getUniProtSTATS

The UniProt stores a <code>STATS</code> file to summarise all available information for their reference proteomes.
Users can now download this file and process it with <code>biomartr</code>.

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

getUniProtSTATS function

<dl><dt>update</dt>
<dd>shall the internal <code>cachedir</code> file be deleted and the <code>STATS</code>
file freshly downloaded from the UniProt FTP servers?</dd></dl>

Arguments

Author

Retrieve UniProt Database Information File (STATS) — getUniProtSTATS

<dl>

<dt>update</dt>
<dd>shall the internal <code>cachedir</code> file be deleted and the <code>STATS</code>
file freshly downloaded from the UniProt FTP servers?</dd>

</dl>

getUniProtSTATS: Retrieve UniProt Database Information File (STATS)

Description

Usage

Arguments

Author

Examples