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.
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()
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.
- 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