restez: Create and Query a Local Copy of GenBank in R

The restez package comes with five families of functions: setup, database, get, entrez and internal/private.

Setup functions

These functions allow a user to set the filepath for where the GenBank files should be stored, create connections and verify these settings.

Database functions

These functions download specific parts of GenBank and create the local SQL-like database.

GenBank functions

These functions allow a user to query the local SQL-like database. A user can use an NCBI accession ID to retrieve sequences or whole GenBank records.

Entrez functions

The entrez functions are wrappers to the entrez_* functions in the rentrez package. e.g the restez's entrez_fetch will first try to search the local database, if it fails it will then call rentrez's rentrez::entrez_fetch() with the same arguments.

Private/internal functions

These functions work behind the scenes to make everything work. If you're curious you can read their documentation using the form ?restez:::functionname.

See also

Useful links:

• https://github.com/ropensci/restez

• https://docs.ropensci.org/restez/

• Report bugs at https://github.com/ropensci/restez/issues

Author

Maintainer: Joel H. Nitta joelnitta@gmail.com (ORCID)

Authors:

• Dom Bennett dominic.john.bennett@gmail.com (ORCID)