An official website of the United States government
GSR: Simulator - SPARSIM
| Attribute | Value |
|---|---|
| Title | SPARSIM |
| Short Description | SPARSim is an R tool used for simulating single cell RNA-seq (scRNA-seq) count tables. |
| Long Description | SPARSim is an scRNA count data simulator based on a Gamma-Multivariate Hypergeometric model. The package generates count data that resembles real data in terms of count intensity, variability and sparsity. The simulator is capable of simulating count matrices that resemble the distribution of different expression intensities observed in real count data. The package can also simulate single cell RNA-seq count tables. |
| Version | 0.9.5 |
| Project Started | 2020 |
| Last Release | 4 years, 11 months ago |
| Homepage | https://gitlab.com/sysbiobig/sparsim |
| Citations | Baruzzo G, Patuzzi I, Di Camillo B, SPARSim single cell: a count data simulator for scRNA-seq data., Bioinformatics, March 1, 2020 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | June 23, 2022 (1030 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 | C or C++, R, |
| License | GNU Public License, |
| 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 SPARSIM.
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]
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]
Ellis D, Roy A, Datta S, Clustering single-cell multimodal omics data with jrSiCKLSNMF., Front Genet, June 9, 2023 [Abstract]