Random forest code

Q&A
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1

Hi Phil, Simone, DepMap team,

I’m interested in running the code underlying the Predictability tabs, which predicts dependency scores from baseline omics. I found the methodology preprint via the readme (https://www.biorxiv.org/content/10.1101/2020.02.21.959627v3), and its apparently-associated github repo (depmap-crispr-vs-rnai/src/ensemble_prediction_pipeline at main · broadinstitute/depmap-crispr-vs-rnai · GitHub).

Can you confirm if this github repo still matches the pipeline you use to generate the predictability tab data? If not, can you please point me to it?

Thank you very much - Brendan

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The code you linked to is an older version than what the portal is using today. Realistically, I don’t think there are any substantive differences between the version you link and the version we use today. (I think most of the differences since that paper was written were just packaging of the code, replacing R code with python, etc)

Regardless, you can find the code that the portal is currently using in this repo: GitHub - broadinstitute/cds-ensemble

Thanks
Phil

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