Cytoscape compatibility

Cytoscape is a powerful solution for network visualization and analysis. It provides countless features and its active community enriches the addons catalogue on a regular basis. RulNet provides the possibility to save network data so you can take advantage of the strength of Cytoscape. Cytoscape is available as a platform-independent open-source Java application, released under the terms of the LGPL. You can download it on the Cytoscape download page.

    Save network data

You can save the network data as a classical tab separated .txt files which contains rule data. When the rules have been generated and filtered as required by your analysis, click on "Export rules" and then click on the "TXT" icon. The rule file saved on your computer is then ready to be uploaded in Cytoscape.

    Upload networks in Cytoscape

Open Cytoscape and choose to "Import" a "Network file" in the file menu. Select the column 1 and 2 as source interaction and target interaction as shown in the picture here below. Select Column 5 as interaction type. In the text file options, choose to transfer the first line as column names. Finally, Click on the header of all the other columns to keep them as edge attributes for further analyses. Click "OK", you are ready to proceed with any analysis available in Cytoscape.

Upload cytoscape
 
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