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immune-pathway-analysis

Run immune pathway GSVA or ssGSEA analysis from a bulk expression matrix, a sample group file, and a local immune Reactome gene-set table, then export differential pathway results and a heatmap for two-group comparison.

68

Quality

82%

Does it follow best practices?

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SecuritybySnyk

Passed

No findings from the security scan

SKILL.md
Quality
Evals
Security

Quality

Content

82%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.

The body is highly actionable and well-organized with strong progressive disclosure, docked only for a dead tests/data/ reference and a missing explicit post-run output-verification checkpoint in an otherwise clear batch workflow.

Suggestions

Either add the tests/ bundle directory or remove the tests/data/ references from the 'When to Read External Files' table and Testing section.

Add an explicit post-run verification step (e.g. confirm expected output files exist under output_dir before reporting) to the Execution Model.

Tighten the worked Completion Format example to a shorter template to recover a few tokens.

DimensionReasoningScore

Conciseness

Mostly lean, table-driven, and free of concept padding, but the full worked Completion Format summary line and a few descriptive sentences could be trimmed further.

4 / 5

Actionability

Provides a copy-paste-ready Rscript command, a complete typed/defaulted Arguments table, concrete input-format specs, and an error-code-to-solution table covering common cases.

5 / 5

Workflow Clarity

Clear 8-step Execution Model with pre-run scope/input validation and a post-run reporting checkpoint that surfaces the FDR-fallback warning; minor gap is the lack of an explicit output-existence verification step.

4 / 5

Progressive Disclosure

Well-structured overview with a situation-to-file navigation table and one-level-deep references that all resolve, except tests/data/ is referenced repeatedly but no tests/ bundle directory exists.

4 / 5

Total

17

/

20

Passed

Description

82%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.

The description is specific, distinct, and trigger-rich but omits an explicit 'Use when...' clause, which caps completeness at the midpoint. Adding a concrete usage-trigger sentence would lift it into the top band.

Suggestions

Append an explicit trigger clause, e.g. 'Use when scoring immune Reactome pathway activity from a bulk expression matrix and comparing two sample groups.'

Mention accepted input formats (CSV/TSV) so users searching by file type land on this skill.

Optionally name the comparison backend (limma) in the description to sharpen distinctiveness from generic enrichment skills.

DimensionReasoningScore

Specificity

Lists multiple concrete actions ('Run immune pathway GSVA or ssGSEA analysis', 'export differential pathway results', 'a heatmap for two-group comparison') with named inputs, matching the comprehensive-coverage anchor.

5 / 5

Completeness

Clearly states what the skill does but has no explicit 'Use when...' trigger clause, so 'when' is only weakly implied — the missing-trigger-guidance rule caps this at 3.

3 / 5

Trigger Term Quality

Covers natural method synonyms users say ('GSVA', 'ssGSEA', 'bulk expression matrix', 'heatmap', 'differential pathway'), matching the comprehensive-synonyms anchor; only minor file-extension terms are absent.

5 / 5

Distinctiveness Conflict Risk

Highly specific niche (immune Reactome gene-set, GSVA/ssGSEA, two-group comparison) with distinct triggers and minimal overlap with other skills.

5 / 5

Total

18

/

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.

Validation15 / 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

Table of Contents

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