Data and code for Rosati, Pogorelyy, Minervina et al 2021.

This repository contains R scripts reproducing the analysis from the manuscript.

0. Download the repository.

1. To reproduce the pipeline from the merged processed single cell dataset, see TCR_analysis.R.

This analysis depends on tcrdist implementation from conga package. Download conga repository, and compile tcrdist:

cd conga/tcrdist_cpp
make

then edit the third line in TCR_analysis.R to include path to your tcrdist folder:

path_tcrdist="path_to_conga_in_your_system/tcrdist_cpp/"

2. To reproduce all the steps to generate merged processed single cell dataset, see the scripts in preprocessing folder (all done by @erosix).