My personal github page:

I also regularly contribute to the MRC IEU github organisation code base:

Causal inference

  • TwoSampleMR R package - Methods for two-sample Mendelian randomization, along with data management and harmonisation functions

  • MR-Base web app - Simple wrapper for the TwoSampleMR R package

  • MR-TRYX R package - Detecting novel pathways to disease by exploiting horizontal pleiotropy (TReasure Your eXceptions!)


  • OpenGWAS API - Rapidly query across hundreds of billions of genetic associations, and perform related LD-based operations such as clumping and identifying tagging variants

  • ieugwasr R package - A simple R interface for convenient access to the OpenGWAS API

  • gwasvcf R package - Rapidly query genetic associations in the GWAS VCF file format

  • gwasglue R package - Connect data from GWAS VCF files or the OpenGWAS API to a range of analytical tools designed for GWAS summary data

  • GoDMC API - Query the cis- and trans-mQTL results from the GoDMC project

  • random-METAL - An edit to the popular software package METAL. This edit enables a DerSimonian-Laird random effects meta-analysis model.

  • simulateGP - R package that contains a collection of methods for simulating and analysing genotype-phenotype relationships

  • ImputePipe - Pipelines for performing imputation of genotyped datasets

  • gctaPower - Power calculator for univariate and bivariate genomic REML analyses

  • epiGPU - Perform exhaustive two-dimensional epistasis scans rapidly using GPU accelerators

  • epiCPU - Perform exhaustive two-dimensional epistasis scans rapidly across multiple CPU cores

  • epiPower web app - Calculate statistical power and significance thresholds for two-dimensional epistasis scans


Random stuff

  • USS Pension model - Collaboration with Neil Davies to illustrate the impact of the planned changes to the UK University pension scheme

  • Shared parental leave calculator - How to divide up shared parental leave? This R package attempts to calculate the cost, time spent with baby and work time lost