motifmatchr
Fast Motif Matching in R
Bioconductor version: Release (3.19)
Quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library, which was developed by Pasi Rastas, Janne Korhonen, and Petri Martinmäki.
Author: Alicia Schep [aut, cre], Stanford University [cph]
Maintainer: Alicia Schep <aschep at gmail.com>
Citation (from within R, enter
citation("motifmatchr")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("motifmatchr")
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("motifmatchr")| motifmatchr | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | MotifAnnotation, Software |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 3.3) |
| Imports | Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, GenomeInfoDb |
| System Requirements | C++11 |
| URL |
See More
| Suggests | testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 |
| Linking To | Rcpp, RcppArmadillo |
| Enhances | |
| Depends On Me | |
| Imports Me | ATACCoGAPS, ATACseqTFEA, enhancerHomologSearch, epiregulon, esATAC, pageRank, spatzie |
| Suggests Me | GRaNIE, MethReg, chromVAR, CAGEWorkflow, MOCHA, Signac |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | motifmatchr_1.26.0.tar.gz |
| Windows Binary (x86_64) | motifmatchr_1.26.0.zip (64-bit only) |
| macOS Binary (x86_64) | motifmatchr_1.26.0.tgz |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/motifmatchr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/motifmatchr |
| Bioc Package Browser | https://code.bioconductor.org/browse/motifmatchr/ |
| Package Short Url | https://bioconductor.org/packages/motifmatchr/ |
| Package Downloads Report | Download Stats |