blupADC

blupADC is an useful and powerful tool for handling genomic data and pedigree data in animal and plant breeding(traditional blup and genomic selection). In the design of this package, most of data analysis problems in breeding have been considered, and the speed of calculation is also the key point. In terms of the speed, the core functions of this package are coded by c++ (Rcpp and RcppArmadillo ) , and it also supports parallel calculation (by applying openMP programming) and big data calculation(by importing bigmemory package).

blupADC provides many useful functions for the whole steps for animal and plant breeding, including pedigree analysis(trace pedigree, rename pedigree, and correct pedigree errors), genotype data format conversion(supports Hapmap, Plink, Blupf90, Numeric, VCF and Haplotype format), genotype data quality control and imputation, construction of kinship matrix(pedigree, genomic and single-step),and genetic evaluation( by interfacing with two famous breeding softwares, DMU and BLUPF90 in an easy way).

Finally, we kindly provides an easier way of applying blupADC, which is a free website(shinyapp). Several functions are still under development. But the pitfall of this website is that it can’t handle big data.