PerturbPlan: An analytical framework for designing Perturb-seq experiments

CRISPR screens with single-cell RNA-seq readouts provide a powerful tool for characterizing the functions of noncoding elements and genes. However, designing these experiments to balance statistical power and cost is challenging, given the large number of design parameters. The only available tool for this purpose is a simulation-based power calculator, but it is computationally costly and requires high-performance computing to run. We derive a novel analytical formula for the power to detect perturbation-expression associations, recapitulating power estimates from the simulation-based tool while reducing runtime by up to seven orders of magnitude. This acceleration unlocks the possibility of interactive single-cell CRISPR screen design. Accordingly, we develop PerturbPlan, an interactive web application built on the analytical power formula. PerturbPlan helps users address 11 design questions for two types of single-cell CRISPR screens, Perturb-seq and targeted Perturb-seq (TAP-seq). We apply PerturbPlan to carry out a comparative analysis of three recent Perturb-seq designs, demonstrating how optimal design varies across experiments of different scales. We also use PerturbPlan to quantify the cost savings of a recent TAP-seq study relative to a hypothetical Perturb-seq study assaying the same perturbations, illustrating how the tool can inform decisions about targeted versus whole-transcriptome readouts. In sum, PerturbPlan is the first tool to facilitate flexible and interactive design of well-powered single-cell CRISPR screen experiments.