title: microclass: an R-package for 16S taxonomy classification.
abstract: BACKGROUND
  Taxonomic classification based on the 16S rRNA gene sequence is important for the profiling of microbial communities. In addition to giving the best possible accuracy, it is also important to quantify uncertainties in the classifications.
  
  
  RESULTS
  We present an R package with tools for making such classifications, where the heavy computations are implemented in C++ but operated through the standard R interface. The user may train classifiers based on specialized data sets, but we also supply a ready-to-use function trained on a comprehensive training data set designed specifically for this purpose. This tool also includes some novel ways to quantify uncertainties in the classifications.
  
  
  CONCLUSIONS
  Based on input sequences of varying length and quality, we demonstrate how the output from the classifications can be used to obtain high quality taxonomic assignments from 16S sequences within the R computing environment. The package is publicly available at the Comprehensive R Archive Network.
authors.affiliation: Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, P.O. Box 5003, N-1432, Norway.|Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, Ås, N-1430, Norway.
authors.forename: Kristian Hovde
authors.initials: KH
authors.lastname: Liland
authors.affiliation: Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, P.O. Box 5003, N-1432, Norway.
authors.forename: Hilde
authors.initials: H
authors.lastname: Vinje
authors.affiliation: Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, P.O. Box 5003, N-1432, Norway. lars.snipen@nmbu.no.
authors.forename: Lars
authors.identifier: http://orcid.org/0000-0002-2883-861X
authors.initials: L
authors.lastname: Snipen
mesh_terms: D019540:Area Under Curve; D001419:Bacteria / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D012336:RNA, Ribosomal, 16S / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D012372:ROC Curve; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: 16S; R; Taxonomy