Work

Phyloseq: a Bioconductor Package for Handling and Analysis of High-throughput Phylogenetic Sequence Data

Year: 2011

Type: conference-paper

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.

Source: Pacific Symposium on Biocomputing (PSB)

DOI: 10.1142/9789814366496_0023

Authors: PAUL J. McMURDIE, SUSAN HOLMES

Institution: Stanford University

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funder: National Institute of General Medical Sciences

Award: Heterogeneous in situ data: Kernals, Distances and Trees