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

License

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