Package: taxonomizr 0.10.6

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:Scott Sherrill-Mix [aut, cre]

taxonomizr_0.10.6.tar.gz
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taxonomizr.pdf |taxonomizr.html
taxonomizr/json (API)

# Install 'taxonomizr' in R:
install.packages('taxonomizr', repos = c('https://sherrillmix.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/sherrillmix/taxonomizr/issues

On CRAN:

8.26 score 69 stars 2 packages 221 scripts 546 downloads 4 mentions 23 exports 21 dependencies

Last updated 11 months agofrom:5df3783cbb. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 22 2024
R-4.5-win-x86_64OKOct 22 2024
R-4.5-linux-x86_64OKOct 22 2024
R-4.4-win-x86_64OKOct 22 2024
R-4.4-mac-x86_64OKOct 22 2024
R-4.4-mac-aarch64OKOct 22 2024
R-4.3-win-x86_64OKOct 22 2024
R-4.3-mac-x86_64OKOct 22 2024
R-4.3-mac-aarch64OKOct 22 2024

Exports:accessionToTaxacondenseTaxagetAccession2taxidgetAccessionsgetCommongetDescendantsgetIdgetId2getNamesAndNodesgetRawTaxonomygetTaxonomygetTaxonomy2lastNotNamakeNewicknormalizeTaxaprepareDatabaseread.accession2taxidread.namesread.names.sqlread.nodesread.nodes.sqlstreamingReadtopoSort

Dependencies:bitbit64blobcachemclicpp11curldata.tableDBIfastmapgluelifecyclememoisepkgconfigplogrR.methodsS3R.ooR.utilsrlangRSQLitevctrs

taxonomizr usage

Rendered fromusage.Rmdusingknitr::rmarkdownon Oct 22 2024.

Last update: 2023-12-14
Started: 2017-03-07