Causal identification of single-cell experimental perturbation effects with CINEMA-OT.

ABSTRACT: Recent advancements in single-cell technologies allow characterization of experimental perturbations at single-cell resolution. While methods have been developed to analyze such experiments, the application of a strict causal framework has not yet been explored for the inference of treatment effects at the single-cell level. Here we present a causal-inference-based approach to single-cell perturbation analysis, termed CINEMA-OT (causal independent effect module attribution + optimal transport). CINEMA-OT separates confounding sources of variation from perturbation effects to obtain an optimal transport matching that reflects counterfactual cell pairs. These cell pairs represent causal perturbation responses permitting a number of novel analyses, such as individual treatment-effect analysis

SUBMITTER: Dong M 

PROVIDER: S-EPMC10630139 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature