recipe bioconductor-cytomapper

Visualization of highly multiplexed imaging data in R

Homepage

https://bioconductor.org/packages/3.14/bioc/html/cytomapper.html

License

GPL (>= 2)

Recipe

/bioconductor-cytomapper/meta.yaml

Highly multiplexed imaging acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualised across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualised on segmented cell areas. This package contains functions for the visualisation of multiplexed read-outs and cell-level information obtained by multiplexed imaging technologies. The main functions of this package allow 1. the visualisation of pixel-level information across multiple channels, 2. the display of cell-level information (expression and/or metadata) on segmentation masks and 3. gating and visualisation of single cells.

package bioconductor-cytomapper

Versions

1.6.0-0,  1.4.1-0,  1.2.1-0,  1.2.0-0,  1.0.0-0

Depends

• bioconductor-biocparallel >=1.28.0,<1.29.0

• bioconductor-delayedarray >=0.20.0,<0.21.0

• bioconductor-ebimage >=4.36.0,<4.37.0

• bioconductor-hdf5array >=1.22.0,<1.23.0

• bioconductor-rhdf5 >=2.38.0,<2.39.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-singlecellexperiment >=1.16.0,<1.17.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• r-base >=4.1,<4.2.0a0

• r-ggbeeswarm

• r-ggplot2

• r-matrixstats

• r-raster

• r-rcolorbrewer

• r-shiny

• r-shinydashboard

• r-svglite

• r-svgpanzoom

• r-viridis

Required By

• bioconductor-imcrtools

• bioconductor-imcdatasets

Installation

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

conda install bioconductor-cytomapper

and update with:

conda update bioconductor-cytomapper

or use the docker container:

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

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

Download stats

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-cytomapper/README.html)