metagene

Metagene Analysis Package

A powerful Python package for metagene profiling analysis and visualization, featuring automatic reference downloading, rich CLI interface, and comprehensive plotting capabilities.

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Quick Start

Installation

pip install metagene

Basic Usage

import metagene

# Load genomic sites
sites = metagene.load_sites("sites.tsv", with_header=True)

# Load reference annotations
reference = metagene.load_reference("GRCh38")  # Auto-downloads if needed

# Run analysis
results = metagene.map_to_transcripts(sites, reference)
normalized = metagene.normalize_positions(results)

# Generate plot
metagene.plot_profile(normalized, "output.png")

Command Line Interface

# Run analysis with built-in reference
metagene -i sites.tsv -o results.tsv -r GRCh38 -p plot.png --with-header

# List available references
metagene --list

# Download specific reference
metagene --download GRCm39

Getting Help