A Systematic Evaluation of Single-Cell Batch Integration Metrics and sBEE: A Robust New Metric (opens in new tab)

Single-cell RNA sequencing (scRNA-seq) datasets generated across laboratories and experimental conditions often exhibit batch effects that obscure biological variation. Numerous computational methods for batch integration have been developed, making rigorous benchmarking critical. Evaluation metrics are central to assessing method performance; however, existing metrics capture only partial aspects of integration quality and often rely on implicit assumptions about cell distributions in the em...