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    14 repositories

    • LevSeq

      Public
      Pipeline for Nanopore sequencing: demultiplexing, variant calling, and quality visualization with error handling.
      Makefile
      •
      GNU General Public License v3.0
      •4•11•0•0•Updated Jan 25, 2026Jan 25, 2026

    • CSR-SALAD

      Public
      Jupyter Notebook
      •0•0•1•0•Updated Nov 14, 2025Nov 14, 2025

    • EnzymeEngineeringDB

      Public
      Database for directed evolution and enzyme engineering
      Jupyter Notebook
      •
      Other
      •2•10•2•0•Updated Oct 10, 2025Oct 10, 2025

    • alde4ssmula

      Public
      ALDE simulation runs for SSMuLA (Site Saturation Mutagenesis Landscape Analysis), the code base paper titled "Evaluation of Machine Learning-Assisted Directed E…
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jun 19, 2025Jun 19, 2025

    • SSMuLA

      Public
      Code base for "Evaluation of Machine Learning-Assisted Directed Evolution Across Diverse Combinatorial Landscapes"
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•15•0•0•Updated Jun 19, 2025Jun 19, 2025

    • LevSeq_db

      Public
      Visualization for the LevSeq project
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated May 22, 2025May 22, 2025

    • substrate_aware_zs

      Public
      Substrate-Aware Zero-Shot Predictors for Non-Native Enzyme Activities
      Python
      •
      GNU General Public License v3.0
      •1•5•0•0•Updated Apr 18, 2025Apr 18, 2025

    • LevSeq_VDB

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 20, 2024Sep 20, 2024

    • evSeq

      Public
      Computational tools for extremely low-cost, massively parallel amplicon-based sequencing of every variant in protein mutant libraries.
      Python
      •
      Other
      •9•34•6•0•Updated Jun 1, 2022Jun 1, 2022

    • MLDE

      Public
      A machine-learning package for navigating combinatorial protein fitness landscapes.
      Python
      •
      Other
      •27•133•3•1•Updated Nov 17, 2021Nov 17, 2021

    • SPGen

      Public
      Jupyter Notebook
      •
      MIT License
      •4•20•2•0•Updated Mar 31, 2021Mar 31, 2021

    • embeddings_reproduction

      Public
      Jupyter Notebook
      •
      Other
      •31•127•6•0•Updated Feb 16, 2021Feb 16, 2021

    • channels

      Public
      Gaussian process models for optimizing channelrhodopsin properties.
      Jupyter Notebook
      •13•13•2•0•Updated May 30, 2020May 30, 2020

    • ProteinGAN

      Public
      Python
      •
      Other
      •74•0•0•0•Updated Oct 3, 2019Oct 3, 2019