Script to calculate gene dependencies

Q&A
1

Three years ago I used this script provided (Revisions · Script based on code from the DepMap portal code to compute the top N pearson correlations and write to a CSV file · GitHub) to calculate co-dependencies for every gene. This was for CERES data. It was very useful for drawing some interaction networks in Cytoscape.

I just used it again for the latest CHRONOS data and the results were nothing like what is up on the website. I used the CRISPRGeneEffect file.

I was wondering if I did something wrong, or this script is outdated for CHRONOS data?

2

No, that script should be just as applicable for CHRONOS as CERES. And I don’t believe anything has changed in the portal for years around how we compute correlation, so that script should continue to provide the same results.

Could you provide an example of the discrepancies you’re seeing?