Functions to Work with NCBI Accessions and Taxonomy

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Documentation for package ‘taxonomizr’ version 0.11.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

accessionToTaxa	Convert accessions to taxa
condenseTaxa	Condense multiple taxonomic assignments to their most recent common branch
getAccession2taxid	Download accession2taxid files from NCBI
getAccessions	Find all accessions for a taxa
getCommon	Find common names for a given taxa
getDescendants	Get descendant ranks for a taxa
getId	Find a given taxa by name
getId2	Find a given taxa by name
getNamesAndNodes	Download names and nodes files from NCBI
getRawTaxonomy	Get all taxonomy for a taxa
getTaxonomy	Get taxonomic ranks for a taxa
getTaxonomy2	Get taxonomic ranks for a taxa
lastNotNa	Return last not NA value
makeNewick	Create a Newick tree from taxonomy
normalizeTaxa	Bring multiple raw taxonomies into alignment
prepareDatabase	Download data from NCBI and set up SQLite database
read.accession2taxid	Read NCBI accession2taxid files
read.names	Read NCBI names file
read.names.sql	Read NCBI names file
read.nodes	Read NCBI nodes file
read.nodes.sql	Read NCBI nodes file
resumableDownload	Download file using curl allowing resumption of interrupted files
streamingRead	Process a large file piecewise
taxonomizrSwitch	Switch from data.table to SQLite
topoSort	Combine multiple sorted vectors into a single sorted vector
trimTaxa	Trim columns from taxa file