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
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libgdal-dev gdal-bin libgeos-dev libglpk-dev make libicu-dev
        libpng-dev libuv1-dev libxml2-dev libssl-dev perl libproj-dev
        python3 libsqlite3-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-08-02 07:34:17 UTC
RemoteUrl: https://github.com/bioc/CySA
RemoteRef: HEAD
RemoteSha: fab459b70225e608bdd7cb18627c68dcd10bd4d0
NeedsCompilation: no
Packaged: 2026-10-29 08:22:39 UTC; root
Author: Bernd Jagla [aut, cre] (ORCID: <https://orcid.org/0000-0002-7696-0484>)
Maintainer: Bernd Jagla <bernd.jagla@pasteur.fr>