﻿Supplementary Software — A dopaminergic eye-brain correspondence in Parkinson's disease

Analysis scripts (Python 3, conda env with numpy/pandas/scipy/scikit-learn/statsmodels/matplotlib;
PyMuPDF for figure export). All input data are public (GEO/PPMI/FCP-INDI; accessions in the manuscript).

signature_genesets_frozen.json  - FROZEN gene-set definitions, incl. the 170-gene signature
                                   (DEG_nominal_p01) and the 11 FDR<0.05 robust core (DEG_significant).
Transcriptomic / signature:      nature_figures.py
Retinal EWCE + dopamine coexpr:  ewce_retina.py
Neuronal-restricted control (C2):ewce_neuronal_control.py, figS6_neuronal_control.py
GWAS genetic enrichment:         fetch_pd_gwas_genes.py, gwas_enrichment.py, gwas_enrichment_figure.py
HPA protein/retina:              fetch_hpa.py, fetch_hpa_background.py, hpa_figure.py
Independent bulk SN (GSE8397):   val_gse8397_step1.py, val_gse8397_step2.py, val_gse8397_figure.py
Single-nucleus SN (Kamath):      kamath_process.py (streams the sparse matrix), kamath_analyze.py
Independent retina (Yan):        yan_analyze.py
Combined validation figure:      fig7_validation_combined.py

Random seeds are fixed in each script for reproducibility. Will be deposited on Zenodo upon publication.
