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Welcome to scParadise documentation!
===================================

`scParadise` is a fast, tunable, high-throughput automatic cell type annotation and modality imputation python framework.

`scParadise` includes three sets of tools: 

    1) `scAdam <https://scparadise.readthedocs.io/en/latest/theory.html#scadam-models>`_ - fast reference-free multi-task multi-class cell type annotation.
    2) `scEve <https://scparadise.readthedocs.io/en/latest/theory.html#sceve-models>`_ - reference-free modality imputation.
    3) `scNoah <https://scparadise.readthedocs.io/en/latest/theory.html#scnoah-metrics>`_ - set of functions for benchmarking cell type annotation and modality imputation. 

`scParadise` enables users to utilize a selection of pre-existing models (`scAdam` or `scEve`) 
as well as to develop, train and optimize custom models tailored to specific research needs. 

`scNoah` facilitates the evaluation of novel models and methods for automated cell type annotation 
and modality imputation in scRNA-seq analysis.

scParadise is now in active development. 

If you have any ideas, enhancements, or bug fixes, please feel free to submit a pull request in a `scParadise GitHub repo <https://github.com/Chechekhins/scParadise>`_.

.. grid:: 3
   :gutter: 2

   .. grid-item-card:: Installation
      :link: installation
      :link-type: doc

      Installation guide for scParadise.

   .. grid-item-card:: Tutorials
      :link: tutorials/index
      :link-type: doc

      Do you want your cells to be annotated and modalities predicted?

   .. grid-item-card:: Model hub
      :link: model_hub/index
      :link-type: doc

      The table of scAdam and scEve models

.. grid:: 3
   :gutter: 2

   .. grid-item-card:: API reference
      :link: api/index
      :link-type: doc

      The API reference of scParadise modules and functions


   .. grid-item-card:: Theory
      :link: theory
      :link-type: doc

      The theory of scParadise key concepts 

   .. grid-item-card:: GitHub
      :link: https://github.com/Chechekhins/scParadise

      The repository where you can try to find a solution of your problem


.. toctree::
   :hidden:
   :maxdepth: 2

   installation
   tutorials/index
   model_hub/index
   api/index
   theory 
   GitHub <https://github.com/Chechekhins/scParadise>
   references
   citation

Contributing
_____________
We warmly welcome contributions to scParadise! If you have any ideas, enhancements, or bug fixes, please feel free to submit a pull request. Additionally, we encourage you to report any issues you encounter while using scParadise. Your feedback is invaluable in helping us improve the tool!

Small jokes from the scParadise team
____________________________________
So Adam gave names to all Monocytes, to the T cells of the blood, and to every living cell. But for Adam there was not found a helper comparable to him.

She became pregnant and gave birth to new modality. Eve said, “With the Lord's help, I have given birth to a surface proteins.”

Pairs of all functions that have the ability to check models quality in them came to Noah and entered the module.