The scripts are used to analyze single cell RNA sequencing data in the paper "Tumor Microenvironment Remodeling after Neoadjuvant Immunotherapy in Non-small Cell Lung Cancer Revealed by Single-Cell RNA Sequencing", https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-023-01164-9, including quality control, clustering, CopyKat, trajectory, CellPhoneDB, Nichenet, and SCENIC analyses. The scripts need modification accroding to the comments(##) in the script before running.
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