chem16S: Chemical Metrics of Community Reference Proteomes

Combines taxonomic classifications of high-throughput 16S rRNA gene sequences with reference proteomes of archaeal and bacterial taxa to generate amino acid compositions of community reference proteomes. Calculates chemical metrics including carbon oxidation state ('Zc'), stoichiometric oxidation and hydration state ('nO2' and 'nH2O'), H/C, N/C, O/C, and S/C ratios, grand average of hydropathicity ('GRAVY'), isoelectric point ('pI'), protein length, and average molecular weight of amino acid residues. Uses precomputed reference proteomes for archaea and bacteria derived from the Genome Taxonomy Database ('GTDB'). Also includes reference proteomes derived from the NCBI Reference Sequence ('RefSeq') database and manual mapping from the 'RDP Classifier' training set to 'RefSeq' taxonomy as described by Dick and Tan (2023) <doi:10.1007/s00248-022-01988-9>. Processes taxonomic classifications in 'RDP Classifier' format or OTU tables in 'phyloseq-class' objects from the Bioconductor package 'phyloseq'.

Version: 1.0.0
Depends: R (≥ 3.5.0)
Imports: plyr, ggplot2, rlang, reshape2, phyloseq
Suggests: tinytest, knitr, patchwork, ggpmisc, rmarkdown
Published: 2023-07-17
Author: Jeffrey Dick ORCID iD [aut, cre]
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
License: GPL-3
URL: https://github.com/jedick/chem16S, https://doi.org/10.5281/zenodo.6793059
NeedsCompilation: no
Materials: README NEWS
CRAN checks: chem16S results

Documentation:

Reference manual: chem16S.pdf
Vignettes: Chemical metrics of reference proteomes
Integration of chem16S with phyloseq
Plotting two chemical metrics

Downloads:

Package source: chem16S_1.0.0.tar.gz
Windows binaries: r-devel: chem16S_1.0.0.zip, r-release: chem16S_1.0.0.zip, r-oldrel: chem16S_1.0.0.zip
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): chem16S_1.0.0.tgz, r-release (x86_64): not available

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