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This is the development version of memes; for the stable release version, see memes.

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

Bioconductor version: Development (3.20)

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))

# The following initializes usage of Bioc devel


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 1.13.0
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)
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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
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Follow Installation instructions to use this package in your R session.

Source Package memes_1.13.0.tar.gz
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macOS Binary (x86_64) memes_1.13.0.tgz
macOS Binary (arm64) memes_1.13.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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