Familia: 'shiny' Application for Population Structure and Ancestry
Assessments
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>). 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>.
| Version: |
1.0.3 |
| Depends: |
R (≥ 4.4.0) |
| Imports: |
BIGpopA, bs4Dash, config, curl, data.table, dplyr, DT, ggplot2, golem, httr, openxlsx, RColorBrewer, scales, shiny, shinydisconnect, shinyjs, shinyWidgets, tibble, tidyr, vcfR (≥
1.15.0), withr, zip |
| Suggests: |
LEA, spelling, testthat |
| Published: |
2026-07-29 |
| DOI: |
10.32614/CRAN.package.Familia (may not be active yet) |
| Author: |
Josue Chinchilla-Vargas [aut, cre],
Alexander M. Sandercock [aut],
Breeding Insight Team [aut] |
| Maintainer: |
Josue Chinchilla-Vargas <josue.chinchilla at ufl.edu> |
| License: |
Apache License (≥ 2) |
| NeedsCompilation: |
no |
| Language: |
en-US |
| Materials: |
README, NEWS |
| CRAN checks: |
Familia results |
Documentation:
Downloads:
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