motifmatchr

DOI: 10.18129/B9.bioc.motifmatchr    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see motifmatchr.

Fast Motif Matching in R

Bioconductor version: 3.7

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("motifmatchr")

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	1.2.0
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
Links To Me
Build Report

Package Archives

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

Source Package	motifmatchr_1.2.0.tar.gz
Windows Binary	motifmatchr_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	motifmatchr_1.2.0.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