SEFF_HCC

Reproducible analysis code and source data for:

GPNMB-state remodelling and persistence of a high-turnover repair front link incomplete fibrosis resolution to hepatocellular carcinoma

This release supports a mechanistic model in which fibrosis regression is a field transition rather than simple programme extinction. Across bulk transcriptomic, single-cell, multi-omic, spatial, paired-biopsy and event-linked cohorts, the analyses resolve:

• a transportable fibrosis backbone and a residual epithelial branch;
• a slower HSC chromatin/Q-transition scar-memory layer;
• stage-dependent GPNMB-positive myeloid repair, matrix-remodelling and antigen/checkpoint states;
• ecological handoff during fibrosis regression;
• within-patient withdrawal of the repair front and GPNMB states;
• a persistent high-turnover repair front associated with incident HCC; and
• a recurrence-phase transition from repair-dominant to matrix/checkpoint-dominant ecology.

Release contents

• 05_CODE/ — frozen Python and JavaScript analysis and submission-assembly scripts.
• 11_MANUSCRIPT/source_data/ — panel-level machine-readable source data for Figures 1–7.
• 11_MANUSCRIPT/Source_Data.xlsx — consolidated source-data workbook.
• 11_MANUSCRIPT/Supplementary_Tables.xlsx — supplementary tables, public claim chain and public execution registry.
• PUBLIC_DATASETS.csv — public source families, accessions, analytical units and roles.
• analysis_execution_map.csv — script-to-output-to-manuscript execution map.
• environment/ and requirements.txt — captured runtime information and Python dependencies.

Reproduction

The scripts assume this repository is the workspace root and therefore remain under 05_CODE/. Raw public matrices are not redistributed because of source size and repository terms. Retrieve them from the accessions in PUBLIC_DATASETS.csv, preserve the documented directory layout under 07_DATA/public_raw/, and run the relevant script from the repository root.

Example:

python -m venv .venv
source .venv/bin/activate
python -m pip install -r requirements.txt
python 05_CODE/analyze_hcc005_gse15654_incident_hcc.py

Many scripts consume frozen intermediate tables generated by earlier analyses. The dependency-aware order and principal outputs are listed in analysis_execution_map.csv. Panel-level source data and the two workbooks permit direct numerical audit without redistributing the original matrices.

Data governance

This public release contains only analyses of public datasets and derived, non-identifiable manuscript source data. Local clinical VCTE/LIS records, patient queues, internal file paths and unrelated project branches are intentionally excluded.

Software and data license

Code, derived source data and documentation are released under the Creative Commons Attribution 4.0 International License. Reuse is permitted with appropriate attribution. Original public datasets remain subject to their source repositories' terms.

Citation

Please cite the versioned Zenodo record for this release:

Ying H, Zhang Z, Ran L, Qiao C, Dong C, Yu H. SEFF_HCC: Reproducible analysis code and source data for the persistent repair-front study. Version 1.0.0. Zenodo, 2026. https://doi.org/10.5281/zenodo.21696550

Citation metadata are also provided in CITATION.cff.

Authors

Hongyu Ying, Ze Zhang, Lisha Ran, Chunping Qiao, Chang Dong, and Hong-wei Yu.

Correspondence: Chang Dong (changdongydy@163.com) and Hong-wei Yu (541014155@qq.com), Department of Clinical Laboratory, Shanghai Pudong Hospital (Fudan University Pudong Medical Center), Shanghai, China.