17. Reproducibility and references

Everything on this page comes from src/run_real_netpert.py, src/make_100_figures.py and src/make_report_style_figures.py (Python 3.13; NumPy, SciPy expm/romb, NetworkX, scikit-learn, Matplotlib), with fixed seeds (edge-drop seed 7, layout seed 7). Full outputs: geneRankings_real.tsv, summary_real.json, figure gallery. Simulation archive: results/archive/.

NetPert paper, PLOS Computational Biology (2024).
Official code repository, which is the reference for the weight calculation (bin/netpert.py).