Package: stJoincount
Type: Package
Title: stJoincount - Join count statistic for quantifying spatial
        correlation between clusters
Version: 1.15.0
Authors@R: c(
    person("Jiarong", "Song", email="songjiar@usc.edu",role=c("cre","aut"), comment = c('ORCID' = "0000-0002-3673-4853")),
    person("Rania", "Bassiouni", email="rbassiou@usc.edu", role=c("aut")),
    person("David","Craig",email="davidwcr@usc.edu", role=c("aut"))
    )
Description: stJoincount facilitates the application of join count
        analysis to spatial transcriptomic data generated from the 10x
        Genomics Visium platform. This tool first converts a labeled
        spatial tissue map into a raster object, in which each spatial
        feature is represented by a pixel coded by label assignment.
        This process includes automatic calculation of optimal raster
        resolution and extent for the sample. A neighbors list is then
        created from the rasterized sample, in which adjacent and
        diagonal neighbors for each pixel are identified. After adding
        binary spatial weights to the neighbors list, a
        multi-categorical join count analysis is performed to tabulate
        "joins" between all possible combinations of label pairs. The
        function returns the observed join counts, the expected count
        under conditions of spatial randomness, and the variance
        calculated under non-free sampling. The z-score is then
        calculated as the difference between observed and expected
        counts, divided by the square root of the variance.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.2.0)
Imports: graphics, stats, dplyr, magrittr, sp, raster, spdep, ggplot2,
        pheatmap, grDevices, Seurat, SpatialExperiment,
        SummarizedExperiment
RoxygenNote: 7.2.1
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
biocViews: Transcriptomics, Clustering, Spatial, BiocViews, Software
Bugreports: https://github.com/Nina-Song/stJoincount/issues
URL: https://github.com/Nina-Song/stJoincount
Config/testthat/edition: 3
Config/pak/sysreqs: libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev
        libglpk-dev make libmagick++-dev gsfonts libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev libproj-dev python3
        libsqlite3-dev libudunits2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:59:18 UTC
RemoteUrl: https://github.com/bioc/stJoincount
RemoteRef: HEAD
RemoteSha: a8ae4f7a74f90f9b09972348425f73e7f0e54722
NeedsCompilation: no
Packaged: 2026-07-03 23:12:17 UTC; root
Author: Jiarong Song [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-3673-4853>),
  Rania Bassiouni [aut],
  David Craig [aut]
Maintainer: Jiarong Song <songjiar@usc.edu>