Get number of pathways

[Eli Kopel]

Hi Anthony,

I have a long list of genes. I am interested in counting the number of pathways from C2 collection each gene appears in (one gene at a time). I known how to do it with one gene, the question is if there is any way I can get that information for many more genes?

Thank you,

Eli

[Anthony Castanza]

Hi Eli,

 

We don’t really offer tools to do this. Your best bet is to read the gene sets into something like R or Python and then iterate over them.

We recently started providing gene sets in .JSON format which might help the process of reading them into R or Python.

 

Sorry I couldn’t be of more help here.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Eli Kopel]

Thank you very much, Anthony

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