CATALYST

DOI: 10.18129/B9.bioc.CATALYST  

Cytometry dATa anALYSis Tools

Bioconductor version: Release (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], 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 "4.3") 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, DataImport, DifferentialExpression, ExperimentalDesign, FlowCytometry, ImmunoOncology, MassSpectrometry, Normalization, Preprocessing, SingleCell, Software, StatisticalMethod, Visualization
Version 1.26.0
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
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 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_1.26.0.tar.gz
Windows Binary CATALYST_1.26.0.zip
macOS Binary (x86_64) CATALYST_1.26.0.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
Old Source Packages for BioC 3.18 Source Archive

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