knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "README-" )
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:
D Commenges, C Alkhassim, R Gottardo, BP Hejblum, R ThiƩbaut, 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 CRAN:
install.packages("cytometree")
Or to get the development version from GitHub:
#install.packages("devtools") devtools::install_github("sistm/cytometree")
-- Chariff Alkhassim & Boris Hejblum
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