PHYLOSEQ: A BIOCONDUCTOR PACKAGE FOR HANDLING AND ANALYSIS OF HIGH-THROUGHPUT PHYLOGENETIC SEQUENCE DATA

By Paul J. McMurdie, Susan P. Holmes. Pacific Symposium on Biocomputing, 2011

328 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/645e93620449e42f94d38bd586ecb58a3d7e2afa

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In Molecular Biology

Citations in the corpus

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data (2013, methodology): “In spite of all of these highly relevant tools, we recently described the lack of a satisfactory standard within Bioconductor [34] (or R generally) for importing the data files from the most popular OTU-clustering applications, or representing this data in a complete, integrated class [31].”
The MG-RAST metagenomics database and portal in 2015 (2015, methodology): “The popular phyloseq R package (18) provides an alternative to the visualizations in MG-RAST or QIIME.”