README.Rmd

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# cytometree <a><img src='man/figures/logo.png' align="right" width="139" /></a>

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[![Downloads](https://cranlogs.r-pkg.org/badges/cytometree?color=blue)](https://www.r-pkg.org/pkg/cytometree)


## Overview

`cytometree` is a package which performs **automatic gating and annotation of flow-cytometry
data**. On top of the [CRAN help files](https://cran.r-project.org/package=cytometree/cytometree.pdf), we also provide a [vignette](https://cran.r-project.org/package=cytometree/vignettes/autogating_cytometree.html) 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>](https://doi.org/10.1002/cyto.a.23601)


## Installation

The easiest way to get `cytometree` is to install it from [CRAN](https://cran.r-project.org/package=cytometree):
```{r CRAN-install, eval=FALSE}
install.packages("cytometree")
```

Or to get the development version from [GitHub](https://github.com/sistm/cytometree):
```{r GitHub-install, eval=FALSE}
#install.packages("devtools")
devtools::install_github("sistm/cytometree")
```