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 

Docker set-up

docker pull

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

docker execute

docker exec -ti pbta-splicing bash

Get project data files

bash download_data.sh

Generate paper figures

bash scripts/run_analyses.sh

Contact

For questions, please submit an issue or send an email to Jo Lynne Rokita (@jharenza): rokita@chop.edu and Ammar S. Naqvi (@naqvia): naqvia@chop.edu.