.. scGPT documentation master file, created by
   sphinx-quickstart on Sun Jul  2 07:16:12 2023.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to scGPT's documentation!

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    :target: https://scgpt.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status

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      :target: https://pypi.python.org/pypi/scgpt
      :alt: PyPI version

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      :target: https://pypi.python.org/pypi/scgpt
      :alt: PyPI supported Python versions

Welcome to the documentation for scGPT, a Python package for single-cell multi-omic data analysis using pretrained foundation models. This package is based on the work of scGPT (`GitHub <https://github.com/bowang-lab/scGPT>`_, `preprint <https://www.biorxiv.org/content/10.1101/2023.04.30.538439>`_) and provides a set of functions for data preprocessing, visualization, and model evaluation.

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

   introduction
   installation

.. toctree::
   :maxdepth: 1
   :caption: Tutorials:

   tutorial_grn
   tutorial_integraion
   tutorial_annotation
   tutorial_perturbation
   tutorial_reference_mapping

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

   scgpt

.. toctree::
   :maxdepth: 2
   :caption: References:

   faq
   references



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

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