Welcome to this repository where we will explore the code used to reproduce the scRNA-seq analysis to create the plots for our paper "Expanding the cytokine receptor alphabet reprograms T cells into diverse cell states".
Our study demonstrates that orthogonal cytokine-receptor engineering leverages the promiscuity of the common gamma chain to redirect and optimize T cell states for a potent antitumor response.
The merged T cells sample data object may be downloaded from Zenodo (contains matrix, genes, barcodes, metadata files).
This repository includes the following scripts:
- scRNA-seq processing:
data-processing.R - Scenic analysis:
RegulonAnalysis.RpySCENIC_Script_Docker.txt(for running in Docker)
- Identification and visualisation of cell surface markers:
SurfaceMarkerAnalysis.R - Cell communication analysis:
CellCellCommunicationAnalysis.LIANA.R