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

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

.. image:: https://img.shields.io/github/tag/mad-lab/transit.svg
    :target: https://github.com/mad-lab/transit
    :alt: GitHub last tag

This page contains the documentation for TRANSIT. Below are a few quick links to some of the most important sections of the documentation, followed by a brief overview of TRANSIT's features.

Quick Links
~~~~~~~~~~~
.. _quick-link:


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


Features
~~~~~~~~
TRANSIT offers a variety of features including:
 
*   More than **8 analysis methods**, including methods for determining **conditional essentiality** as well as **genetic interactions**.

*   Ability to analyze **himar1 or tn5 transposons** datasets.

*   **TrackView** to help visualize read-counts accross the genome.

*   Can **export datasets** into a variety of formats, including **IGV**.

*   Includes a **variety of normalization methods**.

*   **Quality Control** diagnostics, to idenfity poor quality datasets.

*   Ability to install as a **python package**, to import and use in your own personal scripts.   



.. 
 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_interactions_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`

Support
~~~~~~~

For any questions or comments, please contact Dr. Thomas Ioerger, ioerger@cs.tamu.edu.


