Package: Pedixplorer
Version: 1.7.0
Date: 2025-08-26
Title: Pedigree Functions
Authors@R: c(
    person("Louis", "Le Nezet", email="louislenezet@gmail.com",
        role=c("aut","cre","ctb"), comment = c(ORCID = "0009-0000-0202-2703")),
	person("Jason", "Sinnwell", email="sinnwell.jason@mayo.edu", role="aut"),
	person("Terry", "Therneau", role="aut"),
	person("Daniel", "Schaid", role="ctb"),
	person("Elizabeth", "Atkinson", role="ctb"))
Depends: 
	R (>= 4.4.0)
Imports: 
    graphics,
    stats,
    methods,
    ggplot2,
    utils,
    grDevices,
    stringr,
    plyr,
    dplyr,
    tidyr,
    quadprog,
    Matrix,
    S4Vectors,
    shiny,
    readxl,
    DT,
    igraph,
    shinycssloaders,
    shinyhelper,
    shinyjs,
    shinyjqui,
    shinyWidgets,
    htmlwidgets,
    plotly,
    colourpicker,
    shinytoastr
Description: Routines to handle family data with a Pedigree object. The initial
    purpose was to create correlation structures that describe family
    relationships such as kinship and identity-by-descent, which can be used to
    model family data in mixed effects models, such as in the coxme function.
    Also includes a tool for Pedigree drawing which is focused on producing
    compact layouts without intervention. Recent additions include utilities to
    trim the Pedigree object with various criteria, and kinship for the X
    chromosome.
License: Artistic-2.0
Encoding: UTF-8
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
Suggests: 
    diffviewer,
    gridExtra,
    testthat (>= 3.0.0),
    vdiffr,
    rmarkdown,
    BiocStyle,
    knitr,
    withr,
    qpdf,
    shinytest2,
    devtools,
    R.devices,
    usethis,
    rlang,
    magick,
    cowplot
Config/testthat/edition: 3
biocViews: Software, DataRepresentation, Genetics, GraphAndNetwork, Visualization
BugReports: https://github.com/LouisLeNezet/Pedixplorer/issues
URL: https://louislenezet.github.io/Pedixplorer/
BiocType: Software
Collate: 
    'AllValidity.R'
    'AllClass.R'
    'kindepth.R'
    'kinship.R'
    'utils.R'
    'AllConstructor.R'
    'AllAccessors.R'
    'AllGeneric.R'
    'Pedixplorer-package.R'
    'alignped4.R'
    'alignped3.R'
    'alignped2.R'
    'alignped1.R'
    'auto_hint.R'
    'align.R'
    'app.R'
    'app_color_picker.R'
    'app_data_col_sel.R'
    'app_data_download.R'
    'app_data_import.R'
    'app_utils.R'
    'app_family_sel.R'
    'app_health_sel.R'
    'app_inf_sel.R'
    'app_ped_avaf_infos.R'
    'app_plot_resize.R'
    'app_plot_download.R'
    'app_plot_legend.R'
    'app_plot_ped.R'
    'app_plot_all.R'
    'app_server.R'
    'app_ui.R'
    'best_hint.R'
    'bit_size.R'
    'data.R'
    'descendants.R'
    'family_check.R'
    'find_unavailable.R'
    'find_avail_affected.R'
    'find_avail_noninform.R'
    'fix_parents.R'
    'generate_aff_inds.R'
    'generate_colors.R'
    'ibd_matrix.R'
    'is_informative.R'
    'make_famid.R'
    'min_dist_inf.R'
    'norm_data.R'
    'num_child.R'
    'ped_to_legdf.R'
    'ped_to_plotdf.R'
    'plot_fct.R'
    'plot_fromdf.R'
    'plot_pedigree.R'
    'shrink.R'
    'unrelated.R'
    'useful_inds.R'
LazyData: false
git_url: https://git.bioconductor.org/packages/Pedixplorer
git_branch: devel
git_last_commit: 8570263
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
