motifmatchr

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see motifmatchr.

Fast Motif Matching in R

Bioconductor version: 3.6

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 "3.4") 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


Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	MotifAnnotation, Software
Version	1.0.1
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

Suggests	testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19
Linking To	Rcpp, RcppArmadillo
Enhances
Depends On Me
Imports Me
Suggests Me	chromVAR
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	motifmatchr_1.0.1.tar.gz
Windows Binary	motifmatchr_1.0.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	motifmatchr_1.0.1.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
Old Source Packages for BioC 3.6	Source Archive