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    41 repositories

    • 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 to generate all figures in "Comprehensive mutagenesis maps the effect of all single codon mutations in the AAV2 rep gene on AAV production".
      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
      •3•9•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
      •20•58•3•2•Updated Mar 25, 2023Mar 25, 2023

    • UniRep

      Public
      UniRep model, usage, and examples.
      Python
      •96•337•4•1•Updated Jun 21, 2022Jun 21, 2022

    • millstone

      Public
      Genome engineering and analysis software
      Python
      •
      MIT License
      •19•47•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
      •1•1•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
      •18•56•4•0•Updated Apr 8, 2021Apr 8, 2021

    • Deep_diversification_AAV

      Public
      Bioinformatics code for paper associated with deep diversification of AAV
      Jupyter Notebook
      •14•38•0•0•Updated Mar 26, 2021Mar 26, 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
      •13•20•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
      •44•1•0•0•Updated Aug 26, 2018Aug 26, 2018

    • ml-ami-builder

      Public
      Packer scripts to build nvidia-enabled AMIs
      tensorflowcudanvidiapackerami
      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•12•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

    • recoli57

      Public
      Supporting code for Ostrov et al., Science, 2016
      Python
      •
      Other
      •2•0•0•0•Updated Nov 30, 2016Nov 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
      •158•0•0•0•Updated Feb 11, 2016Feb 11, 2016

    • dependence

      Public
      Scripts and data analysis related to NSAA-dependence project
      HTML
      •0•0•0•0•Updated Sep 16, 2015Sep 16, 2015