.. transit documentation master file, created by
   sphinx-quickstart on Wed May  4 13:37:43 2016.

Welcome to TRANSIT's documentation!
===================================


The main documentation for the site is organized into the following sections:

* :ref:`manual-link`
* :ref:`tutorial-link`
* :ref:`tpp-link`
* :ref:`code-link`


Quick Links
~~~~~~~~~~~

* :ref:`install-link`
* :ref:`cheat-link`


Mailing List
~~~~~~~~~~~~

You can join our mailing list to get announcements of new versions, discuss any bugs, or request features! Just head over to the following site and enter your email address:


 + `https://groups.google.com/forum/#!forum/tnseq-transit/join <https://groups.google.com/forum/#!forum/tnseq-transit/join>`_



.. _manual-link:

.. toctree::
   :maxdepth: 2
   :caption: TRANSIT Manual

   transit_overview
   transit_install
   transit_running
   transit_features
   transit_methods
   transit_console_cheatsheet

.. _tutorial-link:

.. toctree::
   :maxdepth: 2
   :caption: TRANSIT Tutorials

   transit_essentiality_tutorial
   transit_genome_tutorial
   transit_comparative_tutorial
   transit_normalization_tutorial
   transit_export_tutorial

.. _tpp-link:

.. toctree::
   :maxdepth: 2
   :caption: TPP Manual

   tpp.rst

.. _code-link:

.. toctree::
   :maxdepth: 2
   :caption: Code Documentation

   transit

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