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BayesSpace

This is the development version of BayesSpace; for the stable release version, see BayesSpace.

Clustering and Resolution Enhancement of Spatial Transcriptomes

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.11.0
In Bioconductor since BioC 3.12 (R-4.0) (3 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
Linking To Rcpp, RcppArmadillo, RcppDist, RcppProgress
Suggests testthat, knitr, rmarkdown, igraph, spatialLIBD, dplyr, viridis, patchwork, RColorBrewer, Seurat
System Requirements C++11
Enhances
URL edward130603.github.io/BayesSpace
Bug Reports https://github.com/edward130603/BayesSpace/issues
See More
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 BayesSpace_1.11.0.tar.gz
Windows Binary BayesSpace_1.11.0.zip (64-bit only)
macOS Binary (x86_64) BayesSpace_1.11.0.tgz
macOS Binary (arm64)
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