stJoincount

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 usc.edu>

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
Bioc Package Browser	https://code.bioconductor.org/browse/stJoincount/
Package Short Url	https://bioconductor.org/packages/stJoincount/
Package Downloads Report	Download Stats