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