This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

motifmatchr

Fast Motif Matching in R

Bioconductor version: Release (3.17)

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 "4.3") 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")
motifmatchr HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews MotifAnnotation, Software
Version 1.22.0
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License GPL-3 + file LICENSE
Depends R (>= 3.3)
Imports Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, GenomeInfoDb
Linking To Rcpp, RcppArmadillo
Suggests testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19
System Requirements C++11
Enhances
URL
See More
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_1.22.0.tar.gz
Windows Binary motifmatchr_1.22.0.zip (64-bit only)
macOS Binary (x86_64) motifmatchr_1.22.0.tgz
macOS Binary (arm64) motifmatchr_1.22.0.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