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) <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'.
Downloads
218
Last 30 days
15074th
405
Last 90 days
405
Last year
Trend: +16.6% (30d vs prior 30d)
CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | ERROR |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | ERROR |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (14 non-OK)
package dependencies
Package required but not available: ‘phyloseq’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
*
*
*
*
*
*
*
*
package dependencies
Package required but not available: ‘phyloseq’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
*
*
*
*
Check History
ERROR 12 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE Mar 9, 2026
package dependencies
Package required but not available: ‘phyloseq’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package required but not available: ‘phyloseq’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.