Package: cytometree 2.0.6

Boris P Hejblum

cytometree: Automated Cytometry Gating and Annotation

Given the hypothesis of a bi-modal distribution of cells for each marker, the algorithm constructs a binary tree, the nodes of which are subpopulations of cells. At each node, observed cells and markers are modeled by both a family of normal distributions and a family of bi-modal normal mixture distributions. Splitting is done according to a normalized difference of AIC between the two families. Method is detailed in: Commenges, Alkhassim, Gottardo, Hejblum & Thiebaut (2018) <doi:10.1002/cyto.a.23601>.

Authors:Chariff Alkhassim [aut], Boris P Hejblum [cre, aut], Anthony Devaux [aut], Van Hung Huynh Tran [aut], Melany Durand [aut]

cytometree_2.0.6.tar.gz
cytometree_2.0.6.zip(r-4.7)cytometree_2.0.6.zip(r-4.6)cytometree_2.0.6.zip(r-4.5)
cytometree_2.0.6.tgz(r-4.6-x86_64)cytometree_2.0.6.tgz(r-4.6-arm64)cytometree_2.0.6.tgz(r-4.5-x86_64)cytometree_2.0.6.tgz(r-4.5-arm64)
cytometree_2.0.6.tar.gz(r-4.7-arm64)cytometree_2.0.6.tar.gz(r-4.7-x86_64)cytometree_2.0.6.tar.gz(r-4.6-arm64)cytometree_2.0.6.tar.gz(r-4.6-x86_64)
cytometree_2.0.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cytometree/json (API)

# Install 'cytometree' in R:
install.packages('cytometree', repos = c('https://sistm.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sistm/cytometree/issues

Pkgdown/docs site:https://sistm.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • DLBCL - Diffuse large B-cell lymphoma data set from the FlowCAP-I challenge.
  • HIPC - HIPC T cell panel data set from HIPC program, patient 1369. The data was analyzed and gated by Stanford.
  • IMdata - Influenza vaccine response dataset

On CRAN:

Conda:

cpp

6.16 score 11 stars 1 packages 22 scripts 421 downloads 10 exports 28 dependencies

Last updated from:2280b5f2f5. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK194
linux-devel-x86_64OK164
source / vignettesOK344
linux-release-arm64OK191
linux-release-x86_64OK187
macos-release-arm64OK109
macos-release-x86_64OK228
macos-oldrel-arm64OK96
macos-oldrel-x86_64OK323
windows-develOK142
windows-releaseOK185
windows-oldrelOK115
wasm-releaseOK170

Exports:AnnotationbootstrapCICytofTreeCytomeTreeFmeasureCFmeasureC_no0plot_cytopopplot_graphplot_nodesRetrievePops

Dependencies:clicowplotcpp11farverggplot2glueGoFKernelgtableigraphisobandKernSmoothlabelinglatticelifecyclemagrittrMatrixmclustpkgconfigR6RColorBrewerRcppRcppArmadillorlangS7scalesvctrsviridisLitewithr

cytoftree: extension of cytometree to analyze mass cytometry data
Introduction to cytoftree | Data transformation | Binary tree construction | Post-hoc annotation | Influenza vaccine response dataset analysis with cytoftree | Data preparation | CytofTree function | High dimensional issues | Annotation function | RetrievePops : providing informations for particular sub-populations | Proportions comparison between manual and automatic gating
Rendered fromcytoftree.Rmdusingknitr::rmarkdown

Last update: 2025-07-24
Started: 2019-07-25

User guide for performing automatic gating with cytometree
Introduction to cytometree | Binary tree construction | Post-hoc annotation | Examples of analysis with cytometree | Diffuse large B-cell lymphoma dataset with 3 markers | Automatic gating step | Post-processing annotation of automatically gated subpopulations | Comparison between manual and automatic gating | PBMC sample from the Human Immunology Project | Semi-supervised gating
Rendered fromautogating_cytometree.Rmdusingknitr::rmarkdown

Last update: 2025-07-24
Started: 2017-07-13