SpaTopic: Topic Inference to Identify Tissue Architecture in Multiplexed Images

A novel spatial topic model to integrate both cell type and spatial information to identify the complex spatial tissue architecture on multiplexed tissue images without human intervention. The Package implements a collapsed Gibbs sampling algorithm for inference. The method is highly scalable to large-scale image datasets without extracting neighborhood information for every single cell. The package supports spatially resolved cell-level data analysis, topic inference, visualization, and downstream biological interpretation of tissue microenvironments.

Version:	1.3.1
Depends:	R (≥ 3.5.0)
Imports:	Rcpp (≥ 0.12.0), RANN (≥ 2.6.0), sf (≥ 1.0-12), methods (≥ 3.4), foreach (≥ 1.5.0), iterators (≥ 1.0)
LinkingTo:	Rcpp, RcppArmadillo, RcppProgress
Suggests:	knitr, rmarkdown, SeuratObject (≥ 4.9.9.9086), doParallel (≥ 1.0), spelling
Published:	2026-05-29
DOI:	10.32614/CRAN.package.SpaTopic
Author:	Xiyu Peng [aut, cre], Nikki Xiao [aut]
Maintainer:	Xiyu Peng <pansypeng124 at gmail.com>
BugReports:	https://github.com/xiyupeng/SpaTopic/issues
License:	GPL (≥ 3)
URL:	https://xiyupeng.github.io/SpaTopic/, https://github.com/xiyupeng/SpaTopic, https://doi.org/10.1038/s41467-025-61821-y
NeedsCompilation:	yes
Language:	en-US
Citation:	SpaTopic citation info
Materials:	README, NEWS
CRAN checks:	SpaTopic results

Documentation:

Reference manual:	SpaTopic.html , SpaTopic.pdf
Vignettes:	SpaTopic Basics (source, R code)

Downloads:

Package source:	SpaTopic_1.3.1.tar.gz
Windows binaries:	r-devel: SpaTopic_1.3.1.zip, r-release: SpaTopic_1.3.1.zip, r-oldrel: SpaTopic_1.3.1.zip
macOS binaries:	r-release (arm64): SpaTopic_1.3.1.tgz, r-oldrel (arm64): SpaTopic_1.3.1.tgz, r-release (x86_64): SpaTopic_1.3.1.tgz, r-oldrel (x86_64): SpaTopic_1.3.1.tgz
Old sources:	SpaTopic archive

Linking:

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