RegionalST

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 (3.20)

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")):

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("RegionalST")

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("RegionalST")
RegionalST HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews KEGG, Reactome, Software, Spatial, Transcriptomics
Version 1.3.0
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
System Requirements
URL
See More
Suggests BiocStyle, knitr, rmarkdown, gplots, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package RegionalST_1.3.0.tar.gz
Windows Binary RegionalST_1.3.0.zip
macOS Binary (x86_64) RegionalST_1.3.0.tgz
macOS Binary (arm64) RegionalST_1.3.0.tgz
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/
Package Downloads Report Download Stats