Gene enrichment analysis of prokaryotes gene

Question

[Genta]

I am wondering what are the good tools (web tools or R-packages) to conduct enrichment analysis using DEG data of prokaryotes (like E. coli, C. perfringens, S. aureus, and so on). Many web tools and R-packages are only available to eukaryotes, especially humans and mice. I really appreciate it if you could let me know.

Answer 1

[dthorbur]

Here is a tutorial on how to use the R package DESeq2 for prokaryotic RNAseq analyses.

Here is a paper describing the tool ProkSeq which incorporates a few RNAseq tools including DESeq2.

Edit: Think I misread the question. If you meant something like KEGG/GO enrichment of outlier genes, then you can use gProfiler2, where you can create a custom datasets for enrichment analyses.