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:
install.packages("cytometree")Or to get the development version from GitHub:
#install.packages("devtools")
devtools::install_github("sistm/cytometree")– Chariff Alkhassim & Boris Hejblum