Rivas Lab

biomarkers

Genetics of blood and urine biomarkers in the UK Biobank

covid19

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.

public-resources

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

snpnet

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

mvpmm

MultiVariate Polygenic Mixture Model

FasTag

FasTag: automatic text classification of unstructured medical narratives

ukbb-tools

Tools for preprocessing, QC, and preliminary analyses from raw UK BioBank data

GlobalBiobankEngine

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

semm

Sex Effects Mixture Model for GWAS summary statistics

mrp

Repo for MRP method.

multisnpnet-Cox

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

degas-risk

Polygenic risk modeling with latent trait-related genetic components

mrpmm

Repo for MRPMM method

multisnpnet-Cox_gpu

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

sex-diff-biomarker-genetics

Bayesian Mixture Models for identifying sex-specific variants in UKBB data.

AncestryOmicsUKB

Code for the paper: "Using Pre-training and Interaction Modeling for ancestry-specific disease prediction using multiomics data from the UK Biobank"

presentations-readings

Repository for lab presentations (abstracts, posters, talks) and readings.

stratified_MR

Codebase for Wainberg et al. PLOS Med 2019 (doi.org/10.1371/journal.pmed.1002982)

ANGPTL7

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

biobank-methods-dev

Method development for Biobank datasets

cGAUGE

covid19_HGI

gbe-power-app

Web app for calculating GWAS power using empirical allele frequency estimates.

hla-assoc

ibd-exomes

All QC, annotation, and analyses for IBD exomes

multisnpnet-Cox-tv

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

PRS

regularizedMR

MR using L1 penalty

snpnet-2.0-paper

Snpnet-2.0 paper supplementary code

snpnet-Cox-paper

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