software

statistical diversity lab

Diversity is a marker of ecosystem health in ecology, microbiology and immunology, with implications for disease diagnosis and infection resistance. However, accurately comparing diversity across environmental gradients is challenging, especially when number of different taxonomic groups in the community is large. DivNet estimates common diversity indices such as the Shannon, Simpson, Bray-Curtis, and Euclidean indices. Unlike other methods, DivNet utilizes covariate and replicate information ("metadata") and models taxa in the ecosystem interacting and co-occuring.

Want to understand the drivers of change in ecological communities? The R package breakaway provides a suite of methods for modelling microbial communities, along with hypothesis testing for alpha-diversity. 

CatchAll is a classic software tool for estimating microbial diversity. The original CatchAll was difficult to run on Mac and Linux operating systems. The Statistical Diversity Lab adopted its maintenance and rewrote it into R.

corncob models the relative abundance of a category in a population. It was specifically developed to analyse microbiome data obtain from high throughput taxonomic profiling techniques. corncob implements a beta-binomial model and permits hypothesis testing for changes in relative abundance and overdispersion.

206.543.8027

Department of Biostatistics
F-657, Box 357232
Health Sciences Building, 1959 NE Pacific St
University of Washington, Seattle, WA 98195

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