Analysis code and data as submitted

Initial public release of the BE WELL analysis code and the de-identified tables used to generate the submitted manuscript. BE WELL (Berry nEctar Working to End Lung cancer) is a phase I/II placebo-controlled trial of black raspberry nectar in long-term smokers at high risk for lung cancer (NCT04267874).

Bittoni MA*, Jahanbakhshi S*, Bibi A, Williamson B, Dravillas C, Williams N, Hoyd R, Nevers L, Heitman K, Webb M, Grainger EM, Tabung FK, Li L, Vodovotz Y, Carbone DP, Clinton SK, Spakowicz D. A phase I/II placebo-controlled trial of black raspberry nectar for cancer prevention in long-term smokers at high risk for developing lung cancer (NCT04267874). Manuscript submitted for publication.

*These authors contributed equally.

This release contains:

• Manuscript notebooks in manuscript/scripts/. Knit them from that directory. They read ../../data and write panels to manuscript/figures/.
• The baseline characteristics table from manuscript/scripts/table1_baseline.R.
• Metagenomic processing scripts in processing/, and the saved clinical analysis object in data/derived/clinical_manuscript.rds.
• De-identified analysis tables in data/, including taxonomy, urine polyphenols, averaged cytokines, diet scores, and the aggregated HUMAnN3 table.
• The trial protocol, 2019C0089_Protocol.pdf.
• The R environment used for the manuscript notebooks: R 4.5.1, with package versions in manuscript/r-packages.txt.
• Code under the MIT license.

These manuscript panels are produced by the notebooks: 2A, 2E, 2F, 3A, 3C, 3D, 3E, 3F, 4A, 4B, 4C, 4D, 4E, and 4F. Figure 3B is the saved file manuscript/figures/fig3B.svg. Figure 1, panels 2C, 2D, and 4G, and the recruitment chart in Figure 2B were prepared outside these notebooks.

Sequencing reads, per-sample profiles, and the reference databases used to process them are on the Ohio Supercomputer Center. Paths are in data/external-files.md. The complete clinical export, the consent-date list, and the study-schedule workbooks remain on the lab drive. processing/prepare_clinical_manuscript.R is the only script that reads that drive; the notebooks use the saved RDS.

Earlier analyses, grant figures, and study-operations notebooks are in exploratory/ and are not part of the submitted results.