Tool to capture spatial colocalization and interaction in the TME using topological analysis in spatial transcriptomics data
- Cite as: Bae S, Lee H, Na KJ, Lee DS, Choi H, Kim YT. STopover captures spatial colocalization and interaction in the tumor microenvironment using topological analysis in spatial transcriptomics data. Genome Med. 2025 Apr 1;17(1):33. doi: 10.1186/s13073-025-01457-1. PMID: 40170080; PMCID: PMC11963362.
conda create -n STopover python=3.8
conda activate STopover
pip install jupyter git+https://github.com/bsungwoo/STopover.git
# Install additional packages for VisiumHD analysis
pip install bin2cell tacco tensorflow
python -m ipykernel install --user --name STopover --display-name STopover
conda activate STopover
python
from STopover import app
app.main()
# Install BiocManager dependencies
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("clusterProfiler")
BiocManager::install("org.Mm.eg.db")
BiocManager::install("org.Hs.eg.db")
# Install STopover
devtools::install_github("bsungwoo/STopover", force = T)
3. Standalone app (packaged with pyinstaller)
Please download file (STopover ver. 1.1.0): STopover_v1_windows.exe
** Python
Please refer to yaml file: Python requirements
** R
Please refer to DESCRIPTION file: R requirements
Please refer to README_Python.md
Please refer to STopover_visium, STopover_visiumHD, STopover_imageST: CosMx, STopover_imageST: Xenium, STopover_imageST: preprocess from cell- to grid-level data
Please refer to the below documents
Link to documents: STopover_visium, STopover_imageST