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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
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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 |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | MassSpectrometry, Preprocessing, SingleCell, Software, StatisticalMethod |
| Version | 1.1.1 |
| In Bioconductor since | BioC 3.5 (R-3.4) (0.5 years) |
| 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.
| Source Package | 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 |
| Source Repository | git clone https://git.bioconductor.org/packages/CATALYST |
| Package Short Url | http://bioconductor.org/packages/CATALYST/ |
| Package Downloads Report | Download Stats |
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