Data and code for: Protein complex covariance and functional dependency in glioblastoma across models and patient proteomes (Additional File 3)

This record is Additional File 3 (AF3) of the manuscript “Protein complex covariance and functional dependency in glioblastoma across models and patient proteomes”. AF3_1_source_data.zip — numerical registers and figure source data: one ledger per main and supplementary panel (81 CSV/JSON files) that reproduce every plotted number. AF3_2_code_and_reproduction.zip — analysis and figure-generation scripts with pinned requirements, the frozen-prediction reproduction resources and the editable figure sources. AF3_3_public_extension.zip — public-data extension specification, download manifest, provenance, scripts and result tables. AF3_README.txt — contents and reproduction instructions. All inputs are public: DepMap Public 24Q4, CCLE and ProCan proteomics, Complex Portal, Proteomic Data Commons studies PDC000204 and PDC000446, GEO GSE240418, and the CPTAC pan-cancer harmonized clinical release. No new patient data were generated; the study is a secondary analysis of de-identified public data.