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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