Characterization of aberrant splicing in pediatric central nervous system tumors reveals CLK1 as a candidate oncogenic dependency

Ammar S. Naqvi, Ryan J. Corbett, Priyanka Seghal, Karina L. Conkrite, Komal S. Rathi, Brian M. Ennis, Katharina E Hayer, Bo Zhang, Miguel A. Brown, Daniel P. Miller, Adam A. Kraya, Joseph M. Dybas, Zhuangzhuang Geng, Christopher Blackden, Shebheel Arif, Antonia Chroni, Aditya Lahiri, Madison L. Hollawell, Phillip B. Storm, Jessica B. Foster, Matuesz Koptyra, Peter J. Madsen, Sharon J. Diskin, Andrei Thomas Tikhonenko, Adam C. Resnick, Jo Lynne Rokita 

This project originated at the Center for Data-Driven Discovery in Biomedicine at Children's Hospital of Philadelphia. For issue and pull request history, please see https://github.com/d3b-center/pbta-splicing.

Clone repository

git clone [email protected]:rokitalab/clk1-splicing.git

Download data

bash download_data.sh

Docker set-up

Pull docker image

docker pull pgc-images.sbgenomics.com/d3b-bixu/pbta-splicing:v1.0.0

docker run

docker run --platform linux/amd64 --name <CONTAINER_NAME> -d -e PASSWORD=pass -p 8787:8787 -v $PWD:/home/rstudio/clk1-splicing pgc-images.sbgenomics.com/d3b-bixu/pbta-splicing:v1.0.0

docker execute

docker exec -ti clk1-splicing bash

Generate paper figures

bash scripts/run_analyses.sh

Code Authors

Ammar S. Naqvi (@naqvia), Jo Lynne Rokita (@jharenza), Ryan Corbett (@rjcorb)

Contact

For questions, please submit an issue.