This repository contains the source code associated with the manuscript
Mayer, Callan: Measures of epitope binding degeneracy from T cell receptor repertoires, PNAS, 2023
It allows reproduction of the statistical analyses and numerical results reported in the manuscript.
For a number of figures final assembly and cosmetic changes were done in Inkscape as a postprocessing step. In these cases the figures will not be reproduced precisely. To help reuse the final edited figures are provided in png/svg format.
The software is written in Python, and was run on Python version 3.6. The code relies on Pyrepseq (version 1.0), a python package for the analysis of immune repertoire sequencing data that we have released to accompany this paper. Other packages used include:
All can be installed using:
pip install -r requirements.txt
Data download and preprocessing is handled by the Snakemake workflow manager, with the help of scripts located within the scripts directory. Data visualization is done within Jupyter notebooks provided for each of the figures.
If you run into any difficulties running the code, please contact us at andimscience@gmail.com.
The source code is freely available under an MIT license. The plots are licensed under a Creative Commons attributions license (CC-BY).