CATALYST
Cytometry dATa anALYSis Tools
Bioconductor version: Release (3.20)
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 at crowell.eu>
citation("CATALYST")):
Installation
To install this package, start R (version "4.4") 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")| 1. Preprocessing | HTML | R Script |
| 2. Differential discovery | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DataImport, DifferentialExpression, ExperimentalDesign, FlowCytometry, ImmunoOncology, MassSpectrometry, Normalization, Preprocessing, SingleCell, Software, StatisticalMethod, Visualization |
| Version | 1.30.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7.5 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.
| Source Package | CATALYST_1.30.0.tar.gz |
| Windows Binary (x86_64) | CATALYST_1.30.0.zip |
| macOS Binary (x86_64) | CATALYST_1.30.0.tgz |
| macOS Binary (arm64) | CATALYST_1.30.0.tgz |
| 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 |