Rivas Lab

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36 repositories

mrp
Public
Repo for MRP method.
Python
•1•3•2•2•Updated Jul 24, 2024Jul 24, 2024
Smiles2Dock
Public
Smiles2Dock: an open large-scale multi-task dataset for ML-based molecular docking
transformers docking chemoinformatics
Python
•
Apache License 2.0
•0•6•0•0•Updated Jun 9, 2024Jun 9, 2024
biomarkers
Public
Jupyter Notebook
•0•2•0•0•Updated May 23, 2024May 23, 2024
AncestryOmicsUKB
Public
Using Pre-training and Interaction Modeling for ancestry-specific disease prediction using multiomics data from the UK Biobank
bioinformatics uk-biobank pretraining
R
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MIT License
•0•1•0•0•Updated May 19, 2024May 19, 2024
snpnet
Public
snpnet - Efficient Lasso Solver for Large-scale genetic variant data
genetics linear-regression statistical-learning prediction sparse survival-analysis cox-regression biobank ukbiobank elastic-net-regression
R
•3•19•3•0•Updated Mar 5, 2024Mar 5, 2024
FasTag
Public
FasTag: automatic text classification of unstructured medical narratives
Jupyter Notebook
•2•5•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
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MIT License
•2•4•13•11•Updated Dec 8, 2022Dec 8, 2022
ukbb-tools
Public
Tools for preprocessing, QC, and preliminary analyses from raw UK BioBank data
gwas phewas ukbiobank grm gwas-summary-statistics ld-score-regression phenotyping-algorithms global-biobank-engine
Jupyter Notebook
•0•8•7•0•Updated Aug 5, 2022Aug 5, 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
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MIT License
•11•24•5•0•Updated Apr 1, 2022Apr 1, 2022
ibd-exomes
Public
All QC, annotation, and analyses for IBD exomes
genetics ulcerative-colitis crohns-disease exome-sequencing inflammatory-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-analysis cox-regression time-varying-covariates
Jupyter Notebook
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MIT License
•1•1•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
gwas genetics polygenic-risk-scores prs principal-component-analysis risk-scores ukbiobank gwas-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
cpu survival-analysis cox-regression cox-model biobank human-genetics survival-prediction multiresponse-sparse-regression cox-ph
R
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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
genetics gpu gpu-acceleration survival-analysis gpu-computing cox-regression prediction-model biobank multiresponse-sparse-regression
C++
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Other
•0•2•0•0•Updated Jan 2, 2021Jan 2, 2021
sex-diff-biomarker-genetics
Public
Bayesian Mixture Models for identifying sex-specific variants in UKBB data.
Jupyter Notebook
•0•2•0•0•Updated Sep 9, 2020Sep 9, 2020
ANGPTL7
Public
Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma
protection genetics finland iop ukbiobank finngen angptl7 therapeutics intraocular-pressure glaucoma
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-analysis cox-regression phenotypes uk-biobank snpnet-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.
genetics hla coronavirus covid-19 sars-cov-2 polygenic-risk-scores uk-biobank blood-group abo-blood
Jupyter Notebook
•7•43•0•0•Updated May 7, 2020May 7, 2020
mvpmm
Public
MultiVariate Polygenic Mixture Model
statistics genetics modeling bayesian-methods stan mixture-model ukbiobank heritability gwas-summary-statistics genetic-correlations
R
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MIT License
•3•6•0•0•Updated Apr 4, 2020Apr 4, 2020
regularizedMR
Public
MR using L1 penalty
genetics lasso causal-inference mendelian-randomization
R
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MIT License
•0•0•0•0•Updated Feb 16, 2020Feb 16, 2020
stratified_MR
Public
Codebase for Wainberg et al. PLOS Med 2019 (doi.org/10.1371/journal.pmed.1002982)
Python
•0•1•0•0•Updated Dec 15, 2019Dec 15, 2019
gbe-power-app
Public
Web app for calculating GWAS power using empirical allele frequency estimates.
R
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MIT License
•0•0•0•0•Updated Apr 13, 2018Apr 13, 2018