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Ularcirc

This is the development version of Ularcirc; for the stable release version, see Ularcirc.

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

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

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

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 1.19.0
In Bioconductor since BioC 3.8 (R-3.5) (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, plotgardener, R.utils, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, yaml
Linking To
Suggests BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene
System Requirements
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URL
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Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Ularcirc_1.19.0.tar.gz
Windows Binary Ularcirc_1.19.0.zip
macOS Binary (x86_64) Ularcirc_1.19.0.tgz
macOS Binary (arm64) Ularcirc_1.19.0.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