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5.0 years ago by
European Union
francesca.defilippis60 wrote:

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

geneanswers kegg metagenome • 968 views
modified 3.4 years ago by Guangchuang Yu1.1k • written 5.0 years ago by francesca.defilippis60
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3.4 years ago by
wangyizhusss0 wrote:

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

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3.4 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

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