universalmotif

DOI: 10.18129/B9.bioc.universalmotif    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see universalmotif.

Import, Modify, and Export Motifs with R

Bioconductor version: 3.9

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]

Maintainer: Benjamin Jean-Marie Tremblay <b2tremblay at uwaterloo.ca>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	Advanced usage: motif and sequence analysis
PDF	R Script	Introduction to "universalmotif"
PDF	R Script	Introduction to sequence motifs
PDF	R Script	Motif import, export, and manipulation
PDF	R Script	Sequence manipulation and scanning
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, GeneRegulation, MotifAnnotation, MotifDiscovery, Software
Version	1.2.1
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
License	GPL-3
Depends	R (>= 3.5.0)
Imports	methods, stats, utils, ggplot2, ape, ggtree, ggseqlogo, gtools, Rcpp, Rdpack (>= 0.7), Biostrings, BiocGenerics, processx, S4Vectors, yaml
LinkingTo	Rcpp
Suggests	spelling, knitr, BiocStyle, TFBSTools, rmarkdown, MotifDb, testthat, Logolas, BiocParallel, seqLogo, motifStack
SystemRequirements
Enhances	MotIV, PWMEnrich, rGADEM, motifRG
URL	https://github.com/bjmt/universalmotif
BugReports	https://github.com/bjmt/universalmotif/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	universalmotif_1.2.1.tar.gz
Windows Binary	universalmotif_1.2.1.zip
Mac OS X 10.11 (El Capitan)	universalmotif_1.2.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/universalmotif
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/universalmotif
Package Short Url	https://bioconductor.org/packages/universalmotif/
Package Downloads Report	Download Stats