HaploBreedR

Superior haplotype discovery and haplotype-guided genomic selection for crop breeding.

HaploBreedR is an end-to-end quantitative genomics and molecular breeding suite. It identifies superior functional haplotypes from nonsynonymous CDS and UTR variants under false discovery rate control, fits two-kernel spectral REML genomic prediction models with the pipeline's superior haplotypes as a feature kernel, performs haplotype-guided cross-usefulness prediction and linkage-aware pyramiding optimization, and selects diverse parent sets with a relatedness ceiling.

📊 One-page infographic — the pipeline at a glance.

Example per-gene figure produced by haplobreed_analysis(plot_style = "gene_list")

*A four-panel summary for a single superior gene: gene model, haplotype network, haplotype table, and trait distribution. Produced automatically by `haplobreed_analysis(plot_style = "gene_list")`.* ---

Installation

# install.packages("devtools")
devtools::install_github("aksruchi/HaploBreedR")