DOI: 10.18129/B9.bioc.memes    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see memes.

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

Bioconductor version: 3.14

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")):


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HTML R Script 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
PDF   Reference Manual
Text   NEWS


biocViews DataImport, FunctionalGenomics, GeneRegulation, MotifAnnotation, MotifDiscovery, SequenceMatching, Software
Version 1.2.5
In Bioconductor since BioC 3.13 (R-4.1) (1 year)
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
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
SystemRequirements Meme Suite (v5.3.3 or above)
Depends On Me
Imports Me
Suggests Me
Links To Me
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