Functions to Work with NCBI Accessions and Taxonomy
Convert accessions to taxa
Condense multiple taxonomic assignments to their most recent common br...
Download accession2taxid files from NCBI
Find all accessions for a taxa
Find common names for a given taxa
Get descendant ranks for a taxa
Find a given taxa by name
Find a given taxa by name
Download names and nodes files from NCBI
Get all taxonomy for a taxa
Get taxonomic ranks for a taxa
Get taxonomic ranks for a taxa
Return last not NA value
Create a Newick tree from taxonomy
Bring multiple raw taxonomies into alignment
Download data from NCBI and set up SQLite database
Read NCBI accession2taxid files
Read NCBI names file
Read NCBI names file
Read NCBI nodes file
Read NCBI nodes file
Download file using curl allowing resumption of interrupted files
Process a large file piecewise
taxonomizr: Functions to Work with NCBI Accessions and Taxonomy
Switch from data.table to SQLite
Combine multiple sorted vectors into a single sorted vector
Trim columns from taxa file
Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to download NCBI data dumps and create a local database for fast and local taxonomic assignment.
Useful links