CATALYST
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CATALYST.
Cytometry dATa anALYSis Tools
Bioconductor version: 3.9
Mass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for preprocessing of cytometry data, including i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation.
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("CATALYST")):
Installation
To install this package, start R (version "3.6") 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")| Differential analysis with CATALYST | HTML | R Script |
| Preprocessing with CATALYST | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, FlowCytometry, ImmunoOncology, MassSpectrometry, Normalization, Preprocessing, SingleCell, Software, StatisticalMethod, Visualization |
| Version | 1.8.7 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 years) |
| License | GPL (>=2) |
| Depends | R (>= 3.6) |
| Imports | Biobase, circlize, ComplexHeatmap, ConsensusClusterPlus, data.table, dplyr, drc, DT, flowCore, FlowSOM, ggplot2, ggrepel, ggridges, graphics, grDevices, grid, gridExtra, htmltools, limma, magrittr, matrixStats, methods, nnls, plotly, purrr, RColorBrewer, reshape2, Rtsne, S4Vectors, scales, scater, shiny, shinydashboard, shinyBS, shinyjs, SingleCellExperiment, stats, SummarizedExperiment, utils |
| System Requirements | |
| URL | https://github.com/HelenaLC/CATALYST |
| Bug Reports | https://github.com/HelenaLC/CATALYST/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, diffcyt, umap |
| Linking To | |
| Enhances | |
| Depends On Me | cytofWorkflow |
| Imports Me | |
| Suggests Me | diffcyt |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CATALYST_1.8.7.tar.gz |
| Windows Binary | CATALYST_1.8.7.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | CATALYST_1.8.7.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 |
| Old Source Packages for BioC 3.9 | Source Archive |