Ularcirc

DOI: 10.18129/B9.bioc.Ularcirc    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see Ularcirc.

Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)

Bioconductor version: 3.8

Ularcirc reads in STAR aligned splice junction files and provides visualisation and analysis tools for splicing analysis. Users can assess backsplice junctions and forward canonical junctions.

Author: David Humphreys [aut, cre]

Maintainer: David Humphreys <d.humphreys at victorchang.edu.au>

Installation

To install this package, start R (version "3.5") and enter:

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

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("Ularcirc")

 

HTML	R Script	Ularcirc.html
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	AlternativeSplicing, Annotation, Coverage, DataRepresentation, DifferentialSplicing, Genetics, Sequencing, Software, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.8 (R-3.5) (0.5 years)
License	file LICENSE
Depends	R (>= 3.5.0)
Imports	data.table (>= 1.9.4), shiny, shinyFiles, gsubfn, Biostrings, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, Sushi, moments, DT, yaml, AnnotationHub, BSgenome, httpuv, mirbase.db
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
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	Ularcirc_1.0.0.tar.gz
Windows Binary	Ularcirc_1.0.0.zip
Mac OS X 10.11 (El Capitan)	Ularcirc_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Ularcirc
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Ularcirc
Package Short Url	http://bioconductor.org/packages/Ularcirc/
Package Downloads Report	Download Stats