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7 hours ago by

Hello!

I work with a Nothobranchius furzeri transcriptome data and want to do the GO enriched pathway analysis using the clusterProfiler R package. I started with the command 'search_kegg_organism'.
The documentation (www.rdocumentation.org/packages/clusterProfiler/versions/3.0.4/topics/search_kegg_organism) says that this function searches directly in the KEGG catalogue (www.genome.jp/kegg/catalog/org_list.html), where Nothobranchius furzeri is present and has a code 'nfu'.
However,

search_kegg_organism('nfu', by='kegg_code')

didn't work. I tried it with other species, and found out that it finds many organisms (e.g. 'mmu', 'dre'), and doesn't find many other organisms (e.g. 'malb', 'els').

What can it depend on?
And does it mean that the package will not work correctly with my species in general?

I would really appreciate if you could help me.



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