DESCRIPTION

Package: phyloseq
Version: 1.41.1
Date: 2022-11-01
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 <joey711@gmail.com>
Author: Paul J. McMurdie <joey711@gmail.com>,
    Susan Holmes <susan@stat.stanford.edu>, with
    contributions from Gregory Jordan and Scott Chamberlain
License: AGPL-3
Imports:
    ade4 (>= 1.7-4),
    ape (>= 5.0),
    Biobase (>= 2.36.2),
    BiocGenerics (>= 0.22.0),
    biomformat (>= 1.0.0),
    Biostrings (>= 2.40.0),
    cluster (>= 2.0.4),
    data.table (>= 1.10.4),
    foreach (>= 1.4.3),
    ggplot2 (>= 2.1.0),
    igraph (>= 1.0.1),
    methods (>= 3.3.0),
    multtest (>= 2.28.0),
    plyr (>= 1.8.3),
    reshape2 (>= 1.4.1),
    scales (>= 0.4.0),
    vegan (>= 2.5)
Depends:
    R (>= 3.3.0)
Suggests:
    BiocStyle (>= 2.4),
    DESeq2 (>= 1.16.1),
    genefilter (>= 1.58),
    knitr (>= 1.16),
    magrittr (>= 1.5),
    metagenomeSeq (>= 1.14),
    rmarkdown (>= 1.6),
    testthat (>= 1.0.2)
VignetteBuilder: knitr
Enhances: doParallel (>= 1.0.10)
biocViews: ImmunoOncology, 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: 6.1.1