memes

DOI: 10.18129/B9.bioc.memes  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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
Text		LICENSE

Details

biocViews	DataImport, FunctionalGenomics, GeneRegulation, MotifAnnotation, MotifDiscovery, SequenceMatching, Software
Version	1.6.0
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
LinkingTo
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)
Enhances
URL	https://snystrom.github.io/memes/ https://github.com/snystrom/memes
BugReports	https://github.com/snystrom/memes/issues
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_1.6.0.tar.gz
Windows Binary	memes_1.6.0.zip
macOS Binary (x86_64)	memes_1.6.0.tgz
macOS Binary (arm64)	memes_1.6.0.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