memes
This is the released version of memes; for the devel version, see memes.
motif matching, comparison, and de novo discovery using the MEME Suite
Bioconductor version: Release (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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1) |
| Imports | Biostrings, dplyr, cmdfun (>= 1.0.2), GenomicRanges, ggplot2, 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, postNet |
| 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_1.20.0.tar.gz |
| Windows Binary (x86_64) | memes_1.20.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | memes_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | memes_1.20.0.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 |