Date: 2025-09-13
Package: chem16S
Version: 1.2.0-6
Title: Chemical Metrics for Microbial Communities
Authors@R: c(
    person("Jeffrey", "Dick", , "j3ffdick@gmail.com", role = c("aut", "cre"),
      comment = c(ORCID = "0000-0002-0687-5890"))
    )
Author: Jeffrey Dick [aut, cre] (0000-0002-0687-5890)
Maintainer: Jeffrey Dick <j3ffdick@gmail.com>
Depends: R (>= 3.5.0)
Imports: plyr, ggplot2, rlang, reshape2, phyloseq, canprot (>= 2.0.0)
Suggests: tinytest, knitr, patchwork, ggpmisc, rmarkdown
Description: 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'.
Encoding: UTF-8
License: GPL-3
VignetteBuilder: knitr
URL: https://github.com/jedick/chem16S
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev zlib1g-dev
Repository: https://jedick.r-universe.dev
Date/Publication: 2025-09-13 10:43:42 UTC
RemoteUrl: https://github.com/jedick/chem16S
RemoteRef: HEAD
RemoteSha: df51f65f63e3cd091bcc55db25ca93dc4e1afc9e
NeedsCompilation: no
Packaged: 2026-10-16 09:24:50 UTC; root