Differential Abundance Analysis (for metagenomics)

Question

[aerotolerant]

Hello,

I would like to use the best statistical test for my data. I have processed the samples using the Anv'io pipeline, and would like to put my mean coverage (mean coverage of a contig divided by overall sample mean coverage) or relative abundance (# of reads recruited to a contig divided by total reads recruited to that contig across all samples) into a differential analysis. The data is non-count, continuous, and non-compositional. I am comparing two groups at the same time point and looking for differential MAGs between them. What would be the best R package? I have used limma, LDM, and ANCOMBC with different results. Thanks.