GSR: Simulator - SimRare

Basic Package Attributes
AttributeValue
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 7 years, 10 months ago
Homepagehttp://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
Documentation
Application
Support

Last evaluated12-05-2018 (682 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers, Haploid DNA Sequence,
VariationsBiallelic Marker, Single Nucleotide Variation, Missing Genotypes, Genotype or Sequencing Error,
Simulation MethodExact Coalescent, Forward-time,
Input
Data TypeAllele Frequencies, Empirical,
File formatOther (Linkage ped file),
Output
Data TypeGenotype or Sequence, Phenotypic Trait, Demographic,
Sequencing ReadsOther (Power/p-values),
File FormatPED,
Sample TypeRandom or Independent, Case-control,
Phenotype
Trait TypeBinary or Qualitative, Quantitative,
DeterminantsSingle Genetic Marker, Multiple Genetic Markers,
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, User Defined,
Gene FlowStepping Stone Models, Island Models,
Spatiality
Life CycleDiscrete Generation Model,
Mating SystemRandom Mating, Polygamous,
FecundityRandomly Distributed, Individually Determined,
Natural Selection
DeterminantSingle-locus, Multi-locus, Fitness of Offspring, Phenotypic Trait,
ModelsMulti-locus models, Random Fitness Effects, Frequency-Dependent,
RecombinationUniform, Varying Recombination Rates,
Mutation ModelsTwo-allele Mutation Model, Infinite-allele Model, Infinite-sites Model,
Events Allowed
Other
InterfaceGraphical User Interface,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageC or C++, R, Python,
LicenseGNU Public License,
GSR CertificationDocumentation, Application,

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]


Propose changes to this simulator