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. (\(\checkmark\)= yes, ✘ = no, (\(\checkmark\)) = yes, but based on user input parameters, i.e., no support for parameter estimation, *requires random splitting of cells into two groups, \(\dag /\ddag\)= internal/prior resampling from empirical parameter distribution, \(\circ\)= no separate estimation step)
From: The shaky foundations of simulating single-cell RNA sequencing data
| Â | Batches | Clusters | Type(s) | Cell # | Parallelization | Availability | Year | Model |
|---|---|---|---|---|---|---|---|---|
BASiCS [37] | \(\checkmark\)  | ✘ | b | ✘ | \(\checkmark\)✘ | 2015 | NB | |
ESCO [38] | \(\checkmark\) | \(\checkmark\) | n,b,k | \(\checkmark\) | \(\checkmark\)\(\checkmark\) | 2020 | Gamma-Poisson | |
hierarchicell [39] | \(\checkmark\) | ✘ | n,b | \(\checkmark\) | ✘✘ | 2021 | NB | |
muscat [40] | \(\checkmark\) | \(\checkmark\) | n,b,k | (\(\checkmark\))\(^\dag\) | ✘✘ | 2020 | NB | |
POWSC [41] | ✘ | \(\checkmark\) | n,k | (\(\checkmark\))\(^\dag\) | ✘✘ | 2020 | zero-inflated, log-normal Poisson mixture | |
powsimR [42] | ✘ | (\(\checkmark\)) | n* | (\(\checkmark\))\(^\dag\) | \(\checkmark\)\(\checkmark\) | 2017 | NB | |
scDD [43] | ✘ | ✘ | n* | \(\checkmark\) | \(\checkmark\)\(\checkmark\) | 2016 | Bayesian NB mixture model | |
scDesign [44] | ✘ | (\(\checkmark\)) | n | \(\checkmark\) | \(\circ\)\(\checkmark\) | 2019 | Gamma-Normal mixture model | |
scDesign2 [45] | ✘ | \(\checkmark\) | n,k | \(\checkmark\) | \(\checkmark\)✘ | 2020 | (zero-inflated) Poisson or NB + Gaussian copula for gene-gene correlations | |
SCRIP [46] | \(\checkmark\) | \(\checkmark\) | n,b,k | \(\checkmark\) | ✘✘ | 2020 | (Beta-)Gamma-Poisson | |
SPARSim [47] | \(\checkmark\) | ✘ | n,b | (\(\checkmark\))\(^\ddag\) | ✘✘ | 2020 | Gamma-multivariate hypergeometric | |
splatter [15] (Splat model) | (\(\checkmark\)) | (\(\checkmark\)) | n | \(\checkmark\) | ✘✘ | 2017 | Gamma-Poisson | |
SPsimSeq [16] | \(\checkmark\) | ✘ | n,b | \(\checkmark\) | \(\circ\)✘ | 2020 | log-linear model-based density estimation + Gaussian copula for gene-gene correlations | |
SymSim [48] | \(\checkmark\) | ✘ | n,b | \(\checkmark\) | ✘✘ | 2019 | kinetic model using MCMC | |
ZINB-WaVE [49] | \(\checkmark\) | \(\checkmark\) | n,b,k | ✘ | ✘✘ | 2018 | zero-inflated NB | |
zingeR [50] | ✘ | ✘ | n | (\(\checkmark\))\(^{\dag \ddag }\) | ✘✘ | 2017 | zero-inflated NB |