Crispr Python Packages

pen-stack

Open infrastructure for genome writing: the Writable Genome (learned safe+durable insertion-site atlas), the Writer Atlas of 33k genome-writing enzymes, an inverse-design Write Planner, and a bridge-recombinase off-target engine. Consolidates 5 prior repos. Pre-registered, blind-validated, single install.

mgsurve

Python package to optimize mosquito traps' positioning in field trials.

monet-mgdrive

MoNeT python package for MGDrivE data analysis

diced

A Rust reimplementation of the MinCED method for identifying CRISPRs in full or assembled genomes.

karyon

Legible, deterministic QC/qualification for bio-AI tool outputs — named-reason contracts + agent skills that compose with NVIDIA BioNeMo.

dotmatch

Fast exact short-DNA known-target assignment for CRISPR guides, barcodes, primers, panels, and whitelists.

genet

Python library for genome editing, CRISPR gRNA design and prediction

spacr

spaCR Spatial phenotype analysis of CRISPR–Cas9 screens (spaCR)

cy

Python module to analyse CRISPR-based libraries

screenpro2

Flexible analysis of high-content CRISPR screening

cctyper

CRISPRCasTyper: Automatic detection and subtyping of CRISPR-Cas operons

spacr-nightly

Spatial phenotype analysis of crisp screens (SpaCr)

crispresso

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from deep sequencing data

crispio

Designing CRISPR-Cas guide RNAs in bacteria.

berets

Base Editing screens' Activity-Normalized variant effect size estimation

fba

Tools for single-cell feature barcoding analysis

crispyx

Memory-efficient streaming analysis of large-scale CRISPR and Perturb-seq screens on disk-backed AnnData files

vintools

Michael Vinyard's utilities

crispr-bean

Base Editor screen analysis with guide Activity Normalization

crisprhawk

CRISPR-HAWK: Haplotype and vAriant-aWare guide design toolKit

py-crispr-analyser

Python module and scripts to analyse CRISPRs and off-targets from a genome

synthego-ice

Synthego - Inference of CRISPR Edits (ICE)

genome-atlas

Unified knowledge graph and embedding space for programmable genome-writing enzymes

mech-class

Mechanism-aware classification of DNA-modifying enzymes