CATALYST

DOI: 10.18129/B9.bioc.CATALYST    

Cytometry dATa anALYSis Tools

Bioconductor version: Release (3.7)

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 [cre], Vito R.T. Zanotelli [aut], St├ęphane Chevrier [aut, dtc], Mark D. Robinson [aut, fnd], Bernd Bodenmiller [fnd]

Maintainer: Helena L. 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CATALYST")

 

HTML R Script Differential analysis with CATALYST
HTML R Script Preprocessing with CATALYST
PDF   Reference Manual
Text   NEWS

Details

biocViews MassSpectrometry, Normalization, Preprocessing, SingleCell, Software, StatisticalMethod
Version 1.4.2
In Bioconductor since BioC 3.5 (R-3.4) (1.5 years)
License GPL (>=2)
Depends R (>= 3.4)
Imports Biobase, circlize, ComplexHeatmap, ConsensusClusterPlus, dplyr, drc, DT, flowCore, FlowSOM, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, htmltools, limma, magrittr, matrixStats, methods, nnls, plotly, RColorBrewer, reshape2, Rtsne, S4Vectors, scales, shiny, shinydashboard, shinyjs, shinyBS, stats, SummarizedExperiment, tidyr, utils
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, testthat, diffcyt
SystemRequirements
Enhances
URL https://github.com/HelenaLC/CATALYST
BugReports https://github.com/HelenaLC/CATALYST/issues
Depends On Me
Imports Me
Suggests Me diffcyt
Links To Me
Build Report  

Package Archives

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

Source Package CATALYST_1.4.2.tar.gz
Windows Binary CATALYST_1.4.2.zip
Mac OS X 10.11 (El Capitan) CATALYST_1.4.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/CATALYST
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CATALYST
Package Short Url http://bioconductor.org/packages/CATALYST/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive

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