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
Software program for generating synthetic datasets for genotypes and phenotypes
quincunx: an R package to query, download and wrangle PGS Catalog data
A toolkit to calculate polygenic scores using PLINK2, PRS-CS, RapidoPGS, or PRSice2.
Python applications and libraries for working with PGS data and the PGS Catalog
Whole genome sequencing analysis pipeline for consumer hardware. 100% local, Docker-powered, free and open source.
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
GAUDI: a penalized regression based PRS method designed specifically for admixed individuals
Exploratory Framework for Genotype-Phenotype Prediction
(superseded by pygscatalog) Utilities for working with PGS Catalog API and scoring files
Tool and library with ui to compute polygenic risk scores
A genomic disease prediction model using Polygenic Risk Scores (PRS), Lasso Logistic Regression, and SNP data from the 1000 Genomes Project. Explores different case-control splits, feature selection strategies, and performance evaluations using AUC metrics.
Web-based Polygenic Risk Score calculator for 50+ diseases using PGS Catalog. Supports 23andMe, AncestryDNA, VCF. Ancestry-aware normalization for EUR/AFR/EAS/SAS/AMR. By Luis Sanchez (UC Berkeley) & Shubhankar Tripathy (Stanford).
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