modtector
  • Overview
    • Key Features
    • Quick Start
      • Installation
      • Example Dataset
      • Basic Usage
    • Workflow Overview
    • Version Information
    • Support
    • Project Links
    • Citation
    • Documentation Contents
      • Documentation Sections
        • Getting Started
        • User Documentation
        • Support & Development
      • Quick Navigation
  • Installation Guide
    • System Requirements
      • Minimum Requirements
      • Required Dependencies
    • Installing Rust
      • Linux/macOS
      • Windows
    • Installing modtector
      • Method 1: Build from Source (Recommended)
      • Method 2: Install via Cargo
    • Dependencies
    • Platform-Specific Notes
      • Linux
      • macOS
      • Windows
    • Verification
    • Troubleshooting
      • Common Issues
      • Getting Help
    • Next Steps
    • Uninstallation
  • Quick Start Guide
    • Prerequisites
    • Example Dataset
    • Step 1: Generate Pileup Data
    • Step 2: Calculate Reactivity Scores
    • Step 3: Normalize Reactivity Signals
    • Step 4: Duet Ensemble Analysis
    • Step 5: Generate Visualizations
    • Step 6: Evaluate Accuracy
    • Expected Outputs
      • Key Output Files
    • Understanding the Results
      • Reactivity Scores
      • Evaluation Metrics
    • Common Issues and Solutions
      • Issue 1: Low Coverage
      • Issue 2: Poor Normalization
      • Issue 3: Low Evaluation Scores
    • Next Steps
    • Getting Help
    • Tips for Success
  • User Guide
    • Table of Contents
    • Understanding RNA Modifications
      • What are RNA Modifications?
      • Common RNA Modifications
      • Detection Methods
    • modtector Workflow
      • Overview
      • Step-by-Step Process
    • Data Preparation
      • Input Requirements
        • BAM Files
        • Reference Sequences
        • Secondary Structure Files
      • Data Quality Checks
      • Batch Processing and Single-cell Mode
        • Batch Mode (--batch)
        • Single-cell Unified Mode (--single-cell)
    • Signal Types
      • Stop Signals
        • Characteristics
        • Analysis
      • Mutation Signals
        • Characteristics
        • Analysis
      • Combined Analysis
    • Normalization Methods
      • Purpose
      • Available Methods
        • 1. Percentile28 Normalization
        • 2. Winsor90 Normalization
        • 3. Boxplot Normalization
      • Window-Based Normalization
        • Fixed Windows
        • Dynamic Windows
        • Sliding Windows
    • Reactivity Calculation
      • Purpose
      • Calculation Methods
        • Stop Signal Methods
        • Mutation Signal Methods
      • Parameters
        • Pseudocount
        • Maximum Score
    • Evaluation Metrics
      • Purpose
      • Available Metrics
        • 1. Area Under the Curve (AUC)
        • 2. F1-Score
        • 3. Accuracy
        • 4. Sensitivity (Recall)
        • 5. Specificity
        • 6. Positive Predictive Value (PPV)
        • 7. Negative Predictive Value (NPV)
      • Evaluation Process
      • Output Files
    • Visualization
      • Purpose
      • Available Plots
        • 1. Signal Distribution Plots
        • 2. Reactivity Plots
        • 3. ROC Curves
        • 4. PR Curves
        • 5. Comparison Plots
        • 6. RNA Structure SVG Plots
        • 7. Interactive HTML Visualizations
      • SVG Plotting
        • Overview
        • SVG-Only Mode
        • Multi-Signal SVG Plotting
        • Interactive HTML Visualization
        • Single Signal SVG Plotting
        • SVG Plotting with Alignment
        • SVG Output Files
      • Plotting Options
        • Basic Plotting
        • With Reactivity Data
        • Custom Thresholds
        • With Genome Annotation
    • Advanced Features
      • Multi-threading
      • Window Analysis
        • Fixed Windows
        • Dynamic Windows
      • Base-Specific Analysis
      • Statistical Testing
      • Auto-shift Correction
      • Base Matching
    • Best Practices
      • Data Quality
      • Parameter Selection
      • Performance Optimization
      • Result Interpretation
      • Troubleshooting
      • Documentation
    • Common Workflows
      • Basic Workflow
      • Advanced Workflow
  • Command Reference
    • Overview
    • count - Data Processing
      • Usage
      • Options
      • Examples
      • Batch and Single-cell Modes
      • Output Format
    • norm - Signal Normalization
      • Usage
      • Options
      • Normalization Methods
      • Examples
    • reactivity - Reactivity Calculation
      • Usage
      • Options
      • Reactivity Methods
        • Stop Signal Methods
        • Mutation Signal Methods
      • K-Factor Prediction Methods
      • Examples
    • compare - Sample Comparison
      • Usage
      • Options
      • Comparison Modes
      • Statistical Tests
      • Examples
    • evaluate - Accuracy Evaluation
      • Usage
      • Options
      • Examples
    • plot - Visualization
      • Usage
        • Regular Mode
        • SVG-Only Mode
      • Options
      • SVG Plotting Options
      • Examples
        • Regular Plotting
        • SVG-Only Mode
        • Combined Mode (Regular + SVG)
      • SVG Plotting Features
        • Signal Type Support
        • Strand Selection
        • Base Filtering
        • Alignment Support
      • Output Files
        • Regular Mode Output
        • SVG Mode Output
        • Combined Mode Output
    • duet - Dynamic Ensemble Decomposition
      • Usage
      • Options
      • Outputs
      • Progress Reporting
      • Examples
    • extract - Extract Gene Regions from Count Results
      • Usage
      • Options
      • How It Works
      • Gene Matching
      • Examples
      • Output Format
      • File Naming
      • Input Formats
        • CSV Format (default)
        • bam-readcount Format
      • Performance Optimization
      • Notes
    • convert - Format Conversion
      • Usage
      • Options
      • Supported Input Formats
      • Examples
      • Input Format (bamreadcount)
      • Output Format (modtector pileup)
      • Conversion Details
      • Performance
      • Progress Reporting
      • Error Handling
      • Use Cases
      • Notes
    • correct - PCR Bias Correction
      • Usage
      • Options
      • How It Works
      • Method Details
      • Examples
      • Output Format
      • Use Cases
      • Notes
    • Global Options
    • Output Files
      • Common Output Formats
      • File Naming Conventions
    • Best Practices
    • Troubleshooting
      • Common Issues
      • Getting Help
  • Examples and Tutorials
    • Table of Contents
    • Basic Example
      • Scenario
      • Data
      • Step-by-Step Process
        • 1. Generate Pileup Data
        • 2. Calculate Reactivity
        • 3. Normalize Reactivity Signals
        • 4. Generate Plots
        • 5. Evaluate Accuracy
      • Expected Outputs
    • Advanced Example
      • Scenario
      • Data
      • Advanced Workflow
        • 1. Batch Processing with Windowing
        • 2. Advanced Normalization
        • 3. Multiple Reactivity Methods
        • 4. Statistical Comparison
        • 5. Comprehensive Evaluation
    • SVG Plotting Examples
      • Scenario
      • Data Requirements
      • Basic SVG Plotting
        • 1. Simple SVG Plot (SVG-Only Mode)
        • 2. Multi-Signal SVG Plotting
        • 3. Single Signal SVG Plotting
      • Advanced SVG Plotting
        • 4. SVG Plotting with Alignment
        • 5. Negative Strand SVG Plotting
        • 6. Both Strands SVG Plotting
      • Combined Mode (Regular + SVG)
        • 7. Generate Both Regular and SVG Plots
      • Real-World Examples
        • Example 1: Human 18S rRNA Structure
        • Example 2: E.coli 16S rRNA Structure
        • Example 3: DMS-seq Specific Analysis
      • SVG Output Files
        • File Naming Convention
        • SVG File Structure
      • Troubleshooting SVG Plotting
        • Common Issues
        • Quality Control
      • Best Practices
    • Batch Processing
      • Scenario
      • Batch Script Example
      • Parallel Processing
    • Custom Analysis
      • Scenario
      • Region-Specific Analysis
      • Custom Normalization Parameters
      • Custom Reactivity Parameters
    • Troubleshooting Examples
      • Low Coverage Issue
      • Memory Issues
      • Poor Normalization
      • Low Evaluation Scores
    • Performance Optimization
      • Large Dataset Processing
      • Memory Optimization
      • Disk Space Management
    • Real-World Examples
      • Example 1: m6A Detection
      • Example 2: m1A Detection
      • Example 3: Pseudouridine Detection
    • Quality Control Examples
      • Data Quality Assessment
      • Result Validation
    • Integration Examples
      • Snakemake Workflow
      • Nextflow Workflow
  • Troubleshooting Guide
    • Table of Contents
    • Installation Issues
      • Rust Not Found
      • Build Failures
      • Permission Errors
    • Data Processing Issues
      • BAM File Issues
      • Reference Sequence Issues
      • Low Coverage
      • Alignment Quality Issues
    • Performance Issues
      • Slow Processing
      • High CPU Usage
      • Disk I/O Issues
    • Output Quality Issues
      • Poor Normalization
      • Low Reactivity Scores
      • Poor Evaluation Scores
    • Memory and Resource Issues
      • Out of Memory
      • Disk Space Issues
    • File Format Issues
      • CSV Format Problems
      • Structure File Issues
      • BAM Index Issues
    • Getting Help
      • Log Files
      • Debug Mode
      • Common Error Messages
        • “BAM file not found”
        • “Reference sequence not found”
        • “Insufficient memory”
        • “Low coverage”
        • “Poor alignment quality”
      • Reporting Issues
      • Community Support
      • Professional Support
    • Prevention Tips
      • Best Practices
      • Regular Maintenance
  • Contributing to modtector
    • Table of Contents
    • Getting Started
      • Prerequisites
      • Fork and Clone
      • Development Setup
    • Contributing Guidelines
      • Types of Contributions
      • Contribution Process
      • Branch Naming
    • Code Style
      • Rust Style Guidelines
      • Code Formatting
      • Linting
      • Documentation
    • Testing
      • Test Structure
      • Running Tests
      • Test Data
      • Integration Tests
    • Documentation
      • Code Documentation
      • User Documentation
      • Documentation Standards
    • Submitting Changes
      • Pull Request Process
      • Pull Request Template
      • Review Process
    • Issue Reporting
      • Bug Reports
      • Feature Requests
      • Issue Template
    • Development Workflow
      • Daily Workflow
      • Release Process
    • Code of Conduct
      • Our Pledge
      • Expected Behavior
      • Unacceptable Behavior
      • Enforcement
    • Getting Help
      • Communication Channels
      • Mentorship
      • Resources
    • Recognition
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