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. 2021 Jun 9;22:177. doi: 10.1186/s13059-021-02394-z

Table 1.

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

Property 1 protocol adaptive 2 gene preserved 3 gene cor. captured 4 cell num. seq. dep. flexible 5 transparent 6 comp. and sample efficient
Simulator
dyngen [77] graphic file with name 13059_2021_2394_Figa_HTML.gif ✗ ✗ graphic file with name 13059_2021_2394_Figb_HTML.gif ✓ ✓
Lun2 [78] graphic file with name 13059_2021_2394_Figc_HTML.gif ✓ ✗ ✓ ✓ ✓
powsimR [75] ✓ ✓ ✗ ✓ ✓ ✓
PROSST [68] graphic file with name 13059_2021_2394_Figd_HTML.gif ✓ ✗ graphic file with name 13059_2021_2394_Fige_HTML.gif ✓ ✓
scDD [74] ✓ ✗ ✗ graphic file with name 13059_2021_2394_Figf_HTML.gif ✓ ✓
scDesign[35] ✓ graphic file with name 13059_2021_2394_Figg_HTML.gif ✗ ✓ ✓ ✓
scGAN [72] ✓ ✓ graphic file with name 13059_2021_2394_Figh_HTML.gif graphic file with name 13059_2021_2394_Figi_HTML.gif ✗ ✗
splat simple[69] ✓ ✗ ✗ ✗ ✓ ✓
splat [69] ✓ ✗ ✗ ✗ ✓ ✓
kersplat [69] ✓ ✗ graphic file with name 13059_2021_2394_Figj_HTML.gif ✗ ✓ ✓
SPARSim [71] ✓ ✓ graphic file with name 13059_2021_2394_Figk_HTML.gif ✗ ✓ ✓
SPsimSeq [79] ✓ ✓ ✓ Inline graphic** ✓ ✓
SymSim[70] ✓ ✗ ✗ ✗ ✓ ✓
ZINB-WaVe[39] ✓ graphic file with name 13059_2021_2394_Figm_HTML.gif graphic file with name 13059_2021_2394_Fign_HTML.gif ✗ ✓ ✓
SERGIO [76] ✓ graphic file with name 13059_2021_2394_Figo_HTML.gif ✗* ✓ ✓ ✓
scDesign2 ✓ ✓ ✓ ✓ ✓ ✓

Property 1: protocol adaptiveness

Property 2: gene preservation

Property 3: gene correlation capture

Property 4: flexible cell number and sequencing depth choices

Property 5: transparency

Property 6: computational and sample efficiency

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

*SERGIO requires a user-specified gene regulatory network, and it does not capture/estimate gene correlations from a real dataset

**SPsimSeq can vary cell number but not sequencing depth