NeuCOVID-Map

Single-Cell Analysis Workflows and Processed Data Across COVID-19 and Influenza A Airway and Circulation: Run Notebook 1 — Lower airway COVID-19 (1_Lower_Airway_Neu.Rmd): Profile baseline PLAU/PLAUR expression states in lower-airway COVID-19 datasets using Bost_Global_Annotated.rds and Wauters_Global_annotated.rds (with BalNeu_Covid.rds as the neutrophil-focused lower-airway object where required). Run Notebook 2 — Upper airway COVID-19 (2_Upper_Airway_Neu.Rmd): Profile baseline PLAU/PLAUR expression states in upper-airway COVID-19 datasets using Chua_Global.rds , Trump_Global.rds, and UpperAirway_Neu_Combined.rds . Run Notebook 3 — Combined airway analysis (3_Combined_Airway_Bulk.Rmd): Integrate the lower- and upper-airway outputs to compare neutrophil, epithelial, and macrophage contributions across Bost, Wauters, Chua, and Trump. The relevant airway objects are Bost_Global_Annotated.rds, Wauters_Global_annotated.rds, Chua_Global.rds, and Trump_Global.rds. Run Notebook 4 — Upper-airway Influenza A (4_Upper_Airway_Flu.Rmd): Introduce the Influenza A airway dataset and perform the local cross-viral comparison using Neu_CovFlu.rds. Run Notebook 5 — Xu circulation cohort (5_Circulation_Xu.Rmd): Map circulating-neutrophil PLAU/PLAUR states using Neu_Xu_Filtered.rds. Run Notebook 6 — Billi circulation cohort: Analyze circulating neutrophils using Neu_Billi_Filtered.rds. Run Notebook 7 — Combes circulation cohort: Analyze circulating neutrophils using Neu_Combes_Filtered.rds. Run Notebook 8 — Wilk circulation cohort: Analyze circulating neutrophils using Neu_Wilk_Filtered.rds. Run Notebook 9 — Circulating-neutrophil atlas (9_Circulation_Atlas.Rmd): Integrate/map systemic COVID-19 neutrophil distributions using CircNeuCovid_Atlas.rds. Run Notebook 10 — Circulating Influenza A (10_Circulation_Flu.Rmd): Evaluate systemic Influenza A circulation to complete the cross-disease and compartment comparison using the Neu_Flu_WB.rds