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cyTRON: a Cytoscape app for the visualization of evolutionary trajectories in cancer progression

TRONCO is an R package that implements state-of-the-art algorithms for the inference of cancer progressions with the ultimate goal of understanding the evolutionary trajectories driving tumor evolution.

In such a multidisciplinary domain, where computer scientists actively cooperate with biologists, being capable of visually understanding the data is crucial to both parties.

cyTRON is a Cytoscape app that was designed for this purpose, i.e., mapping the features provided by the TRONCO R package to a user-friendly and accessible interface.

Documents

The documentation of the cyTRON Cytoscape app is available at the docs folder of this project and includes:

  • the installation guide;
  • a case study example that replicates some of the results published in Caravagna, Giulio, et al. "Algorithmic methods to infer the evolutionary trajectories in cancer progression." Proceedings of the National Academy of Sciences 113.28 (2016): E4025-E4034;
  • a short technical documentation describing the class diagram and the adopted patterns.

In addition, we also provide an installable .jar file (release directory) together with a few example datasets (datasets directory).

Google Summer of Code 2017

cyTRON was developed within the Google Summer of Code program, in collaboration with NRNB (National Resource for Network Biology).

Here is the link to the project.

Starting Point

The starting point of the GSoC2017 project was the code included in the branch base of this repository.

Final Product

The branch master at commit 41a1433 is the final product achieved at the end of the GSoC2017 project.

All the differences between the branch base and commit 41a1433 represent the work carried out during the GSoC2017 conding period.

The app will be added to the Cytoscape App Store.

DEBUG

Please feel free to contact us if you have problems running our tool at daniele.ramazzotti1@gmail.com or edoardo.galimberti1@gmail.com.