Package: chem16S 1.2.0-6

chem16S: Chemical Metrics for Microbial Communities

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) <doi: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:Jeffrey Dick [aut, cre]

chem16S_1.2.0-6.tar.gz
chem16S_1.2.0-6.zip(r-4.7-any)chem16S_1.2.0-6.zip(r-4.6-any)chem16S_1.2.0-6.zip(r-4.5-any)
chem16S_1.2.0-6.tgz(r-4.6-any)chem16S_1.2.0-6.tgz(r-4.5-any)
chem16S_1.2.0-6.tar.gz(r-4.7-any)chem16S_1.2.0-6.tar.gz(r-4.6-any)
chem16S_1.2.0-6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
chem16S/json (API)

# Install 'chem16S' in R:
install.packages('chem16S', repos = c('https://jedick.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jedick/chem16s/issues

Datasets:
  • mouse.GTDB_220 - 'phyloseq-class' objects generated using the DADA2 Pipeline Tutorial
  • mouse.RDP - 'phyloseq-class' objects generated using the DADA2 Pipeline Tutorial
  • mouse.silva - 'phyloseq-class' objects generated using the DADA2 Pipeline Tutorial

On CRAN:

Conda:

16s-rrnacarbon-oxidation-statechemical-metricsgenomic-adaptationmicrobial-communities

4.82 score 4 stars 11 scripts 336 downloads 11 exports 59 dependencies

Last updated from:df51f65f63. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK223
source / vignettesOK295
linux-releaseOK211
macos-releaseOK270
macos-oldrelOK294
windows-develOK138
windows-releaseOK135
windows-oldrelOK126
wasm-releaseOK136

Exports:chemlabget_metadataget_metric_byrankget_metricsmap_taxaplot_metricsplot_ps_metricsplot_ps_metrics2ps_metricsps_taxacountsread_RDP

Dependencies:ade4apeBiobaseBiocGenericsbiomformatBiostringscanprotcliclustercodetoolscpp11crayondata.tabledigestfarverforeachgenericsggplot2gluegtableigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmultcompViewmulttestnlmepermutephyloseqpixmappkgconfigplyrR6RColorBrewerRcppRcppArmadilloreshape2rlangS4VectorsS7scalesSeqinfospstringistringrsurvivalvctrsveganviridisLitewithrXVector

Chemical metrics of reference proteomes for taxa
Required packages | Reference proteomes for taxa | r Zc for genera in selected phyla and classes | Prokaryotic genera, aggregated to phylum | Prokaryotic genera, aggregated to class | Stoichiometric hydration state (r nH2O) | Viruses and prokaryotes | Other metrics | Take-home messages | References
Rendered frommetrics.Rmdusingknitr::rmarkdown

Last update: 2024-12-02
Started: 2023-07-06

Integration of chem16S with phyloseq
Load required packages | Mouse microbiome data | Lowest-level taxa | Taxonomic mapping | From taxonomy to amino acid composition | From taxonomy to chemical metrics | Using GTDB for reference proteomes | Take-home messages | References
Rendered fromphyloseq.Rmdusingknitr::rmarkdown

Last update: 2024-12-02
Started: 2023-07-06

Plotting two chemical metrics
Load required packages | GlobalPatterns | Humboldt Sulfuretum (Marine Sediment) | Qinghai-Tibet Plateau (Hot Springs) | Comparing more datasets | Take-home messages | References
Rendered fromplotting.Rmdusingknitr::rmarkdown

Last update: 2024-12-02
Started: 2023-07-06