Welcome to scCellFie's documentation!
=====================================

.. include:: ../../README.rst
    :end-before: Installation


.. include:: ../../README.rst
    :start-after: ``'organism'``).

Additional Documentation
------------------------
.. toctree::
   :maxdepth: 1

   installation
   api/index


.. toctree::
   :maxdepth: 1
   :hidden:
   :caption: Quick start tutorials

   notebooks/quick_start_human
   notebooks/quick_start_mouse

.. toctree::
   :maxdepth: 1
   :hidden:
   :caption: Extended tutorials

   notebooks/extended_quick_start
   notebooks/metabolic_markers
   notebooks/differential_analysis
   notebooks/tensor_factorization
   notebooks/sc_communication
   notebooks/temporal_patterns

.. toctree::
   :maxdepth: 1
   :hidden:
   :caption: Spatial tutorials

   notebooks/mouse_embryo_spatial
   notebooks/atera_analysis

.. toctree::
   :maxdepth: 1
   :hidden:
   :caption: Visualization tutorials

   notebooks/visualizer
   notebooks/escher_viz



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

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