SPIAT
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see SPIAT.
Spatial Image Analysis of Tissues
Bioconductor version: 3.19
SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.
Author: Anna Trigos [aut] , Yuzhou Feng [aut, cre] , Tianpei Yang [aut], Mabel Li [aut], John Zhu [aut], Volkan Ozcoban [aut], Maria Doyle [aut]
Maintainer: Yuzhou Feng <yuzhou.feng at petermac.org>
citation("SPIAT")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SPIAT")
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("SPIAT")
Details
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Package Archives
Follow Installation instructions to use this package in your R session.