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SPATS Documentation
===================

.. toctree::
   :maxdepth: 1
   :caption: See also:

   install
   quickstart
   tool
   advanced
   reference


Overview
========

See the `SPATS Homepage <http://luckslab.github.io/spats/>`_ for
general information.


See the `installation <install.html>`_ instructions, `quickstart guide
<quickstart.html>`_, or `documentation <tool.html>`_ for information
about getting started with SPATS.


Reference
=========

The SPATS software is based on:

J. B. Lucks, S. A. Mortimer, C. Trapnell, S. Luo, S. Aviran, G. P. Schroth, 
L. Pachter, J. A. Doudna, A. P. Arkin. **Multiplexed RNA structure characterization with selective 2’-hydroxyl acylation
analyzed by primer extension sequencing (SHAPE-Seq).** *PNAS*, 108, 11063, 2011.


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

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