Research notes¶
Informal background research used during pipeline design (analyte choice, MCED landscape, buffy-coat vs cfDNA tradeoffs). These are not canonical user or operator documentation; see ANALYTE_PROFILES.md and the user manual for project-facing guidance.
| Note | Topic |
|---|---|
| BuffyCoat_vs_cfDNA_for_Cancer_Detection.md | Buffy vs cfDNA as MethylPipeline analytes; CHIP/paired designs; synthesizes Gemini + Grok landscape notes |
| omega-cluster-detection.md | Train-healthy Ω clustering → matched-stratum vs all-pairs detection; Buffy results + DomainProgram gate |
| buffy-mvalue-residualization.md | Train-only M-value residualization for confounder-aware buffy DMPs; isolation contract, leakage table, Ω caveat |
| Prostate Cancer Detection.md | Gatekeeper / csPCa clinical framing and wet-lab SOW (source note) |
| Prostate_Cancer_Detection_MethylPipeline_Fitness.md | Fitness analysis of that note vs MethylPipeline (adopt-with-caveats; extensions) |
| Prostate_Cancer_Application_Deep_Dive.md | Application synthesis: buffy/plasma WGBS, EM-Seq GRAIL-style gatekeeper, alignment compare gate, informME/deconv, physician/payer validation story. Operator/researcher options: usage ch.25 |
| Wong2026_EMSeq_mCRPC_MethylPipeline_Gaps.md | Wong et al. 2026 (npj Precis Oncol): targeted EM-Seq + MHB/MHL mCRPC survival vs shipped cfdna_emseq_targeted — what blocks a repeat |
| florida-community-access-partnership-brief.md | External Florida community-access brief (UF/Sylvester HPC + AdventHealth; not Moffitt OCI) |
| florida-hub-partnership-assessment.md | Internal: why Moffitt is the wrong IT partner; Winter Haven hub; UF / Sylvester / AdventHealth targeting |
| GoliathOmics Gaps.md | Completeness vs Wang/Moffitt techniques: cfDNA MHL, clinico-genomic scores, exosomal miRNA/protein, long-read ASM |
| Gemini_on_Cancer_Detection.md | MCED competitors, multiomics platforms, buffy-coat as CHIP filter |
| Grok_on_Gemini_conclusions.md | Verification of Gemini MCED landscape note; performance and regulatory caveats |
| methylpipeline_informme_integration.md | Using informME information-theoretic measures (Ising NME/JSD) in MethylPipeline; read-level data gap and integration options |