NeuroMetBench reproducibility package

NeuroMetBench is a patient-aware evidence-bounding methodology for evaluating transcript-derived metabolic representations across cancer proteogenomic contexts. The framework separates patient-level association, cross-context transport, multiplicity, representation coverage, numerical compatibility, reproducibility, provenance, and claim admissibility so that computationally derived metabolic representations are interpreted only at the level supported by the available evidence.

Version 2.1.0 is a post-rejection scientific revision of the NeuroMetBench reproducibility package. It preserves the rejected v2.0.7 state as immutable historical evidence while reframing the study for integrative genomics and adding a frozen exploratory cross-cohort attenuation analysis. In the evaluated serine representation, RNA-protein concordance was stronger in the LSCC cohort than in the CNS/high-grade-glioma cohort, with Spearman rho values of 0.90705584 and 0.62661458, respectively. The exploratory cross-cohort difference was 0.28044126 with a 100,000-replicate patient-bootstrap 95% interval of 0.14267615 to 0.43803676.

The release preserves adverse, null, unsupported, and non-admitted findings. It does not establish measured metabolic flux, causal metabolic regulation, clinical utility, universal method superiority, independent biochemical validation, or a generally validated metabolic benchmarking framework. The principal RNA-protein endpoint is a same-gene cross-modal comparison and should not be interpreted as direct biochemical or flux validation.

The archive contains the manuscript-associated reproducibility authorities, verification code, figure-generation workflow, statistical authorities, post-rejection analysis records, provenance materials, claim-boundary records, and supporting files required to audit the reported results. Raw third-party molecular matrices are not redistributed where external source licenses or access conditions govern redistribution.

The reusable neurometbench-ref software component remains separately versioned at 1.0.1.