cyTRON in an application for cancer progression analysis. It is an interface to the R library TRONCO and it supports both the visualization of already constructed models and the creation of new analysis.
This application has been developed using NodeJS. In order to run it it is necessary to install the following:
- Clone this repository in a folder in your local machine
- Open the command prompt and cd into the folder
- Run the command
- Type the following:
- For the time being, open the browser and navigate to http://localhost:3000/.
Note: no additional R package is necessary, any missing package will be automatically installed on the application's first run.
Google Summer of Code
cyTRON/JS was developed within the GSoC 2018 program, in collaboration with the NRNB organization.
During the program the following functionalities have been implemented:
- Graph visualization and manipulation: this was accomplished using Cytoscape.js and its extensions.
js-call-r. In particular it is possible to:
- select input data in the formats suported by TRONCO (MAF, GISTIC and a custom boolean table)
- Select an input file with driver mutations
- Select a file with information about clusters into which the data needs to be splitted
- Reconstruct the model using TRONCO's algorithms
- Visualize the contructed model.
The web application was built using the Framework
Express. The code is divided as follows:
- View: this is the folder which contains the interface.
- Routes: in this folder there is the code which maps each HTTP request to the corresponding function in the controller.