Question: GeneAnswer for bacteria metagenomes
gravatar for francesca.defilippis
3.3 years ago by
European Union
francesca.defilippis40 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? 



ADD COMMENTlink modified 19 months ago by Guangchuang Yu890 • written 3.3 years ago by francesca.defilippis40
gravatar for wangyizhusss
19 months ago by
wangyizhusss0 wrote:

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

ADD COMMENTlink written 19 months ago by wangyizhusss0
gravatar for Guangchuang Yu
19 months ago by
Hong Kong
Guangchuang Yu890 wrote:

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

ADD COMMENTlink written 19 months ago by Guangchuang Yu890
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