ⓘ This page was composed with the aid of generative artificial intelligence; it is partially curated.

ZaroPGx Documentation

Welcome to the documentation for ZaroPGx — a containerized pharmacogenomics platform that processes genetic data and generates comprehensive reports.

For Users

Use ZaroPGx to perform pharmacogenomic analysis:

User Guide

• Quick Start Guide
  • Prerequisites
  • Installation
  • First Run-through
  • Supported File Types
  • Next Steps
• Installation Guide
  • System Requirements (minimum for VCF inputs; recommended for others)
  • Docker Installation
  • Deploy ZaroPGx via docker compose
  • Service Ports
  • Initial Setup
  • Troubleshooting
  • Next Steps
• User Guide
  • Web Interface
  • Analysis Workflow
  • Reports
  • API Usage (NEEDS REVIEW)
  • Data Management
• (NOTE: The ZaroPGx Demo Reference server at pgx.zimerguz.net is for DEMO purposes only! Do not upload your sensitive data)
  • Data Export
  • Best Practices
  • Troubleshooting
  • Next Steps
• Supported File Formats [NEEDS CURATION]
  • Variant Call Format (VCF)
  • Binary Alignment Map (BAM)
  • Compressed BAM (CRAM)
  • Sequence Alignment Map (SAM)
  • FASTQ Format
  • Reference Genome Support
  • File Size Considerations
  • Next Steps
• Understanding Reports
  • Report Types
  • Report Structure
  • Understanding Star Alleles
  • Clinical Recommendations
  • Quality Metrics
  • Interpreting Results
  • Export and Integration
  • Troubleshooting Reports
  • Next Steps
• Troubleshooting Guide
  • Installation Issues
  • File Upload Issues
  • Analysis Issues
  • Report Generation Issues
  • Database Issues
  • Network Issues
  • Performance Issues
  • Log Analysis
  • Getting Help
  • Next Steps
• What is ZaroPGx?
• Who is ZaroPGx for?
• How much does ZaroPGx cost?
• What makes ZaroPGx different from other PGx tools?
• Technical Questions
  • Which file formats are supported?
  • What reference genomes are supported?
  • What are the computing hardware requirements?
  • How long does analysis take?
• Clinical Considerations
  • Which pharmacogenes are analyzed?
  • What clinical guidelines does ZaroPGx use?
  • How accurate are the results?
  • Can I use this for clinical decision-making?
• Deployment Questions
  • Can I run this in the cloud?
  • How do I secure my ZaroPGx deployment?
  • Can I scale this for multiple users?
• Data Questions
  • Where is my data stored?
  • Is my data sent anywhere?
  • Can I export my data?
  • How long is data retained?
• Troubleshooting
  • Why is my analysis taking so long?
  • Why are some genes showing “No Call”?
  • Why is my PDF report empty?
• Development
  • Can I contribute to ZaroPGx?
  • How do I report bugs?
  • Can I customize the analysis pipeline?
• See Next

For Developers

Contributing to or extending ZaroPGx:

Developer Guide [NEEDS CURATION]

• System Architecture
  • High-Level Architecture
  • Service Architecture
  • Data Flow Architecture
  • Container Architecture
  • Security Architecture
  • Scalability Architecture
  • Monitoring and Observability
  • Development Architecture
  • Deployment Architecture
  • Next Steps
• API Reference
  • Base URL
  • Authentication
  • API Endpoints
  • Data Models
  • Error Handling
  • Rate Limiting
  • WebSocket Support
  • SDK Examples
  • Next Steps
• Development Setup
  • Prerequisites
  • Environment Setup
  • Local Development
  • Development Workflow
  • Service Development
  • Database Development
  • Frontend Development
  • Testing Development
  • Debugging
  • Performance Development
  • Deployment Development
  • Next Steps
• [CURATION NEEDED]
• Contributing Guide
  • Getting Started
  • Contribution Types
  • Development Workflow
  • Code Review Process
  • Testing Guidelines
  • Documentation Guidelines
  • Release Process
  • Community Guidelines
  • Recognition
  • Next Steps
• Deployment Guide
  • Deployment Overview
  • Prerequisites
  • Environment Configuration
  • Docker Compose Production
  • Cloud Deployment
  • Database Deployment
  • Monitoring and Logging
  • Security Hardening
  • Performance Optimization
  • Backup and Recovery
  • Troubleshooting
  • Next Steps
• Testing Guide
  • Testing Overview
  • Test Structure
  • Unit Testing
  • Integration Testing
  • End-to-End Testing
  • Performance Testing
  • Test Data Management
  • Test Configuration
  • Continuous Integration
  • Test Best Practices
  • Next Steps

Roadmap

Roadmap

• Input Format Support Priorities
• Pipeline Function
• Calling & Tools
• Reporting
• UI/UX
• Data & Database
• FHIR & Exporting
• Security & Privacy
• Docker & CI/CD
• Documentation
• Engineering
• Open Questions

Quick Navigation

• Getting Started: Quick Start Guide

• API Reference: API Reference

• Architecture Overview: System Architecture

• Troubleshooting: Troubleshooting Guide

What is ZaroPGx?

ZaroPGx is a self-hosted, containerized platform that:

• Processes genomic data (VCF, BAM, CRAM, FASTQ) using industry-standard tools

• Performs comprehensive allele calling across 23+ pharmacogenes using PharmCAT, PyPGx, and OptiType

• Generates clinical reports with actionable pharmacogenomic recommendations

• Maintains data privacy through local deployment with no external data transmission

• Integrates with EHR systems via FHIR export capabilities

The platform orchestrates multiple bioinformatics tools through Docker containers, providing a unified interface for pharmacogenomic analysis that would typically require extensive command-line expertise.