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. 2023 Mar 3;24:39. doi: 10.1186/s13059-023-02879-z

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© The Author(s) 2023

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — Benchmarking SRTsim against eight existing scRNAseq simulators for generating SRT data based on the DLPFC reference data. A Violin plots show the distributions of six metrics (six panels) in the reference data (real; x-axis) and in the synthetic data generated by different simulators (x-axis). The six metrics include four gene-wise metrics (expression mean; variance; coefficient of variation, cv; and zero proportion) and two location-wise metrics (zero proportion and library size). The examined simulators include SRTsim, scDesign2, scDesign2 without copula (scDesign2 (ind)), ZINB-WaVE, SPARSim, SymSim, and three variants of the splatter package (kersplat, splat simple, and splat). Results are shown for the reference sample DLPFC 151673. Results for the other reference samples are provided in the supplemental figures. B The spatial expression patterns of three representative genes (MOBP, PCP4, SNAP25) are displayed in the reference data and in the synthetic data generated by SRTsim, scDesign2, ZINB-WaVE, and SPARSim