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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
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Genome Biology

ISSN: 1474-760X

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