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

Bioconductor version: Release (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>

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


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

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


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 1.2.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
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
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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_1.2.0.tar.gz
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macOS Binary (x86_64) RegionalST_1.2.0.tgz
macOS Binary (arm64) RegionalST_1.2.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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