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GSR: Simulator - SymSim
| Attribute | Value |
|---|---|
| Title | SymSim |
| Short Description | SymSim simulates single cell RNA sequencing data thereby allowing users to tune the variation of gene-expression on different levels. |
| Long Description | SymSim models the processes that give rise to data observed in single cell RNA-Seq experiments. The components of the SymSim pipeline pertain to three sources of variation in single cell RNA-Seq data: noise intrinsic to the process of transcription, extrinsic variation indicative of different cell states, and technical variation due to low sensitivity and measurement noise and bias. |
| Version | 0.0.0.9000 |
| Project Started | 2020 |
| Last Release | 5 years, 2 months ago |
| Homepage | https://github.com/YosefLab/SymSim |
| Citations | Zhang X, Xu C, Yosef N, Simulating multiple faceted variability in single cell RNA sequencing., Nat Commun, June 13, 2019 [ 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 | R, |
| License | Other, |
| 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 SymSim.
2023
Boyeau P, Regier J, Gayoso A, Jordan MI, Lopez R, Yosef N, An empirical Bayes method for differential expression analysis of single cells with deep generative models., Proc Natl Acad Sci U S A, May 23, 2023 [Abstract]
2022
Buen Abad Najar CF, Burra P, Yosef N, Lareau LF, Identifying cell state-associated alternative splicing events and their coregulation., Genome Res, July 20, 2022 [Abstract]