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@gitter-lab

Gitter Lab

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

Popular repositories

  1. nn4dms nn4dms Public

    Neural networks for deep mutational scanning data

    Jupyter Notebook 62 16

  2. metl metl Public

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

    Python 21 2

  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 11

Repositories

Showing 10 of 29 repositories
  • metl-sim Public

    High-throughput framework for running molecular simulations for METL

    Python 7 MIT 4 1 0 Updated May 29, 2024
  • SINGE Public

    Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data

    MATLAB 11 MIT 5 14 3 Updated Apr 26, 2024
  • metl Public

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

    Python 21 MIT 2 0 0 Updated Apr 26, 2024
  • metl-pub Public

    Supplementary datasets and scripts for the METL manuscript

    4 MIT 0 1 0 Updated Apr 25, 2024
  • metl-pretrained Public

    Pretrained METL models with minimal dependencies

    Python 13 MIT 0 1 0 Updated Apr 25, 2024
  • active-learning-drug-discovery Public

    End-to-end active learning pipeline for virtual screening and drug discovery

    Jupyter Notebook 3 MIT 0 11 1 Updated Mar 7, 2024
  • min-cost-flow Public

    Pathway reconstruction with a minimum cost flow algorithm

    Python 1 MIT 0 1 1 Updated Jan 29, 2024
  • nn4dms Public

    Neural networks for deep mutational scanning data

    Jupyter Notebook 62 MIT 16 0 0 Updated Jan 5, 2024
  • pria-ams-enamine Public

    Virtual screening on PriA-SSB with the AMS and Enamine REAL libraries

    Jupyter Notebook 6 MIT 1 0 0 Updated Sep 22, 2023
  • hiv1-aurkb Public

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

    Python 1 MIT 1 0 0 Updated Aug 11, 2023