Lncrna Regulatory Network Construction Analysis

What it does

When your agent uses it

• Tasks that involve Bioinformatics
• Tasks that involve Data analysis

Example prompts

• “/lncrna-regulatory-network-construction-analysis”

Workflow steps

9 steps, taken from the first numbered list in SKILL.md.

1. 1Read SKILL.md to confirm that the request is database-driven.
2. 2Use scripts/main.R for actual execution.
3. 3Use --mode analyze to build tables and a saved .rda object.
4. 4Use --mode visualize to reuse the saved object and redraw the PDF without rebuilding the database tables.
5. 5Use --mode full to run both steps in one pass.
6. 6Read reference files only when more detail is needed.
7. 7Before --mode visualize, confirm that output_dir/data/lncrna_network.rda already exists.
8. 8In visualize mode, the saved .rda object is the required input; a missing or invalid reference_dir does not block plot reuse.
9. 9After execution, report the mode, output directory, key files, and either the retained network size or the surfaced skill error code.

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships 6 files in scripts/ (R, from the files we listed), which the agent can run.

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md.

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Lncrna Regulatory Network Construction Analysis loads about 2.7k tokens when it runs, and up to ~19M if it reads all its reference files. Until then it costs about 79 tokens; SKILL.md has 1,028 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~79

When it runs · the whole SKILL.md, loaded when a task matches

~2.7k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~19M

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 1,028 words, ~2,665 tokens.

name

lncrna-regulatory-network-construction-analysis

description

Use this bioinformatics data analysis skill to construct a database-driven lncRNA-mRNA regulatory network from target lncRNA and/or gene lists by projecting shared miRNA evidence from local ceRNA reference tables. It does not infer networks from expression matrices.

license

MIT

author

AIPOCH

Rscript scripts/main.R \
  --mode full \
  --target_genes ./target_genes.txt \
  --target_lncrna ./target_lncrna.txt \
  --mirna_dataset combined \
  --lncrna_strictness High \
  --min_shared_mirna 1 \
  --reference_dir ./references/database \
  --output_dir ./output \
  --seed 42

TP53
BRCA1
MYC

XIST
SNHG16
HNRNPU-AS1

Rscript scripts/main.R \
  --mode full \
  --target_genes ./target_genes.txt \
  --reference_dir ./references/database \
  --output_dir ./output

Rscript scripts/main.R \
  --mode analyze \
  --target_lncrna ./target_lncrna.txt \
  --mirna_dataset starbase \
  --lncrna_strictness Median \
  --output_dir ./lncrna_only_output

Rscript scripts/main.R \
  --mode full \
  --target_genes TP53,BRCA1,MYC \
  --target_lncrna XIST,SNHG16,HNRNPU-AS1 \
  --mirna_dataset combined \
  --lncrna_strictness High \
  --min_shared_mirna 2 \
  --output_dir ./focused_output

Rscript scripts/main.R \
  --mode visualize \
  --output_dir ./focused_output \
  --plot_file reused_network.pdf \
  --layout_type fr

Rscript scripts/main.R --help

Rscript tests/run_tests.R

Rscript scripts/main.R \
  --mode full \
  --target_genes tests/data/target_genes.txt \
  --target_lncrna tests/data/target_lncrna.txt \
  --reference_dir references/database \
  --output_dir tests/output \
  --seed 42

© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 25 other files (scripts, references) in awesome-med-research-skills/Data Analysis/lncrna-regulatory-network-construction-analysis of aipoch/medical-research-skills.

• SKILL.md
• eval_report_lncrna-regulatory-network-construction-analysis_result.json
• references/algorithm.md
• references/cli-guide.md
• references/database/miRDB_miRNA_mRNA.csv
• references/database/miRNA_mRNA.csv
• references/database/miRTarbase_miRNA_mRNA.csv
• references/database/starbase_miRNA_lncRNA_High.csv
• references/database/starbase_miRNA_lncRNA_Low.csv
• references/database/starbase_miRNA_lncRNA_Median.csv
• references/database/starbase_miRNA_mRNA.csv
• references/troubleshooting.md
• scripts/cli_options.R
• scripts/functions.R
• scripts/io.R
• scripts/main.R
• scripts/plot_helpers.R
• scripts/recording.R
• … and 8 more

Open the folder on GitHubat commit 686e09d