Intermediate results for "Specificity-testing gene-set associations in epilepsy transcriptomics: a calibrated permutation pipeline and reporting standard"

Intermediate result tables underlying the manuscript Specificity-testing gene-set associations in epilepsy transcriptomics: a calibrated permutation pipeline and reporting standard. Expression-matched permutation tests for 248 gene sets across four public epilepsy cohorts (GSE256068, GSE213488, GSE128300, GSE272142; 148 samples); comparison of four specificity tests; label-permutation calibration; cell-type composition scores; spiked-in simulation; and the coding of 576 PubMed-indexed epilepsy bioinformatics papers. All primary data are public GEO series; no new sequencing data were generated. Code: https://github.com/mingyueqian0879/epilepsy-geneset-specificity (tag v1.0.0). Random seed 20260922.