COMPASS ICI response prediction dataset

This record contains the Immunotherapy Response Patient (ITRP) dataset used for downstream fine-tuning and validation of the COMPASS foundation model.
The dataset aggregates 1,133 patients from 16 published immunotherapy cohorts (including RNA-seq TPM matrices, clinical annotations, and response labels.), spanning melanoma, bladder, renal, lung, gastric, and brain cancers. Each patient received immune checkpoint inhibitors (anti–PD-1, anti–PD-L1, or anti–CTLA-4).
ContentsThe ZIP archive includes two pandas pickle files:
ITRP.TPM.TABLE — gene-level RNA-seq TPM matrix across 1,133 patients.ITRP.PATIENT.TABLE — clinical metadata table containing cancer type, treatment, and response labels (responder vs. non-responder).These files were preprocessed and harmonized using the official COMPASS data-processing pipeline to ensure consistent gene naming, normalization, and cohort integration.
Documentation and preprocessing scripts are available at:
🔗 https://www.immuno-compass.com/help/index.html#datasets
🔗 https://github.com/mims-harvard/COMPASS-web/tree/main/TCGA_dataset_processing
Data accessDue to data-sharing and privacy regulations, the underlying patient-level data were originally obtained from controlled repositories such as EGA, dbGaP, and ENA.
Redistribution is restricted; users should request access from the corresponding repositories or original publications.