Package: phyloseq
Version: 1.16.2
Date: 2016-04-16
Title: Handling and analysis of high-throughput microbiome census data
Description: phyloseq provides a set of classes and tools
    to facilitate the import, storage, analysis, and
    graphical display of microbiome census data.
Maintainer: Paul J. McMurdie <mcmurdie@stanford.edu>
Author: Paul J. McMurdie <mcmurdie@stanford.edu>,
    Susan Holmes <susan@stat.stanford.edu>, with
    contributions from Gregory Jordan and Scott Chamberlain
License: AGPL-3
Imports: BiocGenerics (>= 0.14.0), ade4 (>= 1.7.2), ape (>= 3.1.1),
        biomformat (>= 0.4.0), Biostrings (>= 2.28.0), cluster (>=
        1.14.4), data.table (>= 1.9.6), foreach (>= 1.4.2), ggplot2 (>=
        2.1.0), igraph (>= 0.7.0), methods (>= 3.1.0), multtest (>=
        2.16.0), plyr (>= 1.8), reshape2 (>= 1.2.2), scales (>= 0.3.0),
        vegan (>= 2.0.10), Biobase
Depends: R (>= 3.2.0)
Suggests: BiocStyle (>= 1.6), DESeq2 (>= 1.8), genefilter (>= 1.50),
        testthat (>= 0.10), knitr (>= 1.10), metagenomeSeq (>= 1.10),
        rmarkdown (>= 0.7)
VignetteBuilder: knitr
Enhances: doParallel (>= 1.0.1)
biocViews: Sequencing, Microbiome, Metagenomics, Clustering,
        Classification, MultipleComparison, GeneticVariability
URL: http://dx.plos.org/10.1371/journal.pone.0061217
BugReports: https://github.com/joey711/phyloseq/issues
Collate: 'allClasses.R' 'allPackage.R' 'allData.R' 'as-methods.R'
        'show-methods.R' 'plot-methods.R' 'extract-methods.R'
        'almostAllAccessors.R' 'otuTable-class.R' 'phyloseq-class.R'
        'taxonomyTable-class.R' 'IO-methods.R' 'merge-methods.R'
        'multtest-wrapper.R' 'ordination-methods.R'
        'transform_filter-methods.R' 'validity-methods.R'
        'assignment-methods.R' 'sampleData-class.R' 'extend_vegan.R'
        'network-methods.R' 'distance-methods.R'
        'deprecated_functions.R' 'extend_DESeq2.R' 'phylo-class.R'
        'extend_metagenomeSeq.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-16 03:15:54 UTC; biocbuild
Built: R 3.3.1; ; 2016-11-13 17:59:00 UTC; unix
