spakowiczlab/ppiio: Code and processed data for Petouhoff et al., Cancer Immunol Immunother (2026)

Processed data and R Markdown notebooks to regenerate the figures and tables in:

Petouhoff A, Hicks R, Husain M, et al. Impact of proton pump inhibitors on immunotherapy is modulated by prior chemotherapy and linked to gut microbiome–immune cell signatures. Cancer Immunol Immunother. 2026;75:98. https://doi.org/10.1007/s00262-026-04346-7

This release includes:

• De-identified Cohort 1 clinical object (manuscript/data/cohort1-cleaned-clinical.RDS)
• Processed Cohort 2 microbiome objects and Cohort 3 MetaPhlAn/CyTOF tables
• Scripts in manuscript/scripts/ mapped to each published figure and table

Raw clinical extracts and sequencing reads are not included. See the README for data locations and how to knit each notebook.