List of software/websites/databases/other stuff for genome engineering
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Jun 20, 2024
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genome-editing
Here are 24 public repositories matching this topic...
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
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May 14, 2026 - Python
FlashFry: The rapid CRISPR target site characterization tool
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Jun 12, 2024 - Scala
Automatically identify non-interfering nucleotide linkers between a pegRNA and 3' motif
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Aug 13, 2025 - Python
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.
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May 8, 2026 - Python
Variant- and Haplotype-aware CRISPR guide design toolkit
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May 25, 2026 - Python
IES retention analysis from PacBio CCS reads
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May 18, 2022 - Python
ALLEGRO is a synthetic biology tool that designs minimal, high activity CRISPR-Cas sgRNA libraries
synthetic-biology linear-programming combinatorial-optimization crispr-cas9 genome-editing sgrna-design
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Apr 10, 2026 - Python
Meganucleases|ZFNs|TALENs|CRISPR-Cas|BaseEditors|PrimeEditor
dataviz protein-structure inkscape data-visualization chimera genome-editing protein-dna-interactions
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Feb 6, 2020
Comparing Cas Activities by Target Superimposition (CATS)
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May 7, 2026 - Python
A large scale off-target analysis tool for CRISPR/Cas9 genome editing system
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Jul 24, 2017 - Perl
A kinetic model of CRISPR-Cas target recognition.
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Mar 19, 2026 - Python
Accelerate DNA gene editing projects with intuitive, AI-powered CRISPR gRNA design and analysis
bioinformatics synthetic-biology computational-biology crispr dna-sequences genome-editing grna bioinformatics-tool guide-rna-library gene-editing streamlit-webapp grna-design
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Apr 29, 2026 - Python
Transcript-unit architecture database for disease-associated large-fragment genome-writing target review.
database clinvar mane genome-editing gencode disease-genomics large-fragment-insertion transcript-architecture genome-writing
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May 26, 2026 - Python
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.
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Oct 22, 2025
Source-aware benchmark and validation-priority resource for high-mismatch genome-editing off-target prioritization.
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May 13, 2026 - Python
Benchmarking BleTIES with Tetrahymena long read data
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Jun 15, 2022 - Jupyter Notebook
PEN-ASSEMBLE: Automated Strategy and Scoring Engine for Molecular Bridge-recombinase Library Engineering | IS110-family design pipeline, 1,029 candidates, 5/5 pre-registered predictions | Part of PEN-STACK
python bioinformatics synthetic-biology computational-biology protein-design genome-editing genetic-engineering gene-therapy pen-stack proteinmpnn genome-atlas bridge-recombinase is110-family penscore deimmunization mech-class
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May 26, 2026 - HTML
Benchmarking BleTIES with simulated long reads
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Jun 15, 2022 - Jupyter Notebook
ALLEGRO is a synthetic biology tool that designs minimal, high activity CRISPR guide RNA libraries
synthetic-biology linear-programming combinatorial-optimization crispr-cas9 genome-editing guide-rna-library
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Apr 3, 2026 - Python
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