Crispr Python Packages

dotmatch

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

spacr

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

pertpy

Single-cell perturbation analysis

diffbio

End-to-end differentiable bioinformatics for JAX/Flax NNX: soft Smith-Waterman alignment, read mapping and assembly, variant calling, RNA-seq, single-cell, epigenomics, CRISPR, metabolomics, multi-omics, protein and RNA structure, molecular dynamics and drug-discovery operators composed into trainable pipelines on the Avitai stack.

mgsurve

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

crispyx

crispyx is a Python package for scalable CRISPR and Perturb-seq screen analysis on disk-backed AnnData files. It provides streaming quality control, normalization, pseudobulk aggregation, and differential expression without loading the full count matrix into memory.

monet-mgdrive

Contains the code for the pypi package to do the data analysis portion of the MGDrivE project.

diced

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

screenpro2

Flexible analysis of high-content CRISPR screening

crispresso

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

pysceptre

Standalone Python port of the statistical engine behind sceptre's discovery analysis for single-cell CRISPR screens.

cctyper

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons

gpudge

Lightweight GPU-only Mann–Whitney U differential expression for single-cell CRISPR perturbation screens

cy

Python module to analyse CRISPR-based libraries

genet

Python library for genome editing, CRISPR gRNA design and prediction

biosuite-ultra

Integrated pure-Python bioinformatics platform: 47 analysis modules, 105 plotting functions, molecular cloning with 169 restriction enzymes, and reproducible workflows through Python, CLI, GUI, and REST API.

berets

Base Editing screens' Activity-Normalized variant effect size estimation

fba

Tools for single-cell feature barcoding analysis

crispio

🌱 Designing CRISPRi experiments in bacteria

karyon

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

vintools

Michael Vinyard's utilities

crisprhawk

Variant- and Haplotype-aware CRISPR guide design toolkit

crispr-bean

Base Editing screens' Activity-Normalized variant effect size estimation

py-crispr-analyser

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