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Bioconductor - CATALYST (development version)

CATALYST

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

Cytometry dATa anALYSis Tools

Bioconductor version: Development (3.22)

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] ORCID: 0000-0002-4801-1767 , Vito R.T. Zanotelli [aut] ORCID: 0000-0001-7268-311X , Stéphane Chevrier [aut, dtc] ORCID: 0000-0002-9216-7910 , Mark D. Robinson [aut, fnd] ORCID: 0000-0002-3048-5518 , Bernd Bodenmiller [fnd] ORCID: 0000-0002-6325-7861

Maintainer: Helena L. Crowell <helena at crowell.eu>

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

To install this package, start R (version "4.5") 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")
Details biocViews Clustering, DataImport, DifferentialExpression, ExperimentalDesign, FlowCytometry, ImmunoOncology, MassSpectrometry, Normalization, Preprocessing, SingleCell, Software, StatisticalMethod, Visualization Version 1.33.0 In Bioconductor since BioC 3.5 (R-3.4) (8 years) License GPL (>=2) Depends R (>= 4.4), 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 spillR, cytofWorkflow 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.

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