// Use when building a ceRNA regulatory network from a key gene list by combining bundled miRNA-mRNA and miRNA-lncRNA database files, with flat-file CSV exports and PDF visualization in a single output directory. NOT for: differential expression, single-cell analysis, enrichment analysis, or workflows without a key gene list.
| name | cerna-analysis |
| description | Use when building a ceRNA regulatory network from a key gene list by combining bundled miRNA-mRNA and miRNA-lncRNA database files, with flat-file CSV exports and PDF visualization in a single output directory. NOT for: differential expression, single-cell analysis, enrichment analysis, or workflows without a key gene list. |
| license | MIT |
| skill-author | Codex |
Use 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.
Use it for:
combined, starbase, or pairwise overlapsDo not use it for:
This skill accepts:
If 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:
"ceRNA Analysis is designed to construct a ceRNA regulatory network from a key gene list using bundled miRNA-mRNA and miRNA-lncRNA reference databases. Your request appears to be outside this scope. Please provide a key gene list and specify a supported miRNA dataset mode, or use a more appropriate skill for differential expression, enrichment analysis, or single-cell workflows."
| Situation | File to Read | Purpose |
|---|---|---|
| Need algorithm details | references/algorithm.md | ceRNA construction logic, dataset combinations, filtering rules. Includes worked examples of pairwise intersection network size vs combined mode. |
| Need to run analysis | scripts/main.R | Execute: Rscript scripts/main.R --key_genes ... --output_dir .... Note: --help requires igraph to be installed. |
| Encounter errors | references/troubleshooting.md | Common errors and solutions |
| Need CLI examples | references/cli-guide.md | Detailed local run examples with measured outputs |
| Need test data | tests/data/ | Sample key-gene input for testing |
Rscript scripts/main.R \
--key_genes tests/data/gene.txt \
--output_dir ./output/ \
--mirna_dataset combined \
--lncrna_strictness High \
--lncrna_freq_thresh 0 \
--timeout_seconds 600 \
--seed 42
Dependency note:
--helpand all analysis modes requireigraphto be installed. Install igraph before running any command. Usereferences/troubleshooting.mdfor installation guidance.
scripts/main.R| Short | Long | Type | Default | Description |
|---|---|---|---|---|
-i | --key_genes | character | required | Key gene file path or comma-separated gene names |
-o | --output_dir | character | ./output/ | Output directory |
-m | --mirna_dataset | character | combined | Dataset: combined, starbase, mirdb, mirtarbase, starbase+mirdb, starbase+mirtarbase, mirdb+mirtarbase |
-l | --lncrna_strictness | character | High | lncRNA interaction strictness: Low, Median, High |
-f | --lncrna_freq_thresh | integer | 0 | Minimum retained lncRNA frequency |
-r | --reference_dir | character | file.path(script_dir, "..", "references", "database") | Database directory |
--plot_width | double | 12 | PDF width in inches | |
--plot_height | double | 8 | PDF height in inches | |
--layout_type | character | kk | Layout: kk, fr, nicely, circle, grid, randomly | |
--mrna_color | character | #D16BA5 | mRNA node color | |
--lncrna_color | character | #008dcd | lncRNA node color | |
--mirna_color | character | #00c9a7 | miRNA node color | |
--node_size_base | double | 15 | Base node size | |
--label_size | double | 0.8 | Node label size | |
--show_legend | logical | TRUE | Show legend in the PDF | |
-t | --timeout_seconds | integer | 3600 | Elapsed timeout limit |
-s | --seed | integer | 42 | Random seed for reproducibility |
key_genes)Plain-text input with one gene symbol per line, or a comma-separated string passed directly on the CLI.
TP53
BRCA1
MYC
Rules:
# are ignoredreference_dir)The bundled database directory is references/database/. Required files depend on the selected mirna_dataset plus the selected lncRNA strictness file.
combined: miRNA_mRNA.csvstarbase: starbase_miRNA_mRNA.csvmirdb: miRDB_miRNA_mRNA.csvmirtarbase: miRTarbase_miRNA_mRNA.csvstarbase+mirdb: starbase_miRNA_mRNA.csv and miRDB_miRNA_mRNA.csvstarbase+mirtarbase: starbase_miRNA_mRNA.csv and miRTarbase_miRNA_mRNA.csvmirdb+mirtarbase: miRDB_miRNA_mRNA.csv and miRTarbase_miRNA_mRNA.csvstarbase_miRNA_lncRNA_High.csv, starbase_miRNA_lncRNA_Median.csv, or starbase_miRNA_lncRNA_Low.csv| File | Description |
|---|---|
ceRNA_network_edges.csv | Edge table with node1,node2 columns |
ceRNA_network_nodes.csv | Node table with node,type,degree columns |
ceRNA_network.pdf | ceRNA network visualization |
session_info.txt | R session details and loaded package versions |
SKILL_INVALID_DATA if no lncRNA interactions remain after filtering, because the ceRNA layer has collapsedcombinedUses the bundled precomputed overlap across three miRNA-mRNA resources for higher-confidence interactions.
starbase+mirdb, starbase+mirtarbase, and mirdb+mirtarbase recompute the overlap between two bundled databases. Pairwise intersections typically yield 20–40% fewer edges than combined mode because only interactions present in both selected databases are retained. Use pairwise modes when you need higher-confidence edges at the cost of reduced network coverage.
High, Median, and Low select different bundled starBase evidence levels for miRNA-lncRNA interactions.
Rscript scripts/main.R \
-i ./key_genes.txt \
-o ./output \
-m combined
Rscript scripts/main.R \
-i ./key_genes.txt \
-o ./output_starbase \
-m starbase \
-l Median \
-f 1
| Error | Cause | Solution |
|---|---|---|
SKILL_FILE_NOT_FOUND | Input file or database file is missing | Check the file path or bundled database directory |
SKILL_EMPTY_FILE | A required file exists but has no content | Replace or regenerate the file |
SKILL_EMPTY_DATA | A required reference table has no usable rows | Verify the input content and regenerate the file if needed |
SKILL_MISSING_COLUMNS | An input table lacks required columns | Verify the expected schema |
SKILL_INVALID_PARAMETER | An invalid CLI value was provided | Use one of the documented parameter values |
SKILL_INVALID_DATA | The input data cannot build a valid ceRNA network, or lncRNA filtering removes the ceRNA layer entirely | Verify the key genes and database files, then lower --lncrna_freq_thresh or choose a different dataset / strictness |
SKILL_DEPENDENCY_MISSING | A required package is not installed (igraph required for all modes including --help) | Install the missing package before running any command |
SKILL_TIMEOUT | The run exceeded the timeout limit | Increase --timeout_seconds |
SKILL_RUNTIME_ERROR | An unexpected runtime failure occurred | Re-run after checking the console error message |
IF error persists, READ: references/troubleshooting.md
# Run with sample data (igraph must be installed first)
Rscript scripts/main.R \
-i tests/data/gene.txt \
-o tests/output/
# Inspect edge output
wc -l tests/output/ceRNA_network_edges.csv
# Check plot exists
ls -la tests/output/ceRNA_network.pdf
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