memes

This package is for version 3.15 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: 3.15

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 "4.2") 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 PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, FunctionalGenomics, GeneRegulation, MotifAnnotation, MotifDiscovery, SequenceMatching, Software

Version 1.4.1

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

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

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