Ularcirc

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8

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

Bioconductor version: Development (3.24)

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")):

David Humphreys. Ularcirc: Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis). doi:10.18129/B9.bioc.Ularcirc, R package version 1.31.0, https://bioconductor.org/packages/Ularcirc.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, Annotation, Coverage, DataRepresentation, DifferentialSplicing, Genetics, Sequencing, Software, Visualization
Version	1.31.0
In Bioconductor since	BioC 3.8 (R-3.5) (8 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, moments, dplyr, plotgardener, R.utils, S4Vectors, shiny, shinydashboard, shinyFiles, shinyjs, yaml
System Requirements
URL

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, r-universe

Package Archives

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

Source Package	Ularcirc_1.31.0.tar.gz
Windows Binary (x86_64)	Ularcirc_1.31.0.zip
macOS Binary (big-sur-x86_64)	Ularcirc_1.31.0.tgz
macOS Binary (sonoma-arm64)	Ularcirc_1.31.0.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