Ularcirc

This package is for version 3.16 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: 3.16

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 "4.2") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AlternativeSplicing, Annotation, Coverage, DataRepresentation, DifferentialSplicing, Genetics, Sequencing, Software, Visualization

Version 1.16.0

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, 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

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Depends On Me

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Build Report Build Report

Package Archives

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

Source Package Ularcirc_1.16.0.tar.gz

Windows Binary Ularcirc_1.16.0.zip

macOS Binary (x86_64) Ularcirc_1.16.0.tgz

macOS Binary (arm64) Ularcirc_1.16.0.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 3.16 Source Archive