Package: CySA
Title: Interactive Cluster Selector for Cytometry Data
Version: 0.99.28
Authors@R: 
    person("Bernd", "Jagla", , "bernd.jagla@pasteur.fr", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-7696-0484"))
Description: CySA provides an interactive Shiny-based tool for analyzing
    flow and mass cytometry data. It supports self-organizing map (SOM)
    based clustering, dimension reduction (t-SNE, UMAP, PCA), and
    statistical comparison of cell populations across sample groups.
    Users can select cell clusters interactively via 2D scatter plots,
    dendrograms, or SOM node grids, and explore marker expression
    patterns across the selected populations.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 8.0.0
biocViews: SingleCell, FlowCytometry, Clustering, Visualization,
        ShinyApps
URL: https://github.com/baj12/CySA
BugReports: https://github.com/baj12/CySA/issues
Depends: R (>= 4.5.0)
Imports: shiny, shinydashboard, shinydashboardPlus, shinyjs, shinyjqui,
        htmltools, SingleCellExperiment, S4Vectors,
        SummarizedExperiment, Matrix, tidyselect, matrixStats,
        RColorBrewer, CATALYST, FlowSOM, dplyr, tidyr, tibble,
        data.table, stringr, purrr, reshape2, rlang, raster, ggplot2,
        plotly, viridis, dendextend, ComplexHeatmap, cowplot, Rtsne,
        umap, DT, collapsibleTree, withr
Suggests: KernSmooth, knitr, jsonlite, rmarkdown, shinytest2, testthat
        (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/CySA
git_branch: devel
git_last_commit: fab459b
git_last_commit_date: 2026-08-02
Repository: Bioconductor 3.24
Date/Publication: 2026-08-31
NeedsCompilation: no
Packaged: 2026-08-31 21:22:34 UTC; biocbuild
Author: Bernd Jagla [aut, cre] (ORCID: <https://orcid.org/0000-0002-7696-0484>)
Maintainer: Bernd Jagla <bernd.jagla@pasteur.fr>
