Cloud-native genomic dataframes and batch computing

A comprehensive tutorial about GWAS and PRS

GWAS Tutorial for Beginners

An open-source toolkit for large-scale genomic analysis

Scalable genetics toolkit

Access share reviewed code & Jupyter Notebooks for use on the UK Biobank (UKBB) Research Application Platform. Includes resources from DNAnexus webinars, online trainings and workshops.

Pan-genome wide association studies

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores

Python command line tool for Multi-Trait Analysis of GWAS (MTAG)

Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.

Codebook from my GWAS cookbook

Single-cell disease relevance score (scDRS)

An R package for creating Q-Q and manhattan plots from GWAS results

A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.

machine learning for genomic variants

Rare variant test software for next generation sequencing data

SEER, reimplemented in python 🐍🔮

PolyFun (POLYgenic FUNctionally-informed fine-mapping)

LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Python API for comprehensive GWAS analysis using GEMMA

Causal Mixture Model for GWAS summary statistics

Rapid standardisation and quality control of GWAS or QTL summary statistics

Find causal cell-types underlying complex trait genetics

🧬High-performance genetics- and genomics-related data visualization using Makie.jl

Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity

A nextflow pipeline to perform state-of-the-art genome-wide association studies.

Open Targets python framework for post-GWAS analysis

Mixed models @lme4 + custom covariances + parameter constraints