Package: BayesSpace
Version: 1.23.0
Date: 2026-01-08
Title: Clustering and Resolution Enhancement of Spatial Transcriptomes
Authors@R: c(
    person("Edward", "Zhao", role=c("aut"), email="edward130603@gmail.com"),
    person("Senbai", "Kang", role=c("aut", "cre"), email="senbai.kang@chuv.ch"),	
    person("Matt", "Stone", role=c("aut"), email="mstone@fredhutch.org"),
    person("Xing", "Ren", role=c("ctb"), email="xren2@fredhutch.org"),
    person("Raphael", "Gottardo", role=c("ctb"), email="rgottard@fredhutch.org"))
Description: 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.
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 (>=
        3.0.0), utils, dplyr, rlang, ggplot2, tibble, rjson, tidyr,
        scales, microbenchmark, BiocFileCache, BiocSingular,
        BiocParallel
License: MIT + file LICENSE
RoxygenNote: 7.3.3
LinkingTo: Rcpp, RcppArmadillo, RcppDist, RcppProgress
NeedsCompilation: yes
SystemRequirements: C++17
Encoding: UTF-8
Suggests: testthat, knitr, rmarkdown, igraph, spatialLIBD, viridis,
        patchwork, RColorBrewer, Seurat
VignetteBuilder: knitr
biocViews: Software, Clustering, Transcriptomics, GeneExpression,
        SingleCell, ImmunoOncology, DataImport
BugReports: https://github.com/edward130603/BayesSpace/issues
URL: edward130603.github.io/BayesSpace
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make
        libharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev
        libwebp-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:53:57 UTC
RemoteUrl: https://github.com/bioc/BayesSpace
RemoteRef: HEAD
RemoteSha: 0411308424722c3271e205fde699d86389e6ee90
Packaged: 2026-06-23 19:10:15 UTC; root
Author: Edward Zhao [aut],
  Senbai Kang [aut, cre],
  Matt Stone [aut],
  Xing Ren [ctb],
  Raphael Gottardo [ctb]
Maintainer: Senbai Kang <senbai.kang@chuv.ch>