[breeding-insight] BIGr 0.7.2

sandercock.alex@gmail.com (Alexander M. Sandercock) — Mon, 18 May 2026 12:03:32 GMT

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) .

[alex-sandercock] castgen 1.0.2

ams866@cornell.edu (Alexander M. Sandercock) — Wed, 02 Apr 2025 20:01:46 GMT

Estimate sample sizes needed to capture target levels of genetic diversity from a population (multivariate allele frequencies) for applications like germplasm conservation and breeding efforts. Compares bootstrap samples to a full population using linear regression, employing the R-squared value to represent the proportion of diversity captured. Iteratively increases sample size until a user-defined target R-squared is met. Offers a parallelized R implementation of a previously developed 'python' method. All ploidy levels are supported. For more details, see Sandercock et al. (2024) .

alex-sandercock.r-universe.dev

[breeding-insight] BIGr 0.7.2

[alex-sandercock] castgen 1.0.2