Hi! I'm interested in pathways enrichment analysis of microbial metagenome from human gut. I already have a list if differentially expressed genes, with relatorive KO and eggNog IDs. now I'd like to know if there is an up or down regulation of some specific pathway. I found the geneAnswer package could be an option for this. Did anybody use it for bacteria metagenome? 

Thanks

francesca

Yes, We have used the geneAnser package for the bacteria metagenomics. It is workable.

you can use `clusterProfiler::enrichKEGG` with organism='ko' and KO ID as input gene.