Repositories list

• Smiles2Dock

  Public
  Smiles2Dock: an open large-scale multi-task dataset for ML-based molecular docking (NeurIPS 2025 AI for Science Workshop)

  transformersdockingchemoinformatics

  Python

  •

  Apache License 2.0

  •0•9•0•0•Updated Nov 16, 2025Nov 16, 2025

• waveform_disease

  Public
  processing waveform data + predicting disease phenotypes

  Python

  •0•1•0•0•Updated Nov 16, 2025Nov 16, 2025

• AncestryOmicsUKB

  Public
  Using Pre-training and Interaction Modeling for ancestry-specific disease prediction in UK Biobank (PLOS One)

  R

  •0•0•0•0•Updated Oct 16, 2025Oct 16, 2025

• phenome-wide-unified-model

  Public
  Python

  •0•0•0•0•Updated Sep 18, 2025Sep 18, 2025

• sh-phewas

  Public
  PheWAS on a sphere. Dashboard for spherical harmonic regression on PheWAS data.

  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 26, 2025Aug 26, 2025

• umr-visualizer

  Public
  Python visualization package for unified meta-regression models

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Mar 31, 2025Mar 31, 2025

• mrp

  Public
  Repo for MRP method.

  Python

  •1•3•2•2•Updated Jul 24, 2024Jul 24, 2024

• biomarkers

  Public
  Jupyter Notebook

  •0•3•0•0•Updated May 23, 2024May 23, 2024

• multiomics-ukb

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Apr 11, 2024Apr 11, 2024

• snpnet

  Public
  snpnet - Efficient Lasso Solver for Large-scale genetic variant data

  geneticslinear-regressionstatistical-learning+ 9predictionlassosparsesurvival-analysiscox-regressionbiobankukbiobank+ 2

  R

  •3•20•3•0•Updated Mar 5, 2024Mar 5, 2024

• FasTag

  Public
  FasTag: automatic text classification of unstructured medical narratives

  Jupyter Notebook

  •2•6•0•2•Updated Mar 24, 2023Mar 24, 2023

• GlobalBiobankEngine

  Public
  A resource for the visualization and exploration of genetic and phenotypic data from biobanks

  HTML

  •

  MIT License

  •2•4•13•11•Updated Dec 8, 2022Dec 8, 2022

• PRS

  Public
  Jupyter Notebook

  •0•0•6•0•Updated Jun 27, 2022Jun 27, 2022

• public-resources

  Public
  Repository for resources we'd like to share with the community.

  Jupyter Notebook

  •

  MIT License

  •11•25•6•0•Updated Apr 1, 2022Apr 1, 2022

• ibd-exomes

  Public
  All QC, annotation, and analyses for IBD exomes

  geneticsulcerative-colitiscrohns-disease+ 2exome-sequencinginflammatory-bowel-disease

  Jupyter Notebook

  •0•0•0•0•Updated Mar 21, 2022Mar 21, 2022

• biobank-methods-dev

  Public
  Method development for Biobank datasets

  Jupyter Notebook

  •0•0•0•0•Updated Oct 28, 2021Oct 28, 2021

• mrpmm

  Public
  Repo for MRPMM method

  Python

  •0•2•0•0•Updated Aug 20, 2021Aug 20, 2021

• multisnpnet-Cox-tv

  Public
  Cox models for time-varying covariate in large population-cohorts

  survival-analysiscox-regressiontime-varying-covariates

  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Jul 27, 2021Jul 27, 2021

• semm

  Public
  Sex Effects Mixture Model for GWAS summary statistics

  C++

  •1•4•0•0•Updated May 25, 2021May 25, 2021

• hla-assoc

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•3•0•Updated May 24, 2021May 24, 2021

• covid19_HGI

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Apr 29, 2021Apr 29, 2021

• snpnet-2.0-paper

  Public
  Snpnet-2.0 paper supplementary code

  R

  •0•0•0•0•Updated Apr 16, 2021Apr 16, 2021

• degas-risk

  Public
  Polygenic risk modeling with latent trait-related genetic components

  gwasgeneticspolygenic-risk-scores+ 5prsprincipal-component-analysisrisk-scoresukbiobankgwas-summary-statistics

  Jupyter Notebook

  •0•2•0•0•Updated Feb 23, 2021Feb 23, 2021

• multisnpnet-Cox

  Public
  Multiresponse time-to-event Cox proportional hazards model - CPU

  cpusurvival-analysiscox-regression+ 6cox-modelbiobankhuman-geneticssurvival-predictionmultiresponse-sparse-regressioncox-ph

  R

  •

  Other

  •0•4•0•0•Updated Feb 9, 2021Feb 9, 2021

• cGAUGE

  Public
  0•0•0•0•Updated Jan 13, 2021Jan 13, 2021

• multisnpnet-Cox_gpu

  Public
  Multiresponse time-to-event Cox proportional hazards model - GPU

  geneticsgpugpu-acceleration+ 6survival-analysisgpu-computingcox-regressionprediction-modelbiobankmultiresponse-sparse-regression

  C++

  •

  Other

  •0•3•0•0•Updated Jan 2, 2021Jan 2, 2021

• ANGPTL7

  Public
  Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma

  protectiongeneticsfinland+ 7iopukbiobankglaucomafinngenangptl7therapeuticsintraocular-pressure

  Jupyter Notebook

  •0•0•0•0•Updated Jul 14, 2020Jul 14, 2020

• snpnet-Cox-paper

  Public
  Repo for "Fast Lasso Method for Large-scale and Ultrahigh-dimensional Cox Model with Applications to UK Biobank"

  survival-analysiscox-regressionphenotypes+ 2uk-biobanksnpnet-cox

  1•0•0•0•Updated May 26, 2020May 26, 2020

• covid19

  Public
  As a part of COVID-19 Host Genetics Initiative, we perform the following set of analyses to better understand the genetic basis of COVID-19 susceptibility and severity.

  geneticspolygenic-risk-scoreshla+ 6uk-biobankblood-groupcoronaviruscovid-19sars-cov-2abo-blood

  Jupyter Notebook

  •7•44•0•0•Updated May 7, 2020May 7, 2020

• mvpmm

  Public
  MultiVariate Polygenic Mixture Model

  statisticsgeneticsmodeling+ 7bayesian-methodsstanmixture-modelukbiobankheritabilitygwas-summary-statisticsgenetic-correlations

  R

  •

  MIT License

  •3•7•0•0•Updated Apr 4, 2020Apr 4, 2020