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Oxford University Press, Bioinformatics, 19(35), p. 3870-3872, 2019

DOI: 10.1093/bioinformatics/btz136

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

Journal article published in 2018 by Nathan D. Olson ORCID, Nidhi Shah, Jayaram Kancherla, Justin Wagner, Joseph N. Paulson ORCID, Hector Corrada Bravo ORCID
This paper was not found in any repository, but could be made available legally by the author.
This paper was not found in any repository, but could be made available legally by the author.

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Abstract

Abstract Summary 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. Availability and implementation https://bioconductor.org/packages/release/bioc/html/metagenomeFeatures.html. Supplementary information Supplementary material is available at Bioinformatics online.