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GSR: Simulator - SPsimSeq
| Attribute | Value |
|---|---|
| Title | SPsimSeq |
| Short Description | SPsimSeq simulates datasets from estimated marginal distributions with Gaussian-copulas. |
| Long Description | SPsimSeq uses an exponential family for density estimation to construct distributions of gene expression levels from RNA sequencing data, thereby simulating a new dataset from marginal distributions with Gaussian-copulas in order to retain the dependence between genes. It also allows for the simulation of multiple groups and batches with any required sample size and library size. |
| Version | v2.0.0 |
| Project Started | 2019 |
| Last Release | 5 years, 11 months ago |
| Homepage | https://github.com/CenterForStatistics-UGent/SPsimSeq |
| Citations | Assefa AT, Vandesompele J, Thas O, SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data., Bioinformatics, May 1, 2020 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | Sept. 30, 2022 (1079 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, Gene Expression, Single-Cell Sequencing, Bulk Sequencing, |
| Variations | |
| Simulation Method | |
| 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 | Command-line, |
| Development | |
| Tested Platforms | |
| Language | R, |
| License | BSD, |
| 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 SPsimSeq.
2023
Crowell HL, Morillo Leonardo SX, Soneson C, Robinson MD, The shaky foundations of simulating single-cell RNA sequencing data., Genome Biol, March 29, 2023 [Abstract]
2020
Takele Assefa A, Vandesompele J, Thas O, On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments., BMC Genomics, April 19, 2020 [Abstract]