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Welcome to Steamboat's documentation!
=======================================

Steamboat is an interpretable machine learning framework leveraging a self-supervised, multi-head attention model that uniquely decomposes the gene expression of a cell into multiple key factors:

* intrinsic cell programs,
* neighboring cell communication, and
* long-range interactions.

These pieces of information are used to generate cell embedding, cell network, and reconstructed gene expression.

In the following sections, you Please refer to respective sections for installation, tutorials, and Steamboat API.

Source code for Steamboat is available as a `GitHub repository <https://github.com/ma-compbio/Steamboat>`_.


.. toctree::
   :maxdepth: 2
   :caption: Contents:
   
   installation
   tutorials
   steamboat/modules
   contact
   

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

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