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.
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.
Google Summer of Code 2017
Here is the link to the project.
The starting point of the GSoC2017 project was the code included in the branch base of this repository.
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.