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Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2.

Tianyi SunDongyuan SongWei Vivian LiJingyi Jessica Li
Published in: Journal of computational biology : a journal of computational molecular cell biology (2022)
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.
Keyphrases
  • single cell
  • gene expression
  • electronic health record
  • rna seq
  • big data
  • dna methylation
  • genome wide
  • stem cells
  • copy number
  • data analysis
  • cell therapy