# Quantifying changes in the T cell receptor repertoire during thymic development

Repository associated with the paper "Quantifying changes in the T cell receptor repertoire during thymic development". 

## Reproduce Plots

In order to reproduce the plots:

1) Extract the file 'CA-lienar_models.tar' in this folder.

2) Install the Required Packages (see section below).

3) Run the corrispondent Jupyter notebook.

## Required Packages

1) Default pip install:
- `numpy`
- `pandas`
- `matplotlib`
- `scipy`
- `scikit-learn`
- `seaborn`
- `tensorflow`
- `sonia`

## Reference

Francesco Camaglia, Arie Ryvkin, Erez Greenstein, Shlomit Reich-Zeliger, Benny Chain, Thierry Mora, Aleksandra M. Walczak, Nir Friedman (2023).
Quantifying changes in the T cell receptor repertoire during thymic development. [https://doi.org/10.7554/eLife.81622](https://doi.org/10.7554/eLife.81622)

## License

Free use of the code is granted under the terms of the [GNU General Public License version 3](LICENSE) (GPLv3).