Package: treekoR
Type: Package
Title: Cytometry Cluster Hierarchy and Proportions to Parent
Version: 1.0.0
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; measure the proportions to parent 
    (proportions of cells each node in the tree relative to the number of cells belonging its
    parent node), in addition to the proportions to all (proportion of cells 
    in each node relative to all cells); 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, magrittr, data.table, ggiraph,
        ggplot2, hopach, ape, ggtree, patchwork, SingleCellExperiment
License: GPL-3
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.1.1
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_13
git_last_commit: 2b645b7
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19
NeedsCompilation: no
Packaged: 2021-05-20 02:46:17 UTC; biocbuild
Author: Adam Chan [aut, cre],
  Ellis Patrick [ctb]
Maintainer: Adam Chan <adam.s.chan@sydney.edu.au>
Built: R 4.1.0; ; 2021-05-20 10:26:26 UTC; windows
