Cell-GPS documentation
======================

Cell-GPS is the reference implementation for Cophenetic Spatial Topology
Embedding (COSTE), a framework for analyzing multiscale tissue architecture
in spatial omics data. These docs cover both the installable Python package
and the manuscript companion code.

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   readme
   manuscript_overview
   manuscript_reproduction
   manuscript_code_index
   reviewer_guide
   installation
   usage
   api
   contributing
   authors
   history

Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`