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>.

Version:	2.0.6
Depends:	R (≥ 3.1.0), Rcpp (≥ 0.12.11)
Imports:	ggplot2, graphics, igraph, mclust, methods, stats, cowplot, GoFKernel
LinkingTo:	Rcpp, RcppArmadillo
Suggests:	knitr, formatR, rmarkdown, viridis, testthat
Published:	2025-07-24
DOI:	10.32614/CRAN.package.cytometree
Author:	Chariff Alkhassim [aut], Boris P Hejblum [cre, aut], Anthony Devaux [aut], Van Hung Huynh Tran [aut], Melany Durand [aut]
Maintainer:	Boris P Hejblum <boris.hejblum at u-bordeaux.fr>
BugReports:	https://github.com/sistm/Cytometree/issues
License:	LGPL-3 | file LICENSE
URL:	https://sistm.github.io/cytometree/, https://github.com/sistm/Cytometree/
NeedsCompilation:	yes
Citation:	cytometree citation info
Materials:	README, NEWS
CRAN checks:	cytometree results

Documentation:

Reference manual:	cytometree.html , cytometree.pdf
Vignettes:	User guide for performing automatic gating with 'cytometree' (source, R code) 'cytoftree': extension of 'cytometree' to analyze mass cytometry data (source, R code)

Downloads:

Package source:	cytometree_2.0.6.tar.gz
Windows binaries:	r-devel: cytometree_2.0.6.zip, r-release: cytometree_2.0.6.zip, r-oldrel: cytometree_2.0.6.zip
macOS binaries:	r-release (arm64): cytometree_2.0.6.tgz, r-oldrel (arm64): cytometree_2.0.6.tgz, r-release (x86_64): cytometree_2.0.6.tgz, r-oldrel (x86_64): cytometree_2.0.6.tgz
Old sources:	cytometree archive

Reverse dependencies:

Reverse imports:

cyanoFilter

Linking:

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