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

Nathan D. Olson; Nidhi Shah; Jayaram Kancherla; Justin Wagner; Joseph Nathaniel Paulson; Héctor Corrada Bravo

doi:10.1093/bioinformatics/btz136

BioinformaticsBioinformaticsFeb 25, 2019

Peer-reviewed journal article

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

Nathan D. Olson iD, Nidhi Shah, Jayaram Kancherla iD, Justin Wagner iD, Joseph Nathaniel Paulson iD, Héctor Corrada Bravo iD

Abstract

We developed the metagenomeFeatures R Bioconductor package along with annotation packages for the three primary 16S rRNA databases (Greengenes, RDP, and SILVA) to facilitate working with 16S rRNA sequence databases and marker-gene survey feature data. The metagenomeFeatures package defines two classes, MgDb for working with 16S rRNA sequence databases, and mgFeatures for working with marker-gene survey feature data. The associated annotation packages provide a consistent interface to the different 16S rRNA databases facilitating database comparison and exploration. The mgFeatures represents a crucial step in the development of a common data structure for working with 16S marker-gene survey data in R.\n\nAvailabilityhttps://bioconductor.org/packages/release/bioc/html/metagenomeFeatures.html\n\nContactnolson@nist.gov

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