Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, GenomeInfoDb
LinkingTo	Rcpp, RcppArmadillo
Suggests	testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements	C++11
Enhances
URL
Depends On Me
Imports Me	ATACCoGAPS, ATACseqTFEA, enhancerHomologSearch, enrichTF, esATAC, pageRank, spatzie
Suggests Me	CAGEWorkflow, chromVAR, GRaNIE, MethReg
Links To Me
Build Report

Package Archives

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

Source Package	motifmatchr_1.20.0.tar.gz
Windows Binary	motifmatchr_1.20.0.zip
macOS Binary (x86_64)	motifmatchr_1.20.0.tgz
macOS Binary (arm64)	motifmatchr_1.20.0.tgz
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