To get the RNAi (Achilles+DRIVE+Marcotte, DEMETER2) codependencies you can use:
(If you copy the URL from the co-dependency tile in the RNAi section, you should see a similar URL there)
Now, this does not compute the correlations, rather it’s just downloading them from tables we’ve precomputed, and we have not be storing p-values or q-values. So this download gives you the data that portal has already precomputed, but does not do anything additional work.
As far as correlation_from_csv.py goes, you would run it once on the DEMETER2 data ( D2_combined_gene_dep_scores.csv ) for RNAi:
python scripts/correlation_from_csv.py D2_combined_gene_dep_scores.csv D2_combined_gene_dep_scores.csv --limit 100 RNAi.csv
and run it a second time using the data from the latest DepMap release for the CRISPR data ( CRISPR_gene_effect.csv ):
python scripts/correlation_from_csv.py CRISPR_gene_effect.csv CRISPR_gene_effect.csv --limit 100 CRISPR.csv