Hello !

I'm looking for an API or package which can perform a joint pathway analysis using a list of genes and a list of metabolites at least. My aim would be to find pathways which include as many items of my lists as possible.

Thanks in advance !

The mogsa package comes to mind.

MetaboAnalyst is another that comes to mind, but this is a web interface.

Kevin

You could also try MOFA:

https://bioconductor.org/packages/release/bioc/html/MOFA.html

okay i'll try them, thank you all !