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).


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install.packages("themetagenomics")

0.1.0 by Stephen Woloszynek, 4 months ago


http://github.com/EESI/themetagenomics


Report a bug at http://github.com/EESI/themetagenomics/issues


Browse source code at https://github.com/cran/themetagenomics


Authors: Stephen Woloszynek [aut, cre]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports ggplot2, lda, lme4, Matrix, plotly, rstan, scales, shiny, stats, stats4, stm

Depends on Rcpp

Suggests assertthat, covr, huge, igraph, inline, knitr, networkD3, proxy, rmarkdown, RcppArmadillo, Rtsne, testthat, vegan, viridis

Linking to Rcpp


See at CRAN