Blood memory CD8 T cell phenotypes in lung cancer patients predict immune checkpoint treatment responses

Rscript for figure generation and data analysis: GenerateFigures.R Seurat objects containing processed data after quality control: NCCS_For_Zenodo.RDS - NCCS discovery cohort. Pavia_For_Zenodo.RDS - Pavia validation cohort. RDS files containing DEGs or differentially abundant surface markers: TestResults2Groups.rds - Cell type specific LTR vs Non Responder DEG TestResults2GroupsADT.rds - Cell type specific LTR vs Non Responder differential surface markers TestResults2GroupsLungOnly.rds - Cell type specific LTR vs Non Responder DEG on lung samples only TestResults2GroupsLungOnlyADT.rds - Cell type specific LTR vs Non Responder differential surface markers on lung samples only TestResults3Groups.rds - Cell type specific LTR vs R vs Non Responder differential DEG TestResults3GroupsGeneralADT.rds - Across cell type LTR vs R vs Non Responder differential surface markers TestResults2GroupsGeneralRNA.rds - Across cell type LTR vs Non Responder DEG TestResults2GroupsGeneralADT.rds - Across cell type LTR vs Non Responder differential surface markers TestResults2GroupsLungOnlyGeneralRNA.rds - Across cell type LTR vs Non Responder DEG on lung samples only TestResults2GroupsLungOnlyGeneralADT.rds - Across cell type LTR vs Non Responder differential surface markers on lung samples only TestResults3GroupsGeneralRNA.rds - Across cell type LTR vs R vs Non Responder differential DEG TestResults3GroupsGeneralADT.rds - Across cell type LTR vs R vs Non Responder differential surface markers Logistic regression models trained on the NCCS discovery cohort: PerCellPredictions <CellType> * - Celltype specific models predicting either LTR, R or control group trained on all NCCS samples PerCellPredictions_2Groups_LungOnly <CellType> * - Celltype specific models predicting either LTR or NonResponder group, trained on lung samples only. PerCellPredictions_2Groups_<CellType> * - Celltype specific models predicting either LTR or NonResponder trained on all NCCS samples