Skip to content

UCLouvain-CBIO/CytoMDS

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

96 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Low Dimensional Projection of Cytometry Samples

Project Status: Active – The project has reached a stable, usable state and is being actively developed. R-CMD-check-bioc license codecov.io

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

The CytoMDS algorithm combines, on the one hand, the concept of Earth Mover's Distance (EMD), a.k.a. Wasserstein metric and, on the other hand, the Multi Dimensional Scaling (MDS) algorithm for the low dimensional projection.

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

License

The CytoMDS code is provided under GPL license version 3.0 or higher. The documentation, including the manual pages and the vignettes, are distributed under a CC BY-SA 4.0 license.

Citation

If you use CytoMDS 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 Package for Low Dimensional Representation of Cytometry Sample Distances.” bioRxiv. https://doi.org/10.1101/2024.07.01.601465.

or run citation("CytoMDS") to get the bibtex entry.

Releases

No releases published

Packages

No packages published