treekoR
This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see treekoR.
Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations
Bioconductor version: 3.15
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.
Author: Adam Chan [aut, cre], Ellis Patrick [ctb]
Maintainer: Adam Chan <adam.s.chan at sydney.edu.au>
citation("treekoR")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("treekoR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("treekoR")| vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DifferentialExpression, FlowCytometry, ImmunoOncology, MassSpectrometry, SingleCell, Software, StatisticalMethod, Visualization |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.1) |
| Imports | stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2, hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt, edgeR, lme4, multcomp |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | treekoR_1.4.0.tar.gz |
| Windows Binary | |
| macOS Binary (x86_64) | treekoR_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/treekoR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/treekoR |
| Bioc Package Browser | https://code.bioconductor.org/browse/treekoR/ |
| Package Short Url | https://bioconductor.org/packages/treekoR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.15 | Source Archive |