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). See
themetagenomics provides functions to explore topics generated from 16S rRNA sequencing information on both the abundance and functional levels. It also provides an R implementation of PICRUSt and wraps Tax4fun, giving users a choice for their functional prediction strategy.
Stephen Woloszynek, Zhengqiao Zhao, Gideon Simpson, Joshua Chang Mell, and Gail Rosen. Gauging the use of topic models as a means to understand microbiome data structure. TBD, 2017
Stan Development Team. 2016. RStan: the R interface to Stan. R package version 2.14.1., 2017.
install.packages('themetagenomics')# To install the developmental version via Github:# install.packages('devtools')devtools::install_github('EESI/themetagenomics',build_vignettes=TRUE)
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