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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>.

Version: 2.0.2
Depends: R (≥ 3.1.0), Rcpp (≥ 0.12.11)
Imports: ggplot2, graphics, igraph, mclust, methods, stats, cowplot, GoFKernel
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, formatR, rmarkdown, viridis
Published: 2019-12-04
DOI: 10.32614/CRAN.package.cytometree
Author: Chariff Alkhassim, Boris P Hejblum, Anthony Devaux, Van Hung Huynh Tran
Maintainer: Boris P Hejblum <boris.hejblum at u-bordeaux.fr>
BugReports: https://github.com/sistm/Cytometree/issues
License: LGPL-3 | file LICENSE
NeedsCompilation: yes
Citation: cytometree citation info
Materials: README NEWS
CRAN checks: cytometree results

Documentation:

Reference manual: cytometree.pdf
Vignettes: User guide for performing automatic gating with 'cytometree'
'cytoftree': extension of 'cytometree' to analyze mass cytometry data

Downloads:

Package source: cytometree_2.0.2.tar.gz
Windows binaries: r-devel: cytometree_2.0.2.zip, r-release: cytometree_2.0.2.zip, r-oldrel: cytometree_2.0.2.zip
macOS binaries: r-release (arm64): cytometree_2.0.2.tgz, r-oldrel (arm64): cytometree_2.0.2.tgz, r-release (x86_64): cytometree_2.0.2.tgz, r-oldrel (x86_64): cytometree_2.0.2.tgz
Old sources: cytometree archive

Reverse dependencies:

Reverse imports: cyanoFilter

Linking:

Please use the canonical form https://CRAN.R-project.org/package=cytometree to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.