memes
motif matching, comparison, and de novo discovery using the MEME Suite
Bioconductor version: 3.23 · Package version: 1.20.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("memes")Details
| Maintainer | Spencer Nystrom <nystromdev@gmail.com> |
| Author | Spencer Nystrom [aut, cre, cph] (ORCID: <https://orcid.org/0000-0003-1000-1579>) |
| License | MIT + file LICENSE |
| URL | https://snystrom.github.io/memes/, https://github.com/snystrom/memes |
| Bug Reports | https://github.com/snystrom/memes/issues |
| System Requirements | Meme Suite (v5.3.3 or above) <http://meme-suite.org/doc/download.html> |
| Downloads rank | 418 |
| Source branch | RELEASE_3_23 |
| biocViews | DataImport, FunctionalGenomics, GeneRegulation, MotifAnnotation, MotifDiscovery, SequenceMatching, Software |
Documentation
- ChIP-seq Analysis
- Denovo Motif Discovery Using DREME
- Install MEME
- Motif Comparison using TomTom
- Motif Enrichment Testing using AME
- Motif Scanning using FIMO
- Tidying Motif Metadata
Download
Dependencies
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
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
Reverse dependencies
Imports Me (2): MotifPeeker, postNet