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two-sample-mr-research-planner

Generates complete two-sample Mendelian randomization (MR) research designs from a user-provided research direction. Use when users want to design, plan, or build a study using two-sample MR to test causal relationships. Triggers:"design a two-sample MR study", "build a publishable MR paper", "test whether this biomarker causally affects this disease", "generate Lite/Standard/Advanced MR plans", "screen multiple exposures with MR", "bidirectional MR design", "causal inference using GWAS summary statistics", or "I want to study X and Y using MR". Always outputs four workload configurations (Lite / Standard / Advanced / Publication+) with a recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, and publication upgrade path.

76

Quality

96%

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SKILL.md
Quality
Evals
Security

Quality

Content

92%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A well-structured instruction skill: fully sequenced workflow with explicit fault-tolerance checkpoints, copy-paste-ready R code with honest placeholder handling, and clean one-level-deep references verified on disk. The only weakness is minor redundancy (repeated summary lines, duplicated reference pointers, and overlapping rule sections) that could be trimmed for token efficiency.

Suggestions

Remove the redundant trailing 'Reference Files' table (the Step 4 inline '→' pointers already link both files), or keep only one of the two placements.

Drop the opening restatement of the frontmatter summary ('Always outputs four workload configurations and a recommended primary plan') since Step 2 states the same requirement in full.

Merge the 'Fault tolerance guidelines' into the relevant Hard Rules (6–8 overlap heavily) to eliminate the double-stated weak-instrument guidance.

DimensionReasoningScore

Conciseness

The body is dense and assumes domain competence (methods are named with thresholds rather than tutored), but has minor redundancy: the opening line repeats the frontmatter summary ('Always outputs four workload configurations and a recommended primary plan'), the trailing 'Reference Files' table duplicates the inline Step 4 pointers already given, and fault-tolerance rules overlap Hard Rules 6–8. Anchor 4 ('efficient; minor instances... that could be trimmed') fits better than 5's 'every token earns its place'.

4 / 5

Actionability

Guidance is fully executable: concrete thresholds ('p < 5×10⁻⁸, LD clumping r² < 0.001 / 10,000 kb', 'F > 10', 'PP.H4 > 0.8'), a complete copy-paste-ready TwoSampleMR R template with the available_outcomes() lookup pattern, and specific fallback methods ('LIML, sisVIVE'). The EXAMPLE-ID placeholders are explicitly justified with inline comments, and per the scoring notes the instruction-style planning guidance is equally concrete.

5 / 5

Workflow Clarity

Steps 1–9 are clearly sequenced with explicit validation checkpoints and feedback loops: 'If IV count falls below 3: warn the user that MR is not feasible', 'If F-statistic < 10 for all IVs: do not proceed with IVW as primary', 'Confirm this fits within any stated time constraints before recommending', and a 'Revision strategy if first-pass findings fail'. This matches the anchor-5 pattern of explicit validation plus error-recovery loops.

5 / 5

Progressive Disclosure

Both referenced files (references/iv_benchmarks.md, references/gwas_databases.md) exist, contain exactly the promised lookup tables, and are one level deep. They are clearly signaled inline in Step 4 with '→' arrows and summarized in a 'Reference Files' table with a 'Used In' step column, while bulky per-exposure-class data is appropriately split out of the overview.

5 / 5

Total

19

/

20

Passed

Description

100%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

An exemplary description: specific third-person statement of what it produces, an explicit 'Use when' clause with realistic trigger phrases covering the major use cases, and tight scoping that minimizes conflict risk. A trivial typo ('Triggers:' missing a space) does not affect any scored dimension.

DimensionReasoningScore

Specificity

The description enumerates multiple concrete actions and outputs — 'Generates complete two-sample Mendelian randomization (MR) research designs' and 'Always outputs four workload configurations (Lite / Standard / Advanced / Publication+) with a recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, and publication upgrade path' — giving comprehensive, specific coverage in third-person voice. Not 4, because no deliverable gaps remain that would justify 'minor gaps in coverage'.

5 / 5

Completeness

It explicitly answers both questions: what ('Generates complete two-sample MR research designs... Always outputs four workload configurations...') and when ('Use when users want to design, plan, or build a study using two-sample MR to test causal relationships') with a list of concrete trigger phrases. This exactly matches the anchor-5 pattern of what + explicit when with concrete trigger phrases.

5 / 5

Trigger Term Quality

Trigger coverage is comprehensive and natural: 'design a two-sample MR study', 'build a publishable MR paper', 'test whether this biomarker causally affects this disease', 'screen multiple exposures with MR', 'bidirectional MR design', 'I want to study X and Y using MR'. Both the full domain term and the common abbreviation (MR) appear, plus screening, bidirectional, and publication-oriented phrasings users would actually say.

5 / 5

Distinctiveness Conflict Risk

The skill occupies a clear niche (two-sample MR study design from GWAS summary statistics) with distinct, domain-specific triggers; it would not fire for generic document, code, or statistics skills. The only conceivable overlap is with a hypothetical general MR-execution skill, which is minimal.

5 / 5

Total

20

/

20

Passed

Validation

93%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

15

/

16

Passed

Repository
aipoch/medical-research-skills
Reviewed

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