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A statistical simulator scDesign for rational scRNA-seq experimental design

Published Web Location

https://www.biorxiv.org/content/early/2018/10/07/437095
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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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