Divergent transcriptomic and proteomic signals of synaptic programs in recurrent glioblastoma: full reproducibility archive

Complete reproducibility archive for the research article "Divergent transcriptomic and proteomic signals of synaptic programs in recurrent glioblastoma" (Briefings in Bioinformatics). The archive contains executable analysis code, minimal analysis inputs, recovered RNA and experimental inputs, reconstructed and derived numerical outputs for every figure and table, and the full technical-benchmark simulation outputs, covering the protein reconstruction (96-patient/182-protein endpoint), the baseline-matched comparator and acquisition-plex sensitivity analyses, the linked-assay and flowcell analyses, the CARE/Wang paired RNA-state models and the measurement-depth benchmark. This study is a secondary analysis of de-identified, publicly archived datasets (GSE274546; GSE174554 and linked GSE138794; PDC000514; PDC000446; PRJNA1252365) and involved no human participants and no animals. Third-party source workbooks are excluded under source terms; source links, minimal eligibility variables and computed outputs are supplied instead.