The way to do different gene abundance analyses using genefamilies.tsv files.

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Hello, after getting the genefamilies.tsv files from metagenomics data. I want to do different gene abundance analyses.

I have looked at some posts, the RPKs data is not appropriate for edgeR and DESeq2, and getting raw counts data is difficult.

In one post Downstream analysis of HUMAnN2 output, paired t-test or Wilcoxon signed-rank test was suggested to do different gene abundance analyses, but it only calculated one gene at a time, and it can't do multiple testing, for example, FDR and BH (Benjaminiand Hochberg).

So could you please recommend some ways to do different gene abundance analyses?

Thanks!

Sarah