RegionalST

DOI: 10.18129/B9.bioc.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 (3.19)

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>

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")

 

HTML	R Script	RegionalST
PDF		Reference Manual
Text		NEWS

Details

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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, gplots, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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/
Package Downloads Report	Download Stats