memes

DOI: 10.18129/B9.bioc.memes    

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

Bioconductor version: Release (3.13)

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 "4.1") and enter:

if (!requireNamespace("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 1.0.2
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
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
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package memes_1.0.2.tar.gz
Windows Binary memes_1.0.2.zip
macOS 10.13 (High Sierra) memes_1.0.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/memes
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/memes
Package Short Url https://bioconductor.org/packages/memes/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive

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