Package: stJoincount
Type: Package
Title: stJoincount - Join count statistic for quantifying spatial
        correlation between clusters
Version: 1.0.0
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, the application of join count analysis to the spatial transcriptomics dataset. 
    This tool converts the spatial map into a raster object (a two-dimensional image as a rectangular matrix or grid of square pixels), 
    where clusters labelled spots are converted to adjacent pixels with a calculated resolution. 
    A neighbors' list was created based on the rasterized sample, which identifies adjacent and diagonal neighbors for each pixel. 
    After adding binary spatial weights to the neighbors' list, a multi-categorical join count analysis is then performed, 
    allowing all possible combinations of cluster pairings to be tabulated. 
    The function returns the observed join counts, the expected count under conditions of spatial randomness, 
    and the variance of observed to expected 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: 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
git_url: https://git.bioconductor.org/packages/stJoincount
git_branch: RELEASE_3_16
git_last_commit: 7b15655
git_last_commit_date: 2022-11-01
Date/Publication: 2022-11-01
NeedsCompilation: no
Packaged: 2022-11-01 23:09:23 UTC; biocbuild
Author: Jiarong Song [cre, aut] (<https://orcid.org/0000-0002-3673-4853>),
  Rania Bassiouni [aut],
  David Craig [aut]
Maintainer: Jiarong Song <songjiar@usc.edu>
Built: R 4.2.2; ; 2022-11-06 02:06:33 UTC; unix
