Title: PHYLOSEQ: A BIOCONDUCTOR PACKAGE FOR HANDLING AND ANALYSIS OF HIGH-THROUGHPUT PHYLOGENETIC SEQUENCE DATA
Abstract: Biocomputing 2012, pp. 235-246 (2011) Open AccessPHYLOSEQ: A BIOCONDUCTOR PACKAGE FOR HANDLING AND ANALYSIS OF HIGH-THROUGHPUT PHYLOGENETIC SEQUENCE DATAPAUL J. McMURDIE and SUSAN HOLMESPAUL J. McMURDIEStatistics Department, Stanford University, Stanford, CA 94305, USA and SUSAN HOLMESStatistics Department, Stanford University, Stanford, CA 94305, USAwww-stat.stanford.edu/˜susan/https://doi.org/10.1142/9789814366496_0023Cited by:26 PreviousNext AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack CitationsRecommend to Library ShareShare onFacebookTwitterLinked InRedditEmail Abstract: We present a detailed description of a new Bioconductor package, phyloseq, for integrated data and analysis of taxonomically-clustered phylogenetic sequencing data in conjunction with related data types. The phyloseq package integrates abundance data, phylogenetic information and covariates so that exploratory transformations, plots, and confirmatory testing and diagnostic plots can be carried out seamlessly. The package is built following the S4 object-oriented framework of the R language so that once the data have been input the user can easily transform, plot and analyze the data. We present some examples that highlight the methods and the ease with which we can leverage existing packages. Keywords: pyrosequencingQIIMEmicrobiomemicrobial ecologyveganadephylophylobaseOTUbase FiguresReferencesRelatedDetailsCited By 26Breed and ruminal fraction effects on bacterial and archaeal community composition in sheepSteven McLoughlin, Charles Spillane, Francis P. Campion, Noel Claffey and Chrystian C. 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