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]

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cytometree.pdf |cytometree.html✨
cytometree/json (API)
NEWS

# 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

6.07 score 11 stars 1 packages 18 scripts 324 downloads 10 exports 28 dependencies

Last updated from:2280b5f2f5. Checks:12 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK154
linux-devel-x86_64OK149
source / vignettesOK349
linux-release-arm64OK149
linux-release-x86_64OK154
macos-devel-arm64OK118
macos-devel-x86_64OK211
macos-release-arm64OK90
macos-release-x86_64OK273
windows-develOK132
windows-releaseOK122
wasm-releaseOK129

Exports:AnnotationbootstrapCICytofTreeCytomeTreeFmeasureCFmeasureC_no0plot_cytopopplot_graphplot_nodesRetrievePops

Dependencies:clicowplotcpp11farverggplot2glueGoFKernelgtableigraphisobandKernSmoothlabelinglatticelifecyclemagrittrMatrixmclustpkgconfigR6RColorBrewerRcppRcppArmadillorlangS7scalesvctrsviridisLitewithr

cytoftree: extension of cytometree to analyze mass cytometry data

Anthony Devaux, Boris Hejblum

Rendered fromcytoftree.Rmdusingknitr::rmarkdownon Mar 30 2026.

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

User guide for performing automatic gating with cytometree

Chariff Alkhassim, Boris Hejblum

Rendered fromautogating_cytometree.Rmdusingknitr::rmarkdownon Mar 30 2026.

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