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gsea

Run GSEA on a ranked gene list and produce the enrichment table, running-score table, and enrichment plots.

62

Quality

74%

Does it follow best practices?

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SecuritybySnyk

Passed

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tessl review fix ./awesome-med-research-skills/Data Analysis/gsea/SKILL.md
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 a well-organized, highly actionable reference with clear navigation to real one-level-deep bundle files and concrete executable commands. The main gap is the large inlined plot-mode argument table, which slightly limits conciseness and progressive-disclosure perfection.

Suggestions

Move the lengthy plot-mode argument table (or its less-common entries) into a reference file and summarize the key options inline, improving both conciseness and progressive disclosure.

Add an explicit validate->fix->retry loop referencing the error codes and troubleshooting doc for the analysis workflow, rather than leaving it implied.

Cross-link the Testing section's expected outputs back to the Output files table to make the verification checkpoint more explicit.

DimensionReasoningScore

Conciseness

The body is lean tabular reference with no padding or explanation of concepts Claude already knows, though the large inlined plot-mode argument table (~50 entries) is bulk that could be trimmed or moved to a reference file.

4 / 5

Actionability

Provides copy-paste-ready `Rscript scripts/main.R ...` commands for both modes, a concrete input CSV example, mode-selection rules, and expected output files covering the common cases.

5 / 5

Workflow Clarity

Mode selection (analysis vs. plot) and precedence are clearly sequenced, and the Testing section supplies a verification checkpoint (expected outputs + exit code 0); the pipeline is not destructive, so the workflow-clarity cap does not apply, but an explicit validate->fix->retry loop is only implied via the error-code/troubleshooting references.

4 / 5

Progressive Disclosure

A "When to read external files" table clearly signals one-level-deep references (algorithm.md, cli-guide.md, troubleshooting.md, scripts/main.R), all verified to exist, and content is appropriately split; the inlined full argument tables keep it just short of the ideal split.

4 / 5

Total

17

/

20

Passed

Description

66%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 and distinctive, clearly stating what the skill does and its concrete outputs. Its main weakness is the absence of an explicit "Use when..." trigger clause, which caps completeness.

Suggestions

Add an explicit trigger clause, e.g. "Use when running gene-set enrichment analysis on a ranked gene list or when the user mentions GSEA, pathway enrichment, or enrichment plots."

Include common synonyms such as "gene set enrichment analysis" and "pathway analysis" to broaden natural keyword coverage.

Mention the supported gene-set families or backends briefly to strengthen specificity and distinctiveness.

DimensionReasoningScore

Specificity

Names the domain ("Run GSEA on a ranked gene list") and lists several concrete outputs ("enrichment table, running-score table, and enrichment plots"), but coverage is limited to outputs rather than the full range of supported operations.

4 / 5

Completeness

Has a clear "what" but no "Use when..." clause or equivalent explicit trigger guidance, so completeness is capped at 3 per the rubric guidelines.

3 / 5

Trigger Term Quality

Includes the canonical term "GSEA" plus natural phrases like "ranked gene list" and "enrichment", but omits common synonyms such as "gene set enrichment analysis", "pathway analysis", or "enrichment analysis".

4 / 5

Distinctiveness Conflict Risk

"GSEA on a ranked gene list" carves a clear niche distinct from general skills, with only minor overlap risk against closely related enrichment analyses (e.g. ORA, ssGSEA).

4 / 5

Total

15

/

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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