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GSR: Simulator - SERGIO
| Attribute | Value |
|---|---|
| Title | SERGIO |
| Short Description | Sergio is a simulator for single-cell gene expression data that models the stochastic nature of the transcription and regulation of genes via transcription factors according to a user-provided gene regulatory network. |
| Long Description | Sergio is a simulator for single-cell gene expression data that models the stochastic nature of the transcription and regulation of genes via transcription factors according to a user-provided gene regulatory network. The package can simulate cell types in steady states or cells differentiating to multiple fates. The datasets generated by SERGIO are statistically comparable to experimental data generated by Illumina HiSeq200, Drop-Seq, Illumina 10x chromium and Smart-seq |
| Version | v1.1.0 |
| Project Started | 2020 |
| Last Release | 5 years ago |
| Homepage | https://github.com/PayamDiba/SERGIO |
| Citations | Dibaeinia P, Sinha S, SERGIO: A Single-Cell Expression Simulator Guided by Gene Regulatory Networks., Cell Syst, Sept. 23, 2020 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | June 23, 2022 (1155 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 | |
| Variations | |
| Simulation Method | |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | |
| 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 | Command-line, |
| Development | |
| Tested Platforms | |
| Language | Python, |
| License | MIT, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used SERGIO.
2023
Li L, Sun L, Chen G, Wong CW, Ching WK, Liu ZP, LogBTF: gene regulatory network inference using Boolean threshold network model from single-cell gene expression data., Bioinformatics, May 4, 2023 [Abstract]
Yang Y, Li G, Zhong Y, Xu Q, Chen BJ, Lin YT, Chapkin RS, Cai JJ, Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks., Nucleic Acids Res, July 21, 2023 [Abstract]