DOI: 10.18129/B9.bioc.CATALYST  

Cytometry dATa anALYSis Tools

Bioconductor version: Release (3.18)

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>

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HTML R Script 1. Preprocessing
HTML R Script 2. Differential discovery
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biocViews Clustering, DataImport, DifferentialExpression, ExperimentalDesign, FlowCytometry, ImmunoOncology, MassSpectrometry, Normalization, Preprocessing, SingleCell, Software, StatisticalMethod, Visualization
Version 1.26.0
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, 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
Links To Me
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