Functions to Work with NCBI Accessions and Taxonomy


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Documentation for package ‘taxonomizr’ version 0.2.2

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accessionToTaxa Convert accessions to taxa
condenseTaxa Condense a taxa table for a single read
getAccession2taxid Download accession2taxid files from NCBI
getId Find a given taxa by name
getNamesAndNodes Download names and nodes files from NCBI
getTaxonomy Get taxonomic ranks for a taxa
lastNotNa Return last not NA value
read.accession2taxid Read NCBI accession2taxid files
read.names Read NCBI names file
read.nodes Read NCBI nodes file
streamingRead Process a large file piecewise
trimTaxa Trim columns from taxa file