R: Functions to Work with NCBI Accessions and Taxonomy

# Functions to Work with NCBI Accessions and Taxonomy

## 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