Overview
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.
Relevant Software and Literature
Stephen Woloszynek, Joshua Chang Mell, Zhengqiao Zhao, Gideon Simpson,
Michael P. O’Connor, and Gail Rosen. Exploring thematic structure and
predicted functionality of 16S rRNA amplicon data. 2019. PLoS
ONE 14(12); doi:
https://doi.org/10.1371/journal.pone.0219235
Margaret E. Roberts, Brandon M. Stewart, and Dustin Tingley (2017).
stm: R Package for Structural Topic
Models, 2016.
Morgan Langille et al. Predictive functional profiling of microbial
communities using 16S rRNA marker gene sequences.
PICRUSt 1.1.1
Kathrin P. Aßhauer, Bernd Wemheuer, Rolf Daniel, and Peter Meinicke.
Tax4Fun: predicting functional profiles from metagenomic 16S rRNA
data
Stan Development Team. 2016. RStan: the R interface to Stan. R package
version 2.14.1., 2017.
Installation
# To install the release version of Themetagenomics:
install.packages('themetagenomics')
# To install the developmental version via Github:
# install.packages('devtools')
devtools::install_github('EESI/themetagenomics',build_vignettes=TRUE)
Development
For future feature requests or suggestions, request an issue:
https://github.com/EESI/themetagenomics/issues