An interface package (beta) for the BIOM file format.
Paul J. McMurdie <mcmurdie@stanford.edu> and the
biom-format team http://biom-format.org/
This is an R package for interfacing with the
BIOM format. This package includes basic tools for
reading biom-format files, accessing and subsetting
data tables from a biom object (which is more complex
than a single table), as well as limited support for
writing a biom-object back to a biom-format file. The
design of this API is intended to match the python API
and other tools included with the biom-format project,
but with a decidedly "R flavor" that should be familiar
to R users. This includes S4 classes and methods, as
well as extensions of common core functions/methods.
'allClasses.R' 'allPackage.R' 'IO-methods.R' 'BIOM-class.R'
'validity-methods.R'

Paul J. McMurdie <mcmurdie@stanford.edu> and the biom-format
team http://biom-format.org/
This is an R package for interfacing with the BIOM format.
Currently in beta form, this package includes basic tools for
reading biom-format files, accessing and subsetting data tables
from a biom object (which is more complex than a single table),
as well as limited support for writing a biom-object back to a
biom-format file. The design of this API is intended to match
the python API and other tools included with the biom-format
project, but with a decidedly "R flavor" that should be
familiar to R users. This includes S4 classes and methods, as
well as extensions of common core functions/methods.

Performing biological data retrieval and functional annotation with R.

Functional Annotation and Biological Data Retrieval with R
knitr (>= 1.6), rmarkdown (>= 0.3.3), devtools (>= 1.6.1),
testthat

Perform biological data retrieval and functional annotation with
R. This tool provides API functions to the BioMart database and genome retrieval
functions for bulk retrieval of genomes.

Perform meta-genomic data retrieval and functional annotation retrieval with
R.

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' (Yates et al. (2016) <doi:10.1093/nar/gkv1157>) 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.