Optimal Transport for Gating Transfer in Cytometry Data with Domain Adaptation

Supervised learning from a source distribution (with known segmentation into cell sub-populations) to fit a target distribution with unknown segmentation. It relies regularized optimal transport to directly estimate the different cell population proportions from a biological sample characterized with flow cytometry measurements. It is based on the regularized Wasserstein metric to compare cytometry measurements from different samples, thus accounting for possible mis-alignment of a given cell population across sample (due to technical variability from the technology of measurements). Supervised learning technique based on the Wasserstein metric that is used to estimate an optimal re-weighting of class proportions in a mixture model Details are presented in Freulon P, Bigot J and Hejblum BP (2023) .


Reference manual

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install.packages("CytOpT")

0.9.8 by Boris Hejblum, 2 years ago


https://sistm.github.io/CytOpT-R/, https://github.com/sistm/CytOpT-R/


Browse source code at https://github.com/cran/CytOpT


Authors: Boris Hejblum [aut, cre] , Paul Freulon [aut] , Kalidou Ba [aut, trl]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports ggplot2, MetBrewer, patchwork, reshape2, reticulate, stats, testthat

Suggests rmarkdown, knitr, covr

System requirements: Python (>= 3.7)


See at CRAN