Man pages for sherrillmix/taxonomizr
Functions to Work with NCBI Accessions and Taxonomy
| accessionToTaxa | Convert accessions to taxa |
| condenseTaxa | Condense multiple taxonomic assignments to their most recent... |
| 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... |
| streamingRead | Process a large file piecewise |
| taxonomizr-package | taxonomizr: Functions to Work with NCBI Accessions and... |
| taxonomizrSwitch | Switch from data.table to SQLite |
| topoSort | Combine multiple sorted vectors into a single sorted vector |
| trimTaxa | Trim columns from taxa file |
