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>
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")| Introduction to stJoincount | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiocViews, Clustering, Software, Spatial, Transcriptomics |
| Version | 1.0.0 |
| 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 |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Old Source Packages for BioC 3.16 | Source Archive |