Automated Cytometry Gating and Annotation

Given the hypothesis of a bimodal 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 bimodal normal mixture distributions. Splitting is done according to a normalized difference of AIC between the two families.


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cytometree is a package which performs automatic gating and annotation of flow-cytometry data. On top of the CRAN help files, we also provide a vignette illustrating the functionnalities of cytometree.

The following article explains what cytometree is about:


The easiest way to get cytometree is to install it from CRAN:


Or to get the development version from GitHub:


-- Chariff Alkhassim & Boris Hejblum


News about the cytometree R package

Main changes in Version 1.1.1 (2017-10-20)

  • Added a 3 component Gaussian mixture option

Main changes in Version 1.1.0 (2017-10-10)

  • Improved the annotation process allowing for 3 levels of expression and using the tree
  • Added a file to track changes to the package.
  • Added a vignette autogating_cytometree
  • Added a README.Rmd

Main changes in Version 1.0.1 (2017-07-03) --- this is only a minor release:

  • bug fix

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.


1.1.1 by Alkhassim Chariff, 8 months ago

Report a bug at

Browse source code at

Authors: Chariff Alkhassim, Boris Hejblum

Documentation:   PDF Manual  

LGPL-3 | file LICENSE license

Imports ggplot2, graphics, igraph, mclust, stats

Depends on Rcpp

Suggests knitr, rmarkdown, viridis

Linking to Rcpp, RcppArmadillo

See at CRAN