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

Rscript for figure generation and data analysis: GenerateFigures_RevisedManuscript.R - A collection of R code used to generate the Figures and perform analyses. Seurat objects containing processed data after quality control and other relevant files NCCS_For_Zenodo.RDS - NCCS discovery cohort. NCCS-Figure1.png - Required for Figure generation Sample_Info_For_Zenodo.txt - Simplified version of the metadat RDS files containing DEGs or differentially abundant 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 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 Logistic regression models trained on the NCCS discovery cohort: PerCellPredictions_2Groups_LungOnly <CellType> * - Celltype specific models predicting either LTR or NonResponder group, trained on lung samples only. Output of third party tools: AUCcellOutput.csv - SCENIC ALL_ligand_target_heatmap_AGN.tsv - NICHENET