Computing

PennPRS

[Preprint]
[Website]
[Offline Pipeline for Large-Scale Analyses]

Software

Literature-derived PRS Benchmarking Database

A literature-derived benchmarking database that contains curated benchmarking data collected from peer-reviewed publications for polygenic risk score (PRS) method benchmarking and code for generating PRS method ranks with uncertainty quantification. [Preprint]

LFVCR

An R package for running LF-VCR (latent-feature-explained varying-coefficient regression), which allows effects of a subset of the observed predictors to vary by a set of lower-dimensional latent features extracted from the predictors. [Preprint]

CaLMR

An R-based command line tool for implementing CaLMR (Causal analysis of Latent exposures using Mendelian Randomization), a powerful method for conducting Mendelian randomization analysis for latent exposures leveraging information from GWAS summary-level information on observed biomarkers. [Preprint]

MUSSEL

An R-based command line tool for implementing MUSSEL (MUltivariate Spike and Slab and Ensemble Learning), a powerful method for developing ancestry-specific polygenic risk scores (PRS) that integrates information from GWAS summary statistics and external LD reference data from multiple populations (ancestry groups). [Paper]

MRLE

An R package for conducting Mendelian randomization analysis for a latent exposure leveraging information from multiple biomarkers. [Paper] [Paper]

T2DAG

An R package for graph-informed detection of disease-associated gene pathways. [Paper]  

COVID-19 Risk Tools

Mortality Risk Calculator

The tool provides an assessment of individualized risks for mortality from COVID-19 using the best publicly available information on risks associated with various pre-existing conditions and socio-demographic factors. We further tailored it to produce absolute risk estimates in future time frames by incorporating information on pandemic dynamics at the community level with projections available from an ensemble of pandemic forecasting models.

Risk Interactive Maps

Developed through a collaborative effort with Eliza Wallace from PolicyMap, the interactive maps show sizes of high-risk populations in the U.S., nationwide and by cities, countries, and states.

[Paper]