RegionalST

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see RegionalST.

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

Bioconductor version: 3.18

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 "4.3") and enter:


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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews KEGG, Reactome, Software, Spatial, Transcriptomics

Version 1.0.1

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

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

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package RegionalST_1.0.1.tar.gz

Windows Binary RegionalST_1.0.1.zip (64-bit only)

macOS Binary (x86_64) RegionalST_1.0.1.tgz

macOS Binary (arm64) RegionalST_1.0.1.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

Old Source Packages for BioC 3.18 Source Archive