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:Xiyu Peng [aut, cre]

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'))

Peer review:

Bug tracker:https://github.com/xiyupeng/spatopic/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • lung5 - Example input data for 'SpaTopic'

openblascppopenmp

3.11 score 13 scripts 543 downloads 3 exports 19 dependencies

Last updated 8 months agofrom:4c8564c489. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-linux-x86_64OKDec 01 2024

Exports:Seurat5obj_to_SpaTopicSpaTopic_inferencestratified_sampling_sf

Dependencies:classclassIntcodetoolsDBIe1071foreachiteratorsKernSmoothmagrittrMASSproxyRANNRcppRcppArmadilloRcppProgresss2sfunitswk

SpaTopic Basics

Rendered fromIntro_SpaTopic.Rmdusingknitr::rmarkdownon Dec 01 2024.

Last update: 2024-04-23
Started: 2024-01-18