scDesign2: a transparent simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured

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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-021-02367-2).