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Published on: September 20, 2016
chem16S: community-level chemical metrics for exploring genomic adaptation to environments
1Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring of Ministry of Education, School of Geosciences and Info-Physics, Central South University, Changsha, Hunan 410083, China.
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.
