themetagenomics (1.0.0)

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Exploring Thematic Structure and Predicted Functionality of 16s rRNA Amplicon Data.

A means to explore the structure of 16S rRNA surveys using a Structural Topic Model coupled with functional prediction. The user provides an abundance table, sample metadata, and taxonomy information, and themetagenomics infers associations between topics and sample features, as well as topics and predicted functional content. Functional prediction can be accomplished via Tax4Fun (for Silva references) and PICRUSt (for GreenGeenes references).

Maintainer: Stephen Woloszynek
Author(s): Stephen Woloszynek [aut, cre]

License: MIT + file LICENSE

Uses: ggplot2, lda, lme4, Matrix, plotly, Rcpp, rstan, scales, shiny, stm, igraph, inline, proxy, vegan, testthat, RcppArmadillo, huge, knitr, assertthat, Rtsne, rmarkdown, networkD3, covr, viridis

Released about 1 month ago.

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