genome-editing

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

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

FlashFry: The rapid CRISPR target site characterization tool

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

Variant- and Haplotype-aware CRISPR guide design toolkit

BEstimate, a Python module that systematically analyses guide RNA (gRNA) targetable sites across given sequences for given Base Editors, and functional and clinical effects of the potential edits on the resulting proteins.

IES retention analysis from PacBio CCS reads

Comparing Cas Activities by Target Superimposition (CATS)

ALLEGRO is a synthetic biology tool that designs minimal, high activity CRISPR-Cas sgRNA libraries

A large scale off-target analysis tool for CRISPR/Cas9 genome editing system

A kinetic model of CRISPR-Cas target recognition.

Meganucleases|ZFNs|TALENs|CRISPR-Cas|BaseEditors|PrimeEditor

Transcript-unit architecture database for disease-associated large-fragment genome-writing target review.

This project critically analyzes the data pipeline of EVO 2, a cutting-edge AI model for genomic research developed by the Arc Institute and collaborators. The focus lies in evaluating its risks, ethical challenges, and governance structures in the context of data privacy, genome editing, and AI-driven biomedical innovation.

Configurable literature collection, triage, ranking, and AI-summarization engine behind Papertrail.

开源的水稻核心组学 + 育种分析技能库 — 18 个分析模块、130 个 R/Python 脚本 + 23 个 shell 封装、541 个精选 agent 技能；覆盖 FASTQ→counts、差异/时间序列、GWAS/TWAS/MR/fine-mapping、mGWAS、泛基因组/T2T、单细胞/空间、编辑设计、CNS 级绘图与论文写作；含方案确认、依赖体检、CI 与工作流导出。

A variant-first, multi-modality CRISPR design framework that unifies SpCas9 nuclease, base-editor, and prime-editor chemistries under a single typed interface to deliver ranked candidate edits complete with calibrated uncertainty intervals, predicted outcome distributions, and ancestry-stratified, population-aware off-target safety reporting.

Source-aware benchmark and validation-priority resource for high-mismatch genome-editing off-target prioritization.

A desktop workstation for non-destructive genome variant editing, prediction and comparison, inspired by digital audio workstations.

Annotates CRISPR–Cas repair outcomes from CRISPResso2 allele tables: cut geometry (blunt vs staggered), deletion orientation and size, microhomology context, and which DNA end participates in repair — with publication-ready charts and statistics.