Paired blood and bronchoalveolar lavage interferon gene scores in sarcoidosis: analysis files for CEI Short Report

Analysis code and patient-pair-level scores for a Short Report comparing a 13-gene interferon score in peripheral blood mononuclear cells (PBMC) with the same score in bronchoalveolar lavage (BAL) cells from 179 paired patients with sarcoidosis (GRADS, GEO GSE109516). Primary analysis: Spearman correlation between compartments against a study-defined benchmark of rho 0.60. Post hoc analyses (bootstrap CIs, agreement of thirds with weighted kappa, subgroups by treatment and Scadding stage, Mann-Whitney tests, 12-gene score without CXCL10, per-gene correlations) are listed in ANALYSIS_PLAN.md. The plan was locally hash-locked before analysis (not preregistered). Files: pair_level_scores.tsv (179 pairs), rerun.py, ANALYSIS_PLAN.md, requirements.txt, MANIFEST.md (SHA-256). Input data: 10.5281/zenodo.23485914. To reproduce, place the three input files from that deposit next to rerun.py and run python3 rerun.py (Python 3.13; pandas, NumPy, SciPy, scikit-learn). Seeds: 20261021 (primary CI), 20261031 (other bootstrap CIs).