PEN-COMPARE Documentation

PEN-COMPARE is the capstone of the PEN-STACK framework — a hierarchical certification system that classifies genome editors as TRUE_WRITER, PROBABLE_WRITER, EMERGING_WRITER, or NOT_WRITER using five pre-registered gates (v3.2).

Getting Started

• Installation
  • Requirements
  • From source
  • Docker (recommended for full pipeline)
  • Streamlit Community Cloud
• Quick Start
  • Certify a single editor
  • CLI usage
  • Run sensitivity analysis
  • Triangulation

Framework

• TrueWriterScore Gates (v3.2)
  • Gate 1 — DSB Avoidance (Necessary)
  • Gate 2 — Programmability (Qualifying)
  • Gate 3 — Native Cargo Capability (Qualifying)
  • Gate 4 — Deliverability (Qualifying)
  • Gate 5 — Experimental Evidence (Qualifying)
  • Tier Ladder
• Tier Ladder
  • Pre-registered outcomes (2026-05-26)
  • Universe composition (Step 5)
  • Scorecard summary
• PEN-COMPARE Model Card
  • Framework Identity
  • Purpose
  • Inputs
  • Outputs
  • Tier Ladder
  • Training Data & Calibration
  • Known Limitations
  • Sensitivity Analysis
  • Pre-Registration Outcomes
  • Citation

API Reference

• Core API
  • pen_compare.core.certify
  • pen_compare.core.gates
  • pen_compare.core.sensitivity
• Triangulation API
  • pen_compare.triangulation
• RAG Q&A API
  • pen_compare.rag
• Server & Cache API
  • pen_compare.server.cache

Results

• Pre-Registration Outcomes
• Sensitivity Analysis
• Triangulation Report

Indices and tables

• Index

• Module Index

• Search Page