synbreed: a framework for the analysis of genomic prediction data using R

Bioinformatics. 2012 Aug 1;28(15):2086-7. doi: 10.1093/bioinformatics/bts335. Epub 2012 Jun 10.


Summary: We present a novel R package named synbreed to derive genome-based predictions from high-throughput genotyping and large-scale phenotyping data. The package contains a comprehensive collection of functions required to fit and cross-validate genomic prediction models. All functions are embedded within the framework of a single, unified data object. Thereby a versatile genomic prediction analysis pipeline covering data processing, visualization and analysis is established within one software package. The implementation is flexible with respect to a wide range of data formats and models. The package fills an existing gap in the availability of user-friendly software for next-generation genetics research and education.

Availability: synbreed is open-source and available through CRAN The latest development version is available from R-Forge. The package synbreed is released with a vignette, a manual and three large-scale example datasets (from package synbreedData).


Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Computer Simulation
  • Electronic Data Processing
  • Genomics / methods*
  • Genotyping Techniques
  • Linear Models
  • Software*