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@ShenLab

Shen Lab at Columbia University

Computational genomics, human genetics, and computational immunology

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  1. SeqDance SeqDance Public

    code for SeqDance, a biophysics-informed protein language model

    Jupyter Notebook 21 2

  2. gMVP gMVP Public

    Python 20 7

  3. missense missense Public

    MVP (Qi et al 2021) source code

    Jupyter Notebook 15 9

  4. CANOES CANOES Public

    R 8 2

  5. ThreaderAI ThreaderAI Public

    Template-based prediction of protein structure with deep-learning

    C++ 6 2

  6. CNV-Espresso CNV-Espresso Public

    A tool designed for confirming copy number variants from exome sequencing predictions in silico

    Python 5

Repositories

Showing 10 of 48 repositories
  • Genetics Public
    ShenLab/Genetics’s past year of commit activity
    Python 1 4 0 2 Updated Nov 23, 2024
  • kif1a Public
    ShenLab/kif1a’s past year of commit activity
    Ruby 0 0 0 0 Updated Nov 21, 2024
  • SeqDance Public

    code for SeqDance, a biophysics-informed protein language model

    ShenLab/SeqDance’s past year of commit activity
    Jupyter Notebook 21 GPL-3.0 2 0 0 Updated Oct 22, 2024
  • shenlab.github.io Public

    large files (PDF or images) for Shen Lab

    ShenLab/shenlab.github.io’s past year of commit activity
    0 0 0 0 Updated Oct 16, 2024
  • PreMode Public

    PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context

    ShenLab/PreMode’s past year of commit activity
    Python 5 1 0 0 Updated Jul 10, 2024
  • CANOES Public
    ShenLab/CANOES’s past year of commit activity
    R 8 MIT 2 1 0 Updated Jun 25, 2024
  • MisFit Public

    Estimation of selection coefficient of missense variants using human population genomes and machine learning

    ShenLab/MisFit’s past year of commit activity
    Python 3 0 0 0 Updated Dec 7, 2023
  • VBASS Public

    A Bayesian Mixture model with learnable prior to integrate single cell gene expression data in rare variants association analysis.

    ShenLab/VBASS’s past year of commit activity
    R 1 0 0 0 Updated Oct 2, 2023
  • AlphaCluster Public

    quantify 3D physical or functional clustering of missense variants

    ShenLab/AlphaCluster’s past year of commit activity
    Python 2 MIT 0 0 1 Updated Apr 5, 2023
  • lollipop Public
    ShenLab/lollipop’s past year of commit activity
    0 CC0-1.0 0 0 0 Updated Feb 5, 2023
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