Package: cytomapper
Version: 1.25.0
Title: Visualization of highly multiplexed imaging data in R
Description: 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.
Authors@R: 
    c(person("Nils", "Eling", role = c("aut"), 
      email = "nils.eling@dqbm.uzh.ch",
      comment = c(ORCID = "0000-0002-4711-1176")),
      person("Nicolas", "Damond", role = c("aut"), 
      email = "nicolas.damond@dqbm.uzh.ch", 
      comment = c(ORCID = "0000-0003-3027-8989")),
      person("Tobias", "Hoch", role = c("ctb")),
      person("Lasse", "Meyer", role = c("cre", "ctb"), 
      email = "lasse.meyer@dqbm.uzh.ch",
      comment = c(ORCID = "0000-0002-1660-1199")))
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
Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat,
        shinytest
biocViews: ImmunoOncology, Software, SingleCell, OneChannel,
        TwoChannel, MultipleComparison, Normalization, DataImport
VignetteBuilder: knitr
URL: https://github.com/BodenmillerGroup/cytomapper
BugReports: https://github.com/BodenmillerGroup/cytomapper/issues
RoxygenNote: 7.3.1
Encoding: UTF-8
Config/pak/sysreqs: cmake libfftw3-dev libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libgdal-dev gdal-bin
        libgeos-dev make libharfbuzz-dev libmagick++-dev gsfonts
        libicu-dev libjpeg-dev libpng-dev libtiff-dev libuv1-dev
        libssl-dev libproj-dev libsqlite3-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:52:15 UTC
RemoteUrl: https://github.com/bioc/cytomapper
RemoteRef: HEAD
RemoteSha: 7f3973c8cc632bf33cefe28121b946f468b9ef29
NeedsCompilation: no
Packaged: 2026-05-28 06:26:51 UTC; root
Author: Nils Eling [aut] (ORCID: <https://orcid.org/0000-0002-4711-1176>),
  Nicolas Damond [aut] (ORCID: <https://orcid.org/0000-0003-3027-8989>),
  Tobias Hoch [ctb],
  Lasse Meyer [cre, ctb] (ORCID: <https://orcid.org/0000-0002-1660-1199>)
Maintainer: Lasse Meyer <lasse.meyer@dqbm.uzh.ch>