Familia
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>.
- BIGapp: A user‐friendly genomic tool kit identified quantitative trait loci for creeping rootedness in alfalfa ( Medicago sativa L.)
- Estimation of genome-wide and locus-specific breed composition in pigs1
- Fast and Efficient Estimation of Individual Ancestry Coefficients
- LEA: An R package for landscape and ecological association studies
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