Ferro-aging in COPD: reproducible analysis code and processed results
Description
Analysis code, processed intermediate tables and figures supporting the manuscript "Ferro-aging in COPD: an iron-driven cellular senescence program enriched in alveolar type II cells". The package reproduces all bulk transcriptomic, WGCNA, machine-learning, single-cell and two-sample Mendelian randomization analyses from publicly available data: GEO (GSE38974, GSE76925, GSE47460, GSE222374, GSE171541); GWAS Catalog (GCST90451683 serum hepcidin; GCST90244098 UK Biobank COPD liability); FinnGen R12 (J10_COPD, J10_EMPHYSEMA). Raw sequencing and GWAS data are NOT bundled (they are already public at the repositories above). The package contains the analysis code, the small processed result tables, the figures, pinned Python dependency specifications, and a one-command reproduction script (reproduce.py). The archive includes the covariate-adjusted analysis of a third, independent cohort (GSE47460, Lung Genomics Research Consortium; 145 COPD vs 91 controls, annotated for age, sex, smoking and spirometry), scripted in analysis8_ageadj_gse47460.py, with results in AGE_ADJ_GSE47460.tsv and AGE_ADJ_GSE47460_summary.txt.