Functions to Work with NCBI Accessions and Taxonomy


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Documentation for package ‘taxonomizr’ version 0.10.6

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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