Sepsis whole-blood transcriptomic benchmark

Version 1.0.0 (release tag v1.0.0) reproducibility release supporting the manuscript “Auditing whole-blood transcriptomic gradients, subtype projection, and mortality informativeness in adult sepsis: a multi-cohort benchmark”.

• Project home: https://github.com/txfengj/sepsis-transcriptomic-benchmark
• Archived release: https://doi.org/10.5281/zenodo.21289941 (DOI: 10.5281/zenodo.21289941)
• Authors: Jun Feng (txfengj@email.ncu.edu.cn) and other authors

Scope

This release contains code, aggregate non-identifiable result tables, figure source data, manuscript source, and MCP-counter signature provenance for an original seven-cohort computational benchmark. It does not contain raw public-cohort downloads, credentialed MIMIC-IV data, CIBERSORTx materials, local package libraries, internal conversations, prompts, handoff notes, reviewer simulations, or obsolete submission drafts.

Reproducibility boundary

• Public cohort accessions and expected analysis sample counts are listed in data/public_cohort_accessions.csv.
• Key staged scripts are under scripts/ and analysis/.
• Aggregate v7 source tables are under results/tables_v7/.
• Figure-level source files are under figure_source_data/.
• The manuscript and supplement source are under manuscript/.
• MCP-counter signatures, upstream commit, license, and checksums are under third_party/MCPcounter/.

Raw expression and metadata files must be retrieved directly from GEO and BioStudies/ArrayExpress under their source terms. MIMIC-IV row-level and derived data are not redistributed; MIMIC-IV is not needed to reproduce the molecular benchmark conclusions.

Tested environment

The released workflow was tested on Ubuntu 24.04.4 LTS (x86_64) with R 4.6.1 and Python 3.12.3. Environment specifications are provided under environment/. This release does not claim platform independence.

Licensing

• Original analysis code: MIT License (LICENSE).
• Original documentation and aggregate derived result tables: Creative Commons Attribution 4.0 International (LICENSE-DATA).
• Third-party material retains its original license and is not relicensed; see THIRD_PARTY_NOTICES.md.

See docs/REPRODUCIBILITY.md and docs/DATA_AND_ACCESS_POLICY.md for the reproducibility and data-access boundaries.

Repository integrity

REPOSITORY_FILE_MANIFEST_v1.0.0.tsv records the category, license class, release reason, size, and SHA256 digest for repository content. SHA256SUMS.txt provides a standard checksum list. The checksum file excludes itself to avoid recursive hashing.