listGenomes

a character string specifying the database for which genome 
availability shall be checked, e.g. <code>db = &quot;refseq&quot;</code>, 
<code>db = &quot;genbank&quot;</code>, <code>db = &quot;ensembl&quot;</code>, <code>db = &quot;ensemblgenomes&quot;</code>.

a character string specifying a potential filter of available 
genomes. Options are <code>type = &quot;all&quot;</code>, <code>type = &quot;kingdom&quot;</code>, 
<code>type = &quot;group&quot;</code>, <code>type = &quot;subgroup&quot;</code>.

type

a character string or character vector specifying a subset of 
<code>type</code>. E.g. if users are interested in retrieving all
<code>Eukaryota</code> species, they can specify: <code>type = &quot;kingdom&quot;</code> and 
<code>subset = &quot;Eukaryota&quot;</code>.

subset

a boolean value specifying whether only the scientific names 
of stored genomes shall be returned (details = FALSE) or all information such
as <code>organism_name</code>,<code>kingdoms</code>, <code>group</code>, <code>subgroup</code>, 
<code>file_size_MB</code>, etc.

details

This function retrieves the names of all genomes available on 
the NCBI ftp:// server and stores the results in a file named &#39;overview.txt&#39; 
inside the directory _ncbi_downloads&#39; that is built inside the workspace.

Perform metagenomic data retrieval and functional annotation
retrieval. In detail, this package aims to provide users with a standardized
way to automate genome, proteome, coding sequence ('CDS'), 'GFF', and metagenome
retrieval from 'NCBI' and 'ENSEMBL' 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. Users can download entire databases such
as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr',
'NCBI nt' and 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>) as
well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.

listGenomes: List All Available Genomes

Description

Usage

Arguments

Details

Examples