memes
This package is for version 3.16 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: 3.16
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>
citation("memes")):
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")| 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, FunctionalGenomics, GeneRegulation, MotifAnnotation, MotifDiscovery, SequenceMatching, Software |
| Version | 1.6.0 |
| 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 | ggmotif |
| 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_1.6.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |