cobind’s documentation

Documentation

• 1. Introduction
  • 1.1. Introductionn
• 2. Definitions
  • 2.1. Symbols definitions
  • 2.2. Spacial Relations of Genomic regions (SROG)
  • 2.3. Collocation coefficient (C)
  • 2.4. Jaccard coefficient (J)
  • 2.5. Sørensen–Dice coefficient (SD)
  • 2.6. Szymkiewicz–Simpson coefficient (SS)
  • 2.7. Pointwise mutual information (PMI)
  • 2.8. Normalized pointwise mutual information (NPMI)
  • 2.9. Which metric to use?
• 3. Installation
  • 3.1. Dependencies
  • 3.2. Install pip
  • 3.3. Install to virtual environment
  • 3.4. Install globally
  • 3.5. Upgrade
  • 3.6. Uninstall
• 4. Input file and data format
  • 4.1. BED format
  • 4.2. BED-like format
  • 4.3. bigBed
  • 4.4. bigWig
• 5. Test dataset
  • 5.1. CTCF ChIP-seq
  • 5.2. RAD21 ChIP-seq
  • 5.3. Other files
• 6. Release history
  • 6.1. Version 1.0.0
  • 6.2. Version 1.0.1

Usage Information

• 1. Overview
  • 1.1. Subcommands description
  • 1.2. Usage
• 2. Collocation coefficient (C)
  • 2.1. Description
  • 2.2. Usage
  • 2.3. Example
• 3. Jaccard coefficient (J)
  • 3.1. Description
  • 3.2. Usage
  • 3.3. Example
• 4. Dice coefficient (SD)
  • 4.1. Description
  • 4.2. Usage
  • 4.3. Example
• 5. Szymkiewicz–Simpson coefficient (SS)
  • 5.1. Description
  • 5.2. Usage
  • 5.3. Example
• 6. Pointwise mutual information (PMI)
  • 6.1. Description
  • 6.2. Usage
  • 6.3. Example
• 7. Normalized pointwise mutual information (NPMI)
  • 7.1. Description
  • 7.2. Usage
  • 7.3. Example
• 8. Cooccurrence
  • 8.1. Description
  • 8.2. Usage
  • 8.3. Example
• 9. Covary
  • 9.1. Description
  • 9.2. Usage
  • 9.3. Example
• 10. Spatial Relation Of Genomic (SROG) intervals
  • 10.1. Description
  • 10.2. Usage
  • 10.3. Example
• 11. Stat
  • 11.1. Description
  • 11.2. Usage
  • 11.3. Example
• 12. Z-score
  • 12.1. Description
  • 12.2. Usage
  • 12.3. Example

Evaluation

• Compare different metrics
• CTCF: Demonstration

Performance

• Performance (CPU & memory usage)

License

• LICENSE

Acknowledgements

• Acknowledgements

Contact

• Contact

Reference

• Reference