siRNAforge Documentation

Comprehensive siRNA design toolkit for gene silencing with multi-species off-target analysis.

🚀 Getting Started

• Installation
• Getting Started & Quick Reference

📖 User Guide

• CLI Reference
• Usage Examples
• Workflows
• Gene Search Functionality
• Scoring Overview
• Thermodynamic Metrics Interpretation Guide
• Tutorials

📚 Reference

• Python API Usage
• API Reference
• Data Models, Filtering & Scoring: Technical Reference
• Chemical Modification Annotation Specification
• Changelog
• Glossary

🔧 Developer

• Developer Documentation
• Chemical Modification Integration Guide for Developers

Quick Start

🚀 Getting Started

Installation, first workflow, and essential commands

Getting Started & Quick Reference

🧬 CLI Reference

Complete command documentation

CLI Reference

📖 Usage Examples

Real-world examples and workflows

Usage Examples

Tutorials

Step-by-step guides

Tutorials

Key Features

• Algorithm-driven design - Thermodynamic asymmetry analysis

• Off-target analysis - Genome-wide prediction

• Rich scoring - Multi-component research-backed metrics

• Structure prediction - ViennaRNA integration

• Containerized - Docker and Nextflow support