| biomartr-package {biomartr} | R Documentation |
Genomic Data Retrieval
Description
This package interacts with a suite of web Application Programming Interfaces and FTP sites to perform automated genomic data retieval and annotation information retrieval.
About
To automate the retrieval process on a meta-genomic scale, this package
provides useful interface functions for genomic sequence retrieval and
functional annotation retrieval.
The major aim of biomartr is to facilitate computational
reproducibility and large-scale handling of genomic data for
(meta-)genomic analyses.
In detail, biomartr aims to provide users with an easy to use
framework to obtain genome, proteome, CDS, GFF (annotation), genome
assembly quality, and metagenome project data. Furthermore, an interface to
the Ensembl Biomart database allows users to retrieve functional annotation
for genomic loci.
Users can download entire databases
such as
-
NCBI RefSeq -
NCBI nr -
NCBI nt -
NCBI Genbank -
NCBI nt -
Ensembl -
Ensembl Genomes -
UniProt
Author(s)
Hajk-Georg Drost hajk-georg.drost@tuebingen.mpg.de