Code
Pipelines, forks and releases. Mostly Hail, R, Python and a great deal of Nextflow-shaped glue.
BRaVa-genetics
The full BRaVa stack: variant annotation, phenotype curation, gene-based association testing and meta-analysis pipelines, plus the harmonised phenotype definitions used across every contributing biobank.
github.com/BRaVa-genetics →UKBB_ldsc
LD score regression applied to the Neale lab round 2 UK Biobank GWAS, with heritability estimates and diagnostics for thousands of phenotypes.
Nealelab/UKBB_ldsc →PHESANT
A fork of PHESANT used to automate phenotype parsing and transformation for Genebass and related UK Biobank exome analyses.
astheeggeggs/PHESANT →mcqueen
The C implementation behind the within-host pathogen evolution work: a Bayesian framework for detecting host influences on viral evolution across large sequence databases.
astheeggeggs/mcqueen →The rest of it
Analysis repositories for individual papers, assorted R and Python utilities, and whatever was necessary to make a deadline.
github.com/astheeggeggs →