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BioMed Central, Genome Biology, 1(17)

DOI: 10.1186/s13059-016-0930-3

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Beyond comparisons of means: understanding changes in gene expression at the single-cell level

Journal article published in 2016 by Catalina A. Vallejos ORCID, Sylvia Richardson ORCID, John C. Marioni ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Abstract Traditional differential expression tools are limited to detecting changes in overall expression, and fail to uncover the rich information provided by single-cell level data sets. We present a Bayesian hierarchical model that builds upon BASiCS to study changes that lie beyond comparisons of means, incorporating built-in normalization and quantifying technical artifacts by borrowing information from spike-in genes. Using a probabilistic approach, we highlight genes undergoing changes in cell-to-cell heterogeneity but whose overall expression remains unchanged. Control experiments validate our methodâ s performance and a case study suggests that novel biological insights can be revealed. Our method is implemented in R and available at https://github.com/catavallejos/BASiCS .