Package: SpaTopic
Type: Package
Title: Topic Inference to Identify Tissue Architecture in Multiplexed
        Images
Version: 1.2.0
Date: 2025-02-27
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
NeedsCompilation: yes
Packaged: 2025-03-03 16:44:38 UTC; xiyupeng
Author: Xiyu Peng [aut, cre] (<https://orcid.org/0000-0003-4232-0910>)
Maintainer: Xiyu Peng <pansypeng124@gmail.com>
Repository: CRAN
Date/Publication: 2025-03-03 17:00:09 UTC
Built: R 4.3.3; x86_64-apple-darwin20; 2025-03-03 17:14:17 UTC; unix
Archs: SpaTopic.so.dSYM
