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GSR: Simulator - HapSim
| Attribute | Value |
|---|---|
| Title | HapSim |
| Short Description | A simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients |
| Long Description | Package for haplotype data simulation. Haplotypes are generated such that their allele frequencies and linkage disequilibrium coefficients match those estimated from an input data set |
| Version | 0.2 |
| Project Started | 2005 |
| Last Release | 18 years, 4 months ago |
| Homepage | http://cran.r-project.org/web/packages/hapsim/index.html |
| Citations | Montana G, HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients., Bioinformatics, 12-01-2005 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | 01-24-2019 (1906 days ago) |
| 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 | Haploid DNA Sequence (Haplotypes), |
| Variations | Biallelic Marker, |
| Simulation Method | Other, |
| Input | |
| Data Type | Allele Frequencies, Other (Ld information), |
| File format | |
| Output | |
| Data Type | Genotype or Sequence (Haplotypes), |
| Sequencing Reads | |
| File Format | |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| 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 (R), |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, Solaris, |
| Language | R, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used HapSim.
2022
Li X, Jiang L, Xue C, Li MJ, Li M, A conditional gene-based association framework integrating isoform-level eQTL data reveals new susceptibility genes for schizophrenia., Elife, 04-12-2022 [Abstract]
Jiang L, Miao L, Yi G, Li X, Xue C, Li MJ, Huang H, Li M, Powerful and robust inference of complex phenotypes' causal genes with dependent expression quantitative loci by a median-based Mendelian randomization., Am J Hum Genet, 05-05-2022 [Abstract]