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BayesSpace

Clustering and Resolution Enhancement of Spatial Transcriptomes


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews Clustering, DataImport, GeneExpression, ImmunoOncology, SingleCell, Software, Transcriptomics
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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
See More
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_1.12.0.tar.gz
Windows Binary BayesSpace_1.12.0.zip (64-bit only)
macOS Binary (x86_64) BayesSpace_1.12.0.tgz
macOS Binary (arm64) BayesSpace_1.12.0.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