CATALYST

DOI: 10.18129/B9.bioc.CATALYST    

This is the development version of CATALYST; for the stable release version, see CATALYST.

Cytometry dATa anALYSis Tools

Bioconductor version: Development (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 <helena.crowell at uzh.ch>, Vito R.T. Zanotelli <vito.zanotelli at uzh.ch>, St├ęphane Chevrier <mark.robinson at imls.uzh.ch>, Mark D. Robinson <helena.crowell at uzh.ch>, Bernd Bodenmiller <vito.zanotelli at uzh.ch>

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CATALYST")

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

Documentation

PDF   Reference Manual

Details

biocViews Clustering, DifferentialExpression, ExperimentalDesign, FlowCytometry, ImmunoOncology, MassSpectrometry, Normalization, Preprocessing, SingleCell, Software, StatisticalMethod, Visualization
Version 1.19.0
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, imcRtools, treekoR
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: