patpy tutorials

Jupyter notebook tutorials for patpy.

This repository is included as a git submodule in patpy/docs/tutorials/notebooks/ and is rendered as part of the patpy documentation on Read the Docs.

Tutorials

• benchmarking_sample_representation_methods.ipynb — using sample representation methods, datasets, and metrics via patpy interface for easy benchmarking.
• sources_of_variation_with_gloscope.ipynb — understanding sources of variation in single-cell data with GloScope.
• Patient_trajectories_example.ipynb — patient trajectory analysis from sample representations.
• supervised_methods_example.ipynb — supervised sample-level methods (MixMIL, PULSAR, PaSCient).
• differential_analysis.ipynb — differential gene expression across condition combinations.
• synthetic_data_generation.ipynb — generating synthetic data with controlled perturbations.
• distances_test_example.ipynb — statistical test for distances between case and control samples.
• immune_aging_multiresolution_composition.ipynb — Immune Health Atlas: CLR, pseudobulk, PILOT, and baselines across AIFI L1–L3; plottable benchmark table plus KNN vs PERMANOVA (CLR) for key phenotypes.

Editing tutorials

See the contributing guide in patpy for the submodule workflow.