.. oligo-designer-toolsuite documentation master file, created by
   sphinx-quickstart on Thu Oct 13 15:49:40 2022.
   You can adapt this file completely to your liking, but it should at least
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*Oligo Designer Toolsuite* - Lightweight Development of Custom Oligo Design Pipelines
=======================================================================================


.. include:: ../../README.md
   :parser: myst_parser.sphinx_
   :start-after: <!-- LINK INTRODUCTION START -->
   :end-before: <!-- LINK INTRODUCTION END -->

.. toctree::
   :maxdepth: 1
   :caption: GETTING STARTED

   _getting_started/installation.rst
   _getting_started/introduction_framework.rst
   _getting_started/build_a_custom_pipeline.rst

.. toctree::
   :maxdepth: 1
   :caption: PIPELINES

   _pipelines/genomic_region_generator
   _pipelines/scrinshot_probe_designer
   _pipelines/merfish_probe_designer
   _pipelines/seqfishplus_probe_designer
   _pipelines/oligoseq_probe_designer


.. toctree::
   :maxdepth: 2
   :caption: API Documentation:

   _api_docs/oligo_designer_toolsuite.rst


Contributing
-------------

.. include:: ../../README.md
   :parser: myst_parser.sphinx_
   :start-after: <!-- LINK CONTRIBUTION START -->
   :end-before: <!-- LINK CONTRIBUTION END -->

How to cite
------------

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   :start-after: <!-- LINK CITE START -->
   :end-before: <!-- LINK CITE END -->

License
--------

.. include:: ../../README.md
   :parser: myst_parser.sphinx_
   :start-after: <!-- LINK LICENSE START -->
   :end-before: <!-- LINK LICENSE END -->