Breeding Insight Genomics Functions for Polyploid and Diploid Species

Functions developed within Breeding Insight to analyze diploid and polyploid breeding and genetic data. 'BIGr' provides the ability to filter variant call format (VCF) files, extract single nucleotide polymorphisms (SNPs) from diversity arrays technology missing allele discovery count (DArT MADC) files, and manipulate genotype data for both diploid and polyploid species. It also serves as the core dependency for the 'BIGapp' 'Shiny' app, which provides a user-friendly interface for performing routine genotype analysis tasks such as dosage calling, filtering, principal component analysis (PCA), genome-wide association studies (GWAS), and genomic prediction. For more details about the included 'breedTools' functions, see Funkhouser et al. (2017) , and the 'updog' output format, see Gerard et al. (2018) .

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BIGr

Core Genomic Analysis Functions for Breeding Insight

BIGr is an R package developed by Breeding Insight that provides a robust set of functions for analyzing genomic and pedigree data in diploid and polyploid breeding programs. It's designed to streamline the analysis of breeding and genetic data, empowering researchers and breeders to make informed decisions.

Installation

To install BIGr, you'll need to have BiocManager installed.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
    install.packages("remotes")

BiocManager::install("Breeding-Insight/BIGr", dependencies = TRUE)
library(BIGr)

Funding

BIGr development is supported by Breeding Insight, a USDA-funded initiative based at Cornell University.

Citation

If you use BIGr in your research, please cite as:

Sandercock, Alexander M., Cristiane H. Taniguti, Josue Chinchilla-Vargas, Dongyan Zhao, Shufen Chen, Meng Lin, Manoj Sapkota, and Breeding Insight Team. 2025. “Breeding Insight Genomics Functions for Polypoid and Diploid Species.” https://github.com/Breeding-Insight/BIGr.