Thank you for @michael.shaffer developing the q2-SCNIC package. I did not know this plugin before and I am planning to run run SparCC in python.
I recently read some article, they use the SparCC method to explore the relationship between environmental factors and microbial community.
Please refer the material and method in the following paper:
I came to have several questions:
Based on the q2-SCNIC tutorial, the input file is OTU table. I saw that SCNIC can run the between table correlations in the github page (but not implemented to using sparcc method currently??). But I am wondering then how can I run the correlations between environmental factor and microbial community. Can you please give me some suggestions. What kind of data file I need to prepare?
If the correlations between OTU table and environmental factor is not available in q2-SCNIC currently. Can I run this kind of correlations in the in the original sparcc package. I want to find some example but cannot find it in their page:
(Can I added more columns to the OTU table to include the environmental factors. And use the new OTU table (include OTU and environmental factor) to run SparCC. So the final output should include the all the correlations not just the correlations between OTU and environmental variables. Is this make sense to you if I want to follow the paper did which I refer above? )
I also saw some people using SPIEC-EASI method to do network analysis. I am trying to figure what are the differences between SparCC and SPIEC-EASI . I am still confused about this two method. If I want to examine the correlations between microbial community and environmental factors, which approach do you suggest? Can you please give me some advice?
Thank you so much for your help!