universalmotif

DOI: 10.18129/B9.bioc.universalmotif    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see universalmotif.

Import, Modify, and Export Motifs with R

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

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	1.14.1
In Bioconductor since	BioC 3.8 (R-3.5) (4 years)
License	GPL-3
Depends	R (>= 3.5.0)
Imports	methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp, Biostrings, BiocGenerics, S4Vectors, rlang, grid
LinkingTo	Rcpp, RcppThread
Suggests	spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio
SystemRequirements
Enhances	PWMEnrich, rGADEM
URL	https://bioconductor.org/packages/universalmotif/
BugReports	https://github.com/bjmt/universalmotif/issues
Depends On Me
Imports Me	circRNAprofiler, memes
Suggests Me	spiky
Links To Me
Build Report

Package Archives

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

Source Package	universalmotif_1.14.1.tar.gz
Windows Binary	universalmotif_1.14.1.zip
macOS Binary (x86_64)	universalmotif_1.14.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/universalmotif
Source Repository (Developer Access)	git clone [email protected]:packages/universalmotif
Package Short Url	https://bioconductor.org/packages/universalmotif/
Package Downloads Report	Download Stats