bsungwoo / STopover

capturing spatial colocalization and interaction in the TME using topological analysis in spatial transcriptomics data

STopover

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. bioRxiv, 2022.
• https://doi.org/10.1101/2022.11.16.516708

Installation and running

1. Python

Install conda environment and add jupyter kernel

  conda create -n STopover python=3.8
  conda activate STopover
  pip install git+https://github.com/bsungwoo/STopover.git
  pip install jupyter
  python -m ipykernel install --user --name STopover --display-name STopover

If you want to annotate cells in image-based ST using TACCO, please install

  conda activate STopover
  pip install tacco

Run GUI for STopover (PyQt)

  conda activate STopover
  python
  from STopover import app
  app.main()

2. R

  # 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_v1_windows.exe

Key packages

** Python
Please refer to yaml file: Python requirements
** R
Please refer to DESCRIPTION file: R requirements

Usage

Python Code Example

Please refer to README_Python.md
Please refer to STopover_visium, STopover_cosmx

R Code Example

Please refer to the below documents
Link to documents: STopover_visium, STopover_cosmx