Simmethods collects and documents 49 popular and common simulation methods for single-cell and spatial transcriptome data. To satisfy user’s requirements in different scenarios, we bundled the simulators comprehensively and users can simulate many kinds of single-cell RNA-seq data (different number of groups, batches, differential expressed genes and even data with differentiation trajectory) using certain methods. If you want to learn how to use a certain simulation method, please check the following chart and commit an issue or send an Email to us when you have any question.
| ID | Method | Language | URL | DOI | Journal |
|---|---|---|---|---|---|
| 1 | BASiCS |  |
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PLoS Computational Biology |
| 2 | BEARscc | |
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Nature Communications |
| 3 | CancerInSilico | |
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PLoS Computational Biology |
| 4 | dropsim | |
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| 5 | dyngen | |
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Nature Communications |
| 6 | dyntoy | |
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| 7 | ESCO | |
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Bioinformatics |
| 8 | ESCO-traj | |
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Bioinformatics |
| 9 | ESCO-tree | |
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Bioinformatics |
| 10 | hierarchicell | |
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BMC Genomics |
| 11 | Kersplat | |
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Genome Biology |
| 12 | Lun | |
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Genome Biology |
| 13 | Lun2 | |
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Genome Biology |
| 14 | MFA | |
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Wellcome Open Research |
| 15 | muscat | |
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Nature Communications |
| 16 | phenopath | |
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bioRxiv |
| 17 | POWSC | |
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Bioinformatics |
| 18 | powsimR | |
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Bioinformatics |
| 19 | PROSSTT |  |
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Bioinformatics |
| 20 | scDD | |
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Genome Biology |
| 21 | scDesign | |
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Bioinformatics |
| 22 | scDesign2 | |
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Genome Biology |
| 23 | scDesign3 | |
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Nature Biotechnology |
| 24 | scDesign3-tree | |
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Nature Biotechnology |
| 25 | scGAN | |
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Nature Communications |
| 26 | scMultiSim | |
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bioRxiv |
| 27 | scMultiSim-tree | |
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bioRxiv |
| 28 | SCRIP-BGP-commonBCV | |
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Bioinformatics |
| 29 | SCRIP-BGP-trendedBCV | |
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Bioinformatics |
| 30 | SCRIP-BP | |
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Bioinformatics |
| 31 | SCRIP-GP-commonBCV | |
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Bioinformatics |
| 32 | SCRIP-GP-trendedBCV | |
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Bioinformatics |
| 33 | SCRIP-paths | |
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Bioinformatics |
| 34 | SimBPDD | |
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Annales Mathematicae et Informaticae |
| 35 | Simple | |
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Genome Biology |
| 36 | SparseDC | |
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Nucleic Acids Research |
| 37 | SPARSim | |
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Bioinformatics |
| 38 | Splat | |
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Genome Biology |
| 39 | Splat-paths | |
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Genome Biology |
| 40 | SplatPop | |
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Genome Biology |
| 41 | SplatPop-paths | |
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Genome Biology |
| 42 | SPsimSeq | |
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Bioinformatics |
| 43 | SRTsim | |
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Genome Bilogy |
| 44 | SymSim | |
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Nature Communications |
| 45 | TedSim | |
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Nucleic Acids Research |
| 46 | VeloSim | |
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bioRxiv |
| 47 | zinbwave | |
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Nature Communications |
| 48 | zinbwaveZinger | |
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Genome Biology |
| 49 | zingeR | |
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Genome Biology |
We are glad to add new simulation methods if some methods are innovative and creative that many users commonly used. If you have the requirements, please tell me by email (duohongrui@cqnu.edu.cn) or raise an issue for that.
Duo H, Li Y, Lan Y, et al. Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios. Genome Biology, 2024, 25(1): 145.