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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 | Package: phyloseq
Version: 1.22.3
Date: 2017-11-04
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 (>= 2.4)
Depends: R (>= 3.4.0)
Suggests: BiocStyle (>= 2.4), DESeq2 (>= 1.16.1), genefilter (>= 1.58),
knitr (>= 1.16), metagenomeSeq (>= 1.14), rmarkdown (>= 1.6),
testthat (>= 1.0.2)
VignetteBuilder: knitr
Enhances: doParallel (>= 1.0.10)
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: 6.0.1
NeedsCompilation: no
Packaged: 2017-11-06 00:01:50 UTC; biocbuild
Built: R 3.4.2; ; 'Sat, 11 Nov 2017 08:37:04 +0100'; unix
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