Brieflow: An Integrated Computational Pipeline for High-Throughput Analysis of Optical Pooled Screening Data.

ABSTRACT: Optical pooled screening (OPS) has emerged as a powerful technique for functional genomics, enabling researchers to link genetic perturbations with complex cellular morphological phenotypes at unprecedented scale. However, OPS data analysis presents challenges due to massive datasets, complex multi-modal integration requirements, and the absence of standardized frameworks. Here, we present Brieflow, a computational pipeline for end-to-end analysis of fixed-cell optical pooled screening data. We demonstrate Brieflow's capabilities through reanalysis of a CRISPR-Cas9 screen encompassing 5,072 fitness-conferring genes, processing more than 70 million cells with multiple phenotypic markers. Our analysis reveals functional gene relationships that were missed in the original study, uncovering co

SUBMITTER: Di Bernardo M 

PROVIDER: S-EPMC12154638 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature