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


BACKGROUND
synbreed is open-source and available through CRAN http://cran.r-project.org/web/packages/synbreed. 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).


BACKGROUND
chris.schoen@wzw.tum.de


BACKGROUND
Supplementary data are available at Bioinformatics online.
Plant Breeding, Technische Universität München, Emil-Ramann-Straße 4, 85354 Freising, Germany.
Valentin
V
Wimmer
Theresa
T
Albrecht
Hans-Jürgen
HJ
Auinger
Chris-Carolin
CC
Schön
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D001330:Electronic Data Processing; D023281:Genomics / Q000379:methods*; D060005:Genotyping Techniques; D016014:Linear Models; D012984:Software