https://josuechinchilla.r-universe.devRecent package updates in josuechinchillaR-universehttps://github.com/josuechinchilla.pnghttps://josuechinchilla.r-universe.devMon, 12 Oct 2026 20:35:48 GMTjosue.chinchilla@ufl.edu (Josue Chinchilla-Vargas)Tools for pedigree quality control and genomic breed/line composition estimation in diploid and polyploid breeding populations. 'BIGpopA' provides functions to check and correct common pedigree errors, assign parentage from SNP genotype data using Mendelian error rates, validate parent-offspring trios, and estimate genome-wide breed or line composition using quadratic programming. Pedigree validation and parentage assignment support any ploidy, using a polysomic Mendelian test for even ploidy and a homozygosity-based check for odd ploidy. Genotypes can be supplied as dosage tables, VCF files, or 'PLINK' .ped files. For more details about the included 'breedTools' functions, see Funkhouser et al. (2017) <doi:10.2527/tas2016.0003>.https://github.com/r-universe/breeding-insight/actions/runs/38321876964Mon, 12 Oct 2026 20:35:48 GMTBIGpopA2.2.0successhttps://breeding-insight.r-universe.devhttps://github.com/breeding-insight/bigpopaBIGpopA.RmdBIGpopA.htmlBIGpopA Tutorial2026-07-16 18:56:322026-10-12 20:30:44josue.chinchilla@ufl.edu (Josue Chinchilla-Vargas)Provides a 'shiny' web application developed by the Breeding Insight team to support pedigree validation and ancestry assessment of plant and animal populations. The app integrates Mendelian error analysis, parentage assignment and genetic composition/ancestry methods to help researchers evaluate genomic relationships through an accessible, web-based interface without requiring command-line tools. Pedigree validation, Mendelian error analysis and parentage assignment build on the 'BIGpopA' package (<https://CRAN.R-project.org/package=BIGpopA>) and support diploid and polyploid data. Ancestry estimation uses the sparse non-negative matrix factorization method of Frichot et al. (2014) <doi:10.1534/genetics.113.160572> as implemented in the 'LEA' package by Frichot and Francois (2015) <doi:10.1111/2041-210X.12382>. Line and breed composition are estimated using the breed composition regression method of Funkhouser et al. (2017) <doi:10.2527/tas2016.0003>, extended to polyploid species by Sandercock et al. (2025) <doi:10.1002/tpg2.70067>.https://github.com/r-universe/breeding-insight/actions/runs/38325770958Mon, 24 Aug 2026 13:30:47 GMTFamilia2.0.0successhttps://breeding-insight.r-universe.devhttps://github.com/breeding-insight/familia