Tutorials

• Python API Tutorial
  • Learning Objectives
  • Prerequisites
  • Getting Started
  • Gene Search API
  • Advanced API Usage
  • Configuration and Customization
  • Testing Your Code
  • Best Practices
  • Next Steps
  • Key API Modules
• Pipeline Integration Tutorial
  • When to Use the Pipeline
  • Prerequisites
  • Step 1 – Prepare Candidates
  • Step 2 – Configure References
  • Step 3 – Run Off-Target Analysis (embedded Nextflow)
  • Running Nextflow Directly (advanced)
  • Step 4 – Inspect Outputs
  • Troubleshooting
  • Additional Resources
• Modular Override Guide
  • Design Philosophy
  • Default Behavior
  • Surgical Overrides
  • Advanced Use Cases
  • Override Hierarchy
  • Cache Management
  • Common Workflows
  • Troubleshooting
  • Implementation Notes
  • Species Normalization
  • API Usage
  • Summary
• Custom Scoring Tutorial
  • Understanding Thermodynamic Asymmetry Scoring
  • Custom Scoring Framework
  • Validation and Performance
  • Advanced Topics
• Chemical Modification Patterns Reference
  • Overview
  • Built-In Modification Patterns
  • FDA-Approved Example: Patisiran (Onpattro)
  • Modification Types Reference
  • Custom Pattern Design
  • Application-Specific Recommendations
  • Synthesis and Ordering
  • Best Practices
  • Integration with siRNAforge
  • Troubleshooting
  • References
  • Contributing Patterns

Tutorial Overview

These tutorials provide step-by-step guidance for using siRNAforge effectively:

• Python API: Using siRNAforge programmatically with Python

• Pipeline Integration: Nextflow workflows for large datasets

• Modular Override Guide: Understanding the single-species design and surgical overrides

• Custom Scoring: Developing application-specific scoring functions

• Modification Patterns Reference: Comprehensive guide to chemical modifications for siRNA stability and therapeutics

Each tutorial includes:

• Clear learning objectives

• Complete, runnable examples

• Expected outputs and interpretation

• Troubleshooting tips

• Links to relevant API documentation