Ularcirc

DOI: 10.18129/B9.bioc.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 (3.17)

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 "4.3") 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

PDF		Reference Manual

Details

biocViews	AlternativeSplicing, Annotation, Coverage, DataRepresentation, DifferentialSplicing, Genetics, Sequencing, Software, Visualization
Version	1.17.0
In Bioconductor since	BioC 3.8 (R-3.5) (4 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
LinkingTo
Suggests	BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr, org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene
SystemRequirements
Enhances
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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