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Bioconductor - universalmotif (development version)

universalmotif

This is the development version of universalmotif; for the stable release version, see universalmotif.

Import, Modify, and Export Motifs with R

Bioconductor version: Development (3.22)

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.

Author: Benjamin Jean-Marie Tremblay [aut, cre] ORCID: 0000-0002-7441-2951 , Spencer Nystrom [ctb] ORCID: 0000-0003-1000-1579

Maintainer: Benjamin Jean-Marie Tremblay <benjamin.tremblay at uwaterloo.ca>

Citation (from within R, enter citation("universalmotif")): Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("universalmotif")

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("universalmotif")
Details biocViews DataImport, GeneRegulation, MotifAnnotation, MotifDiscovery, Software Version 1.27.2 In Bioconductor since BioC 3.8 (R-3.5) (6.5 years) License GPL-3 Depends R (>= 4.1.0) Imports methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid, MatrixGenerics System Requirements URL https://bioconductor.org/packages/universalmotif/ Bug Reports https://github.com/bjmt/universalmotif/issues See More Suggests spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio Linking To Rcpp, RcppThread Enhances PWMEnrich, rGADEM Depends On Me Imports Me ChIPpeakAnno, circRNAprofiler, memes, MotifPeeker Suggests Me Links To Me Build Report Build Report Package Archives

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

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