#clusterProfiler# KEGG enrichment with non-reference species
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googneed • 0
@googneed-11386
Last seen 5.1 years ago

Dear all,

I have some rna-seq data with no reference genome. I got the ko number using the transcript sequences by kaas online servers. I want to know whether the package "clusterProfiler" cound handle the ko numbers to show me the kegg enrichment, or are there some other software/packages instead?

Any infomartion is much appreciated.

clusterprofiler kaas enrichKEGG • 1.7k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

you can use `enrichKEGG` function with input genes of K numbers and `organism="ko"`.

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Great! It works! Thx!

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@renukanayak-13512
Last seen 4.3 years ago

Can you please also clarify what is being used to generate the numbers in the the GeneRatio and BgRatio columns in this case where organism is set to "ko"?

And is there a way to specify a user-specified set of background KO numbers?

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they are based on the ko database. If you want to use your own data, see http://guangchuangyu.github.io/2015/05/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/.

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