Code accompanying Feasibility and clinical utility of whole genome profiling in pediatric and young adult cancers

Shukla N, Levine M F, Gundem G, et al.

📂 Repository Structure

• data/: this directory contains the dataframes necessary to reproduce the results of the study.

• notebooks/: this directory contains notebooks for generating figures and subsampled bams.

🚀 Getting started with this repository

Tested with Python 3.6.5

Clone the repository

To clone this repository on your local computer please run:

$ git clone https://github.com/papaemmelab/Shukla_Levine_Gundem

Install with pip.

cd Shukla_Levine_Gundem
pip install -r requirements.txt

📓 View and run notebooks

It is recommended to view and execute the included notebooks using JupyterLab.

cd notebooks
jupyter lab

The notebooks can then be selected from the top left in the file browser.