Package: SpaTopic 1.1.0
Xiyu Peng
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/>.
Authors:
SpaTopic_1.1.0.tar.gz
SpaTopic_1.1.0.tar.gz(r-4.5-noble)SpaTopic_1.1.0.tar.gz(r-4.4-noble)
SpaTopic_1.1.0.tgz(r-4.4-emscripten)SpaTopic_1.1.0.tgz(r-4.3-emscripten)
SpaTopic.pdf |SpaTopic.html✨
SpaTopic/json (API)
NEWS
| # Install 'SpaTopic' in R: |
| install.packages('SpaTopic', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/xiyupeng/spatopic/issues
- lung5 - Example input data for 'SpaTopic'
Last updated 6 months agofrom:4c8564c489. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 20 2024 |
| R-4.5-linux-x86_64 | OK | Sep 20 2024 |
Exports:Seurat5obj_to_SpaTopicSpaTopic_inferencestratified_sampling_sf
Dependencies:classclassIntcodetoolsDBIe1071foreachiteratorsKernSmoothmagrittrMASSproxyRANNRcppRcppArmadilloRcppProgresss2sfunitswk
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A class of the output from 'SpaTopic' | gibbs.res-class |
| Example input data for 'SpaTopic' | lung5 |
| Convert a Seurat v5 object as the input of 'SpaTopic' | Seurat5obj_to_SpaTopic |
| 'SpaTopic': fast topic inference to identify tissue architecture in multiplexed images | SpaTopic_inference |
| 'SpaTopic' R package | SpaTopic-Package |
| Spatially stratified random sample points from an image. | stratified_sampling_sf |
