RegionalST

DOI: 10.18129/B9.bioc.RegionalST  

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

Bioconductor version: Release (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")

 

HTML R Script RegionalST
PDF   Reference Manual
Text   NEWS

Details

biocViews KEGG, Reactome, Software, Spatial, Transcriptomics
Version 1.0.1
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_1.0.1.tar.gz
Windows Binary RegionalST_1.0.1.zip
macOS Binary (x86_64) RegionalST_1.0.1.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
Old Source Packages for BioC 3.18 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: