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GSR: Simulator - SimRare
| Attribute | Value |
|---|---|
| Title | SimRare |
| Short Description | Rare variant simulation and analysis tool |
| Long Description | A program to generate and analyze sequence-based data for rare variant association studies of quantitative and qualitative traits |
| Version | 1.0.0 |
| Project Started | 2012 |
| Last Release | 12 years, 10 months ago |
| Homepage | http://code.google.com/p/simrare/ |
| Citations | Li B, Wang G, Leal SM, SimRare: a program to generate and analyze sequence-based data for association studies of quantitative and qualitative traits., Bioinformatics, Oct. 15, 2012 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | Dec. 5, 2018 (2474 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, Haploid DNA Sequence, |
| Variations | Biallelic Marker, Single Nucleotide Variation, Missing Genotypes, Genotype or Sequencing Error, |
| Simulation Method | Exact Coalescent, Forward-time, |
| Input | |
| Data Type | Allele Frequencies, Empirical, |
| File format | Other (Linkage ped file), |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait, Demographic, |
| Sequencing Reads | Other (Power/p-values), |
| File Format | PED, |
| Sample Type | Random or Independent, Case-control, |
| Phenotype | |
| Trait Type | Binary or Qualitative, Quantitative, |
| Determinants | Single Genetic Marker, Multiple Genetic Markers, |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, User Defined, |
| Gene Flow | Stepping Stone Models, Island Models, |
| Spatiality | |
| Life Cycle | Discrete Generation Model, |
| Mating System | Random Mating, Polygamous, |
| Fecundity | Randomly Distributed, Individually Determined, |
| Natural Selection | |
| Determinant | Single-locus, Multi-locus, Fitness of Offspring, Phenotypic Trait, |
| Models | Multi-locus models, Random Fitness Effects, Frequency-Dependent, |
| Recombination | Uniform, Varying Recombination Rates, |
| Mutation Models | Two-allele Mutation Model, Infinite-allele Model, Infinite-sites Model, |
| Events Allowed | |
| Other | |
| Interface | Graphical User Interface, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, R, Python, |
| License | GNU Public License, |
| GSR Certification | Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 5
The following 5 publications are selected examples of applications that used SimRare.
2018
Lee S, Kim Y, Choi S, Hwang H, Park T, Pathway-based approach using hierarchical components of rare variants to analyze multiple phenotypes., BMC Bioinformatics, May 8, 2018 [Abstract]
2017
Lee S, Won S, Kim YJ, Kim Y, T2D-Genes Consortium., Kim BJ, Park T, Rare variant association test with multiple phenotypes., Genet Epidemiol, April 1, 2017 [Abstract]
2016
Lee J, Kim YJ, Lee J, T2D-Genes Consortium., Kim BJ, Lee S, Park T, Gene-set association tests for next-generation sequencing data., Bioinformatics, Sept. 1, 2016 [Abstract]
2014
Wen SH, Yeh JI, Cohen's h for detection of disease association with rare genetic variants., BMC Genomics, Oct. 8, 2014 [Abstract]
2013
Moore CB, Wallace JR, Frase AT, Pendergrass SA, Ritchie MD, BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge, BMC Medical Genomics, May 7, 2013 [Abstract]