Package: PathoStat
Type: Package
Title: PathoStat Statistical Microbiome Analysis Package
Version: 1.4.1
Date: 2017-12-06
Author: Solaiappan Manimaran <manimaran_1975@hotmail.com>, Matthew
        Bendall <bendall@gwmail.gwu.edu>, Sandro Valenzuela Diaz
        <sandrolvalenzuelad@gmail.com>, Eduardo Castro
        <castronallar@gmail.com>, Tyler Faits <tfaits@gmail.com>, W.
        Evan Johnson <wej@bu.edu>
Maintainer: Solaiappan Manimaran <manimaran_1975@hotmail.com>
Description: The purpose of this package is to perform Statistical
        Microbiome Analysis on metagenomics results from sequencing
        data samples. In particular, it supports analyses on the
        PathoScope generated report files. PathoStat provides various
        functionalities including Relative Abundance charts, Diversity
        estimates and plots, tests of Differential Abundance, Time
        Series visualization, and Core OTU analysis.
URL: https://github.com/mani2012/PathoStat
BugReports: https://github.com/mani2012/PathoStat/issues
License: GPL (>= 2)
Depends: R (>= 3.3.1)
Imports: MCMCpack, limma, corpcor, rmarkdown, knitr, pander,
        matrixStats, reshape2, scales, ggplot2, rentrez, BatchQC, DT,
        gtools, tidyr, plyr, dplyr, ape, phyloseq, shiny, grDevices,
        stats, methods, XML, graphics, utils, alluvial, BiocStyle,
        edgeR, preprocessCore, DESeq2
Collate: 'pathoStat.R' 'utils.R' 'taxonomy.R' 'confRegion.R'
        'allClasses.R' 'coreOTUModule.R' 'normalization.R'
Suggests: testthat
biocViews: Microbiome, Metagenomics, GraphAndNetwork, Microarray,
        PatternLogic, PrincipalComponent, Sequencing, Software,
        Visualization, RNASeq
SystemRequirements: pandoc (http://pandoc.org/installing.html) for
        generating reports from markdown files.
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2017-12-08 01:48:58 UTC; biocbuild
Built: R 3.4.1; ; 2018-02-16 11:13:16 UTC; unix
