Analysis data for isp-confound-toolkit

This dataset contains cached Geneformer path-D response files, DESeq2/pseudobulk differential-expression outputs, tokenization-coverage diagnostics, path-D validation results, coverage-resampling curves, figure source files, reported-number provenance tables, and supplementary audit files supporting the manuscript “A confound-diagnostic toolkit for foundation-model in-silico perturbation, with a cautionary Geneformer case study”. Source code is maintained separately in the GitHub repository isp-confound-toolkit.