BayesSpace

DOI: 10.18129/B9.bioc.BayesSpace    

Clustering and Resolution Enhancement of Spatial Transcriptomes

Bioconductor version: Release (3.12)

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 "4.0") and enter:

if (!requireNamespace("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")

 

HTML R Script BayesSpace
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Clustering, DataImport, GeneExpression, ImmunoOncology, SingleCell, Software, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
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
LinkingTo Rcpp, RcppArmadillo, RcppDist, RcppProgress
Suggests testthat, knitr, rmarkdown, igraph, spatialLIBD, dplyr, viridis, patchwork, RColorBrewer, Seurat
SystemRequirements C++11
Enhances
URL edward130603.github.io/BayesSpace
BugReports https://github.com/edward130603/BayesSpace/issues
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_1.0.0.tar.gz
Windows Binary BayesSpace_1.0.0.zip
macOS 10.13 (High Sierra) BayesSpace_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BayesSpace
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BayesSpace
Package Short Url https://bioconductor.org/packages/BayesSpace/
Package Downloads Report Download Stats

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