How do I install the Cerna Analysis skill?

Run npx skillmds@latest add aibot88/cerna-analysis in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

What does the Cerna Analysis skill do?

> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills) It is listed under Research & Search on SkillMD.

Is Cerna Analysis safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Cerna Analysis?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Cerna Analysis free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Cerna Analysis?

aibot88 (@aibot88) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Cerna Analysis by aibot88 — Agent Skill

Name: Cerna Analysis
Author: aibot88

Source: https://github.com/aipoch/medical-research-skills

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

When to Read External Files

Situation	File to Read	Purpose
Need algorithm details	`references/algorithm.md`	ceRNA construction logic, dataset combinations, filtering rules
Need to run analysis	`scripts/main.R`	Execute: `Rscript scripts/main.R --key_genes ... --output_dir ...`
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

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.csv
starbase: starbase_miRNA_mRNA.csv
mirdb: miRDB_miRNA_mRNA.csv
mirtarbase: miRTarbase_miRNA_mRNA.csv
starbase+mirdb: starbase_miRNA_mRNA.csv and miRDB_miRNA_mRNA.csv
starbase+mirtarbase: starbase_miRNA_mRNA.csv and miRTarbase_miRNA_mRNA.csv
mirdb+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.

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

Common Errors

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	Install the missing package
`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

# Check help
Rscript scripts/main.R --help

# Run with sample data
Rscript scripts/main.R \
  -i tests/data/gene.txt \
  -o tests/output/

Validation Commands

# Inspect edge output
wc -l tests/output/ceRNA_network_edges.csv

# Check plot exists
ls -la tests/output/ceRNA_network.pdf

Implementation Checklist

CLI parsing with optparse
set.seed() for reproducibility
requireNamespace() dependency checks
Session info recording
File reading instructions in SKILL.md
Modular script structure (scripts/)
Test data provided
Error handling with SKILL_* codes

Last updated: 2026-04-17 | Version: 1.0.0

Cerna Analysis

File contents

ceRNA Analysis

When to Use

When to Read External Files

Usage

Arguments

Main Analysis: `scripts/main.R`

Input Format

Key Genes (`key_genes`)

Database Directory (`reference_dir`)

Output Files

Workflow

Step 1: Validate Input

Step 2: Load Interaction Data

Step 3: Filter the Network

Step 4: Build Outputs

Methods

`combined`

Pairwise Intersections

lncRNA Strictness

Examples

Basic Combined Analysis

Single Database Analysis

Error Handling

Common Errors

Testing

Test with Sample Data

Validation Commands

Implementation Checklist

Frequently asked questions

Cerna Analysis

File contents

ceRNA Analysis

When to Use

When to Read External Files

Usage

Arguments

Main Analysis: scripts/main.R

Input Format

Key Genes (key_genes)

Database Directory (reference_dir)

Output Files

Workflow

Step 1: Validate Input

Step 2: Load Interaction Data

Step 3: Filter the Network

Step 4: Build Outputs

Methods

combined

Pairwise Intersections

lncRNA Strictness

Examples

Basic Combined Analysis

Single Database Analysis

Error Handling

Common Errors

Testing

Test with Sample Data

Validation Commands

Implementation Checklist

Related skills

Frequently asked questions

How do I install the Cerna Analysis skill?

What does the Cerna Analysis skill do?

Is Cerna Analysis safe to use?

Which AI agents work with Cerna Analysis?

Is Cerna Analysis free to use?

Who published Cerna Analysis?

Main Analysis: `scripts/main.R`

Key Genes (`key_genes`)

Database Directory (`reference_dir`)

`combined`