Automated Cytometry Gating and Annotation.
cytometree
Overview
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 A93(11):1132-1140. <doi: 10.1002/cyto.a.23601>
Installation
The easiest way to get cytometree
is to install it from CRAN:
install.packages("cytometree")
Or to get the development version from GitHub:
#install.packages("devtools")
devtools::install_github("sistm/cytometree")
– Chariff Alkhassim & Boris Hejblum.