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Gitter Lab

Computational biology research group at UW-Madison and the Morgridge Institute

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  1. nn4dms nn4dms Public

    Neural networks for deep mutational scanning data

    Jupyter Notebook 66 17

  2. metl metl Public

    Mutational Effect Transfer Learning (METL) framework for pretraining and finetuning biophysics-informed protein language models

    Python 23 3

  3. LPWC LPWC Public

    Lag Penalized Weighted Correlation for Time Series Clustering

    R 20 3

  4. ssps ssps Public

    Sparse Signaling Pathway Sampling: MCMC for signaling pathway inference

    Julia 14

  5. metl-pretrained metl-pretrained Public

    Pretrained METL models with minimal dependencies

    Python 13

  6. prmf prmf Public

    Pathway-Regularized Matrix Factorization

    Python 12

Repositories

Showing 10 of 33 repositories
  • nn4dms Public

    Neural networks for deep mutational scanning data

    gitter-lab/nn4dms’s past year of commit activity
    Jupyter Notebook 66 MIT 17 1 1 Updated Nov 8, 2024
  • ChemLML Public

    Chemical Language Model Linker

    gitter-lab/ChemLML’s past year of commit activity
    Python 2 MIT 0 2 0 Updated Nov 6, 2024
  • metl-pretrained Public

    Pretrained METL models with minimal dependencies

    gitter-lab/metl-pretrained’s past year of commit activity
    Python 13 MIT 0 3 1 Updated Nov 5, 2024
  • hiv1-aurkb Public

    Scripts for analyzing HIV-1 producer cell proteomic and phosphoproteomic data

    gitter-lab/hiv1-aurkb’s past year of commit activity
    Python 1 MIT 1 0 0 Updated Oct 31, 2024
  • metl Public

    Mutational Effect Transfer Learning (METL) framework for pretraining and finetuning biophysics-informed protein language models

    gitter-lab/metl’s past year of commit activity
    Python 23 MIT 3 1 1 Updated Oct 25, 2024
  • metl-pub Public

    Supplementary datasets and scripts for the METL manuscript

    gitter-lab/metl-pub’s past year of commit activity
    Python 5 MIT 0 0 0 Updated Sep 23, 2024
  • benchmarking-structure-based-models Public

    This is a repository of code needed to replicate benchmarks of structure based models in ProteinGym

    gitter-lab/benchmarking-structure-based-models’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 21, 2024
  • min-cost-flow Public

    Pathway reconstruction with a minimum cost flow algorithm

    gitter-lab/min-cost-flow’s past year of commit activity
    Python 1 MIT 1 1 1 Updated Sep 18, 2024
  • metl-sim Public

    High-throughput framework for running molecular simulations for METL

    gitter-lab/metl-sim’s past year of commit activity
    Python 10 MIT 4 2 0 Updated Sep 9, 2024
  • low-n-mlde-review Public

    Low N machine learning-assisted directed evolution perspective written with Manubot

    gitter-lab/low-n-mlde-review’s past year of commit activity
    HTML 0 CC-BY-4.0 0 2 0 Updated Aug 30, 2024