Package: Familia
Title: 'shiny' Application for Population Structure and Ancestry
        Assessments
Version: 2.2.0
Authors@R: 
    c(
              person("Josue", "Chinchilla-Vargas",
                    role = c("aut","cre"),
                    email = "josue.chinchilla@ufl.edu"),
              person(c("Alexander", "M."), "Sandercock",
                    role = "aut"),
              person("Breeding Insight Team",
                    role = "aut"))
Description: 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. Genotypes can be uploaded as dosage
        tables, VCF files, or 'PLINK' .ped files. 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>.
License: Apache License (>= 2)
URL: https://github.com/Breeding-Insight/Familia
BugReports: https://github.com/Breeding-Insight/Familia/issues
Encoding: UTF-8
Depends: R (>= 4.4.0)
biocViews:
Imports: BIGpopA (>= 2.2.0), 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: knitr, LEA, rmarkdown, spelling, svglite, testthat
VignetteBuilder: knitr
Language: en-US
Config/roxygen2/version: 8.1.1
NeedsCompilation: no
Packaged: 2026-10-28 19:16:27 UTC; root
Author: Josue Chinchilla-Vargas [aut, cre], Alexander M. Sandercock
        [aut], Breeding Insight Team [aut]
Maintainer: Josue Chinchilla-Vargas <josue.chinchilla@ufl.edu>
Repository: https://cran.r-universe.dev
Date/Publication: 2026-10-28 10:30:33 UTC
RemoteUrl: https://github.com/cran/Familia
RemoteRef: HEAD
RemoteSha: 9e3fc3f11be1a7e2be7fda412158eb7c5392e4ed