DESCRIPTION

Package: SpaTopic
Type: Package
Title: Topic Inference to Identify Tissue Architecture in Multiplexed Images
Version: 1.1.0.9900
Date: 2024-04-22
Authors@R: person("Xiyu", "Peng", email = "pansypeng124@gmail.com",
  role = c("aut", "cre"),comment = c(ORCID = "0000-0003-4232-0910"))
Description: A novel spatial topic model to integrate both cell type and spatial information to identify the complex spatial tissue architecture on multiplexed tissue images without human intervention. The Package implements a collapsed Gibbs sampling algorithm for inference. 'SpaTopic' is scalable to large-scale image datasets without extracting neighborhood information for every single cell. For more details on the methodology, see <https://xiyupeng.github.io/SpaTopic/>.
License: GPL (>= 3)
Depends: R (>= 3.5.0),
Imports: Rcpp (>= 0.12.0),
         RANN (>= 2.6.0),
         sf (>= 1.0-12),
         methods (>= 3.4),
         foreach (>= 1.5.0),
         iterators (>= 1.0),
LinkingTo: Rcpp, 
           RcppArmadillo,
           RcppProgress,
Suggests: 
    knitr,
    rmarkdown,
    SeuratObject (>= 4.9.9.9086),
    doParallel (>= 1.0),
VignetteBuilder: knitr
RoxygenNote: 7.3.1
Encoding: UTF-8
LazyData: true
URL: https://github.com/xiyupeng/SpaTopic
BugReports: https://github.com/xiyupeng/SpaTopic/issues