EvoAug2 Documentation
======================

**Evolution-Inspired Data Augmentation for Genomic Sequences - DataLoader Version**

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   :alt: PyPI version

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   :target: https://pypi.org/project/evoaug2/
   :alt: Python versions

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   :alt: License

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Welcome to EvoAug2, a Python package that provides evolution-inspired data augmentation techniques for genomic sequence analysis using deep learning. This package implements the two-stage training approach described in the EvoAug2 paper, combining robust augmentation during training with fine-tuning on original data.

.. toctree::
   :maxdepth: 2
   :caption: Getting Started

   installation
   quickstart
   examples

.. toctree::
   :maxdepth: 2
   :caption: API Reference

   api/evoaug
   api/evoaug_utils
   api/examples

.. toctree::
   :maxdepth: 2
   :caption: Examples

   examples/lightning_module
   examples/vanilla_pytorch

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

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

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   <div class="admonition note">
   <p class="admonition-title">Note</p>
   <p>This documentation is for EvoAug2 version 2.0.3. For older versions, please refer to the <a href="https://github.com/aduranu/evoaug/releases">GitHub releases</a>.</p>
   </div>

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   <div class="admonition tip">
   <p class="admonition-title">Tip</p>
   <p>If you're new to EvoAug2, start with the <a href="quickstart.html">Quick Start Guide</a> and then explore the <a href="examples.html">Examples</a> section.</p>
   </div>