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Table 1 Summary of 16 simulators (including our proposed scDesign2) in six properties

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

Property

1

2

3

4

5

6

 

protocol adaptive

gene preserved

gene cor. captured

cell num. seq. dep. flexible

transparent

comp. and sample efficient

Simulator

dyngen [77]

Lun2 [78]

powsimR [75]

PROSST [68]

scDD [74]

scDesign [35]

scGAN [72]

splat simple [69]

splat [69]

kersplat [69]

SPARSim [71]

SPsimSeq [79]

**

SymSim [70]

ZINB-WaVE [39]

SERGIO [76]

scDesign2

  1. Property 1: protocol adaptiveness
  2. Property 2: gene preservation
  3. Property 3: gene correlation capture
  4. Property 4: flexible cell number and sequencing depth choices
  5. Property 5: transparency
  6. Property 6: computational and sample efficiency
  7. For each simulator and each property, a checkmark, checkcross, or cross means that the simulator satisfies, partially satisfies, or does not satisfy the property, respectively
  8. *SERGIO requires a user-specified gene regulatory network, and it does not capture/estimate gene correlations from a real dataset
  9. **SPsimSeq can vary cell number but not sequencing depth