readme.md

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

Ularcirc

An R package that provides analysis and visualisation of canonical and backsplice junctions. Requires output provided by the STAR aligner

Author and maintainer: David Humphreys (d.humphreys at victorchang dot edu dot au)

Pre-print for Ularcirc now on bioarchives.

Installation

You can install Ularcirc using the 'devtools' package

> install.packages("devtools")
> library(devtools)
> devtools::install_github("VCCRI/Ularcirc")

Ularcirc can annotate circRNA with overlapping gene information. This is obtained from available bioconductor databases. Use the following command to identify what databases to download:

> library("Ularcirc")
> all_dbs <- Compatible_Annotation_DBs()
> # List database IDs
> names(all_dbs)
>
> # Select a database and display the commands needed to install
> # Use noquote to correctly format output
> noquote(all_dbs[['Hsapiens.UCSC.hg38']])

To start Ularcirc shiny app

> library('Ularcirc')
  > Ularcirc()

Documentation

Please refer to pdf manual under the docs folder. This document is currently being built so please check back for regular updates.

Please click this link to view a 12 minute screen cast that walks through a simple circRNA analysis using Ularcirc.

Features

• Friendly user interface
• Circular RNA detection independent of gene annotation.
• Provides visualisation of forward AND backsplice junctions
• Recover predicted circRNA sequence
• Recover sequence of backsplice junctions and forward splice junctions
• Support both single-read and paired-end sequencing (paired end prefered).
• Detect miRNA binding sites
• detect putative open reading frame of circRNA

Ularcirc documentation built on Nov. 8, 2020, 6:34 p.m.