Comparing phenotypic manifolds with Kompot: Detecting differential abundance and gene expression at single-cell resolution.

ABSTRACT: Kompot is a statistical framework for holistic comparison of multi-condition single-cell datasets, supporting both differential abundance and differential expression. Differential abundance captures changes in how cells populate the phenotypic manifold across conditions, while differential expression identifies condition-specific changes in gene regulation that may be localized to particular regions of that manifold. Kompot models the distribution of cells and gene expression as continuous functions over a low-dimensional representation of cell states, enabling single-cell resolution inference with calibrated uncertainty estimates. Applying Kompot to aging murine bone marrow, we identified a continuum of shifts in hematopoietic stem cell and mature cell states, transcriptional remodeling o

SUBMITTER: Otto DJ 

PROVIDER: S-EPMC12157388 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature