getKingdomAssemblySummary

Retrieval function of the assembly_summary.txt file 
from NCBI for all kingdoms.
The assembly_summary.txt files store available species on NCBI.

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

getKingdomAssemblySummary function

<dl><dt>db</dt>
<dd>database name. E.g. <code>refseq</code> or <code>genbank</code>.</dd></dl>

Arguments

Author

Retrieve and summarise the assembly_summary.txt files from 
NCBI for all kingdoms — getKingdomAssemblySummary

<dl>

<dt>db</dt>
<dd>database name. E.g. <code>refseq</code> or <code>genbank</code>.</dd>

</dl>

getKingdomAssemblySummary: Retrieve and summarise the assembly_summary.txt files from NCBI for all kingdoms

Description

Usage

Arguments

Author

See Also

Examples