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Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data.

ABSTRACT:

Summary

Highly multiplexed imaging technologies enable spatial profiling of dozens of biomarkers in situ. Here we describe cytomapper, a computational tool written in R, that enables visualisation of pixel- and cell-level information obtained by multiplexed imaging. To illustrate its utility, we analysed 100 images obtained by imaging mass cytometry from a cohort of type 1 diabetes patients. In addition, cytomapper includes a Shiny application that allows hierarchical gating of cells based on marker expression and visualisation of selected cells in corresponding images.

Availability and implementation

The cytomapper package can be installed via https://www.bioconductor.org/packages/release/bioc/html/cytomapper.html. Code for analysis and further instructions can be found at https://github.com/BodenmillerGroup/cytomapper_publication.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Eling N

PROVIDER: S-EPMC8023672 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data.

Eling Nils N Damond Nicolas N Hoch Tobias T Bodenmiller Bernd B

Bioinformatics (Oxford, England) 20210401 24

<h4>Summary</h4>Highly multiplexed imaging technologies enable spatial profiling of dozens of biomarkers in situ. Here, we describe cytomapper, a computational tool written in R, that enables visualization of pixel- and cell-level information obtained by multiplexed imaging. To illustrate its utility, we analysed 100 images obtained by imaging mass cytometry from a cohort of type 1 diabetes patients. In addition, cytomapper includes a Shiny application that allows hierarchical gating of cells ba ...[more]

PMID: 33367748

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