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Question: GeneAnswer for bacteria metagenomes
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gravatar for francesca.defilippis
3.0 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? 

Thanks

francesca

ADD COMMENTlink modified 16 months ago by Guangchuang Yu800 • written 3.0 years ago by francesca.defilippis40
0
gravatar for wangyizhusss
16 months ago by
wangyizhusss0 wrote:

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

ADD COMMENTlink written 16 months ago by wangyizhusss0
0
gravatar for Guangchuang Yu
16 months ago by
Hong Kong
Guangchuang Yu800 wrote:

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

ADD COMMENTlink written 16 months ago by Guangchuang Yu800
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