R/allPackage.R

In phyloseq: Handling and analysis of high-throughput microbiome census data

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#'  Handling and analysis of high-throughput phylogenetic sequence data.
#'
#' 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 \emph{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. \emph{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.
#'
#' @import methods
#' @name phyloseq-package
#' @author Paul J. McMurdie II \email{mcmurdie@@stanford.edu}
#' @references \url{www.stanford.edu/~mcmurdie}
#' @docType package
#' @keywords package
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