universalmotif

DOI: 10.18129/B9.bioc.universalmotif    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see universalmotif.

Import, Modify, and Export Motifs with R

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") 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	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		Reference Manual
Text		NEWS

Details

biocViews	DataImport, GeneRegulation, MotifAnnotation, MotifDiscovery, Software
Version	1.8.5
In Bioconductor since	BioC 3.8 (R-3.5) (2.5 years)
License	GPL-3
Depends	R (>= 3.5.0)
Imports	methods, stats, utils, MASS, ggplot2, ggseqlogo, yaml, IRanges, Rcpp, Rdpack (>= 0.7), Biostrings, BiocGenerics, S4Vectors, rlang, grid
LinkingTo	Rcpp, RcppThread
Suggests	spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, Logolas, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx
SystemRequirements
Enhances	MotIV, PWMEnrich, rGADEM, motifRG
URL	https://bioconductor.org/packages/universalmotif/
BugReports	https://github.com/bjmt/universalmotif/issues
Depends On Me
Imports Me	circRNAprofiler
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	universalmotif_1.8.5.tar.gz
Windows Binary	universalmotif_1.8.5.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	universalmotif_1.8.5.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