| 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 |
ceRNA Analysis
When to Use
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:
- Building a ceRNA network from one gene list and exporting flat CSV plus PDF outputs
- Comparing supported miRNA source modes such as
combined, starbase, or pairwise overlaps
- Re-running the same local workflow with different lncRNA strictness, layout, or plotting parameters
Do not use it for:
- Differential expression, single-cell, enrichment, or survival analysis
- Workflows that do not start from a key gene list
- Cases where you want a miRNA-mRNA-only graph without a retained lncRNA ceRNA layer
Input Validation
This skill accepts:
- A key gene list as a plain-text file (one gene symbol per line) or as a comma-separated string on the CLI
- Optional parameter overrides for dataset mode, lncRNA strictness, layout, colors, and timeout
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."
When to Read External Files
| 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 |
Usage
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: --help and all analysis modes require igraph to be installed. Install igraph before running any command. Use references/troubleshooting.md for installation guidance.
Arguments
Main Analysis: 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 |
Input Format
Key Genes (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:
- Blank lines are ignored
- Lines starting with
# are ignored
- Duplicate genes are removed
- At least one valid gene is required
Database Directory (reference_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.csv- lncRNA file: one of
starbase_miRNA_lncRNA_High.csv, starbase_miRNA_lncRNA_Median.csv, or starbase_miRNA_lncRNA_Low.csv
Output Files
| 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 |
Workflow
Step 1: Validate Input
- Check key-gene input existence or parse comma-separated genes
- Validate parameter choices, numeric limits, timeout, and colors
- Verify the database directory and required files
Step 2: Load Interaction Data
- Load the selected miRNA-mRNA dataset
- Load the selected miRNA-lncRNA dataset by strictness level
- Recompute pairwise intersections when requested
Step 3: Filter the Network
- Retain miRNA-mRNA pairs linked to the provided key genes
- Retain miRNA-lncRNA pairs connected to the retained miRNAs
- Apply the lncRNA frequency threshold
- Stop with
SKILL_INVALID_DATA if no lncRNA interactions remain after filtering, because the ceRNA layer has collapsed
Step 4: Build Outputs
- Construct edge and node tables
- Save CSV, PDF, and session information in the output directory root
Methods
combined
Uses the bundled precomputed overlap across three miRNA-mRNA resources for higher-confidence interactions.
Pairwise Intersections
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.
lncRNA Strictness
High, Median, and Low select different bundled starBase evidence levels for miRNA-lncRNA interactions.
Examples
Basic Combined Analysis
Rscript scripts/main.R \
-i ./key_genes.txt \
-o ./output \
-m combined
Single Database Analysis
Rscript scripts/main.R \
-i ./key_genes.txt \
-o ./output_starbase \
-m starbase \
-l Median \
-f 1
Error Handling
| 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
Testing
Test with Sample Data
Rscript scripts/main.R \
-i tests/data/gene.txt \
-o tests/output/
Validation Commands
wc -l tests/output/ceRNA_network_edges.csv
ls -la tests/output/ceRNA_network.pdf
