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YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data
https://yulab-smu.top/biomedical-knowledge-mining-book/
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KEGG enrichment analysis for gut microbiome #309

Open khemlalnirmalkar opened 3 years ago

khemlalnirmalkar commented 3 years ago

Hello Prof. Yu, I find your clusterProfiler (http://yulab-smu.top/clusterProfiler-book/) a useful tool and tried to follow the tutorial. Since I am working on the gut microbiome and have KEGG pathways for microbiota (mix of bacteria) but not for one bacteria and your tutorial mentioned assigning an organism which is not possible for me. Please can you guide me on, how can I use my KEGG data to do enrichment analysis for microbiota? Many thanks, Khem

GuangchuangYu commented 3 years ago

@mjchen1996 @huerqiang @xiangpin may help.

khemlalnirmalkar commented 3 years ago

Thank you Prof. Yu, I will wait for their response,

khemlalnirmalkar commented 3 years ago

Hello Prof. @GuangchuangYu , I didn't hear anything from @huerqiang @xiangpin Meijun. Please can you suggest to me something to move forward with? Many thanks, Happy New Year, Khem

yanghu2018 commented 3 years ago

Hi Khem,

I am seeking the same answer. And a recent paper might be your interest, but it only mentioned doing GSEA with default setting. Please do let me know if you have any other way to address this issue. Thanks.

Cheers, Yang

Puffer Fish Gut Microbiota Studies Revealed Unique Bacterial Co-Occurrence Patterns and New Insights on Tetrodotoxin Producers.pdf

GuangchuangYu commented 2 years ago

pls try https://github.com/YuLab-SMU/MicrobiomeProfiler.