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GSR: Simulator - EpiReSIM
| Attribute | Value |
|---|---|
| Title | EpiReSIM |
| Short Description | A resampling method of epistatic model without marginal effects using under-determined system of equations |
| Long Description | EpiReSIM provides two strategies for solving eNME models. One is to calculate eNME models using prevalence constraints, and another is by joint constraints of prevalence and heritability. We transform the computation of the model into the problem of solving the under-determined system of equations. Introducing the complete orthogonal decomposition method and Newton’s method, EpiReSIM calculates the solution of the underdetermined system of equations to obtain the eNME model, especially the solution of the high-order model, which is the highlight of EpiReSIM. Second, based on the computed eNME model, EpiReSIM generates simulation data by a resampling method. Experimental results show that EpiReSIM has advantages in preserving the biological properties of minor allele frequencies and calculating high-order models, and it is a convenient and effective alternative method for curre |
| Keywords | GWAS, epistasis model, resampling, penetrance table, prevalence, heritability |
| Project Started | 2022 |
| Homepage | https://github.com/CDMB-lab/EpiReSIM |
| Citations | |
| GSR Certification | This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification. |
| 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 | Genotype at Genetic Markers, |
| Variations | Single Nucleotide Variation, |
| Simulation Method | Resample Existing Data, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | |
| File Format | |
| Sample Type | |
| Phenotype | |
| Trait Type | Binary or Qualitative, |
| 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 | Script-based, |
| Development | |
| Tested Platforms | |
| Language | Other, |
| License | MIT, |
| GSR Certification |
Number of Primary Citations: 0
Number of Non-Primary Citations: 1
The following 1 publications are selected examples of applications that used EpiReSIM.
2022
Shang J, Cai X, Zhang T, Sun Y, Zhang Y, Liu J, Guan B, EpiReSIM: A Resampling Method of Epistatic Model without Marginal Effects Using Under-Determined System of Equations., Genes (Basel), Dec. 4, 2022 [Abstract]