Package: treekoR
Type: Package
Title: Cytometry Cluster Hierarchy and Cellular-to-phenotype
        Associations
Version: 1.21.0
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
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev perl zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:55:45 UTC
RemoteUrl: https://github.com/bioc/treekoR
RemoteRef: HEAD
RemoteSha: e1ad33cc0dafa3642199c9c99353bd912b2736b7
NeedsCompilation: no
Packaged: 2026-07-08 05:37:35 UTC; root
Author: Adam Chan [aut, cre],
  Ellis Patrick [ctb]
Maintainer: Adam Chan <adam.s.chan@sydney.edu.au>