Weak cross-context transfer despite local protein-complex retrieval across perturbation platforms: reproducibility package

This record contains analysis code, processed inputs, frozen benchmark matrices, derived results, manuscript deliverables, environment specifications, and integrity manifests for a cross-context and cross-platform perturbation-profile benchmark. The study evaluates whether a target-similarity representation derived from a mouse whole-brain in vivo Perturb-seq atlas is detectably preserved across human Perturb-seq, PERISCOPE Cell Painting, and GSE106127 L1000 contexts. The analyses provided no evidence of transferable global target geometry under the specified analysis, although selected protein complexes remained locally retrievable within several external matrices. The large whole-brain CRISPR atlas parquet input is not included in this archive. It is identified by its source URL, filename, byte size, and SHA256 checksum and can be retrieved using the included authenticated download script. The corrected main benchmark can be reproduced from the frozen source-benchmark intermediate files included in this record.