We propose the Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) 
method for prioritizing single-guide RNAs, genes and pathways in genome-scale 
CRISPR/Cas9 knockout screens. MAGeCK demonstrates better performance compared 
with existing methods, identifies both positively and negatively selected genes 
simultaneously, and reports robust results across different experimental 
conditions. Using public datasets, MAGeCK identified novel essential genes and 
pathways, including EGFR in vemurafenib-treated A375 cells harboring a BRAF 
mutation. MAGeCK also detected cell type-specific essential genes, including BCR 
and ABL1, in KBM7 cells bearing a BCR-ABL fusion, and IGF1R in HL-60 cells, 
which depends on the insulin signaling pathway for proliferation.