I was interested in using Cytoscape to visualize bacterial metabolomics LC-MS data. I first was hoping to try ClueGO/Pedia, is there a way to enter metabolite names or KEGG Identifiers (I have selected KEGG Ontology). If this only takes gene names/IDs, is there another app that I could use for this?
I'm a bit confused. ClueGO and CluePedia are used for enrichment -- not sure how you were planning on using them for metabolomics visualization. I don't know of an ontology of metabolites that's available for enrichment analysis, but one might exist. If you are just looking to visualize your data, perhaps you can explain a bit more what you are trying to portray and we can provide more help.
