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Bioconductor - memes (development version)

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 (3.22)

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] ORCID: 0000-0003-1000-1579

Maintainer: Spencer Nystrom <nystromdev at gmail.com>

Citation (from within R, enter citation("memes")): Installation

To install this package, start R (version "4.5") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("memes")
Details biocViews DataImport, FunctionalGenomics, GeneRegulation, MotifAnnotation, MotifDiscovery, SequenceMatching, Software Version 1.17.1 In Bioconductor since BioC 3.13 (R-4.1) (4 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 MotifPeeker Suggests Me Links To Me Build Report Build Report Package Archives

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

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