Package: CATALYST
Type: Package
Title: Cytometry dATa anALYSis Tools
Version: 1.33.1
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,
        data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel,
        ggridges, graphics, grDevices, grid, gridExtra, Matrix,
        matrixStats, methods, nnls, purrr, 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: 7.3.2
License: GPL (>=2)
Encoding: UTF-8
LazyData: true
git_url: https://git.bioconductor.org/packages/CATALYST
git_branch: devel
git_last_commit: 0262c36
git_last_commit_date: 2025-07-13
Repository: Bioconductor 3.22
Date/Publication: 2025-07-13
NeedsCompilation: no
Packaged: 2025-07-13 21:59:27 UTC; biocbuild
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 4.5.1; ; 2025-07-14 12:36:53 UTC; windows
