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I would like to know how can i run a network analysis for identifying major OTUs hubs. I wish to build a network of co-occurring OTUs found in different soils samples.
I've started going through the VEGAN R package but i'm not sure it's what i'm looking for. any recommendations network analysis packages ? thank you!
I am going to assume you have a count table that you are starting with. Every tool you decide to use is going to have its own respective instructions so let me get you pointed in a direction to find one that works for you.
I wrote a simple R package for my lab awhile back but there are much better ways to put together Co-occurrence networks (in no particular order):
Now speaking specifically about "hubs", "connectors", and other keystone organisms, I would recommend reading more about what they are and how they were developed. Again, I have a brief summary here but the original "hub" came from a paper on bee pollination networks