RegionalST
This is the development version of RegionalST; for the stable release version, see RegionalST.
Investigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data
Bioconductor version: Development (3.24)
This package analyze spatial transcriptomics data through cross-regional cell type-specific 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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | KEGG, Reactome, Software, Spatial, Transcriptomics |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.3.0) |
| Imports | stats, grDevices, utils, ggplot2, dplyr, scater, gridExtra, BiocStyle, BayesSpace, fgsea, magrittr, SingleCellExperiment, RColorBrewer, Seurat, S4Vectors, tibble, TOAST, assertthat, colorspace, shiny, SummarizedExperiment |
| System Requirements | |
| URL |
See More
| Suggests | 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_1.11.0.tar.gz |
| Windows Binary (x86_64) | RegionalST_1.11.0.zip |
| macOS Binary (big-sur-x86_64) | RegionalST_1.11.0.tgz |
| macOS Binary (sonoma-arm64) | RegionalST_1.11.0.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 |