Genome Editing Python Packages

crisprzip

A kinetic model of CRISPR-Cas target recognition.

crisprhawk

Variant- and Haplotype-aware CRISPR guide design toolkit

pen-assemble

Automated design and scoring engine for IS110-family bridge recombinase variants, nominating 1,029 candidates via an 8-axis PenScore over pre-registered predictions.

helix-dsl

A declarative DSL and compiler for reproducible gene-editing design — with LLM agents and an MCP server so any AI agent can drive it safely.

pen-compare

Hierarchical certification framework (5-gate TrueWriterScore) for programmable genome editors, with sensitivity analysis, cross-pipeline triangulation, and a RAG Q&A layer over the PEN-STACK.

pen-score

Multi-axis scoring framework that ranks programmable genome editors across eight orthogonal axes into a single PenScore to guide experimental design and benchmarking.

crispr-cats

Comparing Cas Activities by Target Superimposition (CATS)