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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "chem16S" in publications use:'
type: software
license: GPL-3.0-only
title: 'chem16S: Chemical Metrics for Microbial Communities'
version: 1.1.0
doi: 10.1093/bioinformatics/btad564
identifiers:
- type: doi
  value: 10.32614/CRAN.package.chem16S
abstract: 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) <https://doi.org/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'.
authors:
- family-names: Dick
  given-names: Jeffrey
  email: j3ffdick@gmail.com
  orcid: https://orcid.org/0000-0002-0687-5890
preferred-citation:
  type: article
  title: '\emphchem16S: community-level chemical metrics for exploring genomic adaptation
    to environments'
  authors:
  - family-names: Dick
    given-names: Jeffrey M.
    email: jeff@chnosz.net
  - family-names: Kang
    given-names: Xun
    email: xunkang@csu.edu.cn
  journal: Bioinformatics
  year: '2023'
  volume: '39'
  issue: '9'
  doi: 10.1093/bioinformatics/btad564
  start: btad564
repository: https://CRAN.R-project.org/package=chem16S
repository-code: https://github.com/jedick/chem16S
url: https://doi.org/10.5281/zenodo.6793059
date-released: '2024-07-01'
contact:
- family-names: Dick
  given-names: Jeffrey
  email: j3ffdick@gmail.com
  orcid: https://orcid.org/0000-0002-0687-5890