Registration Open for Bioc2024
Early registration discount pricing ends May 31!


motif matching, comparison, and de novo discovery using the MEME Suite

Bioconductor version: Release (3.19)

A seamless interface to the MEME Suite family of tools for motif analysis. 'memes' provides data aware utilities for using GRanges objects as entrypoints to motif analysis, data structures for examining & editing motif lists, and novel data visualizations. 'memes' functions and data structures are amenable to both base R and tidyverse workflows.

Author: Spencer Nystrom [aut, cre, cph]

Maintainer: Spencer Nystrom <nystromdev at>

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


To install this package, start R (version "4.4") and enter:

if (!require("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:

ChIP-seq Analysis HTML R Script
Denovo Motif Discovery Using DREME HTML R Script
Install MEME HTML R Script
Motif Comparison using TomTom HTML R Script
Motif Enrichment Testing using AME HTML R Script
Motif Scanning using FIMO HTML R Script
Tidying Motif Metadata HTML R Script
Reference Manual PDF


biocViews DataImport, FunctionalGenomics, GeneRegulation, MotifAnnotation, MotifDiscovery, SequenceMatching, Software
Version 1.12.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports Biostrings, dplyr, cmdfun (>= 1.0.2), GenomicRanges, ggplot2, ggseqlogo, magrittr, matrixStats, methods, patchwork, processx, purrr, rlang, readr, stats, tools, tibble, tidyr, utils, usethis, universalmotif(>= 1.9.3), xml2
System Requirements Meme Suite (v5.3.3 or above)
Bug Reports
See More
Suggests cowplot, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0), knitr, MotifDb, pheatmap, PMCMRplus, plyranges(>= 1.9.1), rmarkdown, covr
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package memes_1.12.0.tar.gz
Windows Binary
macOS Binary (x86_64) memes_1.12.0.tgz
macOS Binary (arm64) memes_1.12.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats