Fig. 1
Overview of Chronos. a Illustration of the model for the simplified case where an sgRNA j is introduced targeting essential gene g in cell line c. Stochastic double-strand repair divides the population of infected cells into two groups, one with (top) and one without (bottom) successful gene knockout, which proliferate at different rates. Successful knockout probability is the product of a per-sgRNA probability pj and a per-cell line probability pc. The population of cells measured at each subsequent time point is a mix of these two populations. Chronos infers the relative change in growth rate rcg. b Typical workflow of a Chronos run. Readcounts driven by outgrowing clones are removed, then gene fitness effects inferred using the readcount matrix, sequence map, and guide map. The inferred gene fitness effects are then corrected for copy number effects. c Number of cell lines in each lineage for the Achilles and Project Score datasets used for comparison