Introduction | Requirements | Installation | Preparation | Assigning taxonomy | Producing accession numbers | Finding taxonomy for NCBI accession numbers | Finding taxonomy for taxonomic names | Finding descendants for a given taxa | Finding common names for taxonomic IDs | Condensing taxonomy a.k.a. lowest common ancestor LCA | Find all taxonomic assignments for a given taxa | Finding accessions for a given taxonomic ID | Convert taxonomy to Newick tree | Note: NCBI name changes in early 2023 | Changelog | v0.11.1 | v0.10.8 | v0.10.7 | v0.10.6 | v0.10.5 | v0.10.4 | v0.10.3 | v0.10.2 | v0.10.1 | v0.9.4 | v0.9.3 | v0.9.2 | v0.8.4 | v0.8.3 | v0.8.2 | v0.8.1 | v0.8.0 | v0.7.1 | v0.7.0 | v0.6.0 | v0.5.3 | v0.5.0 | Manual preparation of database (usually not necessary) | Download names and nodes | Download accession to taxa files | Convert names, nodes and accessions to database | Switch from data.table to SQLite
Package: taxonomizr 0.11.2
Scott Sherrill-Mix
taxonomizr: Functions to Work with NCBI Accessions and Taxonomy
Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment.
Authors:
taxonomizr_0.11.2.tar.gz
taxonomizr_0.11.2.zip(r-4.7)taxonomizr_0.11.2.zip(r-4.6)taxonomizr_0.11.2.zip(r-4.5)
taxonomizr_0.11.2.tgz(r-4.6-x86_64)taxonomizr_0.11.2.tgz(r-4.6-arm64)taxonomizr_0.11.2.tgz(r-4.5-x86_64)taxonomizr_0.11.2.tgz(r-4.5-arm64)
taxonomizr_0.11.2.tar.gz(r-4.7-x86_64)taxonomizr_0.11.2.tar.gz(r-4.6-x86_64)
taxonomizr_0.11.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
taxonomizr/json (API)
| # Install 'taxonomizr' in R: |
| install.packages('taxonomizr', repos = c('https://sherrillmix.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sherrillmix/taxonomizr/issues
Last updated from:218641b806. Checks:2 FAIL, 11 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | FAIL | 3733 | ||
| linux-devel-x86_64 | OK | 153 | ||
| source / vignettes | OK | 158 | ||
| linux-release-arm64 | FAIL | 3734 | ||
| linux-release-x86_64 | OK | 154 | ||
| macos-release-arm64 | OK | 142 | ||
| macos-release-x86_64 | OK | 216 | ||
| macos-oldrel-arm64 | OK | 221 | ||
| macos-oldrel-x86_64 | OK | 278 | ||
| windows-devel | OK | 127 | ||
| windows-release | OK | 120 | ||
| windows-oldrel | OK | 130 | ||
| wasm-release | OK | 111 |
Exports:accessionToTaxacondenseTaxagetAccession2taxidgetAccessionsgetCommongetDescendantsgetIdgetId2getNamesAndNodesgetRawTaxonomygetTaxonomygetTaxonomy2lastNotNamakeNewicknormalizeTaxaprepareDatabaseread.accession2taxidread.namesread.names.sqlread.nodesread.nodes.sqlstreamingReadtopoSort
Dependencies:bitbit64blobcachemclicpp11curldata.tableDBIfastmapgluelifecyclememoisepkgconfigR.methodsS3R.ooR.utilsrlangRSQLitevctrs
