CATALYST

DOI: 10.18129/B9.bioc.CATALYST    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see CATALYST.

Cytometry dATa anALYSis Tools

Bioconductor version: 3.15

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>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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 1.20.1
In Bioconductor since BioC 3.5 (R-3.4) (5.5 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, imcRtools, treekoR
Links To Me
Build Report  

Package Archives

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

Source Package CATALYST_1.20.1.tar.gz
Windows Binary
macOS Binary (x86_64) CATALYST_1.20.1.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

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