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tf-target-gene-regulatory-network

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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.

awesome-med-research-skills/Data Analysis/tf-target-gene-regulatory-network/SKILL.md

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Sep 17, 2026
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# Transcription Factor (TF) Regulatory Network Analysis

## When to Use

- Use this skill when you have a human or mouse gene list and want to identify upstream TFs from the Dorothea database.
- Use it when you need a ready-to-export TF-target network table plus a publication-ready PDF network plot.
- Use it for reproducible CLI execution with saved session information and optional local Dorothea `.rds` databases.

## When Not to Use

- Do not use this skill for differential expression, pathway enrichment, cell type annotation, or survival analysis.
- Do not use it to infer causal direction beyond curated Dorothea TF-target relationships.
- Do not use it when your input genes are aliases or mixed-species symbols that have not been normalized first.
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