stJoincount

DOI: 10.18129/B9.bioc.stJoincount    

stJoincount - Join count statistic for quantifying spatial correlation between clusters

Bioconductor version: Release (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 usc.edu>

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

Installation

To install this package, start R (version "4.2") 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")

 

HTML R Script Introduction to stJoincount
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

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
LinkingTo
Suggests knitr, rmarkdown, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL https://github.com/Nina-Song/stJoincount
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package stJoincount_1.0.0.tar.gz
Windows Binary stJoincount_1.0.0.zip
macOS Binary (x86_64) stJoincount_1.0.0.tgz
macOS Binary (arm64) stJoincount_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/stJoincount
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/stJoincount
Package Short Url https://bioconductor.org/packages/stJoincount/
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