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. ‘Type(s)’ column specifies which type of simulations can be produced (n: “singular” references: single batch or cluster; b: multiple batches; k: multiple clusters). ‘Cell #’ refers to whether the number of cells can be varied. Symbols: $✓$= 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, $\circ$= no separate estimation step)

	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*	$✓$	$✓$$✓$	R/Bioc	2016	Bayesian NB mixture model
scDesign [44]	✘	($✓$)	n	$✓$	$\circ$$✓$	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	$✓$	$\circ$✘	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