tf-target-gene-regulatory-network

Use when analyzing transcription factor (TF) regulatory networks using Dorothea database. Input gene list, identify regulating transcription factors, generate TF-Target network visualization. For: transcription factor enrichment analysis, gene regulatory network research.

Quality

83%

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Securityby

Passed

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Quality

Content

82%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 body is a strong, action-oriented CLI skill reference: executable examples, complete argument and error tables, and a clear workflow. Its weaker spots are light validation/feedback-loop structure in the workflow and a handful of referenced paths that do not exist in the bundle.

Suggestions

Add an explicit validation checkpoint in the workflow (e.g., after generating outputs, verify TF_Network_Plot.pdf and tf_network.xlsx are non-empty; if SKILL_EMPTY_RESULTS, broaden confidence levels and retry) to introduce a validate→fix→retry loop.

Reconcile referenced paths with the bundle: either include tests/data/ and database/database-get.R or remove/guard those references so navigation is not broken.

Trim the bilingual legacy-alias notes (e.g. "节点", "底部") into the visualization-parameters reference to reduce token overhead in the main body.

Dimension	Reasoning	Score
Conciseness	Mostly efficient with table-driven argument and error references and minimal conceptual over-explanation, but some content repeats across sections (e.g. usage shown in both Usage and Examples) and bilingual legacy aliases add token overhead that could be trimmed.	4 / 5
Actionability	Provides copy-paste-ready executable commands ("Rscript scripts/main.R --gene ... --species ..."), a complete arguments table with defaults, and concrete examples covering the common cases (human, mouse, file input, custom styling, local database).	5 / 5
Workflow Clarity	A clear four-step workflow (load database → identify TFs → generate network → visualize) with a post-run file-existence verification, but validation is implicit and there is no explicit validate→fix→retry feedback loop despite the destructive-ish batch write step, so it does not reach 5.	4 / 5
Progressive Disclosure	Good one-level-deep structure with a clear "When to Read External Files" table pointing to references that mostly exist, but several referenced paths are missing from the bundle (tests/data/, database/database-get.R, database/dorothea_hs.rds, dorothea_mm.rds), introducing minor navigation gaps.	4 / 5
	Total	17 / 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 well-constructed: third-person voice, concrete actions, explicit trigger guidance, and a distinct Dorothea-based niche. Its main weakness is slightly incomplete trigger-term synonym coverage rather than any structural defect.

Suggestions

Add a couple of common synonyms such as "gene regulatory network (GRN) construction" and "upstream TF analysis from a gene list" to broaden natural trigger coverage.

Replace "transcription factor enrichment analysis" with more precise wording (e.g., "TF-target enrichment") to reduce overlap with general pathway-enrichment skills.

Dimension	Reasoning	Score
Specificity	Lists several concrete actions — "Input gene list, identify regulating transcription factors, generate TF-Target network visualization" — naming the domain and the specific pipeline steps, with only minor coverage gaps (no mention of confidence filtering or output formats).	4 / 5
Completeness	Explicitly answers both what it does (input gene list → identify TFs → generate network visualization) and when to use it via a leading "Use when analyzing..." clause plus a "For: transcription factor enrichment analysis, gene regulatory network research" trigger list.	5 / 5
Trigger Term Quality	Good natural-term coverage ("transcription factor regulatory networks", "Dorothea", "TF-Target network", "gene regulatory network"); a few common variations like "gene list analysis" or "GRN" are missing, keeping it just below comprehensive.	4 / 5
Distinctiveness Conflict Risk	The Dorothea-specific TF-target niche is clearly distinct, but the trailing "transcription factor enrichment analysis" phrasing carries minor overlap risk with general enrichment skills, so it sits below a 5.	4 / 5
	Total	17 / 20 Passed

Validation

93%

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 — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	15 / 16 Passed

Repository: aipoch/medical-research-skills
Path: awesome-med-research-skills/Data Analysis/tf-target-gene-regulatory-network/SKILL.md
Commit: f5ef65b

Reviewed: ~9 hours ago

Table of Contents

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