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HERCULES
========

.. image:: images/logo-hercules.png
  :width: 250px

A Beta version of Gravity-HERCULES is available for download at the following address `Gravity 1.0.0 Hercules <http://bit.ly/2rY05a4>`_.
Installation instructions are the same as for the main Gravity version.

In this version it is possible to directly open the *.csv* files produced by the Anduril pipeline. No additional steps are necessary and this way, the clinicians are already familiar with the annotations presented to them. If you do not have access to Anduril *.csv* files, please check with your technical HERCULES contact.

To start, you can open an Anduril *.csv* file in Gravity

.. image:: images/open_database.png
  :width: 400px

Then the preferred analysis mode for HERCULES data will be ‘Comparison’. This will allow to observe differences between samples.

.. image:: images/hercules_sample-selection.png
  :width: 400px

For this mode, like for any mode in Gravity, you need to select a few parameters, most of which won’t change between different analyses. The first, Quality settings, relates to the analysis of variants.

.. image:: images/hercules_quality-settings.png
  :width: 400px

After this, network settings can be configured. This will allow the user to focus on specific pathway or list of genes. Or, as in this example, it is possible to select all genes.

.. image:: images/hercules_network-settings.png
  :width: 400px

Then, specific filters can be applied to the data (regarding deleteriousness, frequency or others), and, more importantly, choices for the  display of variants found only in one or the other samples, or a cumulative network of both sets of variants.

.. image:: images/hercules_filters-settings.png
  :width: 400px

Finally, you can create and explore the resulting network.

.. image:: images/hercules_create-network.png
  :width: 400px

.. image:: images/M004_adn.01.cropped.png
  :target: _images/M004_adn.01.cropped.png

It is possible to apply a visual style showing the deleteriousness of mutations (node border color) and indication in the nodes for the sample carrying them (in the following network, the pie charts in the nodes indicate the contribution in terms of CADD of the variant from sample A in blue, and sample B in pink).

.. image:: images/M054_ome.01.cropped.png
  :target: _images/M054_ome.01.cropped.png

.. image:: images/legend.comparison.png
  :width: 400px

The right panel shows additional information on the selected genes and the variants.

.. image:: images/hercules_results.png
  :width: 400px

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To do
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* add more flexibility at loading time on the *csv* formatting
* add more options for the display of variants based on specificity from Anduril