Usage and Examples

To facilitate the use of PIDGINv4, examples of usage are provided below, ordered by expected frequency of use and increasing complexity.

Sections

• Command Line Arguments
  • List of available arguments
  • Detailed explanations for the more complicated arguments
• Getting started
  • Generating predictions for human targets
  • Generating binary predictions
  • Decreasing applicability domain (AD) filter
  • Outputting the AD results
  • Silencing the AD filter
  • Combining model filters
• Extended functionality
  • Generating transposed predictions
  • Increasing trees and getting the standard dev. for input compounds
  • Annotating predictions with known activity
  • Similarity of input compounds to the active compounds in the training set
• Enrichment Predictions
  • List of available arguments
  • Generating enrichment predictions
  • More complicated example
  • References