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Gitter Lab

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

Popular repositories Loading

  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
  • 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 1 Updated Nov 19, 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 Nov 19, 2024
  • nn4dms Public

    Neural networks for deep mutational scanning data

    gitter-lab/nn4dms’s past year of commit activity
    Jupyter Notebook 66 MIT 17 0 0 Updated Nov 13, 2024
  • ChemLML Public

    Chemical Language Model Linker

    gitter-lab/ChemLML’s past year of commit activity
    Python 3 MIT 1 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
  • 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
  • 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

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