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ShinyGPAS: interactive genomic prediction accuracy simulator based on deterministic formulas.

Gota Morota1

  • 1Department of Animal Science, University of Nebraska-Lincoln, PO Box 830908, Lincoln, NE, 68583-0908, USA. morota@unl.edu.

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Summary

This study introduces ShinyGPAS, an interactive tool for simulating genomic prediction accuracy. It helps researchers understand factors influencing accuracy and predict outcomes before extensive computations.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Quantitative Genetics

Background:

  • Deterministic formulas offer insights into genomic prediction accuracy before computationally intensive validation.
  • Interactive visualization of these formulas can enhance understanding of genetic factor influence.

Purpose of the Study:

  • To develop an interactive tool for simulating genomic prediction accuracy using deterministic formulas.
  • To provide a user-friendly platform for exploring factors affecting prediction accuracy.

Main Methods:

  • Implementation of genomic prediction accuracy simulation software in R.
  • Encapsulation of the software as a web-based Shiny application named ShinyGPAS.
  • Dynamic scatter plot generation for visualizing prediction accuracy against genetic factors.

Main Results:

  • ShinyGPAS simulates various deterministic formulas for genomic prediction accuracy.
  • The application displays dynamic scatter plots of prediction accuracy versus influential genetic factors.
  • Interactive exploration is enabled through a web browser interface.

Conclusions:

  • ShinyGPAS is an interactive, shiny-based simulator for genomic prediction accuracy.
  • It facilitates exploration of factors influencing prediction accuracy in genome-enabled prediction.
  • The tool supports pre-genotyping accuracy simulation and educational purposes, offered as open-source software.