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scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured
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scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured
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Journal Article
scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured
2021
Overview
A pressing challenge in single-cell transcriptomics is to benchmark experimental protocols and computational methods. A solution is to use computational simulators, but existing simulators cannot simultaneously achieve three goals: preserving genes, capturing gene correlations, and generating any number of cells with varying sequencing depths. To fill this gap, we propose scDesign2, a transparent simulator that achieves all three goals and generates high-fidelity synthetic data for multiple single-cell gene expression count-based technologies. In particular, scDesign2 is advantageous in its transparent use of probabilistic models and its ability to capture gene correlations via copulas.
Publisher
BioMed Central,Springer Nature B.V,BMC
Subject
