DESCRIPTION

Package: CytoMDS
Title: Low Dimensions projection of cytometry samples
Version: 1.3.2
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: 7.3.2
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'
Depends:
    R (>= 4.4)
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