Supporting data and code for "Non-target expression distorts bulk score correlations: exact decomposition, log-RNA correction and leakage diagnosis"

This record contains supporting data, code and analysis outputs for the study “Non-target expression distorts bulk score correlations: exact decomposition, log-RNA correction and leakage diagnosis”. The archive includes scoring definitions, numerical source tables, analysis and figure-reproduction scripts, figure exports, and the bulk_score_tools Python package (version 0.1.0) with examples and tests. Supplementary Data S1–S4 are indexed in current/DATA_INDEX.csv and current/source_index.csv. FILE_MANIFEST_SHA256.csv provides file-level checksums. The manuscript, supplementary-information document and editable manuscript sources are not included in this deposit. Six input files derived from 3CA annotations or LinkedOmicsKB expression values are provided through source URLs, frozen checksums and tested reconstruction scripts rather than redistributed as data files. See current/external_rebuild/README.md for the reconstruction command, offline use and validation results. Upstream source files are obtained separately under their applicable terms. Software repository: https://github.com/tjw0613-cell/bulk-score-tools The authors’ original software and documentation are licensed under the MIT License. Third-party software, datasets and source-derived resources retain their respective licences and applicable conditions, as documented in the included resource notices.