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This is the development version of RegionalST; for the stable release version, see RegionalST.

Investigating regions of interest and performing cross-regional analysis with spatial transcriptomics data

Bioconductor version: Development (3.19)

This package analyze spatial transcriptomics data through cross-regional analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application.

Author: Ziyi Li [aut, cre]

Maintainer: Ziyi Li <zli16 at mdanderson.org>

Citation (from within R, enter citation("RegionalST")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

RegionalST HTML R Script
Reference Manual PDF


biocViews KEGG, Reactome, Software, Spatial, Transcriptomics
Version 1.1.1
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License GPL-3
Depends R (>= 4.3.0)
Imports stats, grDevices, utils, ggplot2, dplyr, scater, gridExtra, BayesSpace, fgsea, magrittr, SingleCellExperiment, RColorBrewer, Seurat, S4Vectors, tibble, TOAST, assertthat, colorspace, shiny, SummarizedExperiment
System Requirements
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Suggests BiocStyle, knitr, rmarkdown, gplots, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package RegionalST_1.1.1.tar.gz
Windows Binary RegionalST_1.1.1.zip
macOS Binary (x86_64) RegionalST_1.1.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/RegionalST
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RegionalST
Bioc Package Browser https://code.bioconductor.org/browse/RegionalST/
Package Short Url https://bioconductor.org/packages/RegionalST/
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