Table 1 Overview of scRNA-seq simulators compared in this study. Methods are ordered alphabetically and annotated according to their (in)ability to accommodate multiple batches and/or clusters, support for parallelization (parameter estimation and data simulation, respectively), software availability, and publication year. The right-most column catalogues neutral benchmark studies where each simulator was used. (✓ = yes, ✘ = no, (✓) = yes, but based on user input parameters, i.e., no support for parameter estimation, *requires random splitting of cells into two groups, †/‡ = internal/prior resampling from empirical parameter distribution, ∘ = no separate estimation step)
From: Author Correction: The shaky foundations of simulating single-cell RNA sequencing data
Batches | Clusters | Type(s) | Cell # | Parallelization | Availability | Year | Model | |
|---|---|---|---|---|---|---|---|---|
BASiCS [37] | ✓ | ✘ | b | ✘ | ✓✘ | R/Bioc | 2015 | NB |
ESCO [38] | ✓ | ✓ | n,b,k | ✓ | ✓✓ | R/GitHub | 2020 | Gamma-Poisson |
hierarchicell [39] | ✓ | ✘ | n,b | ✓ | ✘✘ | R/GitHub | 2021 | NB |
muscat [40] | ✓ | ✓ | n,b,k | (✓)†| ✘✘ | R/Bioc | 2020 | NB |
POWSC [41] | ✘ | ✓ | n,k | (✓)†| ✘✘ | R/Bioc | 2020 | zero-inflated, log-normal Poisson mixture |
powsimR [42] | ✘ | (✓) | n* | (✓)†| ✓✓ | R/GitHub | 2017 | NB |
scDD [43] | ✘ | ✘ | n* | ✓ | ✓✓ | R/Bioc | 2016 | Bayesian NB mixture model |
scDesign [44] | ✘ | (✓) | n | ✓ | ∘✓ | R/GitHub | 2019 | Gamma-Normal mixture model |
scDesign2 [45] | ✘ | ✓ | n,k | ✓ | ✓✘ | R/GitHub | 2020 | (zero-inflated) Poisson or NB + Gaussian copula for gene–gene correlations |
SCRIP [46] | ✓ | ✓ | n,b,k | ✓ | ✘✘ | R/GitHub | 2020 | (Beta-)Gamma-Poisson |
SPARSim [47] | ✓ | ✘ | n,b | (✓)‡ | ✘✘ | R/GitLab | 2020 | Gamma-multivariate hypergeometric |
splatter [15] (Splat model) | (✓) | (✓) | n | ✓ | ✘✘ | R/Bioc | 2017 | Gamma-Poisson |
SPsimSeq [16] | ✓ | ✘ | n,b | ✓ | ∘✘ | R/Bioc | 2020 | log-linear model-based density estimation + Gaussian copula for gene–gene correlations |
SymSim [48] | ✓ | ✘ | n,b | ✓ | ✘✘ | R/GitHub | 2019 | kinetic model using MCMC |
ZINB-WaVE [49] | ✓ | ✓ | n,b,k | ✘ | ✘✘ | R/Bioc | 2018 | zero-inflated NB |
zingeR [50] | ✘ | ✘ | n | (✓)†‡ | ✘✘ | R/GitHub | 2017 | zero-inflated NB |