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    20 repositories

    • antibody_engineering_scoring

      Public
      Compares simple models (xgboost, xgpr) with fine-tuned LLMs / embeddings on some antibody property prediction tasks
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 25, 2024Oct 25, 2024

    • RESP2

      Public
      Code needed to reproduce experiments from Parkinson / Hard et al. 2024
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 11, 2024Oct 11, 2024

    • Taiji_ALTRA

      Public
      Code for Taiji ALTRA project
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 3, 2024Oct 3, 2024

    • AntPack

      Public
      Tools for annotation, processing and ML for antibody sequences
      C++
      •
      GNU General Public License v3.0
      •2•6•0•0•Updated Oct 2, 2024Oct 2, 2024

    • Taiji2

      Public
      R toolkit for enhanced downstream analysis of Taiji
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Sep 23, 2024Sep 23, 2024

    • Benchmarking-tpLMs

      Public
      Python
      •1•3•0•0•Updated Aug 23, 2024Aug 23, 2024

    • Taiji-reprogram

      Public
      R
      •
      MIT License
      •0•2•0•0•Updated Aug 10, 2024Aug 10, 2024

    • TUnA

      Public
      TUnA: Transformer-based Uncertainty Aware model for PPI Prediction
      Python
      •
      MIT License
      •0•3•0•0•Updated Jun 4, 2024Jun 4, 2024

    • Motif_Finding_Contextual_Regression

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Feb 12, 2024Feb 12, 2024

    • uncertaintyAwareDeepLearn

      Public
      A PyTorch class that implements an approximate Gaussian process as the last layer of a neural network
      HTML
      •
      MIT License
      •2•0•0•0•Updated Jan 29, 2024Jan 29, 2024

    • TIP-RA-CS

      Public
      The code needed to reproduce the analysis of methylation array data in James, Holers, Iyer, Prideaux, et al. 2023.
      Jupyter Notebook
      •0•0•0•0•Updated Oct 11, 2023Oct 11, 2023

    • SomaticMutation

      Public
      Python
      •0•2•0•0•Updated Aug 25, 2023Aug 25, 2023

    • benchmarking_xGPR

      Public
      The code needed to reproduce the experiments associated with Parkinson et al. 2023 for the xGPR library
      Jupyter Notebook
      •
      MIT License
      •2•1•0•0•Updated Jun 23, 2023Jun 23, 2023

    • RESP

      Public
      The code used to generate the results from Parkinson / Hard et al. 2022
      Python
      •7•17•0•0•Updated Apr 13, 2023Apr 13, 2023

    • findRAM

      Public
      Identify the modular organization of 3D genome from histone modifications. For details, please check here (https://github.com/LinaZhengUCSD/findRAM.git)
      Shell
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated May 26, 2022May 26, 2022

    • cbx1_protein_engineering

      Public
      Machine-learning based techniques for identifying likely strong binders from high-throughput datasets
      Jupyter Notebook
      •0•0•0•0•Updated Oct 30, 2020Oct 30, 2020

    • Motto

      Public
      PostScript
      •0•0•0•0•Updated Aug 10, 2020Aug 10, 2020

    • mEpigram

      Public
      Methylated DNA motif discovery tool
      Python
      •
      Other
      •2•1•2•0•Updated Jul 12, 2019Jul 12, 2019

    • Taiji

      Public
      All-in-one analysis pipeline
      Haskell
      •
      BSD 3-Clause "New" or "Revised" License
      •9•1•0•0•Updated Apr 29, 2019Apr 29, 2019

    • EpiSig

      Public
      C++
      •1•1•0•0•Updated Mar 8, 2018Mar 8, 2018