Package: CATALYST
Type: Package
Title: Cytometry dATa anALYSis Tools
Version: 1.37.0
Depends: R (>= 4.5), SingleCellExperiment
Authors@R: c(
	person("Helena L.", "Crowell", 
	    role=c("aut", "cre"),
	    email="helena@crowell.eu", 
	    comment=c(ORCID="0000-0002-4801-1767")),  
	person("Vito R.T.", "Zanotelli", role="aut",
	    comment=c(ORCID="0000-0001-7268-311X")), 
	person("Stéphane", "Chevrier", role=c("aut", "dtc"),
	    comment=c(ORCID="0000-0002-9216-7910")),
	person("Mark D.", "Robinson", role=c("aut", "fnd"), 
	    comment=c(ORCID="0000-0002-3048-5518")),  
	person("Bernd", "Bodenmiller", role="fnd",
	    comment=c(ORCID="0000-0002-6325-7861")))
biocViews: Clustering, DataImport, DifferentialExpression,
        ExperimentalDesign, FlowCytometry, ImmunoOncology,
        MassSpectrometry,Normalization, Preprocessing, SingleCell,
        Software, StatisticalMethod, Visualization
Description: CATALYST provides tools for preprocessing of and
        differential discovery in cytometry data such as FACS, CyTOF,
        and IMC. Preprocessing includes i) normalization using bead
        standards, ii) single-cell deconvolution, and iii) bead-based
        compensation. For differential discovery, the package provides
        a number of convenient functions for data processing (e.g.,
        clustering, dimension reduction), as well as a suite of
        visualizations for exploratory data analysis and exploration of
        results from differential abundance (DA) and state (DS)
        analysis in order to identify differences in composition and
        expression profiles at the subpopulation-level, respectively.
Imports: circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot,
        dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel, ggridges,
        graphics, grDevices, grid, gridExtra, Matrix, matrixStats,
        methods, nnls, RColorBrewer, reshape2, Rtsne,
        SummarizedExperiment, S4Vectors, scales, scater, stats
Suggests: BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto,
        rmarkdown, testthat, uwot
URL: https://github.com/HelenaLC/CATALYST
BugReports: https://github.com/HelenaLC/CATALYST/issues
VignetteBuilder: knitr
RoxygenNote: 7.3.3
License: GPL (>=2)
Encoding: UTF-8
LazyData: true
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libicu-dev libpng-dev libxml2-dev libssl-dev
        perl zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:45:30 UTC
RemoteUrl: https://github.com/bioc/CATALYST
RemoteRef: HEAD
RemoteSha: 4740c0e4b1ae65601eb0fd8f8820c39919952d77
NeedsCompilation: no
Packaged: 2026-07-05 04:06:50 UTC; root
Author: Helena L. Crowell [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4801-1767>),
  Vito R.T. Zanotelli [aut] (ORCID:
    <https://orcid.org/0000-0001-7268-311X>),
  Stéphane Chevrier [aut, dtc] (ORCID:
    <https://orcid.org/0000-0002-9216-7910>),
  Mark D. Robinson [aut, fnd] (ORCID:
    <https://orcid.org/0000-0002-3048-5518>),
  Bernd Bodenmiller [fnd] (ORCID:
    <https://orcid.org/0000-0002-6325-7861>)
Maintainer: Helena L. Crowell <helena@crowell.eu>