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Bioconductor - cytomapper (development version)

cytomapper

This is the development version of cytomapper; for the stable release version, see cytomapper.

Visualization of highly multiplexed imaging data in R

Bioconductor version: Development (3.22)

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.

Author: Nils Eling [aut] ORCID: 0000-0002-4711-1176 , Nicolas Damond [aut] ORCID: 0000-0003-3027-8989 , Tobias Hoch [ctb], Lasse Meyer [cre, ctb] ORCID: 0000-0002-1660-1199

Maintainer: Lasse Meyer <lasse.meyer at dqbm.uzh.ch>

Citation (from within R, enter citation("cytomapper")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("cytomapper")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cytomapper")

Details biocViews DataImport, ImmunoOncology, MultipleComparison, Normalization, OneChannel, SingleCell, Software, TwoChannel Version 1.21.0 In Bioconductor since BioC 3.11 (R-4.0) (5 years) License GPL (>= 2) Depends R (>= 4.0), EBImage, SingleCellExperiment, methods Imports SpatialExperiment, S4Vectors, BiocParallel, HDF5Array, DelayedArray, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5, nnls System Requirements URL https://github.com/BodenmillerGroup/cytomapper Bug Reports https://github.com/BodenmillerGroup/cytomapper/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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