About

I am currently a bioinformatician and software developer at the Center for Statistical Genetics, University of Michigan.

Projects

Projects on which I am currently a maintainer:

Repo	Contributions	Description
LDServer	Commits • PRs	Serves linkage disequilibrium (LD) data over a REST API. Used to calculate LD on-the-fly for the new interactive LocusZoom.js viewer, and score statistics/covariance matrices for use with raremetal.js.
raremetal.js	Commits • PRs	JS package for calculating rare variant aggregation tests. Can calculate in the browser or server-side with node.js. Supports burden, VT, SKAT, and SKAT-O.
LocusZoom API	Commits • PRs	Backend REST API service for LocusZoom.js. Serves information on genes, recombination rates, EBI GWAS catalog variants, genomic interval annotations, dbSNP metadata, and more.

Projects to which I have made a contribution (or at least, attempted to make one):

Repo	Contributions	Description
APEX	Commits • PRs	Toolkit for analysis of molecular quantitative trait loci (xQTLs), such as mRNA expression or methylation levels. Fast and efficient storage of single study summary statisics and covariance matrices.
RAREMETAL	Commits • PRs	Meta-analysis of rare variant burden tests; sharing of summary statistics and covariance matrices.
emeraLD	Commits • PRs	Fast LD calculation from VCFs by exploiting sparsity and haplotype structure.
cget	Commits • PRs	C++ package retrieval for CMake build systems.

Projects no longer under development:

Repo	Contributions	Description
swiss	Commits • PRs	Software to find overlaps between significant GWAS association results and a GWAS catalog of known genetic associations using LD or genomic distance.
locuszoom-standalone	Commits • PRs	Command line version of the original LocusZoom (circa 2010). This has been deprecated in favor of the new interactive LocusZoom.js. Please try it out on the new LocusZoom website.
mvtnorm.js		A test of cross-compiling the multivariate normal distribution function into JS/WASM from Fortran.

Tutorial on using Snakemake.