This GitHub contains all the scripts used to analyze scRNA-seq and functional data from the paper 'Deciphering the state of immune silence in COVID-19 patients'. Our single-cell analysis relies on the Pagoda2 pipeline while the viral landscape of patients' lung was assessed using Viral-Track.
The ScRNA_seq_Verona_cohort_script.R file contains all the code required to generate the analysis and figures linked to scRNA-seq data. Many packages are required and have to be installed before running the script.
The Immune_suppression_analysis.R script details how to analyze the Immune-suppression data and the associated flow-cytometry and cytokine secretion data.
The Clinical_data_processing.R script is required for the analysis of the various biological and clinical data collected, including cytokine and blood cell count data.