recipe bioconductor-cytomapper

Visualization of highly multiplexed imaging data in R

Homepage:

https://bioconductor.org/packages/3.16/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:

1.10.0-0,  1.6.0-0,  1.4.1-0,  1.2.1-0,  1.2.0-0,  1.0.0-0

Depends:

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-delayedarray >=0.24.0,<0.25.0

• bioconductor-ebimage >=4.40.0,<4.41.0

• bioconductor-hdf5array >=1.26.0,<1.27.0

• bioconductor-rhdf5 >=2.42.0,<2.43.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-spatialexperiment >=1.8.0,<1.9.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-ggbeeswarm

• r-ggplot2

• r-matrixstats

• r-nnls

• r-raster

• r-rcolorbrewer

• r-shiny

• r-shinydashboard

• r-svglite

• r-svgpanzoom

• r-viridis

Required By:

• bioconductor-imcdatasets

• bioconductor-imcrtools

• bioconductor-simpleseg

Installation

With an activated Bioconda channel (see 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

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