Package: cytomapper
Version: 1.22.0
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
git_url: https://git.bioconductor.org/packages/cytomapper
git_branch: RELEASE_3_22
git_last_commit: 0d3160a
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 03:21:29 UTC; biocbuild
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>
Built: R 4.5.1; ; 2025-10-30 12:11:53 UTC; unix
