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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 functionalities of cytometree.

The cytometree algorithm rely on the construction of a binary tree, the nodes of which represents cellular (sub)populations. At each node, observed cellular markers are modeled by both a family of normal and a family of normal mixture distributions and splitting of cells into further subpopulations is decided according to a normalized difference of AIC between the two families.

Given the unsupervised nature of such a binary tree, some of the available markers may not be used to find the different cell populations present in a given sample. So in order to recover a complete annotation, we propose a post processing annotation procedure which allows the user to distinguish two or three expression levels per marker.

The following article explains in more details how cytometree works:

Commenges D, Alkhassim C, Gottardo R, Hejblum BP, Thiébaut R (2018). cytometree: a binary tree algorithm for automatic gating in cytometry analysis. Cytometry Part A 93(11):1132-1140. <doi: 10.1002/cyto.a.23601>


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


Or to get the development version from GitHub:


– Chariff Alkhassim & Boris Hejblum