Package: spicyR
Type: Package
Title: Spatial analysis of in situ cytometry data
Version: 1.25.0
Authors@R: c(
    person("Nicolas", "Canete", , "nicolas.canete@sydney.edu.au", role = "aut"),
    person("Ellis", "Patrick", , "ellis.patrick@sydney.edu.au", role = c("aut", "cre")),
    person("Nicholas", "Robertson", , "nicholas.robertson@sydney.edu.au", role = "ctb"),
    person("Alex", "Qin", , "alex.qin@sydney.edu.au", role = "ctb"),
    person("Farhan", "Ameen", ,"farhan.ameen@sydney.edu.au", role = "ctb"),
    person("Shreya", "Rao", ,"shreya.rajeshrao@sydney.edu.au", role = "ctb")
  )
Description: The spicyR package provides a framework for performing
        inference on changes in spatial relationships between pairs of
        cell types for cell-resolution spatial omics technologies.
        spicyR consists of three primary steps: (i) summarizing the
        degree of spatial localization between pairs of cell types for
        each image; (ii) modelling the variability in localization
        summary statistics as a function of cell counts and (iii)
        testing for changes in spatial localizations associated with a
        response variable.
License: GPL (>=2)
LazyData: true
biocViews: SingleCell, CellBasedAssays, Spatial
Encoding: UTF-8
Depends: R (>= 4.1)
VignetteBuilder: knitr
BugReports: https://github.com/SydneyBioX/spicyR/issues
URL: https://ellispatrick.github.io/spicyR/
        https://github.com/SydneyBioX/spicyR,
        https://sydneybiox.github.io/spicyR/
Imports: BiocParallel, ClassifyR, S4Vectors, SingleCellExperiment,
        SpatialExperiment, SummarizedExperiment, cli, concaveman,
        coxme, data.table, dplyr, ggforce, ggh4x, ggnewscale, ggplot2,
        ggthemes, grDevices, lifecycle, lmerTest, magrittr, methods,
        pheatmap, rlang, scales, scam, simpleSeg, spatstat.explore,
        spatstat.geom, stats, survival, tibble, tidyr
Suggests: SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown,
        imcRtools, testthat (>= 3.0.0)
RoxygenNote: 7.3.3
Config/testthat/edition: 3
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
        libuv1-dev libxml2-dev libssl-dev libproj-dev libsqlite3-dev
        libudunits2-dev libnode-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:52:13 UTC
RemoteUrl: https://github.com/bioc/spicyR
RemoteRef: HEAD
RemoteSha: 3effcf4af65009e650a5c895b6545c76d9f99072
NeedsCompilation: no
Packaged: 2026-07-03 23:53:14 UTC; root
Author: Nicolas Canete [aut],
  Ellis Patrick [aut, cre],
  Nicholas Robertson [ctb],
  Alex Qin [ctb],
  Farhan Ameen [ctb],
  Shreya Rao [ctb]
Maintainer: Ellis Patrick <ellis.patrick@sydney.edu.au>