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chem16S  

Chemical Metrics for Microbial Communities
View on CRAN: Click here


Download and install chem16S package within the R console
Install from CRAN:
install.packages("chem16S")

Install from Github:
library("remotes")
install_github("cran/chem16S")

Install by package version:
library("remotes")
install_version("chem16S", "1.2.0")



Attach the package and use:
library("chem16S")
Maintained by
Jeffrey Dick
[Scholar Profile | Author Map]
First Published: 2023-07-17
Latest Update: 2023-07-17
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) . Processes taxonomic classifications in 'RDP Classifier' format or OTU tables in 'phyloseq-class' objects from the Bioconductor package 'phyloseq'.
How to cite:
Jeffrey Dick (2023). chem16S: Chemical Metrics for Microbial Communities. R package version 1.2.0, https://cran.r-project.org/web/packages/chem16S. Accessed 01 Apr. 2025.
Previous versions and publish date:
1.0.0 (2023-07-17 19:10), 1.1.0 (2024-07-01 16:20)
Other packages that cited chem16S R package
View chem16S citation profile
Other R packages that chem16S depends, imports, suggests or enhances
Complete documentation for chem16S
Functions, R codes and Examples using the chem16S R package
Some associated functions: calc_metrics . chem16S-data . chem16S-package . chemlab . get_metadata . get_metrics . map_taxa . phyloseq_integration . plot_metrics . read_RDP . 
Some associated R codes: calc_metrics.R . chemlab.R . get_metadata.R . get_metrics.R . map_taxa.R . phyloseq_integration.R . plot_metrics.R . read_RDP.R . zzz.R .  Full chem16S package functions and examples
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