Reproducibility package for "Resampling-based evaluation of a transcriptomic prognostic model in clear cell renal cell carcinoma: unstable feature selection and variable external performance"

This repository contains the frozen reproducibility package supporting the manuscript “Resampling-based evaluation of a transcriptomic prognostic model in clear cell renal cell carcinoma: unstable feature selection and variable external performance.” The package contains derived data, patient- and fold-level outputs from the primary repeated cross-validation analysis, fixed-panel sensitivity results, locked model parameters, external validation outputs, source data for reported tables and figures where retained, diagnostic records, available analysis code, and provenance documentation. Original public datasets are not redistributed; they remain available from the NCI Genomic Data Commons (TCGA-KIRC), EMBL-EBI ArrayExpress/BioStudies (E-MTAB-1980), and NCBI Gene Expression Omnibus (GSE29609, GSE53757, and GSE40435). The package supports independent verification of the frozen reported results but does not provide exact end-to-end re-execution of the final stabilized primary repeated-cross-validation procedure. The exact final stabilized outer-fold runner could not be recovered from the frozen project archive. Original IPCW bootstrap draw-level replicates and the machine-readable source table used for the Figure 6A Kaplan–Meier plot were also not retained. These provenance limitations are documented in README.md, RELEASE_LIMITATIONS.md, and PLOS_DATA_RELEASE_AUDIT.md. No scientific analyses were rerun and no manuscript results were modified during preparation of this public release.