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Question: clusterProfiler - Non model organism
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gravatar for rozanskide
11 months ago by
rozanskide10
rozanskide10 wrote:

Dear all,

I found clusterprofiler neat and really want to give it a try. However, Im working on a non model organism and without kegg database annotation but with custom compiled kegg representatives for the model.

Is it possible to work with custom kegg annotation using clusterprofiler? Can I provide the custom annotation and then do say kegg enrichment using this custom annotation as reference?

 

Thanks

AndreiR

ADD COMMENTlink modified 11 months ago by Guangchuang Yu1.0k • written 11 months ago by rozanskide10
2
gravatar for Guangchuang Yu
11 months ago by
Guangchuang Yu1.0k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.0k wrote:

clusterProfiler do support non model organisms. For GO you can use AnnotationHub to query GO annotation. For KEGG, it supports all organisms available in KEGG database as it use the online data, see http://guangchuangyu.github.io/2015/02/kegg-enrichment-analysis-with-latest-online-data-using-clusterprofiler/.

If you have customized annotation data, you can also use clusterProfiler to perform ORA or GSEA, please refer to http://guangchuangyu.github.io/2015/05/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/.

ADD COMMENTlink written 11 months ago by Guangchuang Yu1.0k
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