Package: CATALYST
Type: Package
Title: Cytometry dATa anALYSis Tools
Version: 1.35.2
Depends: R (>= 4.4), 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
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-03-09 11:10:35 UTC
RemoteUrl: https://github.com/bioc/CATALYST
RemoteRef: HEAD
RemoteSha: b91b3eda7ebd387551b303b567baf3618d87a564
NeedsCompilation: no
Packaged: 2026-03-10 04:15:07 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>
Built: R 4.6.0; ; 2026-03-10 04:17:49 UTC; windows
