🍑 PEACH: Deep Archetypal Analysis for Single-Cell Biology
===========================================================

PEACH is a deep learning framework for archetypal analysis of single-cell data,
following scverse conventions.

.. toctree::
   :maxdepth: 2
   :caption: Getting Started

   installation
   INDEX

.. toctree::
   :maxdepth: 2
   :caption: Tutorials

   tutorials/index
   tutorials/01_data_loading
   tutorials/02_hyperparameter_search
   tutorials/03_model_training
   tutorials/04_archetype_coordinates
   tutorials/05_gene_enrichment
   tutorials/06_cellrank_integration
   tutorials/08_visualization
   tutorials/09_scatac_analysis
   tutorials/10_spatial_analysis

.. toctree::
   :maxdepth: 2
   :caption: API Reference

   api/index

.. toctree::
   :maxdepth: 1
   :caption: Development

   contributing

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`