phyloseq-package: Handling and analysis of high-throughput phylogenetic sequence data.
Description
There are already several ecology and phylogenetic
packages available in R, including the adephylo, vegan,
ade4, picante, ape, phangorn, phylobase, and OTUbase
packages. These can already take advantage of many of the
powerful statistical and graphics tools available in R.
However, prior to phyloseq a user must devise
their own methods for parsing the output of their
favorite OTU clustering application, and, as a
consequence, there is also no standard within
Bioconductor (or R generally) for storing or sharing the
suite of related data objects that describe a
phylogenetic sequencing project. The phyloseq package
seeks to address these issues by providing a related set
of S4 classes that internally manage the handling tasks
associated with organizing, linking, storing, and
analyzing phylogenetic sequencing data. phyloseq
additionally provides some convenience wrappers for input
from common clustering applications, common analysis
pipelines, and native implementation of methods that are
not available in other R packages.