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DAMUTA documentation
==================================

.. image:: thumbnails/damuta_logo.png
   :width: 200px
   :align: center

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**DAMUTA** is a hierarchical Bayesian probabilistic model that separates DNA damage and misrepair processes.


**Key Capabilities:**

* **Damage-Misrepair Separation**: Infers distinct signatures for DNA damage processes and repair mechanisms
* **Hierarchical Modeling**: Captures sample-specific interactions and tissue-type effects  
* **Pan-Cancer Analysis**: DAMUTA signatures estimated from 18,974 whole genome sequencing samples across 23 cancer types
* **Biological Insights**: Reveals tissue-specificity patterns and DNA damage response deficiencies
* **Compact Representation**: Resolves redundancies in current signature models

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DAMUTA requires only mutation type counts to begin analysis. You can optionally provide:

* Custom signature definitions (damage and misrepair signatures)
* Hierarchical sample groupings for enhanced tissue-specific modeling


.. automodule:: damuta
   :show-inheritance:

.. toctree::
   :maxdepth: 1
   :caption: Get started   

   installation
   examples/quickstart
   examples/index

.. toctree::
   :maxdepth: 3
   :caption: Modules
   :hidden:
   :glob:

   damuta*

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

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