Package: CATALYST
Type: Package
Title: Cytometry dATa anALYSis Tools
Version: 1.35.1
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,
        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: 7.3.3
License: GPL (>=2)
Encoding: UTF-8
LazyData: true
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make
        libharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev
        libwebp-dev libxml2-dev perl zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-11-20 19:04:37 UTC
RemoteUrl: https://github.com/bioc/CATALYST
RemoteRef: HEAD
RemoteSha: a1cad2251f4c1d34617daf11f03c32e9f2405b74
NeedsCompilation: no
Packaged: 2025-11-23 12:33:18 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; ; 2025-11-23 12:35:57 UTC; windows
