Genome wide CRISPR knockout screening

[Zahra Sheybani]

Dear GSEA Team,

I have a question regarding the analysis of CRISPR screening data. 

I have a ranked gene list that includes both enriched (positively selected) and dropped out (negatively selected) genes. For running GSEA, should I analyze the entire ranked list as a whole, or separate the enriched and dropped out genes and run them independently?

I would appreciate your guidance on the best practice for this type of analysis.

Kind regards,

Zahra