Getting started with networks analyses

Here are a few links to help you get started in thinking about networks!

Two types of networks analyses:

1.  Local similarity analysis – includes a time lag, popular for microbial communities

2.  Maximum information-based nonparametric exploration (MINE), from Science

(We have both LSA [R] and MINE [java] up-and-running in the lab, see Ashley for scripts)

A nice visualization software, Cytoscape, a great open-source tool

For analyzing networks (after they are created)

  • A great introductory R package (also other platforms), igraph
  • 1471-2105-12-24 – GraphCrunch haven’t used this one yet but it looks promising

A review by Newman (referenced by over 8,000!), which covers all the nitty-gritty of thinking about networks

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