DOI: 10.18129/B9.bioc.motifmatchr  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see motifmatchr.

Fast Motif Matching in R

Bioconductor version: 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>

Citation (from within R, enter citation("motifmatchr")):


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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
LinkingTo Rcpp, RcppArmadillo
Suggests testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements C++11
Depends On Me
Imports Me ATACCoGAPS, ATACseqTFEA, enhancerHomologSearch, enrichTF, esATAC, pageRank, spatzie
Suggests Me CAGEWorkflow, chromVAR, GRaNIE, MethReg
Links To Me
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