© 2016 The Author(s). The ability to quantify cellular heterogeneity is a major advantage of single-cell technologies. However, statistical methods often treat cellular heterogeneity as a nuisance. We present a novel method to characterize differences in expression in the presence of distinct expression states within and among biological conditions. We demonstrate that this framework can detect differential expression patterns under a wide range of settings. Compared to existing approaches, this method has higher power to detect subtle differences in gene expression distributions that are more complex than a mean shift, and can characterize those differences. The freely available R package scDD implements the approach.
Korthauer, K. D., Chu, L. F., Newton, M. A., Li, Y., Thomson, J., Stewart, R., & Kendziorski, C. (2016). A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. Genome Biology, 17(1). https://doi.org/10.1186/s13059-016-1077-y