Package: BayesSpace
Version: 1.18.4
Date: 2025-06-17
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 (<
        2.0.0), utils, dplyr, rlang, ggplot2, tibble, rjson, tidyr,
        scales, microbenchmark, BiocFileCache, BiocSingular,
        BiocParallel
License: MIT + file LICENSE
RoxygenNote: 7.3.2
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
git_url: https://git.bioconductor.org/packages/BayesSpace
git_branch: RELEASE_3_21
git_last_commit: 1c37eef
git_last_commit_date: 2025-07-15
Repository: Bioconductor 3.21
Date/Publication: 2025-07-17
Packaged: 2025-07-17 23:35:18 UTC; biocbuild
Author: Edward Zhao [aut],
  Senbai Kang [aut, cre],
  Matt Stone [aut],
  Xing Ren [ctb],
  Raphael Gottardo [ctb]
Maintainer: Senbai Kang <senbai.kang@chuv.ch>
Built: R 4.5.1; aarch64-apple-darwin20; 2025-07-19 19:22:53 UTC; unix
