Package: CATALYST
Type: Package
Title: Cytometry dATa anALYSis Tools
Version: 1.16.2
Depends: R (>= 4.0), SingleCellExperiment
Authors@R: c(
	person("Helena L.", "Crowell", email="helena.crowell@uzh.ch", role=c("aut", "cre")),  
	person("Vito R.T.", "Zanotelli", email="vito.zanotelli@uzh.ch", role="aut"), 
	person("Stéphane", "Chevrier", role=c("aut", "dtc")),
	person("Mark D.", "Robinson", email="mark.robinson@imls.uzh.ch", role=c("aut", "fnd")),
	person("Bernd", "Bodenmiller", role="fnd"))
biocViews: Clustering, DifferentialExpression, ExperimentalDesign,
        FlowCytometry, ImmunoOncology, MassSpectrometry, Normalization,
        Preprocessing, SingleCell, Software, StatisticalMethod,
        Visualization
Description: 
	Mass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent 
	tags as reporters to label antibodies, thereby substantially decreasing 
	spectral overlap and allowing for examination of over 50 parameters at the 
	single cell level. While spectral overlap is significantly less pronounced 
	in CyTOF than flow cytometry, spillover due to detection sensitivity, 
	isotopic impurities, and oxide formation can impede data interpretability. 
	We designed CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline 
	for preprocessing of cytometry data, including i) normalization using bead 
	standards, ii) single-cell deconvolution, and iii) bead-based compensation.
Imports: circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot,
        data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel,
        ggridges, graphics, grDevices, grid, gridExtra, magrittr,
        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: 7.1.1
License: GPL (>=2)
LazyData: TRUE
Encoding: UTF-8
git_url: https://git.bioconductor.org/packages/CATALYST
git_branch: RELEASE_3_13
git_last_commit: 5e3b4f4
git_last_commit_date: 2021-07-13
Date/Publication: 2021-07-13
NeedsCompilation: no
Packaged: 2021-07-13 17:53:04 UTC; biocbuild
Author: Helena L. Crowell [aut, cre],
  Vito R.T. Zanotelli [aut],
  Stéphane Chevrier [aut, dtc],
  Mark D. Robinson [aut, fnd],
  Bernd Bodenmiller [fnd]
Maintainer: Helena L. Crowell <helena.crowell@uzh.ch>
Built: R 4.1.0; ; 2021-07-14 14:21:26 UTC; windows
