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universalmotif

Import, Modify, and Export Motifs with R

Bioconductor version: 3.23 · Package version: 1.30.1

Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("universalmotif")

Details

MaintainerBenjamin Jean-Marie Tremblay <benjamin.tremblay@uwaterloo.ca>
AuthorBenjamin Jean-Marie Tremblay [aut, cre] (ORCID: <https://orcid.org/0000-0002-7441-2951>), Spencer Nystrom [ctb] (ORCID: <https://orcid.org/0000-0003-1000-1579>)
LicenseGPL-3
URLhttps://bioconductor.org/packages/universalmotif/
Bug Reportshttps://github.com/bjmt/universalmotif/issues
Downloads rank1559
Source branchRELEASE_3_23
biocViewsDataImport, GeneRegulation, MotifAnnotation, MotifDiscovery, Software

Documentation

Download

Dependencies

Depends: R (>= 4.1.0)

Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid, MatrixGenerics

LinkingTo: Rcpp, RcppThread

Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio

Enhances: PWMEnrich, rGADEM

Reverse dependencies

Imports Me (6): ChIPpeakAnno, circRNAprofiler, memes, MotifPeeker, motifTestR, SEMPLR

Suggests Me (1): epiSeeker