motifmatchr

DOI: 10.18129/B9.bioc.motifmatchr    

Fast Motif Matching in R

Bioconductor version: Release (3.12)

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 "4.0") and enter:

if (!requireNamespace("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")

 

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Details

biocViews MotifAnnotation, Software
Version 1.12.0
In Bioconductor since BioC 3.6 (R-3.4) (3 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 enrichTF, esATAC, pageRank
Suggests Me CAGEWorkflow, chromVAR, MethReg
Links To Me
Build Report  

Package Archives

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

Source Package motifmatchr_1.12.0.tar.gz
Windows Binary motifmatchr_1.12.0.zip
macOS 10.13 (High Sierra) motifmatchr_1.12.0.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

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