Using real genotype data, simulate a complex trait as a function of latent expression, fit eQTL weights in independent data, and perform GWAS/TWAS on complex trait.

SCALLOP-INF analysis

A collection of scripts to run GWAS, regional, gene-oriented, or per-variant analyses.

A ToolKit to perform a Meta-analysis of Genome-Wide Association Studies

Convert GWAS sumstat files into a common format with a common reference for positions, rsids and effect alleles.

Format of GWAS summary statistics.

SpecVar is a convenient tool for estimating interpretable genetic correlation of human complex traits and annotating the SNPs with context specific regulatory networks

SomaLogic data analysis

A ToolKit to perform gene-based association studies using VEGAS or MAGMA

gwas workflow from raw intensity data to in-silico functional mapping

Code and variants to generate results published in Waller RG et al, Hum Mol Genet, 2021.

LABRS: an ancestry-based algorithm that predicts Parkinson's risk by analyzing local genetic variations.

Pipeline to calculate local ancestries using RFMix 1.5 or RFMix 2.0 and Beagle5 or ShapeIT

client to the cimr-d database for continuous integration and analysis using cimr

Detailed GWAS using NARAC data to investigate genetic risk factors for RA. Key steps include genetic data cleaning, PCA, PRS and sex-specific GWAS.

GWAS (Genome wide association study) of ARIC study. Implemented with FAST.2.4 package in linux environment.

Tools for curating and filtering sumstats

Code accompanying the manuscript on Genome variation in alpine bumblebees.

SWATH-MS analysis