STIM provides a comprehensive computational pipeline for the integration and analysis of spatial transcriptomics data. This tool is designed to integrate tissue histology with both high-definition spatial transcriptomics (e.g., Xenium) and transcriptome-wide spatial transcriptomics (e.g., Visium). STIM enables:
- Mapping gene expression across different spatial transcriptomics platforms
- Analyzing cell neighborhoods to identify spatial patterns and interactions
- Inferring ligand-receptor interactions
Installation using pip:
pip install pySTIM
import pySTIM as pst