SpaTopic: Topic Inference to Identify Tissue Architecture in Multiplexed Images
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/>.
| Version: | 1.2.0 |
| 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) |
| Published: | 2025-03-03 |
| DOI: | 10.32614/CRAN.package.SpaTopic |
| Author: | Xiyu Peng  [aut,
cre] |
| Maintainer: | Xiyu Peng <pansypeng124 at gmail.com> |
| BugReports: | https://github.com/xiyupeng/SpaTopic/issues |
| License: | GPL (≥ 3) |
| URL: | https://github.com/xiyupeng/SpaTopic |
| NeedsCompilation: | yes |
| Materials: | README, NEWS |
| CRAN checks: | SpaTopic results |
Documentation:
| Reference manual: | SpaTopic.html , SpaTopic.pdf |
| Vignettes: |
SpaTopic Basics (source, R code) |
Downloads:
| Package source: | SpaTopic_1.2.0.tar.gz |
| Windows binaries: | r-devel: SpaTopic_1.2.0.zip, r-release: SpaTopic_1.2.0.zip, r-oldrel: SpaTopic_1.2.0.zip |
| macOS binaries: | r-release (arm64): SpaTopic_1.2.0.tgz, r-oldrel (arm64): SpaTopic_1.2.0.tgz, r-release (x86_64): SpaTopic_1.2.0.tgz, r-oldrel (x86_64): SpaTopic_1.2.0.tgz |
| Old sources: | SpaTopic archive |
Linking:
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