summary_cds

A summary statistics of specific CDS features is returned.

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

summary_cds function

<dl><dt>file</dt>
<dd>file path to a CDS file in <code>fasta</code> format.</dd>
<dt>organism</dt>
<dd>character string specifying the organism at hand.</dd></dl>

Arguments

Author

Retrieve summary statistics for a coding sequence (CDS) file — summary_cds

<dl>

<dt>file</dt>
<dd>file path to a CDS file in <code>fasta</code> format.</dd>


<dt>organism</dt>
<dd>character string specifying the organism at hand.</dd>

</dl>

summary_cds: Retrieve summary statistics for a coding sequence (CDS) file

Description

Usage

Arguments

Author

Details

See Also