# 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](https://www.biorxiv.org/content/early/2018/05/15/318436).
# 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](https://www.youtube.com/watch?v=BQkCurUF2XQ) 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