Hi, I’m trying to get a rough number of selectively dependent genes. Analogous to the definition of “strongly selective” in the “Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets” paper. I’m guessing a way to do this would be to use a lower threshold of NormLRT. Have you all done, this, can you share any rough estimates of the number of genes that are selective?
We have a definition of “strongly selective” that we use in the portal, which is a threshold of 100 < skewed-LRT.
If you want to see which genes are classified as “strongly selective” you can find that information in the table at https://depmap.org/portal/api/download/gene_dep_summary
Thank you! Feature request, could you share the skewed-LRT values for each gene as well / someday / somehow?
Going to answer my own question now that I’ve finally RTFM’d: in “Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets” supplementary 4 is an excel sheet containing normLRT values calculated for Broad and Sanger. Thank you!