This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

memes

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 (3.18)

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 gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("memes")

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

Documentation

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

browseVignettes("memes")
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
NEWS Text
LICENSE Text

Details

biocViews DataImport, FunctionalGenomics, GeneRegulation, MotifAnnotation, MotifDiscovery, SequenceMatching, Software
Version 1.9.0
In Bioconductor since BioC 3.13 (R-4.1) (2 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
Linking To
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
System Requirements Meme Suite (v5.3.3 or above)
Enhances
URL https://snystrom.github.io/memes/ https://github.com/snystrom/memes
Bug Reports https://github.com/snystrom/memes/issues
See More
Depends On Me
Imports Me ggmotif
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package memes_1.9.0.tar.gz
Windows Binary memes_1.9.0.zip
macOS Binary (x86_64) memes_1.9.0.tgz
macOS Binary (arm64) memes_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/memes
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/memes
Bioc Package Browser https://code.bioconductor.org/browse/memes/
Package Short Url https://bioconductor.org/packages/memes/
Package Downloads Report Download Stats