Ularcirc

DOI: 10.18129/B9.bioc.Ularcirc    

This package is for version 3.11 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: 3.11

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 "4.0") 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
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	AlternativeSplicing, Annotation, Coverage, DataRepresentation, DifferentialSplicing, Genetics, Sequencing, Software, Visualization
Version	1.6.0
In Bioconductor since	BioC 3.8 (R-3.5) (2 years)
License	file LICENSE
Depends	R (>= 3.4.0)
Imports	AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings, BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures, GenomeInfoDb, GenomeInfoDbData, GenomicAlignments, GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments, Organism.dplyr, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, Sushi, yaml
LinkingTo
Suggests	BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene
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_1.6.0.tar.gz
Windows Binary	Ularcirc_1.6.0.zip
macOS 10.13 (High Sierra)	Ularcirc_1.6.0.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	https://bioconductor.org/packages/Ularcirc/
Package Downloads Report	Download Stats