Package: imcRtools
Version: 1.17.0
Title: Methods for imaging mass cytometry data analysis
Description: This R package supports the handling and analysis of
        imaging mass cytometry and other highly multiplexed imaging
        data. The main functionality includes reading in single-cell
        data after image segmentation and measurement, data formatting
        to perform channel spillover correction and a number of spatial
        analysis approaches. First, cell-cell interactions are detected
        via spatial graph construction; these graphs can be visualized
        with cells representing nodes and interactions representing
        edges. Furthermore, per cell, its direct neighbours are
        summarized to allow spatial clustering. Per image/grouping
        level, interactions between types of cells are counted,
        averaged and compared against random permutations. In that way,
        types of cells that interact more (attraction) or less
        (avoidance) frequently than expected by chance are detected.
Authors@R: 
    c(person("Nils", "Eling", role = "aut"),
      person("Tobias", "Hoch", role = "ctb"),
      person("Vito", "Zanotelli", role = "ctb"),
      person("Jana", "Fischer", role = "ctb"),
      person("Daniel", "Schulz", role = c("ctb", "cre"),email = "daniel.schulz@uzh.ch",comment = c(ORCID = "0000-0002-0913-1678")),
      person("Lasse","Meyer", role = "ctb"),
      person("Lutz","Marlene", role = "ctb"),
      person("Schiller","Chiara", role = "ctb"),
      person("Ibañez", "Victor", role = "ctb"))
License: GPL-3
Depends: R (>= 4.1), SpatialExperiment
Imports: S4Vectors, stats, utils, SummarizedExperiment, methods,
        pheatmap, scuttle, stringr, readr, EBImage, cytomapper, abind,
        BiocParallel, viridis, dplyr, magrittr, DT, igraph,
        SingleCellExperiment, vroom, BiocNeighbors, RTriangle, ggraph,
        tidygraph, ggplot2, data.table, sf, concaveman, tidyselect,
        distances, MatrixGenerics, rlang, grDevices
Suggests: CATALYST, grid, tidyr, BiocStyle, knitr, rmarkdown, markdown,
        testthat
biocViews: ImmunoOncology, SingleCell, Spatial, DataImport, Clustering
VignetteBuilder: knitr
URL: https://github.com/BodenmillerGroup/imcRtools
BugReports: https://github.com/BodenmillerGroup/imcRtools/issues
RoxygenNote: 7.3.2
Encoding: UTF-8
Config/pak/sysreqs: libabsl-dev cmake libfftw3-dev libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libgdal-dev gdal-bin
        libgeos-dev libglpk-dev make libharfbuzz-dev libmagick++-dev
        gsfonts libicu-dev libjpeg-dev libpng-dev libtiff-dev
        libxml2-dev libssl-dev libproj-dev libsqlite3-dev
        libudunits2-dev libnode-dev libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:12:28 UTC
RemoteUrl: https://github.com/bioc/imcRtools
RemoteRef: HEAD
RemoteSha: 00166f28885c3f34e2674969b26b85da9a97c15d
NeedsCompilation: no
Packaged: 2025-10-30 06:43:45 UTC; root
Author: Nils Eling [aut],
  Tobias Hoch [ctb],
  Vito Zanotelli [ctb],
  Jana Fischer [ctb],
  Daniel Schulz [ctb, cre] (ORCID:
    <https://orcid.org/0000-0002-0913-1678>),
  Lasse Meyer [ctb],
  Lutz Marlene [ctb],
  Schiller Chiara [ctb],
  Ibañez Victor [ctb]
Maintainer: Daniel Schulz <daniel.schulz@uzh.ch>
Built: R 4.6.0; ; 2025-10-30 06:46:55 UTC; windows
