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 | 11 years, 4 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, 10-15-2012 [ Abstract, cited in PMC ] |
GSR Certification | Accessibility |
Last evaluated | 12-05-2018 (1956 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, 05-08-2018 [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, 04-01-2017 [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, 09-01-2016 [Abstract]
2014
Wen SH, Yeh JI, Cohen's h for detection of disease association with rare genetic variants., BMC Genomics, 10-08-2014 [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, 05-07-2013 [Abstract]