Dear community members,
I’m interested in downloading a list of genes when KO’ed by CRISPR, they have crippling effects on pediatric tumors.
Perhaps I can select a current dataset (CRISPR DepMap Public 24Q2+Score, Chronos), impose a filter (Tumor type- primary and Age Category- pediatric), and add cell line metadata to download. Then, clean the csv choosing the genes with Chronos scores ≤ -1.
Am I on the right track, or am I missing any steps?
As this is my Day1 on DepMap, thanks in advance for any tips.
One thing I’ll point out is that Chronos scores aren’t intended to be used to identify essential genes. Looking at chronos scores <= 1 will certainly identify essential genes, but it will filter out many other genes which are likley to also be essential.
For identifying essential genes, you likely should be using “Probability of dependency” (such as described in Where is probability of dependency used? - #2 by pmontgom )
Taking your suggestion, downloading “CRISPRGeneDependency.csv” and filtering for >= 0.5 seems a less stringent filter than using Chronos scores <= -1 in CRISPR DepMap Public 24Q2+Score, Chronos.
Thanks, pmontgom!
