CATALYST

DOI: 10.18129/B9.bioc.CATALYST    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see CATALYST.

Cytometry dATa anALYSis Tools

Bioconductor version: 3.13

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], Stéphane Chevrier [aut, dtc], Mark D. Robinson [aut, fnd], Bernd Bodenmiller [fnd]

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CATALYST")

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

Documentation

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

browseVignettes("CATALYST")

 

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

Details

biocViews	Clustering, DifferentialExpression, ExperimentalDesign, FlowCytometry, ImmunoOncology, MassSpectrometry, Normalization, Preprocessing, SingleCell, Software, StatisticalMethod, Visualization
Version	1.16.2
In Bioconductor since	BioC 3.5 (R-3.4) (4.5 years)
License	GPL (>=2)
Depends	R (>= 4.0), 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
LinkingTo
Suggests	BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot
SystemRequirements
Enhances
URL	https://github.com/HelenaLC/CATALYST
BugReports	https://github.com/HelenaLC/CATALYST/issues
Depends On Me	cytofWorkflow
Imports Me
Suggests Me	diffcyt, treekoR
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	CATALYST_1.16.2.tar.gz
Windows Binary	CATALYST_1.16.2.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	CATALYST_1.16.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CATALYST
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CATALYST
Package Short Url	https://bioconductor.org/packages/CATALYST/
Package Downloads Report	Download Stats