Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2
Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2
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DOI：
10.1089/cmb.2021.0440
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发表时间：
2022-01
期刊：
影响因子：
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通讯作者：
Tianyi Sun;Dongyuan Song;W. Li;J. Li
中科院分区：
文献类型：
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作者：
Tianyi Sun;Dongyuan Song;W. Li;J. Li
scDesign2是一个透明的模拟器，可以生成高保真的单细胞基因表达计数数据，并捕获基因相关性。本文展示了如何下载和安装scDesign2 R包，如何将概率模型（每个单元类型一个）拟合到实际数据中，并从拟合的模型中模拟合成数据，以及如何使用scDesign2指导实验设计和基准计算方法。最后，在模型拟合和数据仿真之前，将细胞聚类作为预处理步骤。
scDesign2 is a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured. This article shows how to download and install the scDesign2 R package, how to fit probabilistic models (one per cell type) to real data and simulate synthetic data from the fitted models, and how to use scDesign2 to guide experimental design and benchmark computational methods. Finally, a note is given about cell clustering as a preprocessing step before model fitting and data simulation.