Package: CATALYST
Type: Package
Title: Cytometry dATa anALYSis Tools
Version: 1.8.7
Depends: R (>= 3.6)
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: DifferentialExpression, 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: Biobase, circlize, ComplexHeatmap, ConsensusClusterPlus,
        data.table, dplyr, drc, DT, flowCore, FlowSOM, ggplot2,
        ggrepel, ggridges, graphics, grDevices, grid, gridExtra,
        htmltools, limma, magrittr, matrixStats, methods, nnls, plotly,
        purrr, RColorBrewer, reshape2, Rtsne, S4Vectors, scales,
        scater, shiny, shinydashboard, shinyBS, shinyjs,
        SingleCellExperiment, stats, SummarizedExperiment, utils
Suggests: BiocStyle, knitr, rmarkdown, testthat, diffcyt, umap
URL: https://github.com/HelenaLC/CATALYST
BugReports: https://github.com/HelenaLC/CATALYST/issues
VignetteBuilder: knitr
RoxygenNote: 6.1.1
License: GPL (>=2)
LazyData: TRUE
Encoding: UTF-8
git_url: https://git.bioconductor.org/packages/CATALYST
git_branch: RELEASE_3_9
git_last_commit: e1bc86f
git_last_commit_date: 2019-10-14
Date/Publication: 2019-10-14
NeedsCompilation: no
Packaged: 2019-10-15 04:28:10 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 3.6.1; ; 2019-10-15 12:50:12 UTC; windows
