Toward automated and explainable high-throughput perturbation analysis in single cells

Perturbation analysis in single-cell RNA sequencing (scRNA-seq) data is challenging due to the complexity of cellular responses. To address this, Xu and Fleming et al. developed CellCap, a generative deep-learning model that decodes the perturbation effect on a particular cell state. CellCap extracts interpretable latent representations of perturbation response modules, identifying key cellular pathways activated under various conditions. This allows for a deeper understanding of cell-state-specific responses to genetic, chemical, or biological perturbations.