cytometree: Automated Cytometry Gating and Annotation

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) doi: 10.1002/cyto.a.23601 .

Details

The main function in this package is CytomeTree.

Package:	cytometree
Type:	Package
Version:	2.0.4
Date:	2020-08-12
License:	LGPL-3

The algorithm is based on the construction of 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. Given the unsupervised nature of the binary tree, some of the available markers may not be used to find the different cell populations present in a given sample. To recover a complete annotation, we defined, as a post processing procedure, an annotation method which allows the user to distinguish two or three expression levels per marker.

References

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>

See also

Useful links:

• https://sistm.github.io/cytometree/

• https://github.com/sistm/Cytometree/

• Report bugs at https://github.com/sistm/Cytometree/issues

Author

Maintainer: Boris P Hejblum boris.hejblum@u-bordeaux.fr

Authors:

• Chariff Alkhassim

• Anthony Devaux

• Van Hung Huynh Tran

• Melany Durand