Any advice on a community detection algorithm?

1

Gephi

Both Cytoscape and Gephi are options that you can try on Windows; both can run some classic community detection algorithms and can be extended with plugins. Personally, I'd recommend you to use igraph, which can be run as an R or python libraries. Then, about the specific algorithm, I have no experience on amino acid communities, but I would approach the issue thinking the properties that you would like to capture, e.g. Do you want discrete or overlapping communities? Do you have an hypothesized number of communities? etc.

#Diagrams #Flowcharts #Wireframing 31 social mentions

2

Cytoscape

Both Cytoscape and Gephi are options that you can try on Windows; both can run some classic community detection algorithms and can be extended with plugins. Personally, I'd recommend you to use igraph, which can be run as an R or python libraries. Then, about the specific algorithm, I have no experience on amino acid communities, but I would approach the issue thinking the properties that you would like to capture, e.g. Do you want discrete or overlapping communities? Do you have an hypothesized number of communities? etc.

#Diagrams #Data Visualization #Flowcharts 11 social mentions