Data for metabolomics database

Dear team,

My name is Yaara Oren and I am a joint postdoc in the Blainey and the Brugge (HMS) labs. I really enjoyed reading your publications on the cancer cell line metabolism and was wondering what would be the best way to access the data (I was not able to find it in your “Downloads” section). Also, It there an R wrapper that you recommend for accessing the code? I am interested in generating plots looking at the association of copy number with metabolite level across the CCLE, similar to what was done in the paper, and was wondering what is the best way to do so.

Many thanks for your help,


The R wrapper for accessing the DepMap data is maintained by someone outside of the DepMap project. I personally don’t know much about it, but I have heard of others having success with it.

It sounds like you’re looking for the metabolomics dataset which is availible under the “CCLE 2019” data in the download section. I’ve included a screenshot of the file I believe you’re looking for: