GeneAnswer for bacteria metagenomes
2
1
Entering edit mode
@francescadefilippis-7043
Last seen 6.7 years ago
European Union

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 metagenome kegg • 1.2k views
ADD COMMENT
0
Entering edit mode
@wangyizhusss-11059
Last seen 5.1 years ago

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

ADD COMMENT
0
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 7 months ago
China/Guangzhou/Southern Medical Univer…

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

ADD COMMENT

Login before adding your answer.

Traffic: 327 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6