motifmatchr

DOI: 10.18129/B9.bioc.motifmatchr    

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

Fast Motif Matching in R

Bioconductor version: Development (3.8)

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 and enter:

if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("motifmatchr", version = "devel")

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 1.3.0
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 esATAC
Suggests Me chromVAR
Build Report  

Package Archives

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

Source Package motifmatchr_1.3.0.tar.gz
Windows Binary motifmatchr_1.3.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) motifmatchr_1.3.0.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 http://bioconductor.org/packages/motifmatchr/
Package Downloads Report Download Stats

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