Welcome to synbreed project!

Collection of statistical and genetic methods developed for the synbreed project for synergistic plant and animal breeding.

• The R-package synbreed provides a framework for the analysis of genomic prediction data (Genomic Selection, GWAS, QTL-mapping) within an open source software.
  
• Features
• Data processing
• Combining raw data sources to a gpData object
• Conversion from and to class cross in package qtl
• Coding marker data into number of copies of the minor allele
• Preselection of markers according to MAF, % missing values and LD
• Imputation of missing genotypes by marginal allele distribution, family structure for fully homozygous inbred individuals or flanking markers using Beagle
• Data visualization and analysis
• Summary method for classes gpData, pedigree and relationshipMatrix
• Marker map representation for low and high density maps
• LD computation as r2 and LD decay visualization as as scatterplot or stacked histogram
• Pedigree tree and kinship visualization of relatedness between individuals
• Statistical models
• Estimation of pedigree based relationship (additive and dominance)
• Marker based relationship
• Cross-validation for BLUP, Ridge Regression and Bayesian methods
• The package comes with ABSOLUTELY NO WARRANTY; for details see http://www.gnu.org/copyleft/gpl.html (GPL).

To install the latest development version of package synbreed from R-Forge (if you are running a recent R version), use

install.packages("synbreed",repos="http://r-forge.r-project.org")

You can also manually download the source code from
https://r-forge.r-project.org/R/?group_id=710

A stable release is available from CRAN

• Publication in Bioinformatics
• Citation information:
  citation(package="synbreed")
  
• pdf version of the manual
• package vignette with detailed background information and examples:
  library(synbreed)
  vignette("IntroSyn")
  
• overview over the functions
• Poster presented at the 4th International Conference on Quantitative Genetics, June 2012, Edinburgh

• Course slides (2012 - 11 - 08)
• Code of the slides (2012 - 11 - 08)

• Valentin Wimmer , Chair of Plant Breeding, Technische Universität München
• Theresa Albrecht , Chair of Plant Breeding, Technische Universität München
• Hans-Juergen Auinger , Chair of Plant Breeding, Technische Universität München

The development of the package was financially supported by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr ''Synbreed Synergistic plant and animal breeding'' (FKZ 0315528A)