List of software/websites/databases/other stuff for genome engineering
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Jul 29, 2026
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genome-editing
Here are 32 public repositories matching this topic...
Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments
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Jun 12, 2026 - Python
FlashFry: The rapid CRISPR target site characterization tool
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Jul 27, 2026 - Scala
Automatically identify non-interfering nucleotide linkers between a pegRNA and 3' motif
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Aug 13, 2025 - Python
Variant- and Haplotype-aware CRISPR guide design toolkit
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May 25, 2026 - 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
IES retention analysis from PacBio CCS reads
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May 18, 2022 - Python
Comparing Cas Activities by Target Superimposition (CATS)
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May 7, 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
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
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
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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Jul 28, 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
Configurable literature collection, triage, ranking, and AI-summarization engine behind Papertrail.
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Jul 28, 2026 - Python
A declarative DSL and compiler for reproducible gene-editing design — with LLM agents and an MCP server so any AI agent can drive it safely.
python bioinformatics compiler dsl mcp computational-biology crispr genome-editing base-editing gene-editing guide-rna prime-editing llm-agents mcp-server
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Jul 17, 2026 - Python
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.
python rust machine-learning bioinformatics deep-learning genomics computational-biology crispr variant-calling clinvar uncertainty-estimation genome-editing benchmark-datasets pyo3 base-editing populationgenetics prime-editing haplotype-mapping off-target-analysis guide-rna-design
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Jul 29, 2026 - Python
Source-aware benchmark and validation-priority resource for high-mismatch genome-editing off-target prioritization.
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Jul 28, 2026 - Python
Desktop GUI tool for CRISPR/Cas9 guide RNA design — local gRNA search, Doench 16 scoring, secondary structure prediction with custom 2D plotting, interactive genomic map.
bioinformatics crispr-cas9 genome-editing rna-folding grna viennarna bioinformatics-tool guide-rna-design
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Jul 18, 2026 - Python
Quantify CRISPR-Cas9 knockout editing from Nanopore (Plasmidsaurus) amplicon sequencing — a CRISPResso2 workflow with extra tools for multi-guide inter-cut dropouts and large excisions.
bioinformatics nanopore ngs crispr oxford-nanopore indels crispr-cas9 genome-editing amplicon-sequencing long-read-sequencing gene-knockout crispresso2 plasmidsaurus
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Jun 5, 2026 - Python
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