Package: polyICSFlow
Type: Package
Title: Identifying the Frequency of Polyfunctional Antigen-Specific T
        cells in ICS Flow Cytometry Data
Version: 0.99.6
Authors@R: c(person("Lisa", "Loksø Dietz",
                    role = c("aut", "cre"),
                    email = "lisdie@clin.au.dk",
                    comment = c(ORCID = "0000-0002-1797-5766")),
             person("Sofie", "Van Gassen", 
                    role = "aut",
                    email = "sofie.vangassen@ugent.be",
                    comment = c(ORCID = "0000-0002-7119-5330")),
             person("Sarah", "Bonte", 
                    role = "aut",
                    email = "sarahm.bonte@ugent.be",
                    comment = c(ORCID = "0000-0002-0637-4893")),
             person("Yvan", "Saeys", 
                    role = "aut", 
                    email="yvan.saeys@ugent.be",
                    comment = c(ORCID = "0000-0002-0415-1506")),
             person("Ole", "Schmeltz Søgaard", 
                    role = "aut", 
                    email = "ole.schmeltz.sogaard@clin.au.dk",
                    comment = c(ORCID = "0000-0001-9107-2023")))
Imports: flowCore, flowWorkspace, openCyto, FlowSOM, ComplexHeatmap,
        SummarizedExperiment, cowplot, dplyr, forcats, ggtext, rlang,
        scales, stringr, tidyselect, tidyr, magrittr, ggplot2, methods
Description: polyICSFlow systematically identifies all cytokine
        combinations detected in an intracellular cytokine staining
        (ICS) flow cytometry assay and quantifies polyfunctional
        antigen-specific responses to single or multiple antigens. The
        package also offers versatile plotting options for efficient
        data exploration and visualization of cytokine co-expression
        profiles.
URL: https://github.com/SoegaardLab/polyICSFlow
BugReports: https://github.com/SoegaardLab/polyICSFlow/issues
biocViews: FlowCytometry, Immunology, Software, SingleCell
License: GPL (>=2)
Encoding: UTF-8
RoxygenNote: 7.3.3
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), patchwork, ggh4x
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libicu-dev libjpeg-dev libpng-dev libxml2-dev
        libssl-dev perl zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-09-10 07:01:24 UTC
RemoteUrl: https://github.com/bioc/polyICSFlow
RemoteRef: HEAD
RemoteSha: a6b6e7e13e82ce64452478f2dd4d9df0a1d52caf
NeedsCompilation: no
Packaged: 2026-10-11 10:36:34 UTC; root
Author: Lisa Loksø Dietz [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1797-5766>),
  Sofie Van Gassen [aut] (ORCID: <https://orcid.org/0000-0002-7119-5330>),
  Sarah Bonte [aut] (ORCID: <https://orcid.org/0000-0002-0637-4893>),
  Yvan Saeys [aut] (ORCID: <https://orcid.org/0000-0002-0415-1506>),
  Ole Schmeltz Søgaard [aut] (ORCID:
    <https://orcid.org/0000-0001-9107-2023>)
Maintainer: Lisa Loksø Dietz <lisdie@clin.au.dk>
Depends: R (>= 3.5.0)