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    42 repositories

    • recoli57

      Public
      Supporting code for Ostrov et al., Science, 2016
      Python
      •
      Other
      •2•0•0•0•Updated Apr 21, 2026Apr 21, 2026

    • UniRep

      Public
      UniRep model, usage, and examples.
      Python
      •96•362•5•2•Updated Mar 1, 2026Mar 1, 2026

    • Microglia

      Public
      R
      •1•2•1•0•Updated Mar 14, 2025Mar 14, 2025

    • Deep_diversification_AAV

      Public
      Bioinformatics code for paper associated with deep diversification of AAV
      Jupyter Notebook
      •
      MIT License
      •17•42•1•0•Updated Nov 27, 2024Nov 27, 2024

    • aav_rep_scan

      Public
      Contains code used to generate oligonucleotides for AAV2 rep scanning saturation mutagenesis library and to analyze resulting NGS data. Also includes code used …
      Jupyter Notebook
      •1•1•0•0•Updated Mar 13, 2024Mar 13, 2024

    • Generative_AAV_design

      Public
      Code and Data for Generative modeling for AAV design
      Jupyter Notebook
      •
      MIT License
      •4•10•2•0•Updated Nov 13, 2023Nov 13, 2023

    • etfl

      Public
      ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints
      Python
      •
      Apache License 2.0
      •17•0•0•0•Updated Jul 16, 2023Jul 16, 2023

    • UniRep-analysis

      Public
      Analysis and figure code from Alley et al. 2019.
      Jupyter Notebook
      •19•59•3•2•Updated Mar 25, 2023Mar 25, 2023

    • millstone

      Public
      Genome engineering and analysis software
      Python
      •
      MIT License
      •19•46•157•5•Updated Jun 21, 2022Jun 21, 2022

    • optmage

      Public
      Scripts for designing oligos and primers for MAGE (Multiplex Automated Genome Engineering)
      Python
      •
      MIT License
      •2•3•5•2•Updated Jun 21, 2022Jun 21, 2022

    • Vascularized-Organoids

      Public
      Repository for Vascularized Organoids Paper
      R
      •
      MIT License
      •0•1•0•0•Updated Jan 7, 2022Jan 7, 2022

    • lac_repression

      Public
      Code and processed data for Garruss et al. 2021 "Deep Representation Learning Improves Prediction of LacI-mediated Transcriptional Repression"
      Roff
      •
      MIT License
      •2•3•0•0•Updated Jun 30, 2021Jun 30, 2021

    • low-N-protein-engineering

      Public
      Code and data to reproduce analyses in Biswas et al. (2020) "Low-N protein engineering with data-efficient deep learning".
      Jupyter Notebook
      •19•61•4•0•Updated Apr 8, 2021Apr 8, 2021

    • rlr

      Public
      RLR (Schubert & Goodman et al.) - Documentation, Code, and Figures
      MATLAB
      •0•2•0•0•Updated Mar 15, 2021Mar 15, 2021

    • SEER

      Public
      Code and data for SEER publication
      Jupyter Notebook
      •1•0•0•0•Updated Apr 9, 2020Apr 9, 2020

    • AAV_fitness_landscape

      Public
      Analysis for "Comprehensive fitness landscape of AAV capsid reveals a viral gene and enables machine-guided design"
      Jupyter Notebook
      •14•26•4•0•Updated Dec 15, 2019Dec 15, 2019

    • AAV2_library

      Public
      Library of analysis for Comprehensive fitness landscape of AAV capsid reveals a viral gene and enables machine-guided design
      0•0•0•0•Updated Oct 2, 2019Oct 2, 2019

    • pydna

      Public
      Python 3 classes for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut&paste cloning in Jupyter notebooks
      Jupyter Notebook
      •
      Other
      •48•1•0•0•Updated Aug 26, 2018Aug 26, 2018

    • ml-ami-builder

      Public
      Packer scripts to build nvidia-enabled AMIs
      packertensorflowcuda
      packertensorflowcudanvidiaami
      Shell
      •4•19•4•1•Updated Mar 12, 2018Mar 12, 2018

    • aws-utils

      Public
      Docs and scripts for working with Amazon Web Services and compute tasks more generally
      Shell
      •0•2•0•0•Updated Nov 1, 2017Nov 1, 2017

    • churchlab.github.io

      Public
      HTML
      •0•1•1•0•Updated Jul 15, 2017Jul 15, 2017

    • crispr-images

      Public
      Code for Shipman et al. 2017
      Python
      •2•13•0•0•Updated Jul 12, 2017Jul 12, 2017

    • C321evolve

      Public
      Evolving a healthier recoded variant
      Jupyter Notebook
      •0•0•0•0•Updated Jul 2, 2017Jul 2, 2017

    • PyVCF

      Public
      A Variant Call Format reader for Python.
      Python
      •
      Other
      •224•1•0•0•Updated Jun 7, 2017Jun 7, 2017

    • optimizing-complex-phenotypes

      Public
      Supporting code for Kuznetsov, Goodman, Filsinger et al., 2017.
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Mar 15, 2017Mar 15, 2017

    • phip-stat

      Public
      (DEVELOPMENT NOW AT lasersonlab) Analysis tools for PhIP-seq experiments
      Python
      •
      Apache License 2.0
      •9•0•0•0•Updated Dec 30, 2016Dec 30, 2016

    • agr_recoding

      Public
      supporting code and data for Napolitano et al.
      Python
      •
      Other
      •0•2•0•0•Updated Aug 22, 2016Aug 22, 2016

    • analyze_plate_reader_growth

      Public
      Matlab script to analyze bacteria doubling time from plate reader data
      MATLAB
      •1•0•0•0•Updated May 31, 2016May 31, 2016

    • reference_genome_maker

      Public
      Python scripts to create reference genome files (e.g. Genbank) from various inputs (e.g. vcf)
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 29, 2016Apr 29, 2016

    • cloudbiolinux

      Public
      CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
      Python
      •
      MIT License
      •155•0•0•0•Updated Feb 11, 2016Feb 11, 2016
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