basic_grn_inference

This script demonstrates the standard workflow for inferring gene regulatory networks from expression data using GRNBoost2.

Skills
Scientific
2

What it does and how to use it

A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

Install the skill (command above).
In Claude Code, describe what you need - the skill turns on by itself when the context fits.
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Install (Claude Code)

mkdir -p .claude/skills/basic-grn-inference && curl -fsSL https://doutorai.pt/data/lib/skills__basic-grn-inference.md -o .claude/skills/basic-grn-inference/SKILL.md

Paste this command into the terminal, in your project folder, and the component installs automatically.

Content

#!/usr/bin/env python3
"""
Basic GRN inference example using Arboreto.

This script demonstrates the standard workflow for inferring gene regulatory
networks from expression data using GRNBoost2.

Usage:
    python basic_grn_inference.py <expression_file> <output_file> [--tf-file TF_FILE] [--seed SEED]

Arguments:
    expression_file: Path to expression matrix (TSV format, genes as columns)
    output_file: Path for output network (TSV format)
    --tf-file: Optional path to transcription factors file (one per line)
    --seed: Random seed for reproducibility (default: 777)
"""

import argpars

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