shotgun metagenomics degs analysis

Question

[sooni]

Hello. I have shotgun sequencing data. I have a list of bacteria at the species level and a list of genes. What R package do you usually use to view differentially expressed bacteria or genes? I've thought about DESeq2, but I'd like to know if there are any other good packages.

Thank you for help.

Answer 1

[colindaven]

There are quite a few - here is a recent performance comparison and review for 16S data - https://www.nature.com/articles/s41467-022-28034-z

Some of the more sensitive tools are

limma voom, edgeR, Wilcoxon (CLR), and LEfSe

I previously have seen LEfSe used quite widely. edgeR and limma voom are used widely in RNA-seq analyses