DOI: 10.18129/B9.bioc.stJoincount  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see stJoincount.

stJoincount - Join count statistic for quantifying spatial correlation between clusters

Bioconductor version: 3.16

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.

Author: Jiarong Song [cre, aut] , Rania Bassiouni [aut], David Craig [aut]

Maintainer: Jiarong Song <songjiar at>

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biocViews BiocViews, Clustering, Software, Spatial, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.2.0)
Imports graphics, stats, dplyr, magrittr, sp, raster, spdep, ggplot2, pheatmap, grDevices, Seurat, SpatialExperiment, SummarizedExperiment
Suggests knitr, rmarkdown, testthat (>= 3.0.0)
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