.. pysmFISH documentation master file, created by
   sphinx-quickstart on Mon Feb 19 09:46:54 2018.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to pysmFISH!
====================================

pysmFISH is a library for the analysis of single molecule fluorescence hybridization (smFISH).

pysmFISH include an :ref:`API <API>` and a :ref:`pipeline <scripts>` built to analyse large datasets.


.. warning::
    the documentation is still not fully complete and changes will be made frequently


Content
=======

* :ref:`genindex`

.. toctree::
   :hidden:

   self

.. toctree::
    installation/index

.. toctree::
    cluster/index

.. toctree::   
    API/index

.. toctree::
    pipeline/index

.. toctree::
    :hidden:
    tutorials/index
    

.. toctree::
    :hidden:
    notebooks/index

.. toctree::
    license/index


.. toctree::
    citing/index

.. toctree::
    ind_tables/index


Indices and Tables
==================

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