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volcano-plot-script

Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results. Triggered when user needs visualization of gene expression data, p-value vs fold-change scatter plots, publication-ready figures for bioinformatics analysis.

60

Quality

71%

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SecuritybySnyk

Passed

No findings from the security scan

Fix and improve this skill with Tessl

tessl review fix ./scientific-skills/Data Analysis/volcano-plot-script/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

60%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 content is highly actionable with concrete commands, a real packaged script, and a thorough parameter table, and progressive disclosure is sound with verified bundle files. Its main weakness is conciseness: heavy generic boilerplate and verbatim description repetition pad the document well beyond what the task needs.

Suggestions

Remove the verbatim description repetition in 'When to Use' and 'Key Features' and delete generic boilerplate sections (Output Requirements, Response Template, Risk Assessment, Lifecycle Status) that add no volcano-plot-specific value to improve conciseness.

Fix the misformatted code fence in 'Usage' (a shell command currently inside a ```python block) and tighten the workflow steps to volcano-plot-specific actions rather than generic process language.

Move the Security Checklist, Test Cases, and Lifecycle Status into a reference file under references/ so SKILL.md stays a lean overview pointing to detail.

DimensionReasoningScore

Conciseness

The body is noticeably verbose and padded: the description is repeated verbatim in both "When to Use" and "Key Features", the Overview re-explains what volcano plots are, and large generic boilerplate sections (Output Requirements, Response Template, Risk Assessment, Lifecycle Status) add little skill-specific value; not a 1 because there are useful parameter tables and concrete commands mixed in.

2 / 5

Actionability

It provides concrete executable guidance — an "Audit-Ready Commands" block (`python -m py_compile scripts/main.py`, `python scripts/main.py --input deg_results.csv --output volcano_plot.png`), a full parameters table with defaults, and a real packaged `scripts/main.py`; not a 5 because the "Usage" code fence is misformatted (a shell command inside a python block) and a few minor execution details are left implicit.

4 / 5

Workflow Clarity

The "Workflow" section gives a clear 5-step sequence with explicit checkpoints ("stop early if the task would require unsupported assumptions", fallback path on failure) and the "Quick Check" / "Audit-Ready Commands" supply concrete validation; not a 5 because the workflow steps are largely generic process boilerplate rather than volcano-plot-specific, leaving minor validation specificity gaps.

4 / 5

Progressive Disclosure

Structure is good and references are real and one-level-deep: `scripts/main.py`, `assets/example_volcano.R`, and `references/` (best_practices.md, example_deg_data.csv, markers.txt) all exist and are signaled in the body; not a 5 because substantial content (security checklist, lifecycle, test cases) is inlined in SKILL.md that could be split out, leaving minor organization gaps.

4 / 5

Total

14

/

20

Passed

Description

83%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 strong: it concretely states what the skill does and gives explicit trigger conditions in third person, with good domain keyword coverage. Main weakness is trigger-term breadth (missing synonyms and file extensions) and minor overlap with general plotting skills.

DimensionReasoningScore

Specificity

Names the domain and several concrete deliverables — "Generate R/Python code for volcano plots", "p-value vs fold-change scatter plots", "publication-ready figures" — which is several specific actions with only minor coverage gaps; not a 5 because the actions are overlapping variants of one plot-generation task rather than multiple distinct capabilities.

4 / 5

Completeness

It explicitly answers both halves — "what" (Generate R/Python code for volcano plots from DEG results) and "when" ("Triggered when user needs visualization of gene expression data, p-value vs fold-change scatter plots, publication-ready figures"), matching the 5 anchor pattern of concrete trigger phrases; voice is correctly third person with no penalty.

5 / 5

Trigger Term Quality

Good natural-term coverage for the audience ("volcano plots", "DEG", "gene expression data", "publication-ready figures", "bioinformatics"), but it is missing common synonyms and file extensions like "RNA-seq", "differential expression", or ".csv", keeping it just below the comprehensive 5 anchor.

4 / 5

Distinctiveness Conflict Risk

Volcano plots from DEG analysis is a clear niche with distinct triggers and low conflict risk, but there is minor overlap with broader bioinformatics plotting/visualization skills, so it sits at the mostly-distinct 4 anchor rather than the minimal-conflict 5.

4 / 5

Total

17

/

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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