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 (3.14)

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>

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

Installation

To install this package, start R (version "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.11.16
In Bioconductor since BioC 3.8 (R-3.5) (3 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_1.11.16.tar.gz
Windows Binary universalmotif_1.11.16.zip
macOS 10.13 (High Sierra) universalmotif_1.11.16.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

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