Cell-GPS

Cell-GPS is a Python package for spatial topology analysis in spatial omics data. Cell-GPS is used to compute cophenetic distance-based structure maps, analyze cell-cell and transcript-cell relationships, and visualize multiscale tissue organization.

Package names

• Python distribution: Cell-GPS

• Python import package: cellgps

• R package/repository: cellgpsr

• Windows executable: cellgps.exe

• Windows release: latest open v2 DOI https://doi.org/10.5281/zenodo.19482685; version-series route https://zenodo.org/records/17859173

Key features

• Compute cophenetic distance matrices from AnnData objects or coordinate tables.

• Generate StructureMap heatmaps and circular dendrograms.

• Load and preprocess 10x Xenium outputs.

• Run transcript-by-cell analysis for large spatial datasets.

• Support memory-optimized workflows for larger coordinate tables.

Installation

Install from GitHub:

pip install git+https://github.com/hutaobo/cellgps.git

For local inspection:

git clone https://github.com/hutaobo/cellgps.git
cd cellgps
pip install -e .

Reviewer note

The recommended import namespace is src/cellgps/. Legacy compatibility modules remain in src/sfplot/. Curated manuscript figure and supplementary table notebooks are stored in Cell-GPS manuscript code/. See docs/project/REVIEWER_GUIDE.md for a short walkthrough of the repository.