metagenomeFeatures: An R package for working with 16S rRNA reference databases and marker-gene survey feature data.

Published

March 1, 2019

Author(s)

Nathanael David Olson, 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

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DOI Link

Keywords

R Bioconductor, 16S rRNA, software, bioinoformatics

Citation

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 December 3, 2024)