GSR: Simulator - SEQPower

Basic Package Attributes
AttributeValue
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 6 years, 9 months ago
Homepagehttp://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 CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluated02-08-2018 (982 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence,
VariationsBiallelic Marker, Missing Genotypes, Genotype or Sequencing Error,
Simulation MethodForward-time, Resample Existing Data,
Input
Data TypeAllele Frequencies, Empirical, Saved simulation,
File formatProgram Specific,
Output
Data TypeGenotype or Sequence, Phenotypic Trait,
Sequencing Reads
File FormatProgram Specific,
Sample TypeRandom or Independent, Case-control,
Phenotype
Trait TypeBinary or Qualitative, Quantitative,
DeterminantsMultiple Genetic Markers,
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Bottleneck, User Defined,
Gene FlowIsland Models,
Spatiality
Life CycleDiscrete Generation Model,
Mating SystemRandom Mating,
FecundityConstant Number,
Natural Selection
DeterminantMulti-locus,
ModelsMulti-locus models, Random Fitness Effects,
RecombinationUniform,
Mutation ModelsInfinite-sites Model, Others,
Events AllowedPopulation Merge and Split,
Other
InterfaceCommand-line, Script-based,
Development
Tested PlatformsMac OS X, Linux and Unix,
LanguageC or C++, R, Python,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Application, Support,

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]


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