Package: cytometree 2.0.5

Boris P Hejblum

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>.

Authors:Chariff Alkhassim [aut], Boris P Hejblum [cre, aut], Anthony Devaux [aut], Van Hung Huynh Tran [aut], Melany Durand [aut]

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cytometree.pdf |cytometree.html✨
cytometree/json (API)
NEWS

# Install 'cytometree' in R:
install.packages('cytometree', repos = c('https://sistm.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/sistm/cytometree/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • DLBCL - Diffuse large B-cell lymphoma data set from the FlowCAP-I challenge.
  • HIPC - HIPC T cell panel data set from HIPC program, patient 1369. The data was analyzed and gated by Stanford.
  • IMdata - Influenza vaccine response dataset

On CRAN:

10 exports 9 stars 1.71 score 36 dependencies 1 dependents 11 scripts 246 downloads

Last updated 2 years agofrom:b484bed3b5. Checks:OK: 4 NOTE: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 02 2024
R-4.5-win-x86_64NOTESep 02 2024
R-4.5-linux-x86_64NOTESep 02 2024
R-4.4-win-x86_64NOTESep 02 2024
R-4.4-mac-x86_64NOTESep 02 2024
R-4.4-mac-aarch64NOTESep 02 2024
R-4.3-win-x86_64OKSep 02 2024
R-4.3-mac-x86_64OKSep 02 2024
R-4.3-mac-aarch64OKSep 02 2024

Exports:AnnotationbootstrapCICytofTreeCytomeTreeFmeasureCFmeasureC_no0plot_cytopopplot_graphplot_nodesRetrievePops

Dependencies:clicolorspacecowplotcpp11fansifarverggplot2glueGoFKernelgtableigraphisobandKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmclustmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcppRcppArmadillorlangscalestibbleutf8vctrsviridisLitewithr

cytoftree: extension of cytometree to analyze mass cytometry data

Anthony Devaux, Boris Hejblum

Rendered fromcytoftree.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2019-08-19
Started: 2019-07-25

User guide for performing automatic gating with cytometree

Chariff Alkhassim, Boris Hejblum

Rendered fromautogating_cytometree.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2020-04-04
Started: 2017-07-13