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Bioconductor - BayesSpace (development version)

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 (3.22)

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], Senbai Kang [aut, cre], Matt Stone [aut], Xing Ren [ctb], Raphael Gottardo [ctb]

Maintainer: Senbai Kang <senbai.kang at chuv.ch>

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

To install this package, start R (version "4.5") 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")
Details biocViews Clustering, DataImport, GeneExpression, ImmunoOncology, SingleCell, Software, Transcriptomics Version 1.19.3 In Bioconductor since BioC 3.12 (R-4.0) (4.5 years) License MIT + file LICENSE Depends R (>= 4.0.0), SingleCellExperiment Imports Rcpp (>= 1.0.4.6), stats, methods, purrr, scater, scran, SummarizedExperiment, coda, rhdf5, S4Vectors, Matrix, magrittr, assertthat, arrow, mclust, RCurl, DirichletReg, xgboost (< 2.0.0), utils, dplyr, rlang, ggplot2, tibble, rjson, tidyr, scales, microbenchmark, BiocFileCache, BiocSingular, BiocParallel System Requirements C++17 URL edward130603.github.io/BayesSpace Bug Reports https://github.com/edward130603/BayesSpace/issues See More Suggests testthat, knitr, rmarkdown, igraph, spatialLIBD, 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.

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