ncbi: Retrieve and parse data from NCBI databases.

In gschofl/ncbi: Retrieve data from NCBI.

Description

This package provides an R interface to retrieve data from the following NCBI databases: nucleotide, protein, pubmed, taxonomy, nucgss, and nucest.

Important functions

• taxon: Retrieve taxonomy records remotely from NCBI's Taxonomy database.

• createTaxonDB: Install NCBI's Taxonomy database locally.

• taxonDB: Retrieve records from a local install of the Taxonomy database.

• taxonByGeneID: Retrieve records from a local install of the Taxonomy database via NCBI GI numbers.

• pubmed: Retrieve records from the PubMed database.

• protein: Retrieve records from the protein database.

• nucleotide: Retrieve records from the nuccore database.

• GSS: Retrieve records from the nucgss database.

• EST: Retrieve records from the nucest database.

Main classes

• Taxon: A container for data retrieved from the NCBI Taxonomy database.

• TaxonList: A list of Taxa.

• taxonDBConnection: Connection to a local Taxonomy database.

Package options

ncbi uses the following options to configure behaviour:

• ncbi.taxonomy.path: Path to a local installation of the NCBI taxonomy database and (optionally) a GI_to_TaxId database. Defaults to "$HOME/local/db/taxonomy/". You can override the default by setting this option in your .Rprofile file. RuncreateTaxonDB and createGeneidDB to install these databases.

Author(s)

Gerhard Schoefl [e-mail]

gschofl/ncbi documentation built on May 17, 2019, 8:53 a.m.