Package: CytoMDS
Title: Low Dimensions projection of cytometry samples
Version: 1.9.0
Authors@R: 
    c(person(given = "Philippe",
             family = "Hauchamps",
             role = c("aut", "cre"),
             email = "philippe.hauchamps@uclouvain.be",
             comment = c(ORCID = "0000-0003-2865-1852")),
      person(given = "Laurent", family = "Gatto",
             email = "laurent.gatto@uclouvain.be",
             role = "aut",
             comment = c(ORCID = "0000-0002-1520-2268")),
      person(given = "Dan",
             family = "Lin",
             role = "ctb",
             email = "dan.8.lin@gsk.com"))
Description: This 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 exeprimental 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: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
BugReports: https://github.com/UCLouvain-CBIO/CytoMDS/issues
URL: https://uclouvain-cbio.github.io/CytoMDS
biocViews: FlowCytometry, QualityControl, DimensionReduction,
        MultidimensionalScaling, Software, Visualization
Collate: 'CytoMDS-package.R' 'stats.R' 'ggplots.R' 'MDS-class.R'
        'DistSum-class.R'
Depends: R (>= 4.4), Biobase
Imports: methods, stats, rlang, pracma, withr, flowCore, reshape2,
        ggplot2, ggrepel, ggforce, patchwork, transport, smacof,
        BiocParallel, CytoPipeline
Suggests: testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown,
        BiocStyle, HDCytoData
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev make
        libicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev perl
        libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:02:40 UTC
RemoteUrl: https://github.com/bioc/CytoMDS
RemoteRef: HEAD
RemoteSha: 12236215be95e5d73f7c054d5086205db92338aa
NeedsCompilation: no
Packaged: 2026-07-04 06:59:55 UTC; root
Author: Philippe Hauchamps [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2865-1852>),
  Laurent Gatto [aut] (ORCID: <https://orcid.org/0000-0002-1520-2268>),
  Dan Lin [ctb]
Maintainer: Philippe Hauchamps <philippe.hauchamps@uclouvain.be>