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stJoincount

stJoincount - Join count statistic for quantifying spatial correlation between clusters


Bioconductor version: Release (3.18)

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.

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

Maintainer: Jiarong Song <songjiar at usc.edu>

Citation (from within R, enter citation("stJoincount")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("stJoincount")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("stJoincount")
Introduction to stJoincount HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews BiocViews, Clustering, Software, Spatial, Transcriptomics
Version 1.4.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License MIT + file LICENSE
Depends R (>= 4.2.0)
Imports graphics, stats, dplyr, magrittr, sp, raster, spdep, ggplot2, pheatmap, grDevices, Seurat, SpatialExperiment, SummarizedExperiment
System Requirements
URL https://github.com/Nina-Song/stJoincount
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Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package stJoincount_1.4.0.tar.gz
Windows Binary stJoincount_1.4.0.zip
macOS Binary (x86_64) stJoincount_1.4.0.tgz
macOS Binary (arm64) stJoincount_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/stJoincount
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/stJoincount
Bioc Package Browser https://code.bioconductor.org/browse/stJoincount/
Package Short Url https://bioconductor.org/packages/stJoincount/
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