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TheCytoMDS package implements a low dimensional visualization of a setof cytometry samples, in order to visually assess the 'distances' between them.This, in turn, can greatly help the user to identify quality issueslike batch effects or outlier samples, and/or check the presence of potentialsample clusters that might align with the experimental design.

TheCytoMDS algorithm combines, on the one hand, the concept of Earth Mover'sDistance (EMD), a.k.a. Wasserstein metric and, on the other hand,the Multi Dimensional Scaling (MDS) algorithm for the low dimensionalprojection.

Also, the package provides some diagnostic tools for both checking the qualityof the MDS projection, as well as tools to help with the interpretation ofthe axes of the projection.

TheCytoMDS code is provided underGPL license version 3.0 orhigher. The documentation,including the manual pages and the vignettes, are distributed under aCC BY-SA4.0 license.

If you useCytoMDS in your research, please use the following citation:

Hauchamps, Philippe, Simon Delandre, Stephane T. Temmerman,Dan Lin, and Laurent Gatto. 2024.“Visual Quality Control with CytoMDS, a Bioconductor Packagefor Low Dimensional Representation of Cytometry Sample Distances.”bioRxiv.https://doi.org/10.1101/2024.07.01.601465.

or runcitation("CytoMDS") to get the bibtex entry.