Package: chem16S 1.1.0
Jeffrey Dick
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:
chem16S_1.1.0.tar.gz
chem16S_1.1.0.tar.gz(r-4.5-noble)chem16S_1.1.0.tar.gz(r-4.4-noble)
chem16S_1.1.0.tgz(r-4.4-emscripten)chem16S_1.1.0.tgz(r-4.3-emscripten)
chem16S.pdf |chem16S.html✨
chem16S/json (API)
NEWS
| # Installchem16S in R: |
| install.packages('chem16S',repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jedick/chem16s/issues
- mouse.GTDB_214 - '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
Last updated 4 days agofrom:e99315339a
Exports:chemlabget_metadataget_metricsmap_taxaplot_metricsplot_ps_metricsplot_ps_metrics2ps_metricsps_taxacountsread_RDP
Dependencies:ade4apeaskpassBiobaseBiocGenericsbiomformatBiostringscanprotcliclustercodetoolscolorspacecpp11crayoncurldata.tabledigestfansifarverforeachGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemultcompViewmulttestmunsellnlmeopensslpermutephyloseqpillarpixmappkgconfigplyrR6RColorBrewerRcppRcppArmadilloreshape2rhdf5rhdf5filtersRhdf5librlangS4VectorsscalesspstringistringrsurvivalsystibbleUCSC.utilsutf8vctrsveganviridisLitewithrXVectorzlibbioc
Chemical metrics of reference proteomes for taxa
Rendered frommetrics.Rmdusingknitr::rmarkdownon Jul 02 2024.Last update: 2024-07-02
Started: 2023-07-17
Integration of chem16S with phyloseq
Rendered fromphyloseq.Rmdusingknitr::rmarkdownon Jul 02 2024.Last update: 2024-07-02
Started: 2023-07-17
Plotting two chemical metrics
Rendered fromplotting.Rmdusingknitr::rmarkdownon Jul 02 2024.Last update: 2024-07-02
Started: 2023-07-17
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Chemical metrics for microbial communities | chem16S-package chem16S |
| `phyloseq-class` objects generated using the DADA2 Pipeline Tutorial | mouse.GTDB_214 mouse.RDP mouse.silva |
| Formatted labels for chemical metrics | chemlab |
| Template function for metadata | get_metadata |
| Calculate chemical metrics of community reference proteomes | get_metrics |
| Map taxonomic names to NCBI or GTDB taxonomy | map_taxa |
| Process `phyloseq-class` objects to calculate chemical metrics | physeq plot_ps_metrics plot_ps_metrics2 ps_metrics ps_taxacounts |
| Plot chemical metrics of community reference proteomes | plot_metrics |
| Read and filter RDP Classifier output | read_RDP |
