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welchr/README.md

About

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

Projects

Maintainer

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.

Contributor

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.

Archived

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.

Tutorials/Talks

Examples of submitting SLURM jobs on our cluster.

Tutorial on using Snakemake.

@welchr's activity is private