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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 (3.19)

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 gmail.com>

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

Installation

To install this package, start R (version "4.4") 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 1.11.0
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)
URL https://snystrom.github.io/memes/ https://github.com/snystrom/memes
Bug Reports https://github.com/snystrom/memes/issues
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
Enhances
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_1.11.0.tar.gz
Windows Binary memes_1.11.0.zip
macOS Binary (x86_64) memes_1.11.0.tgz
macOS Binary (arm64)
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