Given the hypothesis of a bi-modal distribution of cells for
each marker, the algorithm constructs a binary tree, the nodes of which are
subpopulations of cells. At each node, observed cells and markers are modeled
by both a family of normal distributions and a family of bi-modal normal mixture
distributions. Splitting is done according to a normalized difference of AIC
between the two families. Method is detailed in: Commenges, Alkhassim, Gottardo,
Hejblum & Thiebaut (2018)

`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:

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

`cytometree`

R package- (semi-)supervised option

- improved
`plot_nodes()`

function - added
`plot_cytopop()`

function for displaying populations counts

- Added a 3 component Gaussian mixture option

- Improved the annotation process allowing for 3 levels of expression and using the tree
- Added a
`NEWS.md`

file to track changes to the package. - Added a vignette
`autogating_cytometree`

- Added a
`README.Rmd`

- bug fix