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 |