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dc.contributor.authorLiland, Kristian Hovde
dc.contributor.authorVinje, Hilde
dc.contributor.authorSnipen, Lars-Gustav
dc.date.accessioned2018-06-26T07:58:42Z
dc.date.available2018-06-26T07:58:42Z
dc.date.created2017-09-28T15:02:58Z
dc.date.issued2017
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/11250/2502930
dc.description.abstractBackground 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.
dc.language.isoengnb_NO
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 Internasjonal*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/deed.no*
dc.titlemicroclass: An R-package for 16S taxonomy classificationnb_NO
dc.typeJournal articlenb_NO
dc.typePeer reviewednb_NO
dc.description.versionpublishedVersion
dc.source.volume18nb_NO
dc.source.journalBMC Bioinformaticsnb_NO
dc.source.issue1nb_NO
dc.identifier.doi10.1186/s12859-017-1583-2
dc.identifier.cristin1499864
dc.relation.projectNofima AS: 201702nb_NO
dc.relation.projectNorges forskningsråd: 262308nb_NO
cristin.unitcode192,12,0,0
cristin.unitnameKjemi, bioteknologi og matvitenskap
cristin.ispublishedtrue
cristin.fulltextoriginal
cristin.qualitycode2


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Attribution-NonCommercial-NoDerivatives 4.0 Internasjonal
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