memes
motif matching, comparison, and de novo discovery using the MEME Suite
Bioconductor version: Release (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("memes")
):
Installation
To install this package, start R (version "4.4") 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 | 1.12.0 |
In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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_1.12.0.tar.gz |
Windows Binary | memes_1.12.0.zip |
macOS Binary (x86_64) | memes_1.12.0.tgz |
macOS Binary (arm64) | memes_1.12.0.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 |