.. CAST documentation master file, created by
   sphinx-quickstart on Fri Jun 28 16:03:31 2024.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to CAST's documentation!
================================

**CAST** is a Python library for physically aligning different spatial transcriptome regardless of technologies, magnification, individual variation, and experimental batch effects.
CAST is composed of three modules: CAST Mark, CAST Stack, and CAST Projection. The datasets / jupyter notebooks used in the demos could be found `here <https://drive.google.com/drive/u/1/folders/118IsDqKT5N8LbmgNz42t69rwlb8FZTGR>`_.

`CAST Github <https://github.com/wanglab-broad/CAST>`_


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

   notebooks/demo1_CAST_mark.ipynb
   notebooks/demo2_CAST_Stack_Align_S4_to_S1.ipynb
   notebooks/demo3_CAST_project.ipynb
   notebooks/demo4_STARmap_to_MERFISH.ipynb
   notebooks/demo5_Visium.ipynb
   notebooks/demo6_STARmap_to_SlideSeq.ipynb
   notebooks/demo7_ARTISTA.ipynb
   notebooks/demo8_ARTISTA_delta_Analysis.ipynb

.. toctree::
   :maxdepth: 1
   :caption: API:

   api_source/modules 

.. image:: /_static/Diagram.png
   :alt: Diagram of CAST
   :align: center
   :width: 100%


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

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