recipe bioconductor-catalyst

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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/CATALYST.html

License

GPL (>=2)

Recipe

/bioconductor-catalyst/meta.yaml

package bioconductor-catalyst

(downloads) docker_bioconductor-catalyst

Versions

1.6.0-0

Depends bioconductor-biobase

>=2.42.0,<2.43.0

Depends bioconductor-complexheatmap

>=1.20.0,<1.21.0

Depends bioconductor-consensusclusterplus

>=1.46.0,<1.47.0

Depends bioconductor-flowcore

>=1.48.0,<1.49.0

Depends bioconductor-flowsom

>=1.14.0,<1.15.0

Depends bioconductor-limma

>=3.38.0,<3.39.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-circlize

Depends r-dplyr

Depends r-drc

Depends r-dt

Depends r-ggplot2

Depends r-ggrepel

Depends r-ggridges

Depends r-gridextra

Depends r-htmltools

Depends r-magrittr

Depends r-matrix

Depends r-matrixstats

Depends r-nnls

Depends r-plotly

Depends r-rcolorbrewer

Depends r-reshape2

Depends r-rtsne

Depends r-scales

Depends r-shiny

Depends r-shinybs

Depends r-shinydashboard

Depends r-shinyjs

Depends r-tidyr

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-catalyst

and update with:

conda update bioconductor-catalyst

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-catalyst:<tag>

(see bioconductor-catalyst/tags for valid values for <tag>)