Liao R2 analysis code archive

This archive contains the principal scripts used for the analyses reported in the revised manuscript.

Directory order
1. 01_MR: discovery-stage eQTL processing/MR, GTEx V10 replication-stage MR, and BWMR scripts.
2. 02_Transcriptomics: GSE196533, GSE4290, GSE116520, and cross-cohort meta-analysis scripts.
3. 03_Single_Cell_Virtual_Knockout: GSE131928 audit, annotation integration, patient-balanced sampling, formal scTenifoldKnk analysis, and cross-seed summarization.
4. 04_Enrichment_and_Network: functional enrichment and shared-network analysis.

Reproducibility notes
- R analyses were performed with R 4.4.2. Package versions used in the manuscript are listed in the Supplementary Methods.
- Paths in the archived scripts reflect the original local analysis environment and must be changed before rerunning on another system.
- Controlled-access GBM GWAS files are not redistributed. They remain available from the European Genome-phenome Archive under accession EGAD00010001657, subject to the original data-access conditions.
- Public transcriptomic inputs are available from GEO under GSE196533, GSE4290, GSE116520, and GSE131928.
- The archive contains analysis code only; raw or controlled-access data are not included.
