Package: chem16S 1.1.0-3

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]

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

On CRAN:

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

10 exports 4 stars 1.92 score 75 dependencies 8 scripts 247 downloads

Last updated 2 months agofrom:82f20b437a. Checks:OK: 7. Indexed: yes.

Exports:chemlabget_metadataget_metricsmap_taxaplot_metricsplot_ps_metricsplot_ps_metrics2ps_metricsps_taxacountsread_RDP

Dependencies:ade4apeaskpassBiobaseBiocGenericsbiomformatBiostringscanprotcliclustercodetoolscolorspacecpp11crayoncurldata.tabledigestfansifarverforeachGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemultcompViewmulttestmunsellnlmeopensslpermutephyloseqpillarpixmappkgconfigplyrR6RColorBrewerRcppRcppArmadilloreshape2rhdf5rhdf5filtersRhdf5librlangS4VectorsscalesspstringistringrsurvivalsystibbleUCSC.utilsutf8vctrsveganviridisLitewithrXVectorzlibbioc