Alternative splicing in pediatric central nervous system tumors highlights oncofetal candidate CLK1 exon 4

Ammar S. Naqvi, Patricia J. Sullivan, 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, Alex Sickler, Adam A. Kraya, Kaleem L. Coleman, Joseph M. Dybas, Zhuangzhuang Geng, Christopher Blackden, Shehbeel Arif, Antonia Chroni, Aditya Lahiri, Madison L. Hollawell, Phillip B. Storm, Dalia Haydar, Jessica B. Foster, Mateusz 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.

Our accompanying preprint can be found on bioRxiv.

Clone repository

git clone git@github.com:rokitalab/clk1-splicing.git

Download data

bash download_data.sh

Docker set-up

Pull docker image

docker pull --platform linux/amd64 pgc-images.sbgenomics.com/rokita-lab/pbta-splicing:v1.0.3

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/rokita-lab/pbta-splicing:v1.0.3

docker execute

docker exec -ti clk1-splicing bash

Generate paper figures

bash scripts/run_analyses.sh

Code Authors

Ammar S. Naqvi (@naqvia), Patricia J. Sullivan (@pj-sullivan), Ryan Corbett (@rjcorb), Jo Lynne Rokita (@jharenza)

Contact

For questions, please submit an issue.