RegionalST

Investigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data

Bioconductor version: 3.24 · Package version: 1.11.0

This package analyze spatial transcriptomics data through cross-regional cell type-specific 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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RegionalST")

Details

Maintainer	Ziyi Li <zli16@mdanderson.org>
Author	Ziyi Li [aut, cre]
License	GPL-3
Downloads rank	399
Source branch	devel
biocViews	KEGG, Reactome, Software, Spatial, Transcriptomics

Documentation

Understanding Intrasample Heterogeneity from ST data with RegionalST

Download

Follow the installation instructions to use this package in your R session.

Source package	RegionalST_1.11.0.tar.gz
Windows binary (x86_64)	RegionalST_1.11.0.zip
macOS binary (arm64)	RegionalST_1.11.0.tgz
macOS binary (x86_64)	RegionalST_1.11.0.tgz

Dependencies

Depends: R (>= 4.3.0)

Imports: stats, grDevices, utils, ggplot2, dplyr, scater, gridExtra, BiocStyle, BayesSpace, fgsea, magrittr, SingleCellExperiment, RColorBrewer, Seurat, S4Vectors, tibble, TOAST, assertthat, colorspace, shiny, SummarizedExperiment

Suggests: knitr, rmarkdown, gplots, testthat (>= 3.0.0)