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 |