DESCRIPTION

Package: cytomapper
Version: 1.17.0
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