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Bioconductor - motifmatchr

motifmatchr

This is the released version of motifmatchr; for the devel version, see motifmatchr.

Fast Motif Matching in R

Bioconductor version: Release (3.21)

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 "4.5") 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")
Details biocViews MotifAnnotation, Software Version 1.30.0 In Bioconductor since BioC 3.6 (R-3.4) (7.5 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 ATACseqTFEA, enhancerHomologSearch, epiregulon, esATAC, pageRank, spatzie Suggests Me chromVAR, GRaNIE, MethReg, CAGEWorkflow, Signac Links To Me Build Report Build Report Package Archives

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

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