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@churchlab

Church Lab

George Church's lab at Harvard

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  1. UniRep UniRep Public

    UniRep model, usage, and examples.

    Python 340 96

  2. UniRep-analysis UniRep-analysis Public

    Analysis and figure code from Alley et al. 2019.

    Jupyter Notebook 58 20

  3. low-N-protein-engineering 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 56 18

  4. millstone millstone Public

    Genome engineering and analysis software

    Python 47 19

  5. Deep_diversification_AAV Deep_diversification_AAV Public

    Bioinformatics code for paper associated with deep diversification of AAV

    Jupyter Notebook 39 14

  6. AAV_fitness_landscape AAV_fitness_landscape Public

    Analysis for "Comprehensive fitness landscape of AAV capsid reveals a viral gene and enables machine-guided design"

    Jupyter Notebook 20 13

Repositories

Showing 10 of 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".

    churchlab/aav_rep_scan’s past year of commit activity
    Jupyter Notebook 1 1 0 0 Updated Mar 13, 2024
  • Generative_AAV_design Public

    Code and Data for Generative modeling for AAV design

    churchlab/Generative_AAV_design’s past year of commit activity
    Jupyter Notebook 9 MIT 3 2 0 Updated Nov 13, 2023
  • etfl Public Forked from EPFL-LCSB/etfl

    ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints

    churchlab/etfl’s past year of commit activity
    Python 0 Apache-2.0 18 0 0 Updated Jul 16, 2023
  • UniRep-analysis Public

    Analysis and figure code from Alley et al. 2019.

    churchlab/UniRep-analysis’s past year of commit activity
    Jupyter Notebook 58 20 3 2 Updated Mar 25, 2023
  • UniRep Public

    UniRep model, usage, and examples.

    churchlab/UniRep’s past year of commit activity
    Python 340 96 4 1 Updated Jun 21, 2022
  • millstone Public

    Genome engineering and analysis software

    churchlab/millstone’s past year of commit activity
    Python 47 MIT 19 157 5 Updated Jun 21, 2022
  • optmage Public

    Scripts for designing oligos and primers for MAGE (Multiplex Automated Genome Engineering)

    churchlab/optmage’s past year of commit activity
    Python 3 MIT 2 5 2 Updated Jun 21, 2022
  • Vascularized-Organoids Public

    Repository for Vascularized Organoids Paper

    churchlab/Vascularized-Organoids’s past year of commit activity
    R 1 MIT 0 0 0 Updated Jan 7, 2022
  • lac_repression Public

    Code and processed data for Garruss et al. 2021 "Deep Representation Learning Improves Prediction of LacI-mediated Transcriptional Repression"

    churchlab/lac_repression’s past year of commit activity
    Roff 1 MIT 1 0 0 Updated Jun 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".

    churchlab/low-N-protein-engineering’s past year of commit activity
    Jupyter Notebook 56 18 4 0 Updated Apr 8, 2021
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