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

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons

Synthego ICE - Inference of CRISPR Editing software

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.

Flexible analysis of high-content CRISPR screening

On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs

Python library for genome editing, CRISPR gRNA design and prediction

A Computational Workflow for Designing Libraries of sgRNAs for CRISPR-Mediated Base Editing, and much more

Analysis package for processing counts from genome-wide CRISPR/Cas9 screens

CRISPR/Cas-directed HDR genome editing suite: finds+scores gRNA targets, generates donor DNAs, & produces optimal cPCR primer designs.

Python module to analyse CRISPR-based libraries

Robust and efficient analysis of single-cell perturbation studies

ancestral reconstruction and likelihood analysis for CRISPR spacer arrays

Base Editing screens' Activity-Normalized variant effect size estimation

Automatically identify non-interfering nucleotide linkers between a pegRNA and 3' motif

CROPSR is a python tool designed for genome-wide gRNA design and evaluation for CRISPR experiments, with special focus on complex genomes such as those found in energy-producing crops. CROPSR is a product of the DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI).

CROPSR is a python tool designed for genome-wide gRNA design and evaluation for CRISPR experiments, with special focus on complex genomes such as those found in energy-producing crops. CROPSR is a product of the DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI).

Code for CRISPR activation screen with single-cell RNA-seq readout studying zygotic genome activation

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