Code and artefacts for: fusion-junction antisense oligonucleotides in extraskeletal myxoid chondrosarcoma

The deposit manifest for the fusion-junction ASO submission, whose title and article type are not restated here — they have one home, research/manuscripts/aso/fusion-junction-aso-research-article.md. It names every file the manuscript's availability statements promise, proves each one exists at a stated size and SHA-256, says in one line what each contributes, and records the gaps. It is the working list a human uses to make the deposit and mint the DOI that fills the manuscript's two remaining placeholders. This deposition is the archive cited by the manuscript's availability statement. It carries 483 files taken from https://github.com/trimcrae/Rare-cancers at revision 68acb5a371b7907fe36a7cee939cde2af8c7b606, together with the manifest that names and hashes every one of them. Verifying this archive. Every file's SHA-256 is listed in fusion-junction-aso-archive-manifest.json. That file cannot carry its own hash, so it is recorded here instead: 701583003bb977d69feab489b6584babba2763dc15651047f7561acb568bbf5d. The archive's content digest, derived over the file list, is 1ddbb1e8a03690ec5c31e6a13c07d26204329e33e1d76c19b7c161e442da2de0. Reproducing the results offline. Re-derive the tables from the artifacts: `python3 research/manuscripts/submission_tables.py` — reads the atlas, the locus collapse, the chance baseline and the per-junction screens; writes no network call. Re-derive the graded re-scores under both discrimination bounds: `python3 research/modalities/junction_aso_offtarget.py --rescore research/modalities/junction-aso-offtarget-.json` — the hit set is read from the committed screen and held fixed; only the scoring is recomputed. Re-derive the junction atlas: `python3 research/modalities/nr4a3_fusion_atlas.py` — reads the committed transcript cache (emc-construct-inputs.json) rather than Ensembl. Re-run the reproduction guards: `python3 -m pytest research/modalities/tests/test_aso_submission_numbers.py research/modalities/tests/test_junction_aso_graded.py`. ⚠ What is NOT offline: re-running the BLAST arm of the specificity screen from scratch (`junction_aso_offtarget.py` screening mode) queries NCBI, and re-running the exhaustive arm from scratch downloads the GRCh38.p14 RefSeq RNA set. Neither is needed to reproduce any number reported in the manuscript, all of which are read from the committed screen artifacts in this archive. Research use only. The oligonucleotide sequences in these artefacts are research reagents; nothing here is for administration to any person or animal, and nothing in it asserts efficacy, safety, delivery or clinical readiness.