DOI: 10.18129/B9.bioc.universalmotif    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see universalmotif.

Import, Modify, and Export Motifs with R

Bioconductor version: 3.11

Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.

Author: Benjamin Jean-Marie Tremblay [aut, cre] , Spencer Nystrom [ctb]

Maintainer: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>

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


To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script Introduction to "universalmotif"
PDF R Script Introduction to sequence motifs
PDF R Script Motif comparisons and P-values
PDF R Script Motif import, export, and manipulation
PDF R Script Sequence manipulation and scanning
PDF   Reference Manual
Text   NEWS


biocViews DataImport, GeneRegulation, MotifAnnotation, MotifDiscovery, Software
Version 1.6.4
In Bioconductor since BioC 3.8 (R-3.5) (2 years)
License GPL-3
Depends R (>= 3.5.0)
Imports methods, stats, utils, MASS, ggplot2, ape, ggtree, ggseqlogo, yaml, Rcpp, Rdpack (>= 0.7), Biostrings, BiocGenerics, processx, S4Vectors, rlang
LinkingTo Rcpp, RcppThread
Suggests spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, Logolas, BiocParallel, seqLogo, motifStack, dplyr
Enhances MotIV, PWMEnrich, rGADEM, motifRG
URL https://github.com/bjmt/universalmotif
BugReports https://github.com/bjmt/universalmotif/issues
Depends On Me
Imports Me circRNAprofiler
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package universalmotif_1.6.4.tar.gz
Windows Binary universalmotif_1.6.4.zip (32- & 64-bit)
macOS 10.13 (High Sierra) universalmotif_1.6.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/universalmotif
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/universalmotif
Package Short Url https://bioconductor.org/packages/universalmotif/
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