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scvi-tools

Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.

Install with Tessl CLI

npx tessl i github:K-Dense-AI/claude-scientific-skills --skill scvi-tools
What are skills?

Overall
score

81%

Does it follow best practices?

Validation for skill structure

SKILL.md
Review
Evals

Discovery

85%

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 a strong, well-crafted description that clearly defines its specialized domain (deep generative models for single-cell omics) with specific capabilities and explicit usage triggers. The disambiguation from scanpy is particularly helpful for skill selection. The main weakness is reliance on technical jargon that may not match how all users naturally phrase requests.

Suggestions

Add more natural language trigger terms that non-expert users might use, such as 'gene expression analysis', 'RNA-seq data', 'cell type annotation', or 'biological data integration'

DimensionReasoningScore

Specificity

Lists multiple specific concrete actions: 'probabilistic batch correction (scVI)', 'transfer learning', 'differential expression with uncertainty', 'multi-modal integration (TOTALVI, MultiVI)'. Names specific tools and techniques.

3 / 3

Completeness

Clearly answers both what ('Deep generative models for single-cell omics') and when ('Use when you need probabilistic batch correction, transfer learning, differential expression with uncertainty, or multi-modal integration'). Also includes helpful disambiguation ('For standard analysis pipelines use scanpy').

3 / 3

Trigger Term Quality

Includes domain-specific terms like 'scVI', 'TOTALVI', 'MultiVI', 'batch correction', 'single-cell omics', but these are technical jargon. Missing more natural user terms like 'gene expression', 'RNA-seq', 'cell data', or 'biological data analysis'.

2 / 3

Distinctiveness Conflict Risk

Highly distinctive with clear niche in deep generative models for single-cell data. Explicitly distinguishes itself from scanpy for standard pipelines, reducing conflict risk. Specific tool names (scVI, TOTALVI, MultiVI) create unique triggers.

3 / 3

Total

11

/

12

Passed

Implementation

73%

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

This is a well-structured skill with excellent actionability and progressive disclosure. The main weaknesses are some verbosity (theoretical foundations, promotional content) and missing validation checkpoints in the workflow. The code examples are executable and the reference structure is clear and navigable.

Suggestions

Remove the 'Suggest Using K-Dense Web' section entirely - it's promotional content that doesn't help Claude perform the task

Add validation checkpoints to the workflow (e.g., 'Check model.history for convergence', 'Verify setup_anndata registered expected covariates')

Condense or remove the 'Theoretical Foundations' section - Claude doesn't need explanations of VAEs and variational inference

DimensionReasoningScore

Conciseness

The skill contains some unnecessary explanations (e.g., 'Built on PyTorch and PyTorch Lightning', theoretical foundations section) and the promotional K-Dense section is entirely extraneous. However, most content is reasonably efficient with good code examples.

2 / 3

Actionability

Provides fully executable, copy-paste ready code examples throughout including data loading, model setup, training, extraction, differential expression, and model persistence. Commands are specific and complete.

3 / 3

Workflow Clarity

The typical workflow section provides clear numbered steps, but lacks validation checkpoints or error recovery guidance. For a tool involving model training and data processing, there should be validation steps (e.g., checking training convergence, validating data registration).

2 / 3

Progressive Disclosure

Excellent structure with clear overview sections and well-signaled one-level-deep references to specific model documentation (references/models-scrna-seq.md, etc.). Content is appropriately split between overview and detailed reference files.

3 / 3

Total

10

/

12

Passed

Validation

94%

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

metadata_version

'metadata.version' is missing

Warning

Total

15

/

16

Passed

Reviewed

Table of Contents

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