RegionalST
Investigating regions of interest and performing cross-regional analysis with spatial transcriptomics data
Bioconductor version: Release (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>
citation("RegionalST")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | KEGG, Reactome, Software, Spatial, Transcriptomics |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| 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_1.2.0.tar.gz |
| Windows Binary (x86_64) | RegionalST_1.2.0.zip |
| macOS Binary (x86_64) | RegionalST_1.2.0.tgz |
| macOS Binary (arm64) | RegionalST_1.2.0.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 |