CATALYST

DOI: 10.18129/B9.bioc.CATALYST    

Cytometry dATa anALYSis Tools

Bioconductor version: Release (3.6)

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 Lucia Crowell <crowellh at student.ethz.ch>, Mark D Robinson <mark.robinson at imls.uzh.ch>, Vito RT Zanotelli <vito.zanotelli at uzh.ch>, Stéphane Chevrier, Bernd Bodenmiller

Maintainer: Helena Lucia Crowell <crowellh at student.ethz.ch>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CATALYST")

Documentation

HTML	R Script	Cytometry dATa anALYSis Tools (CATALYST): Tools for preprocessing & analysis of cytometry data
PDF		Reference Manual
Text		NEWS

Details

biocViews	MassSpectrometry, Normalization, Preprocessing, SingleCell, Software, StatisticalMethod
Version	1.2.0
In Bioconductor since	BioC 3.5 (R-3.4) (1 year)
License	GPL (>=2)
Depends	R (>= 3.4)
Imports	drc, flowCore, ggplot2, graphics, grDevices, grid, gridExtra, matrixStats, methods, plotly, RColorBrewer, reshape2, stats, utils
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	CATALYST_1.2.0.tar.gz
Windows Binary	CATALYST_1.2.0.zip
Mac OS X 10.11 (El Capitan)	CATALYST_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CATALYST
Package Short Url	http://bioconductor.org/packages/CATALYST/
Package Downloads Report	Download Stats