:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-cytomapper' .. highlight: bash bioconductor-cytomapper ======================= .. conda:recipe:: bioconductor-cytomapper :replaces_section_title: :noindex: Visualization of highly multiplexed imaging data in R :homepage: https://bioconductor.org/packages/3.18/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. .. conda:package:: bioconductor-cytomapper |downloads_bioconductor-cytomapper| |docker_bioconductor-cytomapper| :versions: ``1.14.0-0``,  ``1.12.0-0``,  ``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: ``>=1.36.0,<1.37.0`` :depends bioconductor-delayedarray: ``>=0.28.0,<0.29.0`` :depends bioconductor-ebimage: ``>=4.44.0,<4.45.0`` :depends bioconductor-hdf5array: ``>=1.30.0,<1.31.0`` :depends bioconductor-rhdf5: ``>=2.46.0,<2.47.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0`` :depends bioconductor-spatialexperiment: ``>=1.12.0,<1.13.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-ggbeeswarm: :depends r-ggplot2: :depends r-matrixstats: :depends r-nnls: :depends r-raster: :depends r-rcolorbrewer: :depends r-shiny: :depends r-shinydashboard: :depends r-svglite: :depends r-svgpanzoom: :depends r-viridis: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install bioconductor-cytomapper and update with:: mamba update bioconductor-cytomapper To create a new environment, run:: mamba create --name myenvname bioconductor-cytomapper with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/bioconductor-cytomapper: (see `bioconductor-cytomapper/tags`_ for valid values for ````) .. |downloads_bioconductor-cytomapper| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-cytomapper.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-cytomapper :alt: (downloads) .. |docker_bioconductor-cytomapper| image:: https://quay.io/repository/biocontainers/bioconductor-cytomapper/status :target: https://quay.io/repository/biocontainers/bioconductor-cytomapper .. _`bioconductor-cytomapper/tags`: https://quay.io/repository/biocontainers/bioconductor-cytomapper?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-cytomapper/README.html