janihuuh / tcrgp_manu_hcc

Analysis of HBV-specificites at the single-cell level in HCC-patients with TCRGP

Analysis of HBV-specificites at the single-cell level in HCC-patients with TCRGP

In order to reproduce the analysis in the publication:

First, clone this repository

git clone https://github.com/janihuuh/tcrgp_manu_hcc

Download the scRNAseq and TCRab data

This is from GEO. We need the GSE98638_HCC.TCell.S5063.count.txt.gz file, rename it zheng_count.txt and add it into the data folder.

(Link)

The TCRαβ data is already provided, downloaded from the Supplementary files from the original Cell publication (Zheng et al., Cell 2017)

Then run the analyze_perc085.R in the same folder

Rscript src/analyze_perc085.R

References

Jokinen et al., biorxiv 2019

Zheng et al., Cell 2017

Chang et al., Sci Immunol 2019