Skip to content

README_docs.md

Latest commit

 

History

History
130 lines (97 loc) · 3.61 KB

README_docs.md

File metadata and controls

130 lines (97 loc) · 3.61 KB

RAPTOR Documentation

Complete documentation for RAPTOR v2.0.0

📚 Documentation Files

Getting Started

  • INSTALLATION.md - Complete installation guide
    • System requirements
    • Python & bioinformatics tools setup
    • Reference genome preparation
    • Verification steps

Core Features

  • PROFILE_RECOMMEND.md - Intelligent pipeline recommendation

    • How the profiling works
    • Understanding recommendations
    • Interpreting data characteristics
    • Advanced customization

  • BENCHMARKING.md - Comprehensive pipeline comparison

    • Running benchmarks
    • Comparing metrics
    • Interpreting results
    • Advanced options

Reference Documentation

  • PIPELINES.md - Deep dive into all 8 pipelines

    • Pipeline components
    • Performance characteristics
    • Use cases and recommendations
    • Running individual pipelines

  • API.md - Python API reference

    • Complete class documentation
    • Method signatures
    • Usage examples
    • Type hints

Support

  • FAQ.md - Frequently asked questions

    • Installation issues
    • Usage questions
    • Technical problems
    • Best practices

  • TROUBLESHOOTING.md - Problem-solving guide

    • Common errors and solutions
    • Debug mode
    • System checks
    • Getting help

📖 Tutorials

Step-by-step guides for common workflows:

  1. 01_quick_start.md - Get started in 5 minutes
  2. 02_profiling_in_depth.md - Master data profiling
  3. 03_benchmarking_guide.md - Run comprehensive benchmarks

🎯 Quick Links by Use Case

I'm new to RAPTOR: → Start with 01_quick_start

I want pipeline recommendations: → See PROFILE_RECOMMEND.md

I need to compare all pipelines: → See BENCHMARKING.md

I want to use Python API: → See API.md

I have installation problems: → Check INSTALLATION.md and TROUBLESHOOTING.md

I need pipeline details: → See PIPELINES.md

📖 Documentation Structure

docs/
├── README.md                      # This file
├── INSTALLATION.md                # Setup guide
├── PROFILE_RECOMMEND.md           # Profiling & recommendations
├── BENCHMARKING.md                # Pipeline comparisons
├── PIPELINES.md                   # Pipeline deep-dive
├── API.md                         # Python API reference
├── FAQ.md                         # Common questions
├── TROUBLESHOOTING.md             # Problem solving
└── tutorials/                     # Step-by-step guides
    ├── 01_quick_start.md
    ├── 02_profiling_in_depth.md
    └── 03_benchmarking_guide.md

🆘 Getting Help

  1. Check documentation - Most answers are here!
  2. Read FAQ - Common questions answered
  3. Try troubleshooting - Solutions to known issues
  4. GitHub Discussions - Ask the community
  5. GitHub Issues - Report bugs
  6. Email - ayehbolouki1988@gmail.com

🤝 Contributing

Found an error or want to improve docs?

  1. Fork the repository
  2. Edit documentation
  3. Submit a pull request

See CONTRIBUTING.md for guidelines.

📄 License

Documentation licensed under MIT License. Same as RAPTOR software.

RAPTOR: Making RNA-seq pipeline selection evidence-based, not guesswork 🦖

Created by Ayeh Bolouki
University of Namur, Belgium
Version 2.0.0