API Reference
=============

Core model
----------

.. automodule:: smoder.models.deconvolution
   :members:
   :undoc-members:
   :show-inheritance:

Pipelines
---------

.. automodule:: smoder.pipelines.mousebrain_h3k27ac
   :members:
   :undoc-members:
   :show-inheritance:

Preprocessing
-------------

RNA preprocessing
~~~~~~~~~~~~~~~~~

.. automodule:: smoder.preprocessing.rna
   :members:
   :undoc-members:
   :show-inheritance:

Second-modality preprocessing
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: smoder.preprocessing.modality2
   :members:
   :undoc-members:
   :show-inheritance:

Postprocessing
--------------

Reconstruction
~~~~~~~~~~~~~~

.. automodule:: smoder.postprocessing.reconstruction
   :members:
   :undoc-members:
   :show-inheritance:

Visualization
-------------

Spatial visualization
~~~~~~~~~~~~~~~~~~~~~

.. automodule:: smoder.visualization.spatial
   :members:
   :undoc-members:
   :show-inheritance:

Configuration
-------------

.. automodule:: smoder.config.defaults
   :members:
   :undoc-members:
   :show-inheritance: