This R code uses aggregated cellranger output (folder libs_aggregate_rev) and adds TCR, UMAP GEX coordinates, GEX cluster, and epitope specificity info for each CD8+ T cell from the study.
Download and unzip libs_aggregate_rev folder from Zenodo
Install neccesary R packages (Seurat version 4.0.4, data.table, igraph, stringr, viridis). Run:
source("postprocessing.R")
This should take a few hours to run all of the analysis and will result in cd8_only_dextr_rev_clean.tsv file (table with aggregated TCR, GEX and MHC-multimer specificity) in the working directory.
Please note, that different Seurat versions might result in slightly different GEX clustering. To reproduce paper results exactly, install Seurat v. 4.0.4