universalmotif

DOI: 10.18129/B9.bioc.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 (3.9)

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>

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

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("universalmotif", version = "3.9")

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 1.1.0
License GPL-3
Depends R (>= 3.5.0)
Imports methods, ggplot2, ape, ggtree, ggseqlogo, stats, utils, gtools, Rdpack (>= 0.7), Biostrings, BiocGenerics, Rcpp, processx
LinkingTo Rcpp
Suggests knitr, BiocStyle, TFBSTools, MotIV, PWMEnrich, motifStack, seqLogo, rmarkdown, MotifDb, testthat, rGADEM, motifRG, motifbreakR, RcisTarget, motifcounter, Logolas, BiocParallel, BCRANK
SystemRequirements
Enhances
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_1.1.0.tar.gz
Windows Binary universalmotif_1.1.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) universalmotif_1.1.0.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 http://bioconductor.org/packages/universalmotif/
Package Downloads Report Download Stats

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