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GSR: Simulator - dyngen
| Attribute | Value |
|---|---|
| Title | dyngen |
| Short Description | Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells |
| Long Description | We present dyngen, a multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. dyngen is more flexible than current single-cell simulation engines, and allows better method development and benchmarking, thereby stimulating development and testing of computational methods. We demonstrate its potential for spearheading computational methods on three applications: aligning cell developmental trajectories, cell-specific regulatory network inference and estimation of RNA velocity. |
| Keywords | Computational models, Gene regulatory networks, single-cell simulation |
| Version | 1.0.2 |
| Project Started | 2016 |
| Last Release | 4 years, 1 month ago |
| Homepage | https://github.com/dynverse/dyngen |
| Citations | Cannoodt R, Saelens W, Deconinck L, Saeys Y, Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells., Nat Commun, June 24, 2021 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | Sept. 30, 2022 (1056 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | RNA, Single-Cell Sequencing, |
| Variations | |
| Simulation Method | Other, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Gene Expression, |
| Sequencing Reads | |
| File Format | |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | |
| Development | |
| Tested Platforms | |
| Language | R, |
| License | MIT, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 3
The following 3 publications are selected examples of applications that used dyngen.
2022
Lange M, Bergen V, Klein M, Setty M, Reuter B, Bakhti M, Lickert H, Ansari M, Schniering J, Schiller HB, et al., CellRank for directed single-cell fate mapping., Nat Methods, Feb. 1, 2022 [Abstract]
Deshpande A, Chu LF, Stewart R, Gitter A, Network inference with Granger causality ensembles on single-cell transcriptomics., Cell Rep, Feb. 8, 2022 [Abstract]
Gorin G, Fang M, Chari T, Pachter L, RNA velocity unraveled., PLoS Comput Biol, Sept. 12, 2022 [Abstract]