.. Renoir documentation master file, created by
   sphinx-quickstart on Sat Apr 15 17:48:05 2023.
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Renoir
======

Renoir is an information-theory-based scoring metric that delineates
spatial communication domains that are cell-type, ligand, and target
specific. It also identifies spatially enriched ligand-target gene sets
and characterizes domain-specific activities between ligands and
targets.

.. raw:: html

   <p align="center">
   <img src="https://raw.githubusercontent.com/Zafar-Lab/Renoir/main/docs/source/images/Overview.png" alt="Overview of RENOIR" width="600"/>
   </p>

Available functionality
-----------------------

- Spatial map of ligand-target interactions
- Spatial map of pathway/De novo ligand-target set activities
- Inference of ligand-target and celltype specific communication domains
- Ranking of ligand specific activity across communication domains
- Overview of ligand-target-celltype interactions (Sankey plot)

.. toctree::
   :maxdepth: 1
   :hidden:

   install_usage
   api.rst
   tips

.. toctree::
   :maxdepth: 1
   :caption: Tutorials
   :hidden:

   notebooks/renoir_downstream_showcase
   notebooks/renoir_visium_tutorial
   notebooks/renoir_cosmx_tutorial
   notebooks/renoir_visiumhd_tutorial
   notebooks/renoir_xenium_tutorial

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

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