Repositories list

• shenlab.github.io

  Public
  large files (PDF or images) for Shen Lab

  0•0•0•0•Updated Nov 7, 2025Nov 7, 2025

• 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•4•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

• MDmis

  Public
  Molecular dynamics simulations for missense variants in intrinsically disordered protein regions

  Python

  •0•1•0•0•Updated May 7, 2025May 7, 2025

• SeqDance

  Public
  code for SeqDance/ESMDance, biophysics-informed protein language models

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •5•41•2•0•Updated Apr 2, 2025Apr 2, 2025

• Genetics

  Public
  Python

  •4•1•0•2•Updated Feb 20, 2025Feb 20, 2025

• CANOES

  Public
  R

  •

  MIT License

  •2•8•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•1•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+ 1sars-cov-2

  Python

  •0•4•0•0•Updated Apr 26, 2020Apr 26, 2020

• igv-classifier

  Public
  HTML

  •4•4•0•0•Updated Mar 16, 2020Mar 16, 2020