Software

We build and maintain open-source tools for gene-environment interaction analysis at biobank scale, along with portable cloud workflows that make these analyses reproducible across platforms.

Gene-environment interaction analysis

GEM — Efficient and statistically rigorous genome-wide GxE testing for large datasets, with robust sandwich-based variance estimation and multi-exposure interaction testing.
Documentation and installation · Manuscript

METAGEM — Flexible meta-analysis of GxE summary statistics across studies and consortia.
Documentation and installation · Manuscript

REGEM — Re-analysis of existing GxE summary statistics under alternative model specifications, without returning to individual-level data.
Documentation and installation · Manuscript

ESPRESSO.GxE.RV — Simulation-based power estimation for set-based GxE tests.
Documentation and installation · Original ESPRESSO manuscript

Note that the genome-wide interaction study-related software programs were developed in close collaboration with Han Chen (NYU) and Alisa Manning (MGH).

Genetic clustering

bNMF clustering — Bayesian non-negative matrix factorization pipeline for partitioning GWAS loci into mechanistically interpretable clusters, including summary statistic preprocessing.

Nutrition and cheminformatics

PhyteByte — Structure-based prediction of food compound bioactivity, using chemical similarity to drugs of known action.
Documentation and installation · Manuscript

Cloud-based analysis workflows

Portable WDL workflows that run across Terra, DNAnexus, and NHLBI BioData Catalyst:

• GEM workflow
• MAGEE workflow
• dbGaP data download and decryption