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YuLab-SMU / biomedical-knowledge-mining-book

:books: Biomedical knowledge mining using GOSemSim and clusterProfiler
https://yulab-smu.top/biomedical-knowledge-mining-book/
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KEGG enrichment analysis - supported organisms #23

Closed tzaquin closed 1 year ago

tzaquin commented 1 year ago

First of all, thank you for this great package!

my question, TLDR: Is there a way to create a custom orgDB for enrichKEGG()?

I have been trying to run a kegg enrichment analyis on non-model organisms. So they are not found in the KEGG dbs. I have run the analysis uing the enricher() command, with good results. However, downstream visualization are lacking (bar plot and dot plot i can do it by myself, but networks not). I'm asking if there is a way to create an orgDB using the Annotationforge package similar to enrichGO so I would be able to use in enrichKEGG?

Tank you

huerqiang commented 1 year ago

It's not clear to me why you want to create the Orgdb package. If you really want to develop such a package, please refer to Bioconductor's document.

GuangchuangYu commented 1 year ago

Maybe this is what you are looking for, https://github.com/YuLab-SMU/createKEGGdb