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GSR: Simulator - SEQPower
| Attribute | Value |
|---|---|
| Title | SEQPower |
| Short Description | Statistical power analysis for sequence-based association studies |
| Long Description | SEQPower is a software to simulate rare variants data associated with complex traits and to perform power and sample size estimation for sequence based association studies. It features on analytic sample size estimates, power comparison of rare variant association methods as well as validation and evaluation of novel association tests under various study designs. |
| Version | 1.0.rc1 |
| Project Started | 2013 |
| Last Release | 10 years, 3 months ago |
| Homepage | http://bioinformatics.org/spower/ |
| Citations | Wang GT, Li B, Lyn Santos-Cortez RP, Peng B, Leal SM, Power analysis and sample size estimation for sequence-based association studies., Bioinformatics, 04-28-2014 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 02-08-2018 (2256 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence, |
| Variations | Biallelic Marker, Missing Genotypes, Genotype or Sequencing Error, |
| Simulation Method | Forward-time, Resample Existing Data, |
| Input | |
| Data Type | Allele Frequencies, Empirical, Saved simulation, |
| File format | Program Specific, |
| Output | |
| Data Type | Genotype or Sequence, Phenotypic Trait, |
| Sequencing Reads | |
| File Format | Program Specific, |
| Sample Type | Random or Independent, Case-control, |
| Phenotype | |
| Trait Type | Binary or Qualitative, Quantitative, |
| Determinants | Multiple Genetic Markers, |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Bottleneck, User Defined, |
| Gene Flow | Island Models, |
| Spatiality | |
| Life Cycle | Discrete Generation Model, |
| Mating System | Random Mating, |
| Fecundity | Constant Number, |
| Natural Selection | |
| Determinant | Multi-locus, |
| Models | Multi-locus models, Random Fitness Effects, |
| Recombination | Uniform, |
| Mutation Models | Infinite-sites Model, Others, |
| Events Allowed | Population Merge and Split, |
| Other | |
| Interface | Command-line, Script-based, |
| Development | |
| Tested Platforms | Mac OS X, Linux and Unix, |
| Language | C or C++, R, Python, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 5
The following 5 publications are selected examples of applications that used SEQPower.
2018
Patricia B. Munroe, Shea Addison, Dominic J. Abrams, Neil J. Sebire, James Cartwright, Ian Donaldson, Marta M. Cohen, Charles Mein, Andrew Tinker, Stephen C. Harmer, Qadeer Aziz, Anna Terry, Monika Struebig, Helen R. Warren, Bhumita Vadgama, Darren J. Fowler, Donald Peebles, Andrew M. Taylor, Peter J. Lally, Sudhin Thayyil, Postmortem Genetic Testing for Cardiac Ion Channelopathies in Stillbirths , Circ Genom Precis Med., 01-11-2018
Phang KC, Akhter A, Tizen NMS, Rahman FA, Zahratul Azma R, Elyamany G, Shabani-Rad MT, Masir N, Mansoor A, Comparison of protein-based cell-of-origin classification to the Lymph2Cx RNA assay in a cohort of diffuse large B-cell lymphomas in Malaysia., J Clin Pathol, 03-01-2018 [Abstract]
2017
Li CI, Samuels DC, Zhao YY, Shyr Y, Guo Y, Power and sample size calculations for high-throughput sequencing-based experiments., Brief Bioinform, 06-09-2017 [Abstract]
Derkach A, Zhang H, Chatterjee N, Power Analysis for Genetic Association Test (PAGEANT) provides insights to challenges for rare variant association studies., Bioinformatics, 11-28-2017 [Abstract]
2016
Wu B, Pankow JS, On Sample Size and Power Calculation for Variant Set-Based Association Tests., Ann Hum Genet, 03-01-2016 [Abstract]