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I have done gene set enrichment analysis which is now straight forward. Such as taking gene set and making a query. For microbiome data it is not that straight forward which I found out.

Step done so far..

  1. Ran Kraken2
  2. Generated OTU table
  3. Downstream analysis using phyloseq.

Now if I have to the functional enrichment from start I would need to use qiime2 which I didn't do earlier.

Now the other option after reading through paper I found kegg can also perform the microbiome functional enrichment

ISSUE
Unlike other database I'm not sure where do I put query in KEGG for the bacterial genus level whatever found.

Any suggestion how to proceed would be really helpful

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