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estimate-immune-score-analysis

Use this skill to compute ESTIMATE immune-related microenvironment scores from a bulk expression matrix, generate an ESTIMATE score heatmap, and optionally generate group-wise ESTIMATE score boxplots plus significance tables when a sample group file is supplied. Trigger keywords: ESTIMATE, immune score, stromal score, tumor microenvironment score. NOT for: immune cell deconvolution, single-cell analysis, differential expression, clinical diagnosis.

71

Quality

88%

Does it follow best practices?

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Adds up to 20 points to the overall score

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SecuritybySnyk

Passed

No findings from the security scan

SKILL.md
Quality
Evals
Security

Quality

Content

88%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, executable skill body with concrete commands, clear validation checkpoints, and proper one-level-deep references to real bundle files. Minor conciseness redundancy and a referenced-but-missing tests/data/ bundle are the only weak spots.

Suggestions

Remove the redundant inline READ pointers (e.g., near Examples and References) that duplicate the 'When to Read External Files' table to tighten conciseness.

Either add the referenced tests/data/ sample files to the bundle or drop the tests/data/ rows from the navigation table so referenced paths all resolve to real files.

DimensionReasoningScore

Conciseness

Efficient body with executable commands, compact argument and output tables, and minimal over-explanation; not 5 due to light redundancy between the 'When to Read External Files' table and the later inline READ pointers and repeated scope statements.

4 / 5

Actionability

Copy-paste ready Rscript commands, a complete arguments table with defaults, concrete input examples, and a full error-code table covering the common cases; matches the fully-executable anchor.

5 / 5

Workflow Clarity

Clear three-step workflow with explicit validation (input existence, numeric columns, unique sample names) and feedback loops (group-failure path preserves core outputs and appends failure records before exiting with a SKILL_* code); matches the explicit-validation anchor.

5 / 5

Progressive Disclosure

Well-organized overview with a one-level-deep 'When to Read External Files' table signaling real reference files (algorithm.md, cli-guide.md, troubleshooting.md) and scripts; not 5 because the referenced tests/data/ bundle is absent and a couple of inline READ pointers are somewhat redundant with the table.

4 / 5

Total

18

/

20

Passed

Description

87%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.

A strong, concrete description that names multiple specific actions and provides explicit trigger guidance plus clear boundary exclusions. It could be marginally improved by adding common synonyms and file extensions to its trigger terms.

Suggestions

Add natural synonyms and file extensions to trigger keywords (e.g., 'expression matrix, bulk RNA-seq, .csv/.tsv') for broader natural-term coverage.

Consider naming the supported input file formats (CSV/TSV) directly in the description to round out capability coverage.

DimensionReasoningScore

Specificity

Lists several concrete actions (compute ESTIMATE scores, generate a heatmap, group-wise boxplots, significance tables), matching the 'several specific actions; minor gaps in coverage' anchor; not 5 because it omits synonyms like file formats and a couple of secondary actions.

4 / 5

Completeness

Explicitly answers both what (compute scores, heatmap, boxplots, significance tables) and when (explicit 'Trigger keywords' plus 'NOT for' boundary), matching the concrete-trigger-phrases anchor; not below because both halves are concrete and explicit.

5 / 5

Trigger Term Quality

Good keyword coverage with natural phrases ('ESTIMATE', 'immune score', 'stromal score', 'tumor microenvironment score'); not 5 because common synonyms and file extensions are not included.

4 / 5

Distinctiveness Conflict Risk

Clear niche (ESTIMATE TME scores from bulk expression) with explicit 'NOT for' exclusions (deconvolution, single-cell, differential expression, diagnosis), minimizing conflict risk; not below because the boundary guidance is strong.

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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