Package: PathoStat
Type: Package
Title: PathoStat Statistical Microbiome Analysis Package
Version: 1.36.0
Date: 2020-03-27
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>,
        Yue Zhao <jasonzhao0307@gmail.com>, 
        Anthony Nicholas Federico <anfed@bu.edu>,
        W. Evan Johnson <wej@bu.edu>
Maintainer: Solaiappan Manimaran <manimaran_1975@hotmail.com>,
 Yue Zhao <jasonzhao0307@gmail.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 (>= 3.5)
Imports: limma, corpcor,matrixStats, reshape2, scales, ggplot2,
        rentrez, DT, tidyr, plyr, dplyr, phyloseq, shiny, stats,
        methods, XML, graphics, utils, BiocStyle, edgeR, DESeq2,
        ComplexHeatmap, plotly, webshot, vegan, shinyjs, glmnet,
        gmodels, ROCR, RColorBrewer, knitr, devtools, ape
Collate: 'pathoStat.R' 'utils.R' 'taxonomy.R' 'biomarker.R'
        'allClasses.R' 'visualization.R' 'differentialAnalysis.R'
biocViews: Microbiome, Metagenomics, GraphAndNetwork, Microarray,
        PatternLogic, PrincipalComponent, Sequencing, Software,
        Visualization, RNASeq, ImmunoOncology
RoxygenNote: 6.1.1
Encoding: UTF-8
Suggests: rmarkdown, testthat
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/PathoStat
git_branch: RELEASE_3_22
git_last_commit: a14c74c
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 05:38:26 UTC; biocbuild
