CATALYST

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

Cytometry dATa anALYSis Tools

Bioconductor version: Development (3.18)

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], 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 "4.3") 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	1.25.1
In Bioconductor since	BioC 3.5 (R-3.4) (6.5 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
Linking To
Suggests	BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto, rmarkdown, testthat, uwot
System Requirements
Enhances
URL	https://github.com/HelenaLC/CATALYST
Bug Reports	https://github.com/HelenaLC/CATALYST/issues

Depends On Me	cytofWorkflow
Imports Me	cytofQC
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_1.25.1.tar.gz
Windows Binary	CATALYST_1.25.1.zip
macOS Binary (x86_64)	CATALYST_1.25.1.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