Documentation

Welcome

• Welcome
  • CheRRI’s workflow
• Installation
  • Install Conda
  • Install CheRRI Conda package
  • Create environment manually
  • Manual installation
  • Install using pip

Usage

• Usage
  • Evaluation of RRIs
    • RRI input format in evaluation mode
    • Example call for CheRRI’s evaluation mode
    • Input parameters in evaluation mode
      • Required:
      • Optional:
    • Output in evaluation mode
    • Validate your model using the eval mode
  • Build a new CheRRI model in training mode
    • Retrieve RNA-RNA interactome files using ChiRA
    • Build RRI interactome file as input for CheRRI
    • Example call for CheRRI’s training mode
    • Input parameters in training mode
      • Required:
      • Optional:
    • Output in training mode
    • Run train in mixed model mode

Documentation

• Documentation
  • CheRRI’s core method scripts
    • RRI detection with find_trusted_RRI.py
      • Input parameters for find_trusted_RRI.py
      • Output of find_trusted_RRI.py
    • Compute occupied regions with find_occupied_regions.py
      • Input parameters for find_occupied_regions.py
      • Output of find_occupied_regions.py
    • Interaction predictions with generate_pos_neg_with_context.py
      • Input parameters for generate_pos_neg_with_context.py
      • IntaRNA parameters used within CheRRI
      • Output of generate_pos_neg_with_context.py
    • Feature extraction with get_features.py
      • Input parameters for get_features.py
      • Output of get_features.py
    • Feature selection and optimization