CRAN DOI R-CMD-check

chem16S calculates chemical metrics for microbial communities by combining taxonomic abundances with genomic reference sequences for proteins. The chemical representation of communities has applications ranging from human microbiomes to Earth-life coevolution.

Supported input formats: * phyloseq-class objects created using phyloseq * RDP Classifier

Supported reference databases:

Description

The chem16S R package combines taxonomic classifications of high-throughput 16S rRNA gene sequences with precomputed amino acid compositions of reference proteomes for archaea and bacteria to obtain the amino acid compositions of community reference proteomes. Chemical metrics of community reference proteomes such as carbon oxidation state (ZC) and stoichiometric hydration state (nH2O) reveal new types of adaptations of microbial genomes to environmental conditions. For instance, an association of lower nH2O with higher salinity in the Baltic Sea suggests a genomically encoded dehydration trend:

Baltic Sea nH2O-Zc plot (example from chem16S::plot_metrics)

PSU stands for practical salinity units. The sequence data analyzed for this plot was taken from Herlemann et al. (2016) and the code to make this plot is available in the help page for chem16S::plot_metrics.

Methods

Installation

First install phyloseq from Bioconductor:

if(!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("phyloseq")

Then install the release version of chem16S from CRAN:

install.packages("chem16S")

Or use install_github from remotes or devtools to install the development version of chem16S from GitHub:

if(!require("remotes", quietly = TRUE)) install.packages("remotes")
remotes::install_github("jedick/chem16S", build_vignettes = TRUE)