Welcome to SPOT's documentation!
===================================

**SPOT** (Spatial Perturbation Omics analysis Toolkit) is a model based toolkit for spaital CRISPR knockout screening analysis.

.. image:: ../_images/LOGO.png
   :align: center

**SPOT** is a free, open-source software for both python and R environment users under the MIT license.
Please cite the paper `Paper here` when using the toolkit.

Offcial documentation `can be found here at <https://spot-tutorial.readthedocs.io/en/latest/>`

Refer to our `SPAC-seq analysis tutorial <https://github.com/pkuTrasond/SPAC-seq/tree/master>`,
it offers a *simple* and *intuitive* API.

Check out the :doc:`Usage` section for further information, including
how to :ref:`Installation` the project.

.. note::

   This project is under active development.

Contents
--------

.. toctree::

   Installation
   Preprocessing
   NMF
   Cellcharter
   ClusterDependent
   ClusterIndependent
   Tutorial
   API