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3.5 years ago
Hello all, I hope you all are doing good. I have made clusters of a string PPI network using MCODE from cytoscape but I am not sure how to do the analysis? How do I evaluate the significance of the clusters obtained? Is the highest scoring network considered the best? This is the first time I am doing clustering. Would really appreciate it if someone could take out their valuable time to help me. Thank you.
You may have seen these already, but there are tutorial and documentation links from both the MCODE app and clusterMaker2 apps, which can each perform MCODE clustering:
If you are asking about MCODE clustering in general, perhaps this paper is a good place to start: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-4-2