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review-zoom-hic-methods-glossary

Review zoom Hi-C methods: explain O/E, mcool, Mantel, Pore-C, Dip-C, mouse

Metadata

Statusdone
Assignedagent-978
Agent identity3577bc75d6ed4f1947509aa5c086c91ce7c997c7806dab6bf6affac647452647
Created2026-05-06T20:26:26.486333640+00:00
Started2026-05-06T20:57:02.488579031+00:00
Completed2026-05-06T21:10:09.533487312+00:00
Tagsbog-this-week, bog-deck, review-zoom, revision-fanout, eval-scheduled, git-provenance
Eval score0.96
└ blocking impact0.97
└ completeness0.96
└ constraint fidelity0.85
└ coordination overhead0.98
└ correctness0.96
└ downstream usability0.97
└ efficiency0.92
└ intent fidelity0.86
└ style adherence0.95

Description

User review points 13-17 plus 14 and 15.

Goal: produce a deep but slide-usable breakdown of the 3D evidence block so Erik can explain each Hi-C/Pore-C/Dip-C/mouse panel precisely.

Questions to answer:

  • What is O/E contact in this repo's figures?
  • What is .mcool / 5mcool in this context?
  • What exactly does the Mantel exclusions plot show, and what does each point/axis mean?
  • What does Fig 3 panel A show: rows/columns, ordering, color scale, platform, resolution?
  • What is Fig 3 panel C single-cell 3D trying to show?
  • What is Fig 4 panel D mouse meiotic Hi-C showing, and why should zygotene matter?
  • Which captions/scripts/source TSVs are authoritative for these answers?

Requirements:

  • Inspect paper_prep/figures/fig3, fig4, ed5 captions/scripts and any relevant survey/crosswalk notes.
  • Produce a concise glossary plus per-slide speaker notes for 10a, 10b, 11, 12a, 12b.
  • Flag any unclear/ambiguous labels that final slides must fix.
  • Do not edit deck source.

Deliverables:

  • slides/v2-review-zoom/_revision_assets/hic_methods/README.md with definitions, source references, and speaker-ready explanations.

Depends on

Required by

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