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Welcome to scGPT's documentation!
.. image:: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat
: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.
=================================
.. 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`
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