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>

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

Installation

To install this package, start R (version "4.0") and enter:


if (!require("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")
Ularcirc HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews AlternativeSplicing, Annotation, Coverage, DataRepresentation, DifferentialSplicing, Genetics, Sequencing, Software, Visualization
Version 1.6.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 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
System Requirements
URL
See More
Suggests BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/Ularcirc/
Package Short Url https://bioconductor.org/packages/Ularcirc/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive