Package: treekoR
Type: Package
Title: Cytometry Cluster Hierarchy and Cellular-to-phenotype
        Associations
Version: 1.20.0
Authors@R: c(person("Adam", "Chan", role = c("aut", "cre"),
                     email = "adam.s.chan@sydney.edu.au"),
             person("Ellis", "Patrick", role = "ctb"))
biocViews: Clustering, DifferentialExpression, FlowCytometry,
        ImmunoOncology, MassSpectrometry, SingleCell, Software,
        StatisticalMethod, Visualization
Description: treekoR is a novel framework that aims to utilise the hierarchical 
    nature of single cell cytometry data to find robust and interpretable associations 
    between cell subsets and patient clinical end points. These associations are aimed to 
    recapitulate the nested proportions prevalent in workflows inovlving manual gating, 
    which are often overlooked in workflows using automatic
    clustering to identify cell populations. We developed treekoR to:
    Derive a hierarchical tree structure of cell clusters; quantify a cell types as 
    a proportion relative to all cells in a sample (%total), and, as 
    the proportion relative to a parent population (%parent); perform significance 
    testing using the calculated proportions; and provide an 
    interactive html visualisation to help highlight key results.
Depends: R (>= 4.1)
Imports: stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2,
        hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt,
        edgeR, lme4, multcomp
License: GPL-3
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.2.3
Suggests: knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/treekoR
git_branch: RELEASE_3_23
git_last_commit: fdda490
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
NeedsCompilation: no
Packaged: 2026-04-29 01:15:55 UTC; biocbuild
Author: Adam Chan [aut, cre],
  Ellis Patrick [ctb]
Maintainer: Adam Chan <adam.s.chan@sydney.edu.au>
