.. spMetaTME documentation master file, created by
   sphinx-quickstart on Sat Sep 13 01:19:50 2025.
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Welcome to spMetaTME's documentation!
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**spMetaTME** spMetaTME: A spatial atlas of tumour microenvironment metabolism and interactions


Unlike traditional flux estimation approaches, spMetaTME represents the metabolic network as a directed hypergraph, where metabolites are represented as nodes and reactions as hyperedges, enabling the modelling of directional reactant-to-product flux propagation. By leveraging self-supervised hypergraph learning, spMetaTME captures the intrinsic metabolic dependencies and directional flux propagation across spatially adjacent cells or spots.


.. toctree::
   :maxdepth: 2
   :caption: Contents:
   
   installation
   usage
   docker
   cli

   Estimate_fluxes
   Metabolic_visualisations
   Metabolic_interactions
   Metabolite_analysis


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

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

Please cite
=================
* Verma, S., Doan, L. M. T., Kang, J. H., Colombo, G., Serganov, I., Zappasodi, R., Occhipinti, A., & Angione, C. spMetaTME: A spatial atlas of tumour microenvironment metabolism and interactions.