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stefpeschel / NetCoMi

Network construction, analysis, and comparison for microbial compositional data
GNU General Public License v3.0
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How to find a "good" algorithm and parameter set #110

Closed antonkratz closed 7 months ago

antonkratz commented 7 months ago

I am interested in differential microbiome networks. I have networks before and after treatment. I expect the difference between the two networks to be subtle, i.e. the treatment does not have a very strong impact on the microbiome. I know that because when searching for differentially abundant microbiota with ANCOM and other techniques, I do not get any significant hits.

NetCoMi offers a large number of algorithms for network construction, each with its own set of parameters (how to filter taxa, how to deal with zero counts...).

How could a meaningful workflow look like? Is the idea of NetCoMi to go through a large number of algorithms and parameter sets until some combination of method and parameters sets detects significant hits? Or to try go through a very large space and try to find a consensus?

antonkratz commented 7 months ago

Closing my issue as I realize the question is too open ended.