getKingdoms

A short list of available kingdoms of life

Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized
way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome
retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL',
and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database
(Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve
functional annotation for genomic loci. In addition, users can download entire databases such
as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr',
'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.

Hajk-Georg Drost

biomartr

Genomic Data Retrieval

Haakon Tjeldnes

getKingdoms function

<dl><dt>db</dt>
<dd>a character string specifying the database from which the genome
shall be retrieved: <code>db = "refseq"</code>, <code>db = "genbank"</code>,
<code>db = "ensembl"</code>, <code>db = "ensemblgenomes"</code>.
Default is <code>db = "refseq"</code>.</dd></dl>

Arguments

Author

Retrieve available kingdoms of life — getKingdoms

<dl>

<dt>db</dt>
<dd>a character string specifying the database from which the genome
shall be retrieved: <code>db = "refseq"</code>, <code>db = "genbank"</code>,
<code>db = "ensembl"</code>, <code>db = "ensemblgenomes"</code>.
Default is <code>db = "refseq"</code>.</dd>

</dl>

getKingdoms: Retrieve available kingdoms of life

Description

Usage

Arguments

Author

See Also

Examples