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

Versions

1.8.6-0, 1.6.0-0

Depends

• bioconductor-biobase >=2.44.0,<2.45.0

• bioconductor-complexheatmap >=2.0.0,<2.1.0

• bioconductor-consensusclusterplus >=1.48.0,<1.49.0

• bioconductor-flowcore >=1.50.0,<1.51.0

• bioconductor-flowsom >=1.16.0,<1.17.0

• bioconductor-limma >=3.40.0,<3.41.0

• bioconductor-s4vectors >=0.22.0,<0.23.0

• bioconductor-scater >=1.12.0,<1.13.0

• bioconductor-singlecellexperiment >=1.6.0,<1.7.0

• bioconductor-summarizedexperiment >=1.14.0,<1.15.0

• r-base >=3.6,<3.7.0a0

• r-circlize

• r-data.table

• r-dplyr

• r-drc

• r-dt

• r-ggplot2

• r-ggrepel

• r-ggridges

• r-gridextra

• r-htmltools

• r-magrittr

• r-matrixstats

• r-nnls

• r-plotly

• r-purrr

• r-rcolorbrewer

• r-reshape2

• r-rtsne

• r-scales

• r-shiny

• r-shinybs

• r-shinydashboard

• r-shinyjs

Required By

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>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-catalyst/README.html)