Package: Familia
Title: 'shiny' Application for Population Structure and Ancestry
        Assessments
Version: 2.0.0
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. 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
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.4.0)
biocViews:
Imports: BIGpopA (>= 2.0.0), 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: LEA, spelling, testthat
Language: en-US
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libssl-dev
        zlib1g-dev
Repository: https://breeding-insight.r-universe.dev
Date/Publication: 2026-08-24 13:30:47 UTC
RemoteUrl: https://github.com/breeding-insight/familia
RemoteRef: HEAD
RemoteSha: 03a5beded1e2f96f118cac87bc5ad94737d5ef88
NeedsCompilation: no
Packaged: 2026-10-13 00:12:09 UTC; root
Author: Josue Chinchilla-Vargas [aut, cre],
  Alexander M. Sandercock [aut],
  Breeding Insight Team [aut]
Maintainer: Josue Chinchilla-Vargas <josue.chinchilla@ufl.edu>