Unique patterns of mutations in childhood cancer highlight chemotherapy’s disease-defining role at relapse

Scripts and Notebooks to reproduce figures in the above paper.

v 0.2

This repository includes

• 6 Notebooks to reproduce Main Figures
• 10 Notebooks to reproduce Extended Data Figures
• 1 Notebook to reproduce Supplementary Figures
• 1 helper script with all the plotting functions
• 2 helper scripts with 10s of analysis functions
• 1 script to run the logistic regression model
• 1 source data directory containing all the data needed to reproduce the figures (some sensitive data will be added after manuscript decision)

Dependencies

- scikit-learn==1.3.0
- shap==0.46.0
- ipykernel==6.25.2
- ipython==8.15.0
- pandas>2.1.0
- numpy==1.24.4
- scipy==1.11.2
- matplotlib==3.7.3
- seaborn==0.13.2
- plotly==5.16.1
- pywaffle==1.1.0
- xgboost==1.7.6
- catboost==1.2.1
- UpSetPlot==0.9.0
- nbformat==5.10.4
- patsy==1.0.1
- networkx==3.4.2
- statsmodels==0.14.4
- pydeseq2==0.5.1
- ipykernel
- jupyter

Download

To install, you can directly download zipped folder from menu above or run this command:

git clone https://github.com/shlienlab/mutsigs_therapy

Installation

We recommended installing the required packages into a python virtual environment.

1. Create the virtual environment in the specified path of your choice

python3 -m venv /your_path/your_env_name

2. Activate the virtual environment

source /your_path/your_env_name/bin/activate

3. Install requirements (from inside the root directory of the repository)

pip install -r requirements.txt

4. Add the new environment to kernels list

python3 -m ipykernel install --name "your_env_name" --user

Otherwise, skip the virtual environment steps, navigate to the root directory and type the following:

pip install -r requirements.txt

Usage

After installation, you can open and run the Jupyter notebooks in any compatible (e.g., VS Code). If you created a virtual environment, make sure to select it as your kernel.

Some source files might be missing due to GitHub's file size limit. These will be uploaded somewhere else soon.

Citation

When using this library, please cite

Layeghifard M., ..., and Shlien A., "Unique patterns of mutations in childhood cancer highlight chemotherapy’s disease-defining role at relapse" (under review).

Contributions

This library is still a work in progress. Contributions are always welcome.