cytometree is a package which performs automatic gating and
annotation of flow-cytometry data. On top of the CRAN help
also provide a
illustrating the functionalities of
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
D Commenges, C Alkhassim, R Gottardo, BP Hejblum, R Thiébaut, cytometree: a binary tree algorithm for automatic gating in cytometry analysis, Cytometry: Part A, (in press), 2018.
The easiest way to get
cytometree is to install it from
Or to get the development version from GitHub:
– Chariff Alkhassim & Boris Hejblum