BayesSpace

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see BayesSpace.

Clustering and Resolution Enhancement of Spatial Transcriptomes

Bioconductor version: 3.19

Tools for clustering and enhancing the resolution of spatial gene expression experiments. BayesSpace clusters a low-dimensional representation of the gene expression matrix, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.

Author: Edward Zhao [aut], Matt Stone [aut, cre], Xing Ren [ctb], Raphael Gottardo [ctb]

Maintainer: Matt Stone <mstone at fredhutch.org>

Citation (from within R, enter citation("BayesSpace")):

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("BayesSpace")

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("BayesSpace")

BayesSpace	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, DataImport, GeneExpression, ImmunoOncology, SingleCell, Software, Transcriptomics
Version	1.14.0
In Bioconductor since	BioC 3.12 (R-4.0) (4 years)
License	MIT + file LICENSE
Depends	R (>= 4.0.0), SingleCellExperiment
Imports	Rcpp (>= 1.0.4.6), stats, purrr, scater, scran, SummarizedExperiment, coda, rhdf5, S4Vectors, Matrix, assertthat, mclust, RCurl, DirichletReg, xgboost, utils, ggplot2, scales, BiocFileCache, BiocSingular
System Requirements	C++11
URL	edward130603.github.io/BayesSpace
Bug Reports	https://github.com/edward130603/BayesSpace/issues

Suggests	testthat, knitr, rmarkdown, igraph, spatialLIBD, dplyr, viridis, patchwork, RColorBrewer, Seurat
Linking To	Rcpp, RcppArmadillo, RcppDist, RcppProgress
Enhances
Depends On Me
Imports Me	RegionalST
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	BayesSpace_1.14.0.tar.gz
Windows Binary (x86_64)	BayesSpace_1.14.0.zip (64-bit only)
macOS Binary (x86_64)	BayesSpace_1.14.0.tgz
macOS Binary (arm64)	BayesSpace_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BayesSpace
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BayesSpace
Bioc Package Browser	https://code.bioconductor.org/browse/BayesSpace/
Package Short Url	https://bioconductor.org/packages/BayesSpace/
Package Downloads Report	Download Stats