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  3. Perturbplan: An Analytical Framework For Designing Perturb-seq Experiments.
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  3. Perturbplan: An Analytical Framework For Designing Perturb-seq Experiments.

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PerturbPlan: An analytical framework for designing Perturb-seq experiments.

Ziang Niu, Yihui He, James Galante

    Biorxiv : the Preprint Server for Biology
    |June 4, 2026

    View abstract on PubMed

    Summary
    This summary is machine-generated.

    Designing CRISPR screens for gene function studies is complex. A new analytical formula and the PerturbPlan app drastically speed up power calculations, enabling interactive and cost-effective experimental design for Perturb-seq and TAP-seq.

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    Area of Science:

    • Genomics
    • Molecular Biology
    • Bioinformatics

    Background:

    • CRISPR screens coupled with single-cell RNA sequencing (scRNA-seq) are vital for understanding gene and noncoding element functions.
    • Designing these complex experiments requires balancing statistical power and experimental costs, a challenge due to numerous parameters.

    Purpose of the Study:

    • To develop a computationally efficient method for power calculation in single-cell CRISPR screens.
    • To create an interactive tool that facilitates optimal experimental design for Perturb-seq and targeted Perturb-seq (TAP-seq).

    Main Methods:

    • Derived a novel analytical formula for calculating the statistical power of detecting perturbation-expression associations.
    • Developed PerturbPlan, a web application implementing the analytical formula for interactive experimental design.
  • Applied PerturbPlan to analyze and compare different single-cell CRISPR screen designs.

    • Main Results:

    • The analytical formula reduces runtime for power calculations by up to seven orders of magnitude compared to simulation-based methods.
    • PerturbPlan successfully guided comparative analyses of existing Perturb-seq designs and quantified cost-effectiveness of TAP-seq.
    • Demonstrated how optimal experimental design choices vary with scale and readout type.

    Conclusions:

    • PerturbPlan offers the first flexible and interactive solution for designing well-powered single-cell CRISPR screens.
    • The tool aids researchers in making informed decisions regarding experimental scale, design, and readout strategies (e.g., TAP-seq vs. Perturb-seq).
    • Accelerated power calculations enable more accessible and efficient experimental planning in functional genomics.