A statistical simulator scDesign for rational scRNA-seq experimental design

Li, W. V.; Li, J. J.

doi:10.1101/437095

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bioRxiv · 10.1101/437095

A statistical simulator scDesign for rational scRNA-seq experimental design

Li, W. V.·Li, J. J.

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Abstract

Single-cell RNA-sequencing (scRNA-seq) has revolutionized biological sciences by revealing genome-wide gene expression levels within an individual cell. However, a critical challenge faced by researchers is how to optimize the choices of sequencing platforms, sequencing depths, and cell numbers in designing scRNA-seq experiments, so as to balance the exploration of the depth and breadth of transcriptome information. Here we present a flexible and robust simulator, scDesign, the first statistical framework for researchers to quantitatively assess practical scRNA-seq experimental design in the context of differential gene expression analysis. In addition to experimental design, scDesign also assists computational method development by generating high-quality synthetic scRNA-seq datasets under customized experimental settings. In an evaluation based on 17 cell types and six different protocols, scDesign outperformed four state-of-the-art scRNA-seq simulation methods and led to rational experimental design.

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Li, W. V., Li, J. J.. 2018-10-07. A statistical simulator scDesign for rational scRNA-seq experimental design. https://doi.org/10.1101/437095

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