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Gravity
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GRAVITY (for “Gene inteRaction Analysis of Variants in Individuals: a Tool for You”) is a new open-source Cytoscape app that allows an efficient visualisation and analysis of all the exonic variants by mapping them on a protein-protein interaction (PPI).

.. figure:: images/gravity_introduction.png
  :figclass: align-center

  *Cytoscape with GRAVITY network displayed.*

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Features
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* Visualise sequencing data from cohorts using a standard VCF file or a GEMINI database.
* Uses the pedigree informations to enrich the representations and analysis available.
* Integrate interactions between the genes using different PPI networks.
* Different modes of analysis are available:

  * **Trio:** to focus on the mutations of a single individual while integrating, when available, the knowledge of his/her parents.
  * **Complete pedigree:** to focus on finding similarities/differences between the affected and unaffected members of a family (dominant, recessive, compound heterozygous variants)
  * **Comparison of 2 samples:** to focus on similarities/differences between 2 samples. This is particularly interesting for somatic variants that can be observed across tissues, conditions, time, etc.

* A *Cohort panel* to quickly find other individuals in your cohort are sharing variants in the currently selected genes.

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Next releases
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We are still developing this app and are planing to add some new functionalities based on needs and requests.

* Other types of interactions networks such as coexpression or regulation.
* Work on the CNV integration
* Allow other annotations than VEP for the input data

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Licence
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This work is licensed under a `Creative Commons Attribution-NonCommercial 4.0 International License <http://creativecommons.org/licenses/by-nc/4.0/>`_.

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Contents:
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.. toctree::
   :maxdepth: 2

   installation
   getting_started
   input
   controls
   results
   settings

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Acknowledgments
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We would like to thank Yang-Min Kim for the design of the logo. Logo font `Faune, Alice Savoie / Cnap <http://www.cnap.graphismeenfrance.fr/faune/>`_.