Taxonomy format overview | Prefix-based formats | UNITE format (k__/p__ prefixes) | SINTAX / UTAX format | Greengenes2 format (d__/p__ prefixes) | Positional formats | Unprefixed semicolon-delimited (generic) | PR2 format (no prefixes, 9 levels) | Sequence name placement | Working with taxonomy formats in dbpq | Detecting the format | Getting rank information | Summarizing databases | Listing ranks | Converting between formats | Downloading databases in specific formats | Database formats and classification algorithms | Choosing a database and classifier
Package: dbpq 0.1.0.9000
dbpq: Manage FASTA Reference Databases for Taxonomic Assignment
Download, format, summarize, and modify FASTA reference databases used for taxonomic assignment in metabarcoding pipelines. Supports major databases ('UNITE', 'SILVA', 'PR2', 'Greengenes2', 'RDP', 'MIDORI2', 'BOLD', 'Diat.barcode', 'MaarjAM', 'Eukaryome') and converts between taxonomy header formats ('dada2', 'SINTAX', 'Greengenes2'). Part of the 'pqverse' ecosystem.
Authors:
dbpq_0.1.0.9000.tar.gz
dbpq_0.1.0.9000.zip(r-4.7-any)dbpq_0.1.0.9000.zip(r-4.6-any)dbpq_0.1.0.9000.zip(r-4.5-any)
dbpq_0.1.0.9000.tgz(r-4.6-any)dbpq_0.1.0.9000.tgz(r-4.5-any)
dbpq_0.1.0.9000.tar.gz(r-4.7-any)dbpq_0.1.0.9000.tar.gz(r-4.6-any)
dbpq_0.1.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dbpq/json (API)
| # Install 'dbpq' in R: |
| install.packages('dbpq', repos = c('https://adrientaudiere.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/adrientaudiere/dbpq/issues
Pkgdown/docs site:https://adrientaudiere.github.io
Last updated from:3483ddfea2. Checks:7 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | ERROR | 236 | ||
| source / vignettes | OK | 255 | ||
| linux-release | ERROR | 218 | ||
| macos-release | ERROR | 175 | ||
| macos-oldrel | ERROR | 177 | ||
| windows-devel | ERROR | 184 | ||
| windows-release | ERROR | 185 | ||
| windows-oldrel | ERROR | 172 | ||
| wasm-release | OK | 146 |
Exports:add_sh_to_taxonomycount_pattern_dbcount_seq_dbcount_unwanted_taxcutadapt_rm_primers_dbdetect_tax_formatdiagnose_dbdownload_bold_dbdownload_diatbarcode_dbdownload_eukaryome_dbdownload_greengenes2_dbdownload_ksgp_dbdownload_ltplus_dbdownload_marjaam_dbdownload_midori2_dbdownload_pr2_dbdownload_rdp_dbdownload_silva_dbdownload_unite_dbfilter_dbfind_vsearchformat_fasta_dbformat2dada2format2dada2_speciesformat2sintaxget_file_extensionis_vsearch_installedlist_ranks_dbprofile_dbsearch_taxa_dbsummarize_dbtax_prefixes
Dependencies:BiocGenericsBiostringsclicpp11crayondplyrgenericsglueIRangesjsonlitelifecyclemagrittrpillarpkgconfigpurrrR6rlangS4VectorsSeqinfostringistringrtibbletidyrtidyselectutf8vctrswithrXVector
