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 (3.23)
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 "4.6") 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
| Reference Manual |
Details
| biocViews | DataImport, FunctionalGenomics, GeneRegulation, MotifAnnotation, MotifDiscovery, SequenceMatching, Software |
| Version | 1.19.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (4.5 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| 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 |
| Package Short Url | https://bioconductor.org/packages/memes/ |
| Package Downloads Report | Download Stats |