Chronos: Gene Fitness Effect Inference from CRISPR

Dataset provided in support of "Chronos: a model of cell population dynamics in CRISPR knockout screens that improves inference of gene dependency" by Dempster et al. Includes the jupyter notebook Analysis.ipynb together with all files needed to generate the panels in that manuscript. Also includes MAGeCK-MLE, CRISPRCleanR, CERES, and Chronos inference of gene fitness effects for the genome-wide pan-cancer CRISPR knockout experiments Project Achilles (public 20Q2) and Project Score.

v2: Additional analysis and supporting information.

To conserve space and speed up data loading, large matrices are provided as hdf5 files where dim_0 stores row names, dim_1 stores column names, and data stores the matrix as a 2D array. UTF8 encoding was used. Python users can load the matrices as Pandas dataframes using read_hdf5 from the Chronos package at https://github.com/broadinstitute/chronos.