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GSR: Simulator - EpiGEN
| Attribute | Value |
|---|---|
| Title | EpiGEN |
| Short Description | An epistasis simulation pipeline |
| Long Description | EpiGEN is an easy-to-use epistasis simulation pipeline written in Python. It supports epistasis models of arbitrary size, which can be specified either extensionally or via parametrized risk models. Moreover, the user can specify the minor allele frequencies (MAFs) of both noise and disease SNPs, and provide a biased target distribution for the generated phenotypes to simulate observation bias. |
| Keywords | epistasis |
| Project Started | 2020 |
| Homepage | https://github.com/daisybio/epigen |
| Citations | Blumenthal DB, Viola L, List M, Baumbach J, Tieri P, Kacprowski T, EpiGEN: an epistasis simulation pipeline., Bioinformatics, Dec. 8, 2020 [ Abstract, cited in PMC ] |
| 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 | Forward-time, Resample Existing Data, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | Other, |
| 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 | Command-line, |
| Development | |
| Tested Platforms | |
| Language | Python, |
| License | GNU Public License, |
| GSR Certification |
Number of Primary Citations: 1
Number of Non-Primary Citations: 1
The following 1 publications are selected examples of applications that used EpiGEN.
2022
Russ D, Williams JA, Cardoso VR, Bravo-Merodio L, Pendleton SC, Aziz F, Acharjee A, Gkoutos GV, Evaluating the detection ability of a range of epistasis detection methods on simulated data for pure and impure epistatic models., PLoS One, Feb. 18, 2022 [Abstract]