Whole genome sequencing analysis pipeline for consumer hardware. 100% local, Docker-powered, free and open source.

Poster Presented at FLUX 2025

For my MDS capstone, I conducted an independent study on the polygenic risk scoring for autism.

Reproducible code for the Mixture-of-Experts PRS (MoEPRS) paper (2025)

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).

End-to-end GWAS pipeline for rheumatoid arthritis (NARAC): QC, PCA-based stratification control, sex-stratified mixed-model association testing, PRS, and LD score regression.

A Dockerized 5D multimodal pipeline for Alzheimer's prediction, integrating 3D-MRI (PCA), SNP analysis, and clinical biomarkers using optimized SVM models and Digital Twin (XAI) validation.

CoMorMent-Containers

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

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

A simple desktop application for analyzing human genome sequence data against the GWAS Catalog, now featuring polygenic risk score analysis. This is an exploration tool, not a medical instrument.

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.

This short course is designed to equip scientists based in Africa with the skills and knowledge to perform polygenic risk scores (PRS) analysis.

Pipeline for PRS computation integrating diverse PRS algorithms into a unique Snakemake workflow.

Thai Symposium & Workshop on Genomic Medicine, Therapeutics and Health

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

Exploratory Framework for Genotype-Phenotype Prediction

Variational Inference of Polygenic Risk Scores

Exploring the genetic and behavioral factors behind the fertility-longevity trade-off, this project uses survival analysis and polygenic risk scores to uncover the complex interplay of reproductive behavior, socio-demographic influences, and genetic predispositions in shaping human lifespan.

Julia implementation of Ge et al's PRScs