cerna-analysis

1# ceRNA Analysis
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3## When to Use
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5Use this skill when you need to construct a ceRNA regulatory network from a known key-gene list using the bundled miRNA-mRNA and miRNA-lncRNA reference tables.
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7Use it for:
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9- Building a ceRNA network from one gene list and exporting flat CSV plus PDF outputs
10- Comparing supported miRNA source modes such as `combined`, `starbase`, or pairwise overlaps
11- Re-running the same local workflow with different lncRNA strictness, layout, or plotting parameters
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13Do not use it for:
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15- Differential expression, single-cell, enrichment, or survival analysis
16- Workflows that do not start from a key gene list
17- Cases where you want a miRNA-mRNA-only graph without a retained lncRNA ceRNA layer
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19## Input Validation
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21This skill accepts:
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23- A key gene list as a plain-text file (one gene symbol per line) or as a comma-separated string on the CLI
24- Optional parameter overrides for dataset mode, lncRNA strictness, layout, colors, and timeout
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26If the user's request does not involve building a ceRNA regulatory network from a key gene list — for example, asking to run differential expression, enrichment analysis, single-cell workflows, or survival analysis — do not proceed with the workflow. Instead respond:
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