Cytosape is an open source software. You can visualize complex networks and integrate them with a lot of attribute data. A lot of Apps are available and increase what you can do !
You can find more details in their website: https://cytoscape.org/index.html
1 Tutorials
You can also find tutorials with examples: https://github.com/cytoscape/cytoscape-tutorials/wiki.
2 Download
The downloading page is different according your platform.
2.1 Windows and MAC OS
Java 11 is automatically installed. You have just to install Cytoscape.
2.2 Linux
Then, set the JAVA_HOME variable with the correct location of JDK executable. You can find many tutorials on internet.
3 Add apps
You can find a list and description of each app available here: https://apps.cytoscape.org/.
You can directly install apps inside Cytoscape with the Apps manager (Figure 3.1).
Figure 3.1: Cytoscape View - App Manager on the menu tab at the top of the Cytoscape window.
A new window appears. You can search by key words or using the app name. Then, you click on the Install button (Figure 3.2).
Figure 3.2: App Manager View - Search the app you want, and install it easily.
4 Requirement for the training session
For the training session, you need to install several apps:
- yFiles Layout Algorithm:
1.1.2 - LegendCreator:
1.1.6 - stringApps:
1.5.1 - Omics visualize:
1.3.0
Notice that, the version available could depend on your version of Cytoscape.