DOI: 10.18129/B9.bioc.CATALYST    

Cytometry dATa anALYSis Tools

Bioconductor version: Release (3.6)

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 Lucia Crowell <crowellh at>, Mark D Robinson <mark.robinson at>, Vito RT Zanotelli <vito.zanotelli at>, St├ęphane Chevrier, Bernd Bodenmiller

Maintainer: Helena Lucia Crowell <crowellh at>

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biocViews MassSpectrometry, Normalization, Preprocessing, SingleCell, Software, StatisticalMethod
Version 1.2.0
In Bioconductor since BioC 3.5 (R-3.4) (1 year)
License GPL (>=2)
Depends R (>= 3.4)
Imports drc, flowCore, ggplot2, graphics, grDevices, grid, gridExtra, matrixStats, methods, plotly, RColorBrewer, reshape2, stats, utils
Suggests BiocStyle, knitr, rmarkdown, testthat
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