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 <doi:10.1371/journal.pone.0219235>.
| Version: | 1.0.2 |
| Depends: | R (≥ 3.2.5), Rcpp (≥ 0.11.3) |
| Imports: | ggplot2, lda, lme4 (≥ 1.1.12), Matrix, plotly (≥ 4.5.6), rstan (≥ 2.14.0), scales, shiny (≥ 1.0.0), stats, stats4, stm (≥ 1.1.4) |
| LinkingTo: | Rcpp |
| Suggests: | assertthat, covr, huge, igraph, inline, knitr, networkD3, proxy, rmarkdown, RcppArmadillo, Rtsne, testthat, vegan, viridis |
| Published: | 2020-04-30 |
| Author: | Stephen Woloszynek [aut, cre] |
| Maintainer: | Stephen Woloszynek <sw424 at drexel.edu> |
| BugReports: | http://github.com/EESI/themetagenomics/issues |
| License: | MIT + file LICENSE |
| URL: | http://github.com/EESI/themetagenomics |
| NeedsCompilation: | yes |
| Citation: | themetagenomics citation info |
| Materials: | README NEWS |
| CRAN checks: | themetagenomics results |
| Reference manual: | themetagenomics.pdf |
| Vignettes: |
Predicting Functional Content Finding Thematic Structure in the David Dataset |
| Package source: | themetagenomics_1.0.2.tar.gz |
| Windows binaries: | r-devel: themetagenomics_1.0.2.zip, r-release: themetagenomics_1.0.2.zip, r-oldrel: themetagenomics_1.0.2.zip |
| macOS binaries: | r-release: themetagenomics_1.0.2.tgz, r-oldrel: themetagenomics_1.0.2.tgz |
| Old sources: | themetagenomics archive |
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