Reviewer Guide

This repository contains the code used to develop the Cell-GPS workflow described in the manuscript.

Package naming

Suggested reading order

  • README.md

  • src/cellgps/analysis/searcher_findee_score.py

  • src/cellgps/preprocessing/data_processing.py

  • src/cellgps/analysis/tbc_analysis.py

Repository map

  • src/cellgps/: Python package and implementation modules

  • docs/: package documentation

  • Cell-GPS manuscript/: curated manuscript figure and table notebooks

  • examples/: compact package usage examples and small example data files

  • packaging/: historical packaging recipes and Windows executable build assets

Minimal install

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

Manuscript validation scope

The manuscript-validated scope is the COSTE/SSS workflow and the figure/table analyses mapped in Cell-GPS manuscript/ and docs/cellgps_science_manuscript_code_inventory.md. Ligand-receptor topology, pathway topology, Visium helpers, GUI entry points and other convenience APIs are included for reuse and development, but should be treated as optional or exploratory unless a manuscript notebook or documentation page explicitly maps them to a reported analysis.

Input contract

For the DataFrame workflow, the minimal required columns are x, y, and celltype.

Reproducibility note

Raw datasets are not bundled in this repository because of size and data-distribution constraints. The repository is intended to expose the code, analysis structure, and plotting workflows used in the study.