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CATALYST

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

Cytometry dATa anALYSis Tools


Bioconductor version: Development (3.19)

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 uzh.ch>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("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

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

browseVignettes("CATALYST")
1. Preprocessing HTML R Script
2. Differential discovery HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, DataImport, DifferentialExpression, ExperimentalDesign, FlowCytometry, ImmunoOncology, MassSpectrometry, Normalization, Preprocessing, SingleCell, Software, StatisticalMethod, Visualization
Version 1.27.0
In Bioconductor since BioC 3.5 (R-3.4) (7 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
System Requirements
URL https://github.com/HelenaLC/CATALYST
Bug Reports https://github.com/HelenaLC/CATALYST/issues
See More
Suggests BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot
Linking To
Enhances
Depends On Me cytofWorkflow, spillR
Imports Me cytofQC
Suggests Me diffcyt, imcRtools, treekoR
Links To Me
Build Report Build Report

Package Archives

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

Source Package CATALYST_1.27.0.tar.gz
Windows Binary CATALYST_1.27.0.zip
macOS Binary (x86_64) CATALYST_1.27.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/CATALYST
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CATALYST
Bioc Package Browser https://code.bioconductor.org/browse/CATALYST/
Package Short Url https://bioconductor.org/packages/CATALYST/
Package Downloads Report Download Stats