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Cytometry dATa anALYSis Tools

Bioconductor version: Release (3.19)

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.

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>

Citation (from within R, enter citation("CATALYST")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

1. Preprocessing HTML R Script
2. Differential discovery HTML R Script
Reference Manual PDF


biocViews Clustering, DataImport, DifferentialExpression, ExperimentalDesign, FlowCytometry, ImmunoOncology, MassSpectrometry, Normalization, Preprocessing, SingleCell, Software, StatisticalMethod, Visualization
Version 1.28.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL (>=2)
Depends R (>= 4.4), SingleCellExperiment
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
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Suggests BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot
Linking To
Depends On Me spillR, cytofWorkflow
Imports Me cytofQC
Suggests Me diffcyt, imcRtools, treekoR
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package CATALYST_1.28.0.tar.gz
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macOS Binary (x86_64) CATALYST_1.28.0.tgz
macOS Binary (arm64)
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Source Repository (Developer Access) git clone
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