T-cell receptor analysis of synucleinopathy

This repository holds scripts for generating the T-cell receptor repertoire analysis figures for the manuscript: Intestinal macrophages modulate synucleinopathy along the gut–brain axis.

Installation

To run the scripts, first install the local package via running the following command in the top level directory:

pip install .

Structure

All plots used in the manuscript are located within ./publication/. Additional plots are located in ./additional/.

Data

All data used in these plots can be obtained from the SRA: PRJNA1321765. To obtain aligned repertoires, use decombinator.

Example command:

decombinator pipeline -c <chain> -in <filename> -br R2 -sp mouse -bl 42 -ol M13

See the readme of decombinator for further details.