pydeseq2

Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.

Quality

73%

Does it follow best practices?

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Securityby

Passed

No findings from the security scan

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tessl review fix ./backend/cli/skills/biology/pydeseq2/SKILL.md

Quality

Content

65%Weight 40%Scale 1-3

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

A highly actionable, well-sequenced DESeq2 workflow skill with real, properly signaled bundle references, held back by length/redundancy and by validation guidance that lives in troubleshooting rather than as inline workflow checkpoints.

Suggestions

Remove redundant content: the 'Two-Group Comparison' pattern duplicates Quick Start, and several 'Key Reminders' restate step content — consolidate to tighten the body.

Add explicit inline validation checkpoints in the main workflow (e.g. 'verify counts and metadata indices align before fitting') rather than only surfacing these checks in Troubleshooting.

Move the full visualization code and detailed troubleshooting into references/workflow_guide.md, keeping SKILL.md a lean overview that points to it.

Dimension	Reasoning	Score
Conciseness	The ~550-line body is mostly efficient and assumes Claude's competence, but contains redundancy — the 'Two-Group Comparison' pattern repeats the Quick Start nearly verbatim and the 8 'Key Reminders' restate content already covered in the workflow steps.	2 / 3
Actionability	Provides fully executable, copy-paste-ready code throughout (imports, concrete parameters, result column definitions) plus a complete CLI invocation with all flags, giving concrete actionable guidance.	3 / 3
Workflow Clarity	Steps 1-6 are clearly sequenced with diagnostic QC and troubleshooting sections, but for a batch analysis operation the main workflow lacks explicit inline 'validate before proceeding' checkpoints — validation is reactive (in Troubleshooting) rather than gated, capping clarity at 2.	2 / 3
Progressive Disclosure	Real bundle files (references/api_reference.md, references/workflow_guide.md, scripts/run_deseq2_analysis.py) are referenced by exact path and clearly signaled one level deep, but the SKILL.md body is long with substantial inline content (full visualization code, troubleshooting) that could be split into references.	2 / 3
	Total	9 / 12 Passed

Description

82%Weight 40%Scale 1-3

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 specific, distinctive description with good natural trigger terms, weakened only by the lack of an explicit 'Use when...' clause that would fully answer when to invoke the skill.

Suggestions

Add an explicit trigger clause, e.g. 'Use when analyzing bulk RNA-seq count data for differential expression, or when users mention DESeq2, differential expression, or RNA-seq analysis.'

Consider adding common user phrasings like 'gene expression analysis' to broaden natural trigger coverage.

Dimension	Reasoning	Score
Specificity	Lists multiple specific concrete actions — 'Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots' — naming distinct operations and outputs rather than vague domain language.	3 / 3
Completeness	Clearly answers 'what' (the analysis actions) but the 'when' is only implied by the trailing 'for RNA-seq analysis' rather than an explicit 'Use when...' trigger clause, which caps completeness at 2 per the guidelines.	2 / 3
Trigger Term Quality	Includes natural terms a user would say ('differential gene expression', 'RNA-seq', 'DESeq2', 'DE genes'); these are the actual phrases bioinformatics users employ, though a few common variations are absent.	3 / 3
Distinctiveness Conflict Risk	Occupies a clear niche (Python DESeq2 for bulk RNA-seq differential expression) with distinct triggers unlikely to fire for unrelated skills.	3 / 3
	Total	11 / 12 Passed

Validation

81%

Warnings & errors only

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

Validation — 13 / 16 Passed

Validation for skill structure

Criteria	Description	Result
skill_md_line_count	SKILL.md is long (559 lines); consider splitting into references/ and linking	Warning
metadata_version	'metadata.version' is missing	Warning
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	13 / 16 Passed

Repository: synthetic-sciences/openscience
Path: backend/cli/skills/biology/pydeseq2/SKILL.md
Commit: dc00e07

Reviewed: 11 days ago

Table of Contents

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