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@ShenLab Shen Lab at Columbia University

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    51 repositories

    • MDmis

      Public
      Molecular dynamics simulations for missense variants in intrinsically disordered protein regions
      Jupyter Notebook
      •0•1•0•0•Updated Feb 24, 2026Feb 24, 2026

    • SPARK3

      Public
      scripts used in autism exome data analysis in Qiao et al 2026
      R
      •
      MIT License
      •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • Genetics

      Public
      Python
      •4•1•0•2•Updated Feb 4, 2026Feb 4, 2026

    • SeqDance

      Public
      code for SeqDance/ESMDance, biophysics-informed protein language models
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •7•59•3•0•Updated Jan 28, 2026Jan 28, 2026

    • shenlab.github.io

      Public
      large files (PDF or images) for Shen Lab
      0•0•0•0•Updated Jan 23, 2026Jan 23, 2026

    • kif1a

      Public
      Ruby
      •
      MIT License
      •1•0•0•0•Updated Oct 2, 2025Oct 2, 2025

    • MisFit

      Public
      Estimation of selection coefficient of missense variants using human population genomes and machine learning
      Python
      •1•5•0•0•Updated Sep 29, 2025Sep 29, 2025

    • mutable-sh

      Public
      HTML
      •0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

    • PreMode

      Public
      Python
      •0•5•0•0•Updated Jul 7, 2025Jul 7, 2025

    • PreModeArchive

      Public
      PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context
      Python
      •1•7•0•0•Updated Jul 1, 2025Jul 1, 2025

    • CANOES

      Public
      R
      •
      MIT License
      •2•9•1•0•Updated Jun 25, 2024Jun 25, 2024

    • VBASS

      Public
      A Bayesian Mixture model with learnable prior to integrate single cell gene expression data in rare variants association analysis.
      R
      •0•1•0•0•Updated Oct 2, 2023Oct 2, 2023

    • AlphaCluster

      Public
      quantify 3D physical or functional clustering of missense variants
      Python
      •
      MIT License
      •0•2•0•1•Updated Apr 5, 2023Apr 5, 2023

    • gMVP

      Public
      Python
      •
      MIT License
      •7•21•0•0•Updated Nov 15, 2022Nov 15, 2022

    • rescve

      Public
      Representation of missense variants for predicting modes of action
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Oct 16, 2022Oct 16, 2022

    • CNV-Espresso

      Public
      A tool designed for confirming copy number variants from exome sequencing predictions in silico
      Python
      •
      MIT License
      •0•6•0•0•Updated Sep 19, 2022Sep 19, 2022

    • SPARK_Analysis_V1

      Public
      Perl
      •1•2•0•0•Updated Jun 15, 2022Jun 15, 2022

    • spark

      Public
      SPARK and genetics analysis of ASD
      Perl
      •1•0•0•0•Updated Apr 27, 2022Apr 27, 2022

    • noncoding

      Public
      Predict site-specific RNA binding protein - mRNA binding and functional impact of noncoding variants based on RBP binding and population genomes.
      R
      •0•1•0•0•Updated Jun 2, 2021Jun 2, 2021

    • pathways

      Public
      Pathway enrichment analysis of de novo or rare variants.
      R
      •0•0•0•0•Updated May 17, 2021May 17, 2021

    • missense

      Public
      MVP (Qi et al 2021) source code
      Jupyter Notebook
      •9•17•1•0•Updated May 11, 2021May 11, 2021

    • x-TADA

      Public
      A new model to integrate functional genomics data in identifying de novo risk genes.
      R
      •0•0•0•0•Updated May 10, 2021May 10, 2021

    • TCR

      Public
      Jupyter Notebook
      •6•0•0•0•Updated May 3, 2021May 3, 2021

    • US_UK_combine

      Public
      R
      •1•0•0•0•Updated Apr 2, 2021Apr 2, 2021

    • VariableThresholdTest

      Public
      Perl
      •1•1•0•0•Updated Apr 2, 2021Apr 2, 2021

    • ThreaderAI

      Public
      Template-based prediction of protein structure with deep-learning
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •2•7•0•0•Updated Jan 2, 2021Jan 2, 2021

    • A-risk

      Public
      F-risk, plausibility of risk genes of autism
      Jupyter Notebook
      •1•1•0•0•Updated Oct 28, 2020Oct 28, 2020

    • mosaicism

      Public
      R
      •1•2•0•0•Updated May 19, 2020May 19, 2020

    • pipeline

      Public
      Python
      •3•2•0•0•Updated May 6, 2020May 6, 2020

    • viralTCR

      Public
      A machine learning method to predict TCR-peptide binding
      deep-learningtcrcovid-19
      deep-learningtcrcovid-19sars-cov-2
      Python
      •0•4•0•0•Updated Apr 26, 2020Apr 26, 2020
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