Statistics/machine learning


Metastats is software for detecting differentially abundant features in metagenomic case/control studies. It is the first tool developed in the context of metagenomic data comprising multiple samples, and relies on a non-parametric t-test. This software is no longer current, not recommended for use, and is not being provided anymore. Newer tools exist in this space, such as metagenomeseq, corncob, and others.

Metagenomic Assembly

Assembly and Analysis Software for Exploring the Human Microbiome

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Gene Finding

Metagenomic assembly

Principal Investigators


Bayesian tool to integrate genetic and epigenetic data to find causal expression regulatory polymorphisms


Modeling microbial communities

Principal Investigators

Students and Postdoctoral researchers:


Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can add d3 visualizations.


MetaPath can identify differentially abundant pathways in metagenomic data-sets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge.

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