The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation

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.

CoMorMent-Containers

Variational Inference of Polygenic Risk Scores

A toolkit to calculate polygenic scores using PLINK2, PRS-CS, RapidoPGS, or PRSice2.

quincunx: an R package to query, download and wrangle PGS Catalog data

Software program for generating synthetic datasets for genotypes and phenotypes

Toolkit to aid generation of advanced Polygenic Risk Scores (PRS) including SNP-allele tagging and interaction models, especially in HLA. Developed and maintained by Seth Sharp ([email protected]).

Toolkit for the efficient construction and analysis of polygenic risk scores in R.

Multi Kernel Linear Mixed Models for Complex Phenotype Prediction

quincunx: an R package to query, download and wrangle PGS Catalog data

Python applications and libraries for working with PGS data and the PGS Catalog

PRS Africa 2023

Tokyo Symposium on Genomic Medicine (2024)

(superseded by pygscatalog) Utilities for working with PGS Catalog API and scoring files

This repository contains the programming codes used in Genetic analysis of amyotrophic lateral sclerosis identifies contributing pathways and cell types https://advances.sciencemag.org/content/7/3/eabd9036

Polygenic risk modeling with latent trait-related genetic components

power calculator for Genetic Risk Scores (GRS)

Those are the code files for producing the PheWAS analyses in the manuscript "Phenome-Wide Association Study of Polygenic Risk Score for Alzheimer’s Disease in Electronic Health Records". Part of our analyses included sensitive genomic data. Codes to produce AD PRS were not included here.

Machine Learning in Genomics and Healthcare (COMP 565) Project