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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 (3.19)

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] , Spencer Nystrom [ctb]

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 "4.4") 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")
Introduction to "universalmotif" PDF R Script
Introduction to sequence motifs PDF R Script
Motif comparisons and P-values PDF R Script
Motif import, export, and manipulation PDF R Script
Sequence manipulation and scanning PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, GeneRegulation, MotifAnnotation, MotifDiscovery, Software
Version 1.21.2
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-3
Depends R (>= 3.5.0)
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, cowplot, GenomicRanges, ggbio
Linking To Rcpp, RcppThread
Enhances PWMEnrich, rGADEM
Depends On Me
Imports Me ChIPpeakAnno, circRNAprofiler, memes
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package universalmotif_1.21.2.tar.gz
Windows Binary universalmotif_1.21.2.zip
macOS Binary (x86_64) universalmotif_1.21.2.tgz
macOS Binary (arm64) universalmotif_1.21.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/universalmotif
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/universalmotif
Bioc Package Browser https://code.bioconductor.org/browse/universalmotif/
Package Short Url https://bioconductor.org/packages/universalmotif/
Package Downloads Report Download Stats