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arboreto

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

88

1.31x
Quality

82%

Does it follow best practices?

Impact

100%

1.31x

Average score across 3 eval scenarios

SecuritybySnyk

Passed

No known issues

SKILL.md
Quality
Evals
Security

Quality

Discovery

100%

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

This is an excellent skill description that clearly defines a specific bioinformatics capability with concrete algorithms, data types, and use cases. It uses proper third-person voice, includes an explicit 'Use when' clause with natural domain-specific trigger terms, and occupies a highly distinctive niche that minimizes conflict risk with other skills.

DimensionReasoningScore

Specificity

Lists multiple specific concrete actions: 'Infer gene regulatory networks (GRNs)', 'scalable algorithms (GRNBoost2, GENIE3)', 'identify transcription factor-target gene relationships and regulatory interactions', 'distributed computation for large-scale datasets'.

3 / 3

Completeness

Clearly answers both 'what' (infer GRNs using GRNBoost2/GENIE3, identify TF-target relationships, supports distributed computation) and 'when' (explicit 'Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships').

3 / 3

Trigger Term Quality

Excellent coverage of natural terms a bioinformatics user would say: 'gene regulatory networks', 'GRNs', 'gene expression data', 'GRNBoost2', 'GENIE3', 'transcriptomics', 'bulk RNA-seq', 'single-cell RNA-seq', 'transcription factor', 'regulatory interactions'. These are the exact terms domain users would use.

3 / 3

Distinctiveness Conflict Risk

Highly distinctive niche — gene regulatory network inference is a very specific bioinformatics task. The mention of specific algorithms (GRNBoost2, GENIE3) and specific data types (RNA-seq, transcriptomics) makes it extremely unlikely to conflict with other skills.

3 / 3

Total

12

/

12

Passed

Implementation

64%

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

The skill provides strong actionable guidance with executable code examples covering multiple real-world use cases. However, it suffers from some redundancy (duplicate installation sections, overlapping Quick Start and Use Cases), lacks validation checkpoints in workflows, and references bundle files that don't exist. Tightening the content and adding inline validation steps would significantly improve quality.

Suggestions

Add explicit validation checkpoints to workflows, e.g., verify DataFrame shape/columns after loading, check that TF names overlap with gene names before inference, and validate output is non-empty before saving.

Remove the duplicate installation section and consolidate the Quick Start example with the Common Use Cases to reduce redundancy.

Either provide the referenced bundle files (references/basic_inference.md, references/algorithms.md, etc.) or remove the references and keep the essential content inline.

Trim explanatory text that Claude already knows (e.g., 'Original multiple regression approach', 'Transcription factor (regulator)') to improve token efficiency.

DimensionReasoningScore

Conciseness

The skill is mostly efficient but includes some redundancy—the Quick Start and Common Use Cases sections overlap significantly, and the algorithm comparison section explains things Claude would already know (e.g., what gradient boosting and random forests are). The installation section appears twice. Some sections like 'Integration with pySCENIC' and 'Comparative Analysis' add moderate value but could be tighter.

2 / 3

Actionability

The skill provides fully executable, copy-paste ready Python code throughout, with concrete examples for multiple use cases (single-cell, bulk RNA-seq, distributed computing). Commands include specific parameters, import statements, and output handling. The CLI script invocation is also concrete.

3 / 3

Workflow Clarity

While individual steps are clear, there are no explicit validation checkpoints in the workflows. For a data analysis pipeline that can fail silently (wrong data format, empty results, memory issues), there should be validation steps between loading data and running inference. The troubleshooting section partially compensates but is reactive rather than integrated into the workflow. The pySCENIC integration workflow is incomplete (Step 2 defers entirely).

2 / 3

Progressive Disclosure

The skill references external files (references/basic_inference.md, references/algorithms.md, references/distributed_computing.md, scripts/basic_grn_inference.py) which is good structure, but no bundle files are provided, meaning these references are broken. The main file also contains substantial inline content that overlaps with what the referenced files presumably cover, suggesting the split between overview and detail isn't clean.

2 / 3

Total

9

/

12

Passed

Validation

90%

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

Validation10 / 11 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

Total

10

/

11

Passed

Repository
K-Dense-AI/claude-scientific-skills
Reviewed

Table of Contents

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