DESCRIPTION

Package: spicyR
Type: Package
Title: Spatial analysis of in situ cytometry data
Version: 1.19.3
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: 
    ggplot2,
    concaveman,
    BiocParallel,
    spatstat.explore,
    spatstat.geom,
    lmerTest,
    S4Vectors,
    methods,
    pheatmap,
    rlang,
    grDevices,
    stats,
    data.table,
    dplyr,
    tidyr,
    scam,
    SingleCellExperiment,
    SpatialExperiment,
    SummarizedExperiment,
    ggforce,
    ClassifyR,
    tibble,
    magrittr,
    cli,
    survival,
    ggthemes,
    ggh4x,
    coxme,
    ggnewscale,
    lifecycle,
    simpleSeg
Suggests: 
    SpatialDatasets,
    BiocStyle,
    knitr,
    rmarkdown,
    pkgdown,
    imcRtools,
    testthat (>= 3.0.0)
RoxygenNote: 7.3.2
Config/testthat/edition: 3