List of software/websites/databases/other stuff for genome engineering

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

Mining CRISPRs in Environmental Datasets

Cutting-edge Full-stack AI Platform delivered as a SaaS (Software as a Service). Built on a robust technology stack, integrated with powerful APIs such as OpenAI and Replicate, offers a seamless experience for code generation, conversation simulation, image creation, music composition, and video generation.

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons

FlashFry: The rapid CRISPR target site characterization tool

Synthego ICE - Inference of CRISPR Editing software

A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).

SpacePHARER CRISPR Spacer Phage-Host pAiRs findER

:earth_americas: Complex Topics Explained For Your Level And Background. :pencil2:

Predicting Cell Health with Morphological Profiles

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

The CRISPR assembler

A better, faster way to count guides in CRISPR screens.

Flexible analysis of high-content CRISPR screening

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

Comprehensive design of CRISPR gRNAs for nucleases and base editors

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

A software tool for personalized and allele-specific CRISPR editing.

a guideRNA database generation tool

GEMINI: A variational Bayesian approach to identify genetic interactions from combinatorial CRISPR screens

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

Collection of R packages that work in harmony for CRISPR gRNA design

Robust and efficient analysis of single-cell perturbation studies

Tutorials for the crisprVerse

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

An interactive exploration/visualization platform to help you lift the fog from your CRISPR analyses.