Package: spicyR
Type: Package
Title: Test Changes in the Co-Localisation of Cell Types Between Groups
        of Patients
Version: 1.99.11
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("Sadiq", "Dohadwalla", role = "aut"),
    person("Elijah", "Willie", , "ewillie0004@gmail.com", role = "aut"),
    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: spicyR tests whether the spatial co-localisation of pairs
        of cell types differs between groups of patients, or is
        associated with patient outcome, in cell-resolution spatial
        omics data (imaging mass cytometry, CODEX, MIBI, Xenium, CosMx
        and others). Its default method, spicyR Cell, counts the cells
        of one type within a radius of each cell of another and
        compares the count with its exact expectation under random
        labelling of the observed cells. Images are combined within
        patients by a frailty generalised estimating equation, and
        differences are tested with a small-sample cluster-robust (CR2)
        variance with patients as the units. Covariates, several
        conditions, several radii and survival outcomes are supported,
        and the original image-level test is kept as an option. The
        computations run in a C++ core shared with the Python package
        spicyr.
License: GPL (>=2)
Copyright: The C++ port of concaveman in src/concaveman.cpp: see
        inst/COPYRIGHTS.
LazyData: false
biocViews: SingleCell, CellBasedAssays, Spatial, Survival
Encoding: UTF-8
Depends: R (>= 4.5.0)
VignetteBuilder: knitr
BugReports: https://github.com/SydneyBioX/spicyR/issues
URL: https://sydneybiox.github.io/spicyR/,
        https://github.com/SydneyBioX/spicyR
Imports: Rcpp, methods, stats, utils, grDevices, grid, splines,
        parallel, ggplot2, S4Vectors, survival
LinkingTo: Rcpp, RcppEigen
SystemRequirements: C++17
Suggests: SummarizedExperiment, plotly, dplyr, SingleCellExperiment,
        SpatialExperiment, lmerTest, lme4, scam, coxme, spatstat.geom,
        spatstat.explore, BiocParallel, SpatialDatasets, BiocStyle,
        knitr, rmarkdown, testthat (>= 3.0.0)
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Roxygen: list(markdown = TRUE)
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-10 02:18:39 UTC
RemoteUrl: https://github.com/bioc/spicyR
RemoteRef: HEAD
RemoteSha: 56ee2842c6b83cec2825d9767db31c5f7b4972cb
NeedsCompilation: yes
Packaged: 2026-10-10 07:26:25 UTC; root
Author: Nicolas Canete [aut],
  Ellis Patrick [aut, cre],
  Sadiq Dohadwalla [aut],
  Elijah Willie [aut],
  Nicholas Robertson [ctb],
  Alex Qin [ctb],
  Farhan Ameen [ctb],
  Shreya Rao [ctb]
Maintainer: Ellis Patrick <ellis.patrick@sydney.edu.au>