stJoincount
This is the development version of stJoincount; for the stable release version, see stJoincount.
stJoincount - Join count statistic for quantifying spatial correlation between clusters
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Jiarong Song <songjiar at usc.edu>
citation("stJoincount")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 1.9.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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 | BiocStyle, 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_1.9.0.tar.gz |
| Windows Binary (x86_64) | stJoincount_1.9.0.zip |
| macOS Binary (x86_64) | stJoincount_1.9.0.tgz |
| macOS Binary (arm64) | |
| 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 |