Chem16S: community-level chemical metrics for exploring genomic adaptation to environments.
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ABSTRACT: Summary
The chem16S package combines taxonomic classifications of 16S rRNA gene sequences with amino acid compositions of prokaryotic reference proteomes to generate community reference proteomes. Taxonomic classifications from the RDP Classifier or data objects created by the phyloseq R package are supported. Users can calculate and visualize a variety of chemical metrics in order to explore the effects of redox, salinity, and other physicochemical variables on the genomic adaptation of protein sequences at the community level.Availability and implementation
Development of chem16S is hosted at https://github.com/jedick/chem16S. Version 1.0.0 is freely available from the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/package=chem16S.
SUBMITTER: Dick JM
PROVIDER: S-EPMC10505500 | biostudies-literature | 2023 Sep
REPOSITORIES: biostudies-literature
Publications
chem16S: community-level chemical metrics for exploring genomic adaptation to environments.
Bioinformatics (Oxford, England) 20230901 9
<h4>Summary</h4>The chem16S package combines taxonomic classifications of 16S rRNA gene sequences with amino acid compositions of prokaryotic reference proteomes to generate community reference proteomes. Taxonomic classifications from the RDP Classifier or data objects created by the phyloseq R package are supported. Users can calculate and visualize a variety of chemical metrics in order to explore the effects of redox, salinity, and other physicochemical variables on the genomic adaptation of ...[more]
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