Olson, N.
, Shah, N.
, Kancherla, J.
, Wagner, J.
and Corrada Bravo, H.
(2019),
metagenomeFeatures: An R package for working with 16S rRNA reference databases and marker-gene survey feature data., Bioinformatics, [online], https://doi.org/10.1093/bioinformatics/btz136
(Accessed April 28, 2024)
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metagenomeFeatures: An R package for working with 16S rRNA reference databases and marker-gene survey feature data.
Published
Author(s)
, Nidhi Shah, Jayaram Kancherla, Justin Wagner, Hector Corrada Bravo
Abstract
We developed the metagenomeFeatures R Bioconductor package along with annotation packages for three 16S rRNA databases (Greengenes, RDP and SILVA) to facilitate working with 16S rRNA databases and marker-gene survey feature data. The metagenomeFeatures package defines two classes, MgDb for working with 16S rRNA sequence databases, and mgFeatures for marker-gene survey feature data. The associated annotation packages provide a consistent interface to the different databases facilitating database comparison and exploration. The mgFeatures-class represents a crucial step in the development of a common data structure for working with 16S marker-gene survey data in R.Citation
Bioinformatics
Issue
19
Pub Type
Journals
Download Paper
Keywords
R Bioconductor, 16S rRNA, software, bioinoformatics
Citation
Created March 1, 2019, Updated February 1, 2024