DOI: 10.18129/B9.bioc.CATALYST  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see CATALYST.

Cytometry dATa anALYSis Tools

Bioconductor version: 3.17

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.

Author: Helena L. Crowell [aut, cre] , Vito R.T. Zanotelli [aut], St├ęphane Chevrier [aut, dtc], Mark D. Robinson [aut, fnd], Bernd Bodenmiller [fnd]

Maintainer: Helena L. Crowell <helena.crowell at>

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biocViews Clustering, DataImport, DifferentialExpression, ExperimentalDesign, FlowCytometry, ImmunoOncology, MassSpectrometry, Normalization, Preprocessing, SingleCell, Software, StatisticalMethod, Visualization
Version 1.24.0
In Bioconductor since BioC 3.5 (R-3.4) (6.5 years)
License GPL (>=2)
Depends R (>= 4.2), SingleCellExperiment
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
Depends On Me cytofWorkflow
Imports Me cytofQC
Suggests Me diffcyt, imcRtools, treekoR
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