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chem16S
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", "1.1.0")
Attach the package and use:
library("chem16S")
Maintained by
Jeffrey Dick
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
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 1.1.0, https://cran.r-project.org/web/packages/chem16S. Accessed 22 Dec. 2024.
Previous versions and publish date:
1.0.0 (2023-07-17 19:10)
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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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