To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

CATALYST

 

   

Cytometry dATa anALYSis Tools

Bioconductor version: Release (3.5)

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 Robinson <mark.robinson at imls.uzh.ch>, Vito Zanotelli <vito.zanotelli at uzh.ch>, St<c3><a9>phane Chevrier, Bernd Bodenmiller

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

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

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, Preprocessing, SingleCell, Software, StatisticalMethod
Version 1.1.1
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
License GPL (>=2)
Depends R (>= 3.4)
Imports flowCore, ggplot2, graphics, grDevices, grid, gridExtra, matrixStats, methods, plotly, RColorBrewer, stats, utils
LinkingTo
Suggests BiocStyle, knitr, rmarkdown
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.

Package Source CATALYST_1.1.1.tar.gz
Windows Binary CATALYST_1.1.1.zip
Mac OS X 10.11 (El Capitan) CATALYST_1.1.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/CATALYST/tree/release-3.5
Package Short Url http://bioconductor.org/packages/CATALYST/
Package Downloads Report Download Stats

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