Question

clusterProfiler - Non model organism

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rozanskide ▴ 10

@rozanskide-14307

Last seen 7.2 years ago

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

clusterprofiler • 6.8k views

ADD COMMENT • link updated 7.2 years ago by Guangchuang Yu ★ 1.2k • written 7.2 years ago by rozanskide ▴ 10

score 2 · Accepted Answer · 2017-11-02

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/.