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Add IFS and CMN reference evidence - #476

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iskandr merged 2 commits into
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agent/473-475-ifs-cmn-references
Aug 2, 2026
Merged

Add IFS and CMN reference evidence#476
iskandr merged 2 commits into
mainfrom
agent/473-475-ifs-cmn-references

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@iskandr

@iskandr iskandr commented Aug 2, 2026

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Summary

  • add CMN as a canonical, non-classifying entity and expose public Treehouse PolyA/RiboD and GSE11482 physical source evidence without pooling protocols
  • add donor-aware sample provenance and structured heterogeneous IFS/CMN driver spectra; diagnosis-only samples remain molecularly unknown
  • use one assay-independent technical-RNA gene set for every assay and replace its clean-TPM composition with a fixed Treehouse PolyA profile
  • rebuild all expression artifacts under sample-QC v3 and make source selection authoritative rather than gene-count-driven

Controlled EGA, St. Jude, and CCDI expression remains explicitly access-required. Public sample-level molecular annotations are included where available; no controlled expression or fusion calls are inferred. GSE11482 remains a non-linear, rank-only TPM proxy and is never claimed to be absolute RNA-seq TPM.

Releases

  • source matrices: source-v5.22.10 (133 validated assets)
  • derived bundle: v5.23.17
  • package version: 1.8.171

Verification

  • 1035 passed in 56.55s
  • Ruff lint and changed-file formatting pass
  • MkDocs strict build passes
  • sdist and wheel build successfully
  • all four IFS/CMN public physical-source views load through cancer_reference_expression

Closes #473
Closes #474
Closes #475

@iskandr
iskandr merged commit e03351b into main Aug 2, 2026
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@iskandr
iskandr deleted the agent/473-475-ifs-cmn-references branch August 2, 2026 17:47
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