Mostly efficient domain-specific guidance, but the rows-vs-sites pitfall is explained three times (TOP-OF-MIND RULE, PRIMARY SCRIPT section, and the "Distinguish rows vs unique sites" section) with two overlapping question-phrasing tables that could be merged, so it fits the score-2 "could be tightened" anchor rather than the lean score-3 anchor.

The primary script invocation is fully executable and copy-paste ready ("python skills/.../methylation_density.py --cpg ... --chr-lengths ... --filter-meth-extremes 90 10") with a concrete output-field table, but Phases 1–7 are high-level bullets (e.g., "Differential methylation: T-test/Wilcoxon between groups + FDR") and delegate implementations to CODE_REFERENCE.md, which is not present in the bundle, leaving key details missing as in the score-2 anchor.

A clearly sequenced Phase 0–7 workflow with RULE ZERO precedence and explicit feedback loops ("Sanity check: if your filtered count is two orders of magnitude smaller than the GT range ... Re-run with the other axis and compare") matches the score-3 anchor of clear sequence with explicit validation and error-recovery checkpoints; operations are analytical/read-only rather than destructive, so the destructive-cap does not apply.

References are one-level-deep and clearly signaled (inline "See CODE_REFERENCE.md" plus a Reference Files list), but four referenced files (CODE_REFERENCE.md, TOOLS_REFERENCE.md, ANALYSIS_PROCEDURES.md, QUICK_START.md) do not exist in the bundle — only scripts/methylation_density.py is present — so navigation leads nowhere and the structure is only partly realized, fitting the score-2 "could be better organized" anchor rather than the well-split score-3 anchor.

Lists multiple concrete analysis capabilities ("DNA methylation (CpG, 5mC, 5hmC, bisulfite, RRBS), m6A RNA modification (MeRIP-seq), ChIP-seq peaks, ATAC-seq accessibility, histone modifications, chromatin state, multi-omics integration") and concrete actions ("genome-wide epigenomic statistics, methylation analysis, and chromatin-genome integration"), matching the score-3 anchor of multiple specific concrete actions rather than the partial score-2 anchor.

Clearly answers both what (the enumerated analysis types) and when via the explicit trigger clause "Use for genome-wide epigenomic statistics, methylation analysis, and chromatin-genome integration," satisfying the "Use when…" equivalent guidance that would otherwise cap completeness at 2.

Contains natural terms a genomics user would actually say ("DNA methylation", "CpG", "ChIP-seq", "ATAC-seq", "histone", "methylation analysis", "multi-omics") with broad coverage including common variations, so it sits above the score-2 "some relevant keywords but missing common variations" anchor.

Targets a clear epigenomics/epitranscriptomics niche with distinct triggers (methylation, ChIP-seq, ATAC-seq, histone, chromatin state) unlikely to fire for unrelated skills, fitting the score-3 "clear niche with distinct triggers" anchor rather than the score-2 overlap anchor.