# 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