Package: phyloseq
Version: 1.8.2
Date: 2014-05-23
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: ade4 (>= 1.6.2), ape (>= 3.1.1), biom (>= 0.3.9), Biostrings
        (>= 2.28.0), cluster (>= 1.14.4), data.table (>= 1.9.2), DESeq2
        (>= 1.4.0), foreach (>= 1.4.2), ggplot2 (>= 1.0.0), igraph (>=
        0.6.5.2), methods (>= 3.0.0), multtest (>= 2.16.0), plyr (>=
        1.8), reshape2 (>= 1.2.2), scales (>= 0.2.3), vegan (>= 2.0.10)
Depends: R (>= 3.0.0)
Suggests: genefilter (>= 1.42.0), testthat (>= 0.7.1), knitr (>= 1.3)
VignetteBuilder: knitr
Enhances: doParallel (>= 1.0.1)
biocViews: Clustering, Classification, MultipleComparisons,
        QualityControl, GeneticVariability, HighThroughputSequencing
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'
Packaged: 2014-05-24 10:14:03 UTC; biocbuild
Built: R 3.1.0; ; 2014-05-24 15:36:58 UTC; windows
