cascade-reg

Contents:

  • Installation guide
  • Tutorials
    • Stage 1: Data preprocessing
    • Stage 2: Model training
    • Stage 3: Counterfactual prediction
    • Stage 4: Intervention design
  • Resources
  • Python interface
  • Command line interface
cascade-reg
  • Tutorials
  • View page source

Tutorials

An cascade-reg workflow can be divided into the following two stages. We provide separate tutorials for each stage.

  • Stage 1: Data preprocessing
    • Read data
    • Data format requirements
    • Cell and gene selection
    • Encode intervention regime
    • Encode technical covariates
    • Data normalization
    • Neighbor-based imputation
    • Configure dataset
    • Construct scaffold graph
    • Prepare gene function embeddings
    • Save processed data files
    • Afterwords
  • Stage 2: Model training
    • Read preprocessed data
    • Build the CASCADE model
    • Run causal discovery
    • Remove remaining cycles
    • Model tuning
  • Stage 3: Counterfactual prediction
    • Read data and model
    • Specify counterfactual condition
    • Run counterfactual prediction
    • Counterfactual differential expression comparison
    • Explain counterfactual prediction
  • Stage 4: Intervention design
    • Prepare source data
    • Prepare target data
    • Define gene weights
    • Specify candidate genes
    • Run intervention design
    • Determine design score cutoff
    • Verify design with counterfactual prediction
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