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Enhancements
- Added support for a custom ranking function in
run_one_enrichment()andrun_all_enrichment(), with tests - Added a mini gene dictionary (~2% of the original, ~75MB) for lightweight usage
- Added FDR q-value metric to robust result output
- New tutorial notebooks: 3 quick-start covering core functionalities and an advanced tutorial detailing all parameters and statistical relevance
Breaking changes
- Removed
multi_contrastcomputation fromplot_significant_results(),run_all_enrichment_test(),check_robustness(), andget_robust_significant_results() - Removed simultaneous up- and downregulated enrichment computation
Maintenance
- Made plotting packages optional dependencies
- Improved code robustness via default arguments, assertions, and type hints
- Restructured formatting and logging, unified parameter documentation
- Updated documentation