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GSR: Simulator - scDesign
| Attribute | Value |
|---|---|
| Title | scDesign |
| Short Description | scDesign assess scRNA-seq experimental design in the context of differential gene expression analysis. |
| Long Description | scDesign quantitatively assesses scRNA-seq experimental design. The software also assists in computational method development by generating high-quality synthetic scRNA-seq datasets under customized experimental settings. scDesign is reproducible across biological replicates and independent studies. |
| Version | 1.0.0 |
| Project Started | 2018 |
| Last Release | 4 years, 8 months ago |
| Homepage | https://github.com/Vivianstats/scDesign |
| Citations | Li WV, Li JJ, A statistical simulator scDesign for rational scRNA-seq experimental design., Bioinformatics, July 15, 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 | Other, |
| License | |
| 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 scDesign.
2023
Fan S, Dang D, Ye Y, Zhang SW, Gao L, Zhang S, scHi-CSim: a flexible simulator that generates high-fidelity single-cell Hi-C data for benchmarking., J Mol Cell Biol, June 1, 2023 [Abstract]
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]