Visually Comparing Hi-C Networks: Demo Presentation CytoHiC in 10 Steps

1. Download CytoHiC Plugin*: toHiC/CytoHiCPlugin.jar toHiC/CytoHiCPlugin.jar * Make sure you have Cytoscape (or later version) installed on your computer

2. Place it in Cytoscape’s plugins directory

3. Launch Cytoscape: CytoHiC menu will appear under the Plugins menu

4. Open the View Dialog

5. Upload a bin file, a contact file and a landmarks file* Example files are available at: The genomic location of each segment (bin) Contact values between bins The genomic location of landmarks of interest

*Example Files

6. Click OK: a network will be generated

7. Explore the network by hovering or through the node/edge browser

8. Use the right click menu or the CytoHiC menu to compare networks

9. Compare Hi-C networks a. Use indices to compare landmarks b. Use hovering and browsers to view landmarks details

10. Learn more with CytoHiC’s user guide