universalmotif

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see universalmotif.

Import, Modify, and Export Motifs with R

Bioconductor version: 3.11

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 <b2tremblay at uwaterloo.ca>

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

Installation

To install this package, start R (version "4.0") and enter:


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

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, GeneRegulation, MotifAnnotation, MotifDiscovery, Software
Version	1.6.4
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, ape, ggtree, ggseqlogo, yaml, Rcpp, Rdpack (>= 0.7), Biostrings, BiocGenerics, processx, S4Vectors, rlang
System Requirements
URL	https://github.com/bjmt/universalmotif
Bug Reports	https://github.com/bjmt/universalmotif/issues

Suggests	spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, Logolas, BiocParallel, seqLogo, motifStack, dplyr
Linking To	Rcpp, RcppThread
Enhances	MotIV, PWMEnrich, rGADEM, motifRG
Depends On Me
Imports Me	circRNAprofiler
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_1.6.4.tar.gz
Windows Binary	universalmotif_1.6.4.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	universalmotif_1.6.4.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
Old Source Packages for BioC 3.11	Source Archive