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GSR: Simulator - metaSPARSim
| Attribute | Value |
|---|---|
| Title | metaSPARSim |
| Short Description | metaSPARSim is a sparse count matrix simulator intended for usage in the development of pipelines for 16S rRNA metagenomic data processing. |
| Long Description | metaSPARSim is a sparse count matrix simulator intended for usage in development of pipelines 16S rRNA metagenomic data processing. metaSPARSim implements a new generative process that models the sequencing process with a Multivariate Hypergeometric in order to realistically reproduce these data considering their characteristic aspects, such as compositionality and sparsity. It provides ready-to-use count matrices and comes with the possibility to reproduce different pre-coded scenarios or to tune internal parameters in order to create a tailored count matrix that better fits some prior information or specific characteristic an expert user may want to consider. |
| Version | v.1.1.2 |
| Project Started | 2019 |
| Last Release | 5 years, 6 months ago |
| Homepage | https://gitlab.com/sysbiobig/metasparsim |
| Citations | Patuzzi I, Baruzzo G, Losasso C, Ricci A, Di Camillo B, metaSPARSim: a 16S rRNA gene sequencing count data simulator., BMC Bioinformatics, Nov. 22, 2019 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | March 8, 2022 (1286 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 | Gene Expression, |
| 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: 2
The following 2 publications are selected examples of applications that used metaSPARSim.
2022
Cappellato M, Baruzzo G, Di Camillo B, Investigating differential abundance methods in microbiome data: A benchmark study., PLoS Comput Biol, Sept. 8, 2022 [Abstract]
Viljanen M, Boshuizen H, llperm: a permutation of regressor residuals test for microbiome data., BMC Bioinformatics, Dec. 12, 2022 [Abstract]