Distinct transcriptional programs characterize neoantigen-specific T cells in lung cancers treated with neoadjuvant PD-1 blockade
- PCA_CCA: perform Principal Component Analysis and conduct Canonical Correlation Analysis.
- Monte_Carlo_simulation: perform complementary test for Fig4e.
- Raisin: perform differential analysis for CD3 T cell clusters
- Pseudotime: perform differential analysis along pseudotime axis
- Figures: code to generate figures in the manuscript